Citing Reactome

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This is a listing of 468 articles, 159 reviews, 174 books and other references citing Reactome Publications.

We also provide a list of publications, citing the use of Reactome pathway data to assist biologists, clinicians, geneticists and bioinformaticians to answer important biological questions.

If your publication cites one of the Reactome Publications and is not listed below, please let us know by sending an email to HelpDesk and we will update the list.

2011

AHMED, J., MEINEL, T., DUNKEL, M., MURGUEITIO, M. S., ADAMS, R., BLASSE, C., ECKERT, A., PREISSNER, S. & PREISSNER, R. (2011) CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. Nucleic Acids Research, 39, 960-967.
ANDREINI, C., BERTINI, I., CAVALLARO, G., DECARIA, L. & ROSATO, A. (2011) A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms. Journal of Chemical Information and Modeling, 51, 730-8.
BENSON, D. A., KARSCH-MIZRACHI, I., LIPMAN, D. J., OSTELL, J. & SAYERS, E. W. (2011) GenBank. Nucleic Acids Research, 39, 32-37.
BORDRON, P., EVEILLARD, D. & RUSU, I. (2011) SIPPER : A flexible method to integrate heterogeneous data into a metabolic network. Proceedings of Computational Advances in Bio and Medical Sciences (ICCABS).
BURKARD, T. R., PLANYAVSKY, M., KAUPE, I., BREITWIESER, F. P., BUERCKSTUEMMER, T., BENNETT, K. L., SUPERTI-FURGA, G. & COLINGE, J. (2011) Initial characterization of the human central proteome. BMC Systems Biology, 5, 17.
CAVILL, R., KAMBUROV, A., ELLIS, J. K., ATHERSUCH, T. J., BLAGROVE, M. S. C., HERWIG, R., EBBELS, T. M. D. & KEUN, H. C. (2011) Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells. PLoS Computational Biology, 7, e1001113.
CERAMI, E. G., GROSS, B. E., DEMIR, E., RODCHENKOV, I., BABUR, O., ANWAR, N., SCHULTZ, N., BADER, G. D. & SANDER, C. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Research, 39, 685-690.
CHAKRABORTY, C., ROY, S. S., HSU, M. J. & AGORAMOORTHY, G. (2011) Landscape mapping of functional proteins in insulin signal transduction and insulin resistance: a network-based protein-protein interaction analysis. PLoS one, 6, e16388.
CHAO, S.-Y., CHIANG, J.-H., HUANG, A.-M. & CHANG, W.-S. (2011) An integrative approach to identifying cancer chemoresistance-associated pathways. BMC Medical Genomics, 4, 23.
CHEN, C., HUANG, H. & WU, C. H. (2011) Protein Bioinformatics Databases and Resources. Methods in Molecular Biology, 694, 3.
COHEN, O., GOPHNA, U. & PUPKO, T. (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular Biology and Evolution, 28, 1481-1489.
CUTTS, R. J., GADALETA, E., HAHN, S. A., CRNOGORAC-JURCEVIC, T., LEMOINE, N. R. & CHELALA, C. (2011) The Pancreatic Expression database: 2011 update. Nucleic Acids Research, 39, 1023-1028.
DAVIS, A. P., KING, B. L., MOCKUS, S., MURPHY, C. G., SARACENI-RICHARDS, C., ROSENSTEIN, M., WIEGERS, T. & MATTINGLY, C. J. (2011) The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Research, 1-6.
D'EUSTACHIO, P. (2011) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, 694, 49-61.
FUCILE, G., DI BIASE, D., NAHAL, H., LA, G., KHODABANDEH, S., CHEN, Y., EASLEY, K., CHRISTENDAT, D., KELLEY, L. & PROVART, N. J. (2011) ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web. PLoS one, 6, e15237.
JONES, P. (2011) Analysing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMart. Methods in Molecular Biology, 696, 107-121.
JØRGENSEN, K. M., HJELLE, S. M., OYE, O. K., PUNTERVOLL, P., REIKVAM, H., SKAVLAND, J., ANDERSSEN, E., BRUSERUD, O. & GJERTSEN, B. T. (2011) Untangling the intracellular signalling network in cancer - a strategy for data integration in acute myeloid leukaemia. Journal of Proteomics, 74, 269-281.
KAMBUROV, A., PENTCHEV, K., GALICKA, H., WIERLING, C., LEHRACH, H. & HERWIG, R. (2011) ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Research, 39, 712-717.
KARINEN, S., HEIKKINEN, T., NEVANLINNA, H. & HAUTANIEMI, S. (2011) Data Integration Workflow for Search of Disease Driving Genes and Genetic Variants. PLoS ONE, 6, e18636.
KARP, P. D. & CASPI, R. (2011) A survey of metabolic databases emphasizing the MetaCyc family. Archives of Toxicology.
KERRIGAN, J. J., XIE, Q., AMES, R. S. & LU, Q. (2011) Production of protein complexes via co-expression. Protein Expression and Purification, 75, 1-14.
KHATRI, P. & SARWAL, M. M. (2011) Immunologic Signatures of Rejection. Analysis, 239-256.
KIM, Y.-A., WUCHTY, S. & PRZYTYCKA, T. M. (2011) Identifying Causal Genes and Dysregulated Pathways in Complex Diseases. PLoS Computational Biology, 7, e1001095.
LASHER, C. D., RAJAGOPALAN, P. & MURALI, T. M. (2011) Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures. PLoS one, 6, e15247.
LATINO, D. (2011) Classification of chemical reactions and chemoinformatic processing of enzymatic transformations. Methods in Molecular Biology, 672, 325-340.
LEE, S., LEE, E., LEE, K. H. & LEE, D. (2011) Predicting disease phenotypes based on the molecular networks with condition-responsive correlation. International Journal of Data Mining and Bioinformatics, 5, 131-42.
LI, Q., LI, X., LI, C., CHEN, L., SONG, J., TANG, Y. & XU, X. (2011) A Network-Based Multi-Target Computational Estimation Scheme for Anticoagulant Activities of Compounds. PLoS one, 6, e14774.
LOURENÇO, A., CARNEIRO, S., ROCHA, M., FERREIRA, E. C. & ROCHA, I. (2011) Challenges in integrating Escherichia coli molecular biology data. Briefings in Bioinformatics, 12, 91-103.
MAGLOTT, D., OSTELL, J., PRUITT, K. D. & TATUSOVA, T. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research, 39, 52-57.
MAQUNGO, M., KAUR, M., KWOFIE, S. K., RADOVANOVIC, A., SCHAEFER, U., SCHMEIER, S., OPPON, E., CHRISTOFFELS, A. & BAJIC, V. B. (2011) DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research, 39, D980-5.
MEWES, H. W., RUEPP, A., THEIS, F., RATTEI, T., WALTER, M., FRISHMAN, D., SUHRE, K., SPANNAGL, M., MAYER, K. F. X., STÜMPFLEN, V. & ANTONOV, A. (2011) MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Research, 39, 220-224.
MILANOWSKA, K., KRWAWICZ, J., PAPAJ, G., KOSINSKI, J., POLESZAK, K., LESIAK, J., OSINSKA, E., ROTHER, K. & BUJNICKI, J. M. (2011) REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Research, 39, 788-792.
MURALI, T., PACIFICO, S., YU, J., GUEST, S., ROBERTS, G. G. & FINLEY, R. L. (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Research, 39, D736-43.
NATALE, D. A., ARIGHI, C. N., BARKER, W. C., BLAKE, J. A., BULT, C. J., CAUDY, M., DRABKIN, H. J., D'EUSTACHIO, P., EVSIKOV, A. V., HUANG, H., NCHOUTMBOUBE, J., ROBERTS, N. V., SMITH, B., ZHANG, J. & WU, C. H. (2011) The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Research, 39, 539-545.
PAZ, A., BROWNSTEIN, Z., BER, Y., BIALIK, S., DAVID, E., SAGIR, D., ULITSKY, I., ELKON, R., KIMCHI, A., AVRAHAM, K. B., SHILOH, Y. & SHAMIR, R. (2011) SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Research, 39, D793-9.
PERLMAN, L., GOTTLIEB, A., ATIAS, N., RUPPIN, E. & SHARAN, R. (2011) Combining drug and gene similarity measures for drug-target elucidation. Journal of Computational Biology, 18, 133-45.
PETRI, V., SHIMOYAMA, M., HAYMAN, G. T., SMITH, J. R., TUTAJ, M., DE PONS, J., DWINELL, M. R., MUNZENMAIER, D. H., TWIGGER, S. N. & JACOB, H. J. (2011) The rat genome database pathway portal. Database, 2011, bar010.
ROSSIN, E. J., LAGE, K., RAYCHAUDHURI, S., XAVIER, R. J., TATAR, D., BENITA, Y., COTSAPAS, C. & DALY, M. J. (2011) Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology. PLoS Genetics, 7, e1001273.
SAYERS, E. W., BARRETT, T., BENSON, D. A., BOLTON, E., BRYANT, S. H., CANESE, K., CHETVERNIN, V., CHURCH, D. M., DICUCCIO, M., FEDERHEN, S., FEOLO, M., FINGERMAN, I. M., GEER, L. Y., HELMBERG, W., KAPUSTIN, Y., LANDSMAN, D., LIPMAN, D. J., LU, Z., MADDEN, T. L., MADEJ, T., MAGLOTT, D. R., MARCHLER-BAUER, A., MILLER, V., MIZRACHI, I., OSTELL, J., PANCHENKO, A., PHAN, L., PRUITT, K. D., SCHULER, G. D., SEQUEIRA, E., SHERRY, S. T., SHUMWAY, M., SIROTKIN, K., SLOTTA, D., SOUVOROV, A., STARCHENKO, G., TATUSOVA, T. A., WAGNER, L., WANG, Y., WILBUR, W. J., YASCHENKO, E. & YE, J. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 39, 38-51.
SCHAEFER, U., SCHMEIER, S. & BAJIC, V. B. (2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research, 39, D106.
SHIRDEL, E. A., XIE, W., MAK, T. W. & JURISICA, I. (2011) NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs. PLoS one, 6, e17429.
SUCAET, Y. & DEVA, T. (2011) Evolution and applications of plant pathway resources and databases. Briefings in Bioinformatics.
SUN, J. & ZHAO, Z. (2011) A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics, 11 Suppl 3, S5.
SZKLARCZYK, D., FRANCESCHINI, A., KUHN, M., SIMONOVIC, M., ROTH, A., MINGUEZ, P., DOERKS, T., STARK, M., MULLER, J., BORK, P., JENSEN, L. J. & MERING, C. V. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research, 39, 561-568.
TABOUREAU, O., NIELSEN, S. K., AUDOUZE, K., WEINHOLD, N., EDSGÄRD, D., ROQUE, F. S., KOUSKOUMVEKAKI, I., BORA, A., CURPAN, R., JENSEN, T. S., BRUNAK, S. & OPREA, T. I. (2011) ChemProt: a disease chemical biology database. Nucleic Acids Research, 39, 367-372.
TROPSHA, A., OPREA, T. I., MAY, E. E. & LEITA, A. (2011) Chemoinformatics and Computational Chemical Biology. Methods in Molecular Biology, 672.
VELANKAR, S. & KLEYWEGT, G. J. (2011) The Protein Data Bank in Europe (PDBe): bringing structure to biology. Acta Crystallographica Section D Biological Crystallography, 67, 324-330.
VIZCAÍNO, J. A., REISINGER, F. & CÔTÉ, R. (2011) Data Mining in Proteomics. Methods in Molecular Biology, 696, 93-105.
WANG, Z., ZHANG, X.-C., LE, M. H., XU, D., STACEY, G. & CHENG, J. (2011) A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One, 6, e17906.
WEBB, R. L. & MA'AYAN, A. (2011) Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code for Biology and Medicine, 6, 5.
XU, Y., HU, W., CHANG, Z., DUANMU, H., ZHANG, S., LI, Z., LI, Z., YU, L. & LI, X. (2011) Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. Interface, 8, 555-67.
YAKHINI, Z. & JURISICA, I. (2011) Cancer Computational Biology. BMC Bioinformatics, 12, 120.
YANG, X., YE, Y., WANG, G., HUANG, H., YU, D. & LIANG, S. (2011) VeryGene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery. Physiological Genomics, 43, 457-60.
ZHANG, G. L., DELUCA, D. S. & BRUSIC, V. (2011) Protein Microarray for Disease Analysis. Methods in Molecular Biology, 723.
ZHANG, K. X. & OUELLETTE, B. F. F. (2011) CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data. PLoS Computational Biology, 7, e1001114.
ZHAO, Z., XIA, J., TASTAN, O., SINGH, I., KSHIRSAGAR, M., CARBONELL, J. & KLEIN-SEETHARAMAN, J. (2011) Virus interactions with human signal transduction pathways. International Journal of Computational Biology and Drug Design, 4, 83-105.

2010

ALEXOPOULOS, L. G., MELAS, I. N., CHAIRAKAKI, A. D., SAEZ-RODRIGUEZ, J. & MITSOS, A. (2010) Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. Proceedings of 32nd Annual International Conference of the IEEE EMBS.
ALEXOPOULOS, L. G., SAEZ-RODRIGUEZ, J., COSGROVE, B. D., LAUFFENBURGER, D. A. & SORGER, P. K. (2010) Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes. Molecular and Cellular Proteomics, 9, 1849-65.
ALIFERIS, K. A. & CHRYSAYI-TOKOUSBALIDES, M. (2010) Metabolomics in pesticide research and development: review and future perspectives. Metabolomics, 7, 35-53.
ANATSKAYA, O. V. & VINOGRADOV, A. E. (2010) Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome. Functional and Integrative Genomics, 433-446.
ANDERSON, M. W. & SCHRIJVER, I. (2010) Next Generation DNA Sequencing and the Future of Genomic Medicine. Genes, 1, 38-69.
ANTONELL, A., VILARDELL, M. & PÉREZ JURADO, L. A. (2010) Transcriptome profile in Williams-Beuren syndrome lymphoblast cells reveals gene pathways implicated in glucose intolerance and visuospatial construction deficits. Human Genetics, 128, 27-37.
ANTONOV, A. V. (2010) Mining protein lists from proteomics studies: applications for drug discovery. Expert Opinion on Drug Discovery, 5, 323-331.
ANTONOV, A. V., SCHMIDT, E. E., DIETMANN, S., KRESTYANINOVA, M. & HERMJAKOB, H. (2010) R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Research, 38, W78-83.
ARAB, S., SADEGHI, M., ESLAHCHI, C., PEZESHK, H. & SHEARI, A. (2010) A pairwise residue contact area-based mean force potential for discrimination of native protein structure. BMC Bioinformatics, 11, 16.
ARANDA, B., ACHUTHAN, P., ALAM-FARUQUE, Y., ARMEAN, I., BRIDGE, A., DEROW, C., FEUERMANN, M., GHANBARIAN, A. T., KERRIEN, S., KHADAKE, J., KERSSEMAKERS, J., LEROY, C., MENDEN, M., MICHAUT, M., MONTECCHI-PALAZZI, L., NEUHAUSER, S. N., ORCHARD, S., PERREAU, V., ROECHERT, B., VAN EIJK, K. & HERMJAKOB, H. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Research, 38, D525-31.
BABUR, O., DOGRUSOZ, U., DEMIR, E. & SANDER, C. (2010) ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics, 26, 429-31.
BAUDOT, A., DE LA TORRE, V. & VALENCIA, A. (2010) Mutated genes, pathways and processes in tumours. EMBO Reports, 11, 6-11.
BERGER, S. I., MA'AYAN, A. & IYENGAR, R. (2010) Systems pharmacology of arrhythmias. Science Signaling, 3, ra30.
BESTEIRO, S., VO DUY, S., PERIGAUD, C., LEFEBVRE-TOURNIER, I. & VIAL, H. J. (2010) Exploring metabolomic approaches to analyse phospholipid biosynthetic pathways in Plasmodium. Parasitology, 137, 1343-56.
BLINOV, M. L., RUEBENACKER, O., SCHAFF, J. C. & MORARU, I. I. (2010) Modeling without Borders: Creating and Annotating VCell Models Using the Web. Proceedings of 6th International Symposium, ISBRA.
BROOKSBANK, C., CAMERON, G. & THORNTON, J. (2010) The European Bioinformatics Institute's data resources. Nucleic Acids Research, 38, D17-25.
BUDCZIES, J., DENKERT, C., MÜLLER, B. M. & BROCKMÖLLER, S. F. (2010) METAtarget – extracting key enzymes of metabolic regulation from high-throughput metabolomics data using KEGG REACTION information. Lecture Notes in Informatics, 103-112.
CAKMAK, A., DSOUZA, A., HANSON, R. W. & OZSOYOGLU, M. (2010) Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10. New York, New York, USA, ACM Press.
CAKMAK, A., OZSOYOGLU, G. & HANSON, R. W. (2010) Querying Metabolism Under Different Physiological Constraints. Journal of Bioinformatics and Computational Biology, 08, 247.
CAMPBELL, S. J., GAULTON, A., MARSHALL, J., BICHKO, D., MARTIN, S., BROUWER, C. & HARLAND, L. (2010) Visualizing the drug target landscape. Drug Discovery Today, 15, 3-15.
CEOL, A., CHATR ARYAMONTRI, A., LICATA, L., PELUSO, D., BRIGANTI, L., PERFETTO, L., CASTAGNOLI, L. & CESARENI, G. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Research, 38, D532-9.
CHARRO, N., HOOD, B. L., FARIA, D., PACHECO, P., AZEVEDO, P., LOPES, C., DE ALMEIDA, A. B., COUTO, F. M., CONRADS, T. P. & PENQUE, D. (2010) Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC-MS/MS approach. Journal of Proteomics, 74, 110-126.
CHAURASIA, G. & FUTSCHIK, M. E. (2010) Interactomics and Cancer. An Omics Perspective on Cancer Research, 167-182.
CHEN, H. & XIE, G. (2010) The use of web ontology languages and other semantic web tools in drug discovery. Expert Opinion on Drug Discovery, 5, 413-423.
CHEN, S., YANG, P., JIANG, F., WEI, Y., MA, Z. & KANG, L. (2010) De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits. PLoS One, 5, e15633.
CHESLER, E. J. & BAKER, E. J. (2010) The importance of open-source integrative genomics to drug discovery. Current opinion in Drug Discovery & Development, 13, 310-6.
CHIA, N.-Y., CHAN, Y.-S., FENG, B., LU, X., ORLOV, Y. L., MOREAU, D., KUMAR, P., YANG, L., JIANG, J., LAU, M.-S., HUSS, M., SOH, B.-S., KRAUS, P., LI, P., LUFKIN, T., LIM, B., CLARKE, N. D., BARD, F. & NG, H.-H. (2010) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature, 468, 316-320.
COTTRET, L. & JOURDAN, F. (2010) Graph methods for the investigation of metabolic networks in parasitology. Parasitology, 1-15.
DAEMEN, A., SIGNORETTO, M., GEVAERT, O., SUYKENS, J. A. K. & DE MOOR, B. (2010) Improved microarray-based decision support with graph encoded interactome data. PLoS one, 5, e10225.
DAIGLE, B. J., SRINIVASAN, B. S., FLANNICK, J. A., NOVAK, A. F. & BATZOGLOU, S. (2010) Systems Biology for Signaling Networks. Systems Biology.
DALE, J. M., POPESCU, L. & KARP, P. D. (2010) Machine learning methods for metabolic pathway prediction. BMC Bioinformatics, 11, 15.
DALL'OLIO, G. M., BERTRANPETIT, J. & LAAYOUNI, H. (2010) The annotation and the usage of scientific databases could be improved with public issue tracker software. Database, 2010, baq035-baq035.
DANIELS, C., GODOY, P., DUQUE, E., MOLINA-HENARES, M. A., DE LA TORRE, J., DEL ARCO, J. M., HERRERA, C., SEGURA, A., GUAZZARONI, M. E., FERRER, M. & RAMOS, J. L. (2010) Global regulation of food supply by Pseudomonas putida DOT-T1E. Journal of Bacteriology, 192, 2169-81.
DE BRUIN, J. & KOK, J. (2010) Combining subgroup discovery and permutation testing to reduce reduncancy. Proceedings of the 4th International Conference on Leveraging applications of formal methods, verification, and validation. Springer.
DE MATOS, P., ALCÁNTARA, R., DEKKER, A., ENNIS, M., HASTINGS, J., HAUG, K., SPITERI, I., TURNER, S. & STEINBECK, C. (2010) Chemical Entities of Biological Interest: an update. Nucleic Acids Research, 38, D249-54.
DEL SOL, A., BALLING, R., HOOD, L. & GALAS, D. (2010) Diseases as network perturbations. Current Opinion in Biotechnology, 21, 566-571.
DELISI, C., FAN, Y., KIM, S., KON, M. & LOUISE, R. (2010) Regularization Techniques for Machine Learning on Graphs and Networks with Biological Applications. Communications in Mathematical Analysis, 8, 136-145.
DEMIR, E., CARY, M. P., PALEY, S., FUKUDA, K., LEMER, C., VASTRIK, I., WU, G., D'EUSTACHIO, P., SCHAEFER, C., LUCIANO, J., SCHACHERER, F., MARTINEZ-FLORES, I., HU, Z., JIMENEZ-JACINTO, V., JOSHI-TOPE, G., KANDASAMY, K., LOPEZ-FUENTES, A. C., MI, H., PICHLER, E., RODCHENKOV, I., SPLENDIANI, A., TKACHEV, S., ZUCKER, J., GOPINATH, G., RAJASIMHA, H., RAMAKRISHNAN, R., SHAH, I., SYED, M., ANWAR, N., BABUR, Ö., BLINOV, M., BRAUNER, E., CORWIN, D., DONALDSON, S., GIBBONS, F., GOLDBERG, R., HORNBECK, P., LUNA, A., MURRAY-RUST, P., NEUMANN, E., REUBENACKER, O., SAMWALD, M., VAN IERSEL, M., WIMALARATNE, S., ALLEN, K., BRAUN, B., WHIRL-CARRILLO, M., CHEUNG, K.-H., DAHLQUIST, K., FINNEY, A., GILLESPIE, M., GLASS, E., GONG, L., HAW, R., HONIG, M., HUBAUT, O., KANE, D., KRUPA, S., KUTMON, M., LEONARD, J., MARKS, D., MERBERG, D., PETRI, V., PICO, A., RAVENSCROFT, D., REN, L., SHAH, N., SUNSHINE, M., TANG, R., WHALEY, R., LETOVKSY, S., BUETOW, K. H., RZHETSKY, A., SCHACHTER, V., SOBRAL, B. S., DOGRUSOZ, U., MCWEENEY, S., ALADJEM, M., BIRNEY, E., COLLADO-VIDES, J., GOTO, S., HUCKA, M., NOVÈRE, N. L., MALTSEV, N., PANDEY, A., THOMAS, P., WINGENDER, E., KARP, P. D., SANDER, C. & BADER, G. D. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28, 935-942.
DEY, S. K. & JAMIL, H. (2010) A hierarchical approach to reachability query answering in very large graph databases. Proceedings of the 19th ACM international conference on Information and knowledge management. ACM.
DILEK, A., BELVIRANLI, M. E. & DOGRUSOZ, U. (2010) VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Research, 38, W150-4.
DODERER, M. S., YOON, K. & ROBBINS, K. A. (2010) SIDEKICK: Genomic data driven analysis and decision-making framework. BMC Bioinformatics, 11, 611.
DYER, M. D., NEFF, C., DUFFORD, M., RIVERA, C. G., SHATTUCK, D., BASSAGANYA-RIERA, J., MURALI, T. M. & SOBRAL, B. W. (2010) The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS one, 5, e12089.
EASTON, J. M., HARRIS, L. M., VIANT, M. R., PEET, A. C. & ARVANITIS, T. N. (2010) Linked metabolites: a tool for the construction of directed metabolic graphs. Computers in Biology and Medicine, 40, 340-9.
EMIG, D., SALOMONIS, N., BAUMBACH, J., LENGAUER, T., CONKLIN, B. R. & ALBRECHT, M. (2010) AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research, 38 Suppl, W755-62.
FANG, H., YANG, Y., LI, C., FU, S., YANG, Z., JIN, G., WANG, K., ZHANG, J. & JIN, Y. (2010) Transcriptome analysis of early organogenesis in human embryos. Developmental Cell, 19, 174-84.
FERREIRA, G. B., MATHIEU, C. & OVERBERGH, L. (2010) Understanding dendritic cell biology and its role in immunological disorders through proteomic profiling. Proteomics Clin Appl, 4, 190-203.
FOKKENS, L., BOTELHO, S. M. C., BOEKHORST, J. & SNEL, B. (2010) Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics, 11, 86.
FREEMAN, T. C. (2010) Systems Biology for Signaling Networks. Systems Biology, 139-157.
FREEMAN, T. C., RAZA, S., THEOCHARIDIS, A. & GHAZAL, P. (2010) The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. BMC Systems Biology, 4, 65.
FROLKIS, A., KNOX, C., LIM, E., JEWISON, T., LAW, V., HAU, D. D., LIU, P., GAUTAM, B., LY, S., GUO, A. C., XIA, J., LIANG, Y., SHRIVASTAVA, S. & WISHART, D. S. (2010) SMPDB: The Small Molecule Pathway Database. Nucleic Acids Research, 38, D480-7.
GADALETA, E., LEMOINE, N. R. & CHELALA, C. (2010) Online resources of cancer data: barriers, benefits and lessons. Briefings in Bioinformatics, 12, 52-63.
GARCIA-GARCIA, J., GUNEY, E., ARAGUES, R., PLANAS-IGLESIAS, J. & OLIVA, B. (2010) Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics, 11, 56.
GEER, L. Y., MARCHLER-BAUER, A., GEER, R. C., HAN, L., HE, J., HE, S., LIU, C., SHI, W. & BRYANT, S. H. (2010) The NCBI BioSystems database. Nucleic Acids Research, 38, D492-6.
GEHLENBORG, N., O'DONOGHUE, S. I., BALIGA, N. S., GOESMANN, A., HIBBS, M. A., KITANO, H., KOHLBACHER, O., NEUWEGER, H., SCHNEIDER, R., TENENBAUM, D. & GAVIN, A.-C. (2010) Visualization of omics data for systems biology. Nature Methods, 7, S56-68.
GILLE, C., BÖLLING, C., HOPPE, A., BULIK, S., HOFFMANN, S., HÜBNER, K., KARLSTÄDT, A., GANESHAN, R., KÖNIG, M., ROTHER, K., WEIDLICH, M., BEHRE, J. & HOLZHÜTTER, H.-G. (2010) HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Molecular Systems Biology, 6, 411.
GILLESPIE, M., SHAMOVSKY, V. & D'EUSTACHIO, P. (2010) Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mammalian Genome, 130-138.
GLAAB, E., BAUDOT, A., KRASNOGOR, N. & VALENCIA, A. (2010) Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics, 11, 597.
GLAAB, E., GARIBALDI, J. M. & KRASNOGOR, N. (2010) Learning pathway-based decision rules to classify microarray cancer samples. Lecture Notes in Informatics, 123-134.
GO, E. P. (2010) Database resources in metabolomics: an overview. Journal of Neuroimmune Pharmacology, 5, 18-30.
GONÇALVES, J. P., MADEIRA, S. C. & MOREAU, Y. (2010) Network-Based Disease Candidate Gene Prioritization : Towards Global Diffusion in Heterogeneous Association Networks. Workshop on Dynamic Networks and Knowledge Discovery (DyNaK 2010).
GUBB, E. & MATTHIESEN, R. (2010) Bioinformatics Methods in Clinical Research. Methods in Molecular Biology, 593.
HACKL, H., STOCKER, G., CHAROENTONG, P., MLECNIK, B., BINDEA, G., GALON, J. & TRAJANOSKI, Z. (2010) Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy. Pharmacology and Therapeutics, 128, 488-498.
HAO, T., MA, H.-W., ZHAO, X.-M. & GORYANIN, I. (2010) Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics, 11, 393.
HARRIS, T. W., ANTOSHECHKIN, I., BIERI, T., BLASIAR, D., CHAN, J., CHEN, W. J., DE LA CRUZ, N., DAVIS, P., DUESBURY, M., FANG, R., FERNANDES, J., HAN, M., KISHORE, R., LEE, R., MÜLLER, H.-M., NAKAMURA, C., OZERSKY, P., PETCHERSKI, A., RANGARAJAN, A., ROGERS, A., SCHINDELMAN, G., SCHWARZ, E. M., TULI, M. A., VAN AUKEN, K., WANG, D., WANG, X., WILLIAMS, G., YOOK, K., DURBIN, R., STEIN, L. D., SPIETH, J. & STERNBERG, P. W. (2010) WormBase: a comprehensive resource for nematode research. Nucleic Acids Research, 38, D463-7.
HIGGINS, J. A., BAILEY, P. C. & LAURIE, D. A. (2010) Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS one, 5, e10065.
HOANG, L. T., LYNN, D. J., HENN, M., BIRREN, B. W., LENNON, N. J., LE, P. T., DUONG, K. T. H., NGUYEN, T. T. H., MAI, L. N., FARRAR, J. J., HIBBERD, M. L. & SIMMONS, C. P. (2010) The early whole-blood transcriptional signature of dengue and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. Journal of Virology, 84, 12982-12994.
HUANG, D., HUANG, Y., KLUKAS, C., HOFESTADT, R. & CHEN, M. (2010) PBSK Browser: navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats. Proceedings of Bioinformatics and Biomedicine Workshops (BIBMW). IEEE.
HUANG, N., LEE, I., MARCOTTE, E. M. & HURLES, M. E. (2010) Characterising and Predicting Haploinsufficiency in the Human Genome. PLoS Genetics, 6, e1001154.
HUDSON, T. (2010) International network of cancer genome projects. Nature, 464, 993-8.
HUR, J., SULLIVAN, K. A., SCHUYLER, A. D., HONG, Y., PANDE, M., STATES, D. J., JAGADISH, H. V. & FELDMAN, E. L. (2010) Literature-based discovery of diabetes- and ROS-related targets. BMC Medical Genomics, 3, 49.
HUTHMACHER, C., HOPPE, A., BULIK, S. & HOLZHÜTTER, H.-G. (2010) Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Systems Biology, 4, 120.
HUTTENHOWER, C. & HOFMANN, O. (2010) A Quick Guide to Large-Scale Genomic Data Mining. PLoS Computational Biology, 6, e1000779.
IADEVAIA, S., LU, Y., MORALES, F. C., MILLS, G. B. & RAM, P. T. (2010) Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. Cancer Research, 70, 6704-14.
IHARA, Y., KIHARA, Y., HAMANO, F., YANAGIDA, K., MORISHITA, Y., KUNITA, A., YAMORI, T., FUKAYAMA, M., ABURATANI, H., SHIMIZU, T. & ISHII, S. (2010) The G protein-coupled receptor T-cell death-associated gene 8 (TDAG8) facilitates tumor development by serving as an extracellular pH sensor. Proceedings of the National Academy of Sciences of the United States of America, 8.
ISSERLIN, R., MERICO, D., ALIKHANI-KOUPAEI, R., GRAMOLINI, A., BADER, G. D. & EMILI, A. (2010) Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics, 10, 1316-27.
JAISWAL, P., DHARMAWARDHANA, P. & NAITHANI, S. (2010) A model plant genome resource and comparative genomics. Acta Horticulturae, 859, 31-41.
JANSSON, A. & JIRSTRAND, M. (2010) Biochemical modeling with Systems Biology Graphical Notation. Drug Discovery Today, 15, 365-70.
JASSAL, B., JUPE, S., CAUDY, M., BIRNEY, E., STEIN, L., HERMJAKOB, H. & D'EUSTACHIO, P. (2010) The systematic annotation of the three main GPCR families in Reactome. Database, 2010, baq018.
JENNEN, D. G. J., GAJ, S., GIESBERTZ, P. J., VAN DELFT, J. H. M., EVELO, C. T. & KLEINJANS, J. C. S. (2010) Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes. Drug Discovery Today, 15, 851-8.
JESMIN, J., RASHID, M. S., JAMIL, H., HONTECILLAS, R. & BASSAGANYA-RIERA, J. (2010) Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. BMC Medical Genomics, 3, 45.
JIA, P., SUN, J., GUO, A. Y. & ZHAO, Z. (2010) SZGR: a comprehensive schizophrenia gene resource. Molecular Psychiatry, 15, 453-62.
JIA, P. & ZHAO, Z. (2010) Convergent evidence for Wnt signaling pathway in psychotic disorders. Proceedings of 2010 Biomedical Sciences and Engineering Conference. IEEE.
JIAO, Q., YANG, Z. & HUANG, J. (2010) Construction of a gene regulatory network for Arabidopsis based on metabolic pathway data. Chinese Science Bulletin, 55, 158-162.
JIMÉNEZ, B. G., LEDEZMA, A. & SANCHIS, A. (2010) MMRF for Proteome Annotation Applied to Human Protein Disease Prediction. Proceedings of 20th International Conference on Inductive Logic Programming (ILP 2010).
KANDASAMY, K., MOHAN, S. S., RAJU, R., KEERTHIKUMAR, S., KUMAR, G. S. S., VENUGOPAL, A. K., TELIKICHERLA, D., NAVARRO, J. D., MATHIVANAN, S., PECQUET, C., GOLLAPUDI, S. K., TATTIKOTA, S. G., MOHAN, S., PADHUKASAHASRAM, H., SUBBANNAYYA, Y., GOEL, R., JACOB, H. K. C., ZHONG, J., SEKHAR, R., NANJAPPA, V., BALAKRISHNAN, L., SUBBAIAH, R., RAMACHANDRA, Y. L., RAHIMAN, B. A., PRASAD, T. S. K., LIN, J.-X., HOUTMAN, J. C. D., DESIDERIO, S., RENAULD, J.-C., CONSTANTINESCU, S. N., OHARA, O., HIRANO, T., KUBO, M., SINGH, S., KHATRI, P., DRAGHICI, S., BADER, G. D., SANDER, C., LEONARD, W. J. & PANDEY, A. (2010) NetPath: a public resource of curated signal transduction pathways. Genome Biology, 11, R3.
KANN, M. G. (2010) Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Briefings in Bioinformatics, 11, 96-110.
KARLAS, A., MACHUY, N., SHIN, Y., PLEISSNER, K.-P., ARTARINI, A., HEUER, D., BECKER, D., KHALIL, H., OGILVIE, L. A., HESS, S., MÄURER, A. P., MÜLLER, E., WOLFF, T., RUDEL, T. & MEYER, T. F. (2010) Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature, 463, 818-22.
KARP, P. D., PALEY, S. M., KRUMMENACKER, M., LATENDRESSE, M., DALE, J. M., LEE, T. J., KAIPA, P., GILHAM, F., SPAULDING, A., POPESCU, L., ALTMAN, T., PAULSEN, I., KESELER, I. M. & CASPI, R. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics, 11, 40-79.
KELDER, T., CONKLIN, B. R., EVELO, C. T. & PICO, A. R. (2010) Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets. PLoS Biology, 8, e1000472.
KILNER, J., ZHU, L., OW, S. Y., EVANS, C. & CORFE, B. (2010) Assessing the Loss of Information through Application of the ‘Two-hit Rule’ in iTRAQ Datasets. Journal of Integrated OMICS, 1.
KLINGSTRÖM, T. & PLEWCZYNSKI, D. (2010) Protein-protein interaction and pathway databases, a graphical review. Briefings in Bioinformatics.
KLOMP, J., TEH, B. & FURGE, K. (2010) An Integrated Oncogenomic Approach: From Genes to Pathway Analyses. An Omics Perspective on Cancer Research.
KOH, J. L. Y., DING, H., COSTANZO, M., BARYSHNIKOVA, A., TOUFIGHI, K., BADER, G. D., MYERS, C. L., ANDREWS, B. J. & BOONE, C. (2010) DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Research, 38, D502-7.
KORCSMÁROS, T., FARKAS, I. J., SZALAY, M. S., ROVÓ, P., FAZEKAS, D., SPIRÓ, Z., BÖDE, C., LENTI, K., VELLAI, T. & CSERMELY, P. (2010) Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics, 26, 2042-50.
KORMEIER, B., HIPPE, K., TÖPEL, T. & HOFESTÄDT, R. (2010) CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases. Journal of Integrative Bioinformatics, 7, 142.
KUHN, M., SZKLARCZYK, D., FRANCESCHINI, A., CAMPILLOS, M., VON MERING, C., JENSEN, L. J., BEYER, A. & BORK, P. (2010) STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research, 38, D552-6.
LACHMANN, A. & MA'AYAN, A. (2010) Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics, 11, 87.
LATENDRESSE, M. & KARP, P. D. (2010) An advanced web query interface for biological databases. Database, 2010, baq006.
LAUKENS, K., HOLLUNDER, J., DANG, T. H., DE JAEGER, G., KUIPER, M., WITTERS, E., VERSCHOREN, A. & VAN LEEMPUT, K. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics, 11, 360.
LI, C., DONIZELLI, M., RODRIGUEZ, N., DHARURI, H., ENDLER, L., CHELLIAH, V., LI, L., HE, E., HENRY, A., STEFAN, M. I., SNOEP, J. L., HUCKA, M., LE NOVÈRE, N. & LAIBE, C. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology, 4, 92.
LI, J., DUNCAN, D. T. & ZHANG, B. (2010) CanProVar: a human cancer proteome variation database. Human Mutation, 31, 219-28.
LI, P., DADA, J. O., JAMESON, D., SPASIC, I., SWAINSTON, N., CARROLL, K., DUNN, W., KHAN, F., MALYS, N., MESSIHA, H. L., SIMEONIDIS, E., WEICHART, D., WINDER, C., WISHART, J., BROOMHEAD, D., GOBLE, C. A., GASKELL, S. J., KELL, D. B., WESTERHOFF, H. V., MENDES, P. & PATON, N. W. (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics, 11, 582.
LI, Y. (2010) Systems Biology for Signaling Networks. Systems Biology, 491-504.
LIKIĆ, V. A., MCCONVILLE, M. J., LITHGOW, T. & BACIC, A. (2010) Systems Biology: The Next Frontier for Bioinformatics. Advances in Bioinformatics.
LYNN, D. J., GARDY, J. L., FJELL, C. D., HANCOCK, R. E. W. & BRINKMAN, F. S. L. (2010) Systems Biology for Signaling Networks. Systems Biology, 531-560.
MALIK, R., DULLA, K., NIGG, E. A. & KÖRNER, R. (2010) From proteome lists to biological impact--tools and strategies for the analysis of large MS data sets. Proteomics, 10, 1270-83.
MARTIN, A., OCHAGAVIA, M. E., RABASA, L. C., MIRANDA, J., FERNANDEZ-DE-COSSIO, J. & BRINGAS, R. (2010) BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics, 11, 91.
MASSA, M. S., CHIOGNA, M. & ROMUALDI, C. (2010) Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, 4, 121.
MATSUOKA, Y., GHOSH, S., KIKUCHI, N. & KITANO, H. (2010) Payao: a community platform for SBML pathway model curation. Bioinformatics, 26, 1381-3.
MEDINA, I., CARBONELL, J., PULIDO, L., MADEIRA, S. C., GOETZ, S., CONESA, A., TÁRRAGA, J., PASCUAL-MONTANO, A., NOGALES-CADENAS, R., SANTOYO, J., GARCÍA, F., MARBÀ, M., MONTANER, D. & DOPAZO, J. (2010) Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research, 1-4.
MEINEL, T. & WIG, R. H. (2010) Web-Based Applications in Healthcare and Biomedicine. Information Systems, 7, 101-116.
MERICO, D., ISSERLIN, R., STUEKER, O., EMILI, A. & BADER, G. D. (2010) Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation. PLoS one, 5, e13984.
MINGUEZ, P. & DOPAZO, J. (2010) Functional genomics and networks: new approaches in the extraction of complex gene modules. Expert Review of Proteomics, 7, 55-63.
MONTANER, D. & DOPAZO, J. (2010) Multidimensional Gene Set Analysis of Genomic Data. PLoS one, 5, e10384.
MORRIS, J. H., MENG, E. C. & FERRIN, T. E. (2010) Computational tools for the interactive exploration of proteomic and structural data. Molecular and Cellular Proteomics, 9, 1703-15.
MOSCA, E., ALFIERI, R., MERELLI, I., VITI, F., CALABRIA, A. & MILANESI, L. (2010) A multilevel data integration resource for breast cancer study. BMC Systems Biology, 4, 76.
NOOKAEW, I., GABRIELSSON, B. G., HOLMÄNG, A., SANDBERG, A.-S. & NIELSEN, J. (2010) Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice. PLoS one, 5, e12361.
ONSONGO, G., XIE, H. & GRIFFIN, T. (2010) Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data. Association for Computing Machinery.
ORCHARD, S., JONES, A., ALBAR, J.-P., CHO, S. Y., KWON, K.-H., LEE, C. & HERMJAKOB, H. (2010) Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics, 10, 3062-6.
OV, A. & VINOGRADOV, A. (2010) Somatic polyploidy associated metabolic changes revealed by modular biology. Tsitologiia, 52, 52-62.
PAE, C.-U., DRAGO, A., FORLANI, M., PATKAR, A. A. & SERRETTI, A. (2010) Investigation of an epistastic effect between a set of TAAR6 and HSP-70 genes variations and major mood disorders. American Journal of Medical Genetics, 153B, 680-3.
PARK, I., LEE, K. H. & LEE, D. (2010) Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets. Bioinformatics, 26, 1506-12.
PATIL, S., PINCAS, H., SETO, J., NUDELMAN, G., NUDELMAN, I. & SEALFON, S. C. (2010) Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. BMC Systems Biology, 4, 137.
PATTIN, K. A., GUI, J. & MOORE, J. H. (2010) Employing Publically Available Biological Expert Knowledge from Protein-Protein Interaction Information. Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics 2010 (PRIB'10).
RAAB, M., DAXECKER, H., EDWARDS, R. J., TREUMANN, A., MURPHY, D. & MORAN, N. (2010) Protein interactions with the platelet integrin alpha(IIb) regulatory motif. Proteomics, 2790-2800.
RAMACHANDRARAO, S. P., TALWAR, P., RAVASI, T. & SHARMA, K. (2010) Novel systems biology insights using antifibrotic approaches for diabetic kidney disease. Expert Review of Endocrinology & Metabolism, 5, 127-135.
RANEA, J. A. G., MORILLA, I., LEES, J. G., REID, A. J., YEATS, C., CLEGG, A. B., SANCHEZ-JIMENEZ, F. & ORENGO, C. (2010) Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling. PLoS Computational Biology, 6, e1000945.
RAZA, S., MCDERMENT, N., LACAZE, P. A., ROBERTSON, K., WATTERSON, S., CHEN, Y., CHISHOLM, M., ELEFTHERIADIS, G., MONK, S., O'SULLIVAN, M., TURNBULL, A., ROY, D., THEOCHARIDIS, A., GHAZAL, P. & FREEMAN, T. C. (2010) Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. BMC Systems Biology, 4, 63.
REBOIRO-JATO, M., GLEZ-PEÑA, D., DOMINGUEZ, R., GÓMEZ-LÓPEZ, G., PISANO, D., CAMPOS, C. & FDEZ-RIVEROLA, F. (2010) PathAgent: Multi-agent System for Updated Pathway Information Integration. Trends in Practical Applications of Agents and Multiagent Systems, 77-85.
REIMAND, J., VAQUERIZAS, J. M., TODD, A. E., VILO, J. & LUSCOMBE, N. M. (2010) Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Research, 38, 4768-4777.
RENKONEN, J., MATTILA, P., PARVIAINEN, V., JOENVÄÄRÄ, S., TOPPILA-SALMI, S. & RENKONEN, R. (2010) A network analysis of the single nucleotide polymorphisms in acute allergic diseases. Allergy, 65, 40-7.
RODRÍGUEZ-PRADOS, J.-C., TRAVÉS, P. G., CUENCA, J., RICO, D., ARAGONÉS, J., MARTÍN-SANZ, P., CASCANTE, M. & BOSCÁ, L. (2010) Substrate Fate in Activated Macrophages: A Comparison Between Innate, Classic, and Alternative Activation. Journal of Immunology.
ROMANO, G. H., GURVICH, Y., LAVI, O., ULITSKY, I., SHAMIR, R. & KUPIEC, M. (2010) Different sets of QTLs influence fitness variation in yeast. Molecular Systems Biology, 6, 346.
RUEBENACKER, O. & BLINOV, M. (2010) Using views of Systems Biology Cloud: application for model building. Theory in Biosciences.
SARDER, P., ZHANG, W., COBB, J. P. & NEHORAI, A. (2010) Link Mining: Models, Algorithms, and Applications. Link Mining: Models, Algorithms, and Applications, 557-568.
SATAGOPAM, V. P., THEODOROPOULOU, M. C., STAMPOLAKIS, C. K., PAVLOPOULOS, G. A., PAPANDREOU, N. C., BAGOS, P. G., SCHNEIDER, R. & HAMODRAKAS, S. J. (2010) GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database, 2010, baq019-baq019.
SCHELLENBERGER, J., PARK, J. O., CONRAD, T. M. & PALSSON, B. Ø. (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics, 11, 213.
SCHNACKENBERG, L. K., SUN, J., PENCE, L., BHATTACHARYYA, S., SONKO, B. J. & BEGER, R. D. (2010) Metabolomics for Personalized Nutrition Research and Clinical Applications. Current Pharmacogenomics and Personalized Medicine, 8, 202-217.
SEALFON, R. A. & SEALFON, S. C. (2010) Systems Biology for Signaling Networks. Systems Biology, 75-83.
SIMS, D., BURSTEINAS, B., GAO, Q., JAIN, E., MACKAY, A., MITSOPOULOS, C. & ZVELEBIL, M. (2010) ROCK: a breast cancer functional genomics resource. Breast Cancer Research and Treatment, 124, 567-72.
SIMS, D., BURSTEINAS, B., JAIN, E., GAO, Q., BAUM, B. & ZVELEBIL, M. (2010) The flight Drosophila RNAi database: 2010 update. Fly, 4, 1-5.
SINGH, I. & KLEIN-SEETHARAMAN, J. (2010) Comparison of Virus Interactions with Human Signal Transduction Pathways. Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology.
SOH, D., DONG, D., GUO, Y. & WONG, L. (2010) Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics, 11, 449.
SÖLLNER, J., HEINZEL, A., SUMMER, G., FECHETE, R., STIPKOVITS, L., SZATHMARY, S. & MAYER, B. (2010) Concept and application of a computational vaccinology workflow. Immunome Research, 6 Suppl 2, S7.
STEFANINI, I., TRABOCCHI, A., MARCHI, E., GUARNA, A. & CAVALIERI, D. (2010) A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of saccharomyces cerevisiae mutants. The Journal of Biological Chemistry, 285, 23477-85.
STEGMAIER, P., KRULL, M., VOSS, N., KEL, A. E. & WINGENDER, E. (2010) Molecular mechanistic associations of human diseases. BMC Systems Biology, 4, 124.
STINGO, F., CHEN, Y. A., TADESSE, M. & VANNUCCI, M. (2010) Incorporating biological information into linear models: a bayesian approach to the selection of pathways and genes. Annals of Applied Statistics, 1-26.
SUN, J. & ZHAO, Z. (2010) Functional Features, Biological Pathways, and Protein Interaction Networks of Addiction-Related Genes. Chemistry and Biodiversity, 7, 1153-1162.
SWAINSTON, N., GOLEBIEWSKI, M., MESSIHA, H. L., MALYS, N., KANIA, R., KENGNE, S., KREBS, O., MIR, S., SAUER-DANZWITH, H., SMALLBONE, K., WEIDEMANN, A., WITTIG, U., KELL, D. B., MENDES, P., MÜLLER, W., PATON, N. W. & ROJAS, I. (2010) Enzyme kinetics informatics: from instrument to browser. The FEBS Journal, 277, 3769-79.
SZKLARCZYK, R. & HUYNEN, M. A. (2010) Mosaic origin of the mitochondrial proteome. Proteomics, 10, 4012-4024.
TARI, L., ANWAR, S., LIANG, S., HAKENBERG, J. & BARAL, C. (2010) Synthesis of pharmacokinetic pathways through knowledge acquisition and automated reasoning. Pacific Symposium on Biocomputing, 465-76.
TRANCHEVENT, L.-C., CAPDEVILA, F. B., NITSCH, D., DE MOOR, B., DE CAUSMAECKER, P. & MOREAU, Y. (2010) A guide to web tools to prioritize candidate genes. Briefings in Bioinformatics, 12, 22-32.
ULITSKY, I., MARON-KATZ, A., SHAVIT, S., SAGIR, D., LINHART, C., ELKON, R., TANAY, A., SHARAN, R., SHILOH, Y. & SHAMIR, R. (2010) Expander: from expression microarrays to networks and functions. Nature Protocols, 5, 303-22.
VAN DELFT, J. H. M., MATHIJS, K., STAAL, Y. C. M., VAN HERWIJNEN, M. H. M., BRAUERS, K. J. J., BOORSMA, A. & KLEINJANS, J. C. S. (2010) Time series analysis of benzo[A]pyrene-induced transcriptome changes suggests that a network of transcription factors regulates the effects on functional gene sets. Toxicological Sciences, 117, 381-92.
VAN HEMERT, J. L. & DICKERSON, J. A. (2010) PathwayAccess: CellDesigner plugins for pathway databases. Bioinformatics, 26, 2345-6.
VAN LEENE, J., HOLLUNDER, J., EECKHOUT, D., PERSIAU, G., VAN DE SLIJKE, E., STALS, H., VAN ISTERDAEL, G., VERKEST, A., NEIRYNCK, S., BUFFEL, Y., DE BODT, S., MAERE, S., LAUKENS, K., PHARAZYN, A., FERREIRA, P. C. G., ELOY, N., RENNE, C., MEYER, C., FAURE, J.-D., STEINBRENNER, J., BEYNON, J., LARKIN, J. C., VAN DE PEER, Y., HILSON, P., KUIPER, M., DE VEYLDER, L., VAN ONCKELEN, H., INZÉ, D., WITTERS, E. & DE JAEGER, G. (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Molecular Systems Biology, 6, 397.
VASKE, C. J., BENZ, S. C., SANBORN, J. Z., EARL, D., SZETO, C., ZHU, J., HAUSSLER, D. & STUART, J. M. (2010) Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics, 26, i237-i245.
VINOGRADOV, A. E. (2010) Human transcriptome nexuses: basic-eukaryotic and metazoan. Genomics, 95, 345-54.
VIZCAÍNO, J. A., CÔTÉ, R., REISINGER, F., BARSNES, H., FOSTER, J. M., RAMESEDER, J., HERMJAKOB, H. & MARTENS, L. (2010) The Proteomics Identifications database: 2010 update. Nucleic Acids Research, 38, D736-42.
VIZCAÍNO, J. A., FOSTER, J. M. & MARTENS, L. (2010) Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. Journal of Proteomics, 73, 2136-46.
VIZCAÍNO, J. A., REISINGER, F., CÔTÉ, R. & MARTENS, L. (2010) PRIDE: Data submission and analysis. Current protocols in protein science / editorial board, John E. Coligan ... [et al.], Chapter 25, Unit 25.4.
VOIGHT, B. F., SCOTT, L. J., STEINTHORSDOTTIR, V., MORRIS, A. P., DINA, C., WELCH, R. P., ZEGGINI, E., HUTH, C., AULCHENKO, Y. S., THORLEIFSSON, G. & OTHERS (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nature Genetics, 42, 579-589.
WANG, M., SHANG, X., LEI, X. & LI, Z. (2010) Mining Maximal Frequent Dense Subgraphs without Candidate Maintenance in PPI Networks. Proceedings of 2nd International Workshop on Intelligent Systems and Applications. Ieee.
WARDE-FARLEY, D., DONALDSON, S. L., COMES, O., ZUBERI, K., BADRAWI, R., CHAO, P., FRANZ, M., GROUIOS, C., KAZI, F., LOPES, C. T., MAITLAND, A., MOSTAFAVI, S., MONTOJO, J., SHAO, Q., WRIGHT, G., BADER, G. D. & MORRIS, Q. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research, 38, W214-W220.
WATANABE, T., WATANABE, S. & KAWAOKA, Y. (2010) Cellular networks involved in the influenza virus life cycle. Cell Host & Microbe, 7, 427-39.
WATTERSON, S. & GHAZAL, P. (2010) Use of logic theory in understanding regulatory pathway signaling in response to infection. Future Microbiology, 5, 163-76.
WOELKE, A. L., MURGUEITIO, M. S. & PREISSNER, R. (2010) Theoretical modeling techniques and their impact on tumor immunology. Clinical and Developmental Immunology, 2010, 271794.
WU, C.-C., ASGHARZADEH, S., TRICHE, T. J. & D'ARGENIO, D. Z. (2010) Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning. Bioinformatics, 26, 807-13.
WU, G., FENG, X. & STEIN, L. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biology, 11, R53.
WU, Z.-J., ZHU, Y., HUANG, D.-R. & WANG, Z.-Q. (2010) Constructing the HBV-Human Protein Interaction Network to Understand the Relationship Between HBV and Hepatocellular Carcinoma. Journal of experimental & clinical cancer research : CR, 29, 146.
WUCHTY, S., SIWO, G. & FERDIG, M. T. (2010) Viral organization of human proteins. PLoS one, 5, e11796.
WUCHTY, S., ZHANG, A., WALLING, J., AHN, S., LI, A., QUEZADO, M., OBERHOLTZER, C., ZENKLUSEN, J.-C. & FINE, H. A. (2010) Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. Journal of Biomedical Informatics, 43, 945-52.
XIA, J. & WISHART, D. S. (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Research, 38, W71-7.
XU, H., SCHANIEL, C., LEMISCHKA, I. R. & MA'AYAN, A. (2010) Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Systems Biology and Medicine, 2, 708-33.
YANG, M. Q., LAFLAMME, K., GOTEA, V., JOINER, C. H., SEIDEL, N. E., WONG, C., PETRYKOWSKA, H. M., LICHTENBERG, J., LEE, S., WELCH, L., GALLAGHER, P. G., BODINE, D. M. & ELNITSKI, L. (2010) Genome-wide detection of a TFIID localization element from an initial human disease mutation. Lecture Notes in Comput Science, 39, 2175-2187.
YAO, C., LI, H., ZHOU, C., ZHANG, L., ZOU, J. & GUO, Z. (2010) Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. BMC Systems Biology, 4, 151.
YOU, Q. & FANG, S. (2010) GeneTerrain: visual exploration of differential gene expression profiles organized in native biomolecular interaction networks. Information Visualization.
YU, W.-H., HU, H., ZHOU, Q., XIA, Y. & AMAR, S. (2010) Bioinformatics Analysis of Macrophages Exposed to Porphyromonas gingivalis: Implications in Acute vs. Chronic Infections. PLoS one, 5, e15613.
ZAMBACH, S. & HANSEN, J. (2010) Logical knowledge representation of regulatory relations in biomedical pathways. Proceedings of Information Technology in Bio-and Medical Informatics, ITBAM 2010, 186-200.
ZHANG, K. X. & OUELLETTE, B. F. F. (2010) Pandora, a pathway and network discovery approach based on common biological evidence. Bioinformatics, 26, 529-35.
ZHANG, M. & LU, L. J. (2010) Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics, 11, 466.
ZHANG, P., DREHER, K., KARTHIKEYAN, A., CHI, A., PUJAR, A., CASPI, R., KARP, P., KIRKUP, V., LATENDRESSE, M., LEE, C., MUELLER, L. A., MULLER, R. & RHEE, S. Y. (2010) Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants. Plant Physiology, 153, 1479-1491.
ZHANG, Y., XUAN, J., DE LOS REYES, B. G., CLARKE, R. & RESSOM, H. W. (2010) Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS one, 5, e10268.
ZHANG, Z. & ZHANG, Z.-G. (2010) Integrating Heterogeneous Protein-Protein Interaction Databases Based on Metadata. Chinese Journal of Biomedical Engineering, 02.
ZHU, J., XIAO, H., SHEN, X., WANG, J., ZOU, J., ZHANG, L., YANG, D., MA, W., YAO, C., GONG, X., ZHANG, M., ZHANG, Y. & GUO, Z. (2010) Viewing cancer genes from co-evolving gene modules. Bioinformatics, 26, 919-24.
ZOU, J., LUO, S.-D., WEI, Y.-Q. & YANG, S.-Y. (2010) Integrated computational model of cell cycle and checkpoint reveals different essential roles of Aurora-A and Plk1 in mitotic entry. Molecular Biosystems, 169-179.

2009

ADLER, P., PETERSON, H., AGIUS, P., REIMAND, J. & VILO, J. (2009) Ranking genes by their co-expression to subsets of pathway members. Annals of the New York Academy of Sciences, 1158, 1-13.
ALFIERI, R., BARBERIS, M., CHIARADONNA, F., GAGLIO, D., MILANESI, L., VANONI, M., KLIPP, E. & ALBERGHINA, L. (2009) Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. BMC Bioinformatics, 10 Suppl 1, S16.
ANTEZANA, E., EGAÑA, M., BLONDÉ, W., ILLARRAMENDI, A., BILBAO, I., DE BAETS, B., STEVENS, R., MIRONOV, V. & KUIPER, M. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology, 10, R58.
ANTEZANA, E., KUIPER, M. & MIRONOV, V. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics, 10, 392-407.
ARAKAWA, K., TAMAKI, S., KONO, N., KIDO, N., IKEGAMI, K., OGAWA, R. & TOMITA, M. (2009) Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics, 10, 31.
ARIGHI, C. N., LIU, H., NATALE, D. A., BARKER, W. C., DRABKIN, H., BLAKE, J. A., SMITH, B. & WU, C. H. (2009) TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics, 10 Suppl 5, S3.
BALAKRISHNAN, S., TASTAN, O., CARBONELL, J. & KLEIN-SEETHARAMAN, J. (2009) Alternative paths in HIV-1 targeted human signal transduction pathways. BMC Genomics, 10 Suppl 3, S30.
BAUDOT, A., GÓMEZ-LÓPEZ, G. & VALENCIA, A. (2009) Translational disease interpretation with molecular networks. Genome Biology, 10, 221.
BAUER-MEHREN, A., FURLONG, L. I., RAUTSCHKA, M. & SANZ, F. (2009) From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. BMC Bioinformatics, 10 Suppl 8, S6.
BAUER-MEHREN, A., FURLONG, L. I. & SANZ, F. (2009) Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Molecular Systems Biology, 5, 290.
BAYÉS, A. & GRANT, S. G. N. (2009) Neuroproteomics: understanding the molecular organization and complexity of the brain. Nature Reviews Neuroscience, 10, 635-46.
BEN-SHLOMO, I., RAUCH, R., AVSIAN-KRETCHMER, O. & HSUEH, A. J. W. (2009) Matching Receptome Genes with Their Ligands for Surveying Paracrine/ Autocrine Signaling Systems. Molecular Endocrinology, 2009-2014.
BENITA, Y., KIKUCHI, H., SMITH, A. D., ZHANG, M. Q., CHUNG, D. C. & XAVIER, R. J. (2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Research, 37, 4587-602.
BERNTHALER, A., MÜHLBERGER, I., FECHETE, R., PERCO, P., LUKAS, A. & MAYER, B. (2009) A dependency graph approach for the analysis of differential gene expression profiles. Molecular Biosystems, 5, 1720-31.
BOSSI, A. & LEHNER, B. (2009) Tissue specificity and the human protein interaction network. Molecular Systems Biology, 5, 260.
BRAECKMAN, B. P., HOUTHOOFD, K. & VANFLETEREN, J. R. (2009) Intermediary metabolism. WormBook: The Online Review of C. elegans Biology, 1-24.
BRASS, A. L., HUANG, I.-C., BENITA, Y., JOHN, S. P., KRISHNAN, M. N., FEELEY, E. M., RYAN, B. J., WEYER, J. L., VAN DER WEYDEN, L., FIKRIG, E., ADAMS, D. J., XAVIER, R. J., FARZAN, M. & ELLEDGE, S. J. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell, 139, 1243-54.
BUSH, W. S., DUDEK, S. M. & RITCHIE, M. D. (2009) Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pacific Symposium on Biocomputing, 379, 368-79.
CALDAS, J., GEHLENBORG, N., FAISAL, A., BRAZMA, A. & KASKI, S. (2009) Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics, 25, i145-53.
CARE, M. A., BRADFORD, J. R., NEEDHAM, C. J., BULPITT, A. J. & WESTHEAD, D. R. (2009) Combining the interactome and deleterious SNP predictions to improve disease gene identification. Human Mutation, 30, 485-92.
CARRARO, S., GIORDANO, G., RENIERO, F., PERILONGO, G. & BARALDI, E. (2009) Metabolomics: a new frontier for research in pediatrics. The Journal of Pediatrics, 154, 638-44.
CHAURASIA, G., MALHOTRA, S., RUSS, J., SCHNOEGL, S., HÄNIG, C., WANKER, E. E. & FUTSCHIK, M. E. (2009) UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. Nucleic Acids Research, 37, D657-60.
CHEN, H., DING, L., WU, Z., YU, T., DHANAPALAN, L. & CHEN, J. Y. (2009) Semantic web for integrated network analysis in biomedicine. Briefings in Bioinformatics, 10, 177-92.
CHOWBINA, S. R., WU, X., ZHANG, F., LI, P. M., PANDEY, R., KASAMSETTY, H. N. & CHEN, J. Y. (2009) HPD: an online integrated human pathway database enabling systems biology studies. BMC Bioinformatics, 10 Suppl 1, S5.
DAVIS, A. P., MURPHY, C. G., SARACENI-RICHARDS, C. A., ROSENSTEIN, M. C., WIEGERS, T. C. & MATTINGLY, C. J. (2009) Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Research, 37, D786-92.
DIETMANN, S., GEORGII, E., ANTONOV, A., TSUDA, K. & MEWES, H.-W. (2009) The DICS repository: module-assisted analysis of disease-related gene lists. Bioinformatics, 25, 830-1.
DOGRUSOZ, U., CETINTAS, A., DEMIR, E. & BABUR, O. (2009) Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinformatics, 10, 376.
DRISCOLL, T., DYER, M. D., MURALI, T. M. & SOBRAL, B. W. (2009) PIG--the pathogen interaction gateway. Nucleic Acids Research, 37, D647-50.
DURINCK, S., SPELLMAN, P. T., BIRNEY, E. & HUBER, W. (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols, 4, 1184-91.
EISENACHER, M., MARTENS, L., HARDT, T., KOHL, M., BARSNES, H., HELSENS, K., HÄKKINEN, J., LEVANDER, F., AEBERSOLD, R., VANDEKERCKHOVE, J., DUNN, M. J., LISACEK, F., SIEPEN, J. A., HUBBARD, S. J., BINZ, P.-A., BLÜGGEL, M., THIELE, H., COTTRELL, J., MEYER, H. E., APWEILER, R. & STEPHAN, C. (2009) Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics, 9, 3928-33.
ENDLER, L., RODRIGUEZ, N., JUTY, N., CHELLIAH, V., LAIBE, C., LI, C. & LE NOVÈRE, N. (2009) Designing and encoding models for synthetic biology. Interface, 6 Suppl 4, S405-17.
ESSACK, M., RADOVANOVIC, A., SCHAEFER, U., SCHMEIER, S., SESHADRI, S. V., CHRISTOFFELS, A., KAUR, M. & BAJIC, V. B. (2009) DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer, 9, 219.
EVSIKOV, A. V., DOLAN, M. E., GENRICH, M. P., PATEK, E. & BULT, C. J. (2009) MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biology, 10, R84.
FAURÉ, A. & THIEFFRY, D. (2009) Logical modelling of cell cycle control in eukaryotes: a comparative study. Molecular Biosystems, 5, 1569-1581.
FAUST, K., CROES, D. & VAN HELDEN, J. (2009) Metabolic pathfinding using RPAIR annotation. Journal of Molecular Biology, 388, 390-414.
GERSTEN, M., ALIREZAEI, M., MARCONDES, M. C. G., FLYNN, C., RAVASI, T., IDEKER, T. & FOX, H. S. (2009) An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. The Journal of Neuroscience, 29, 12467-76.
GLEZ-PEÑA, D., GÓMEZ-LÓPEZ, G., PISANO, D. G. & FDEZ-RIVEROLA, F. (2009) WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis. Nucleic Acids Research, 37, W329-34.
HAIDER, S., BALLESTER, B., SMEDLEY, D., ZHANG, J., RICE, P. & KASPRZYK, A. (2009) BioMart Central Portal--unified access to biological data. Nucleic Acids Research, 37, W23-7.
HAN, J., DATLA, R., CHAN, S. & BORCHERS, C. H. (2009) Mass spectrometry-based technologies for high-throughput metabolomics. Bioanalysis, 1, 1665-84.
HEAP, G. A., TRYNKA, G., JANSEN, R. C., BRUINENBERG, M., SWERTZ, M. A., DINESEN, L. C., HUNT, K. A., WIJMENGA, C., VANHEEL, D. A. & FRANKE, L. (2009) Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Medical Genomics, 2, 1.
HU, J. C., KARP, P. D., KESELER, I. M., KRUMMENACKER, M. & SIEGELE, D. A. (2009) What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology, 17, 269-78.
HUMINIECKI, L., GOLDOVSKY, L., FREILICH, S., MOUSTAKAS, A., OUZOUNIS, C. & HELDIN, C.-H. (2009) Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. BMC Evolutionary Biology, 9, 28.
HUTTENHOWER, C., HALEY, E. M., HIBBS, M. A., DUMEAUX, V., BARRETT, D. R., COLLER, H. A. & TROYANSKAYA, O. G. (2009) Exploring the human genome with functional maps. Genome Research, 1093-1106.
IHEKWABA, A. E. C., NGUYEN, P. T. & PRIAMI, C. (2009) Elucidation of functional consequences of signalling pathway interactions. BMC Bioinformatics, 10, 370.
IOSSIFOV, I., RODRIGUEZ-ESTEBAN, R., MAYZUS, I., MILLEN, K. J. & RZHETSKY, A. (2009) Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Computational Biology, 5, e1000559.
ISOKPEHI, R. D., LEWIS, S. A., OYELEYE, T. O., AYENSU, W. K. & GERALD, T. M. (2009) Comorbidity of bipolar disorder with substance abuse: selection of prioritized genes for translational research. Proceedings of Summit on Translational Bioinformatics.
JENSEN, L. J., KUHN, M., STARK, M., CHAFFRON, S., CREEVEY, C., MULLER, J., DOERKS, T., JULIEN, P., ROTH, A., SIMONOVIC, M., BORK, P. & VON MERING, C. (2009) STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37, D412-6.
JIANG, K., HUANG, Y. & ROBERTSON, J. (2009) A method of biological pathway similarity search using high performance computing. Proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society., 2009, 4933-6.
KAHLEM, P., CLEGG, A., REISINGER, F., XENARIOS, I., HERMJAKOB, H., ORENGO, C. & BIRNEY, E. (2009) ENFIN--A European network for integrative systems biology. Comptes Rendus Biologies, 332, 1050-8.
KAMBUROV, A., WIERLING, C., LEHRACH, H. & HERWIG, R. (2009) ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Research, 37, D623-8.
KAUR, M., RADOVANOVIC, A., ESSACK, M., SCHAEFER, U., MAQUNGO, M., KIBLER, T., SCHMEIER, S., CHRISTOFFELS, A., NARASIMHAN, K., CHOOLANI, M. & BAJIC, V. B. (2009) Database for exploration of functional context of genes implicated in ovarian cancer. Nucleic Acids Research, 37, D820-3.
KAYANO, M., TAKIGAWA, I., SHIGA, M., TSUDA, K. & MAMITSUKA, H. (2009) Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinformatics, 25, 2735-43.
KELDER, T., PICO, A. R., HANSPERS, K., VAN IERSEL, M. P., EVELO, C. & CONKLIN, B. R. (2009) Mining biological pathways using WikiPathways web services. PLoS one, 4, e6447.
KIND, T., SCHOLZ, M. & FIEHN, O. (2009) How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS one, 4, e5440.
KIPP, A., BANNING, A., VAN SCHOTHORST, E. M., MÉPLAN, C., SCHOMBURG, L., EVELO, C., COORT, S., GAJ, S., KEIJER, J., HESKETH, J. & BRIGELIUS-FLOHÉ, R. (2009) Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon. Molecular Nutrition and Food Research, 53, 1561-72.
KONO, N., ARAKAWA, K., OGAWA, R., KIDO, N., OSHITA, K., IKEGAMI, K., TAMAKI, S. & TOMITA, M. (2009) Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS one, 4, e7710.
KREMER, H. & CREMERS, F. P. M. (2009) Auditory and Vestibular Research. Methods in Molecular Biology, 493.
KRÜGER, B. & DANDEKAR, T. (2009) Bioinformatical Approaches to Detect and Analyze Protein Interactions. Methods in Molecular Biology, 564.
KRUSHEVSKAYA, D., PETERSON, H., REIMAND, J., KULL, M. & VILO, J. (2009) VisHiC--hierarchical functional enrichment analysis of microarray data. Nucleic Acids Research, 37, W587-92.
KUMAR, P., HAN, B. C., SHI, Z., JIA, J., WANG, Y. P., ZHANG, Y. T., LIANG, L., LIU, Q. F., JI, Z. L. & CHEN, Y. Z. (2009) Update of KDBI: Kinetic Data of Bio-molecular Interaction database. Nucleic Acids Research, 37, D636-41.
LATINO, D. A. R. S. & AIRES-DE-SOUSA, J. (2009) Assignment of EC numbers to enzymatic reactions with MOLMAP reaction descriptors and random forests. Journal of Chemical Information and Modeling, 49, 1839-46.
LEE, H., KANG, R., HAHN, Y., YANG, Y., KIM, S. S., CHO, S. H., CHUNG, S. I. & YOON, Y. (2009) Antiobesity Effect of Baicalin involves the Modulations of Proadipogenic and Antiadipogenic Regulators of the Adipogenesis Pathway. Phytotherapy Research, 23, 1615-1623.
LEE, S., LEE, E., LEE, K. H. & LEE, D. (2009) Disease Classification Based on the Activities of Interacting Molecular Modules with Condition-Responsive Correlation. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine. Ieee.
LEE, T.-L., PANG, A. L.-Y., RENNERT, O. M. & CHAN, W.-Y. (2009) Genomic landscape of developing male germ cells. Birth Defects Research, 87, 43-63.
LEWIS, N. E., JAMSHIDI, N., THIELE, I. & PALSSON, B. Ø. (2009) Metabolic Systems Biology. Encyclopedia of Encyclopedia and Systems Science, 13, 5535-5552.
LI, F., PENG, Y., XU, W., YU, G., LI, P., BO, X. & WANG, S. (2009) Towards a Comprehensive HBV-Human Interaction Map. Proceedings of 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 311-314.
LI, L., ZHANG, K., LEE, J., CORDES, S., DAVIS, D. P. & TANG, Z. (2009) Discovering cancer genes by integrating network and functional properties. BMC Medical Genomics, 2, 61.
LICHTENBERG, J., JACOX, E., WELCH, J. D., KURZ, K., LIANG, X., YANG, M. Q., DREWS, F., ECKER, K., LEE, S. S., ELNITSKI, L. & WELCH, L. R. (2009) Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics, 10 Suppl 1, S18.
LINGHU, B., SNITKIN, E. S., HU, Z., XIA, Y. & DELISI, C. (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biology, 10, R91.
LYSENKO, A., LYSENKO, A., HINDLE, M. M., TAUBERT, J., SAQI, M. & RAWLINGS, C. J. (2009) Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases. Briefings in Bioinformatics, 10, 676-93.
MANAKOV, S. A., GRANT, S. G. N. & ENRIGHT, A. J. (2009) Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation. BMC Genomics, 10, 419.
MANNING, M., AGGARWAL, A., GAO, K. & TUCKER-KELLOGG, G. (2009) Scaling the walls of discovery: using semantic metadata for integrative problem solving. Briefings in Bioinformatics, 10, 164-76.
MILANESI, L., ROMANO, P., CASTELLANI, G., REMONDINI, D. & LIÒ, P. (2009) Trends in modeling Biomedical Complex Systems. BMC Bioinformatics, 10 Suppl 1, I1.
MONTANER, D., MINGUEZ, P., AL-SHAHROUR, F. & DOPAZO, J. (2009) Gene set internal coherence in the context of functional profiling. BMC Genomics, 10, 197.
MORRISSEY, E. R. & DIAZ-URIARTE, R. (2009) Pomelo II: finding differentially expressed genes. Nucleic Acids Research, 37, W581-6.
NAVRATIL, V., DE CHASSEY, B., MEYNIEL, L., DELMOTTE, S., GAUTIER, C., ANDRÉ, P., LOTTEAU, V. & RABOURDIN-COMBE, C. (2009) VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Research, 37, D661-8.
PAE, C.-U., DRAGO, A., PATKAR, A. A., JUN, T.-Y. & SERRETTI, A. (2009) Epistasis between a set of variations located in the TAAR6 and HSP-70 genes toward schizophrenia and response to antipsychotic treatment. European Neuropsychopharmacology, 19, 806-11.
PATTIN, K. A. & MOORE, J. H. (2009) Role for protein-protein interaction databases in human genetics. Expert Review of Proteomics, 6, 647-59.
PRICKETT, D. & WATSON, M. (2009) Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria. BMC Proceedings.
PURVIS, J. E., RADHAKRISHNAN, R. & DIAMOND, S. L. (2009) Steady-state kinetic modeling constrains cellular resting states and dynamic behavior. PLoS Computational Biology, 5, e1000298.
QU, X. A., GUDIVADA, R. C., JEGGA, A. G., NEUMANN, E. K. & ARONOW, B. J. (2009) Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. BMC Bioinformatics, 10 Suppl 5, S4.
RAMACHANDRARAO, S. P., ZHU, Y., RAVASI, T., MCGOWAN, T. A., TOH, I., DUNN, S. R., OKADA, S., SHAW, M. A. & SHARMA, K. (2009) Pirfenidone is renoprotective in diabetic kidney disease. Journal of the American Society of Nephrology, 20, 1765-75.
RAMAN, K. & CHANDRA, N. (2009) Flux balance analysis of biological systems: applications and challenges. Briefings in Bioinformatics, 10, 435-49.
RICHARDSON, C. J., GAO, Q., MITSOPOULOUS, C., ZVELEBIL, M., PEARL, L. H. & PEARL, F. M. G. (2009) MoKCa database--mutations of kinases in cancer. Nucleic Acids Research, 37, D824-31.
ROMASCHIN, A. D., YOUSSEF, Y., CHOW, T.-F. F., SIU, K. W. M., DESOUZA, L. V., HONEY, R. J., STEWART, R., PACE, K. T. & YOUSEF, G. M. (2009) Exploring the pathogenesis of renal cell carcinoma: pathway and bioinformatics analysis of dysregulated genes and proteins. Biological Chemistry, 390, 125-35.
RUEBENACKER, O., MORARU, I. I., SCHAFF, J. S. & BLINOV, M. L. (2009) Integrating BioPAX knowledge with SBML models. Systems Biology, IET, 3, 317-328.
SAHA, S., HARRISON, S. H. & CHEN, J. Y. (2009) Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics, 9, 470-84.
SCHAEFER, C. F., ANTHONY, K., KRUPA, S., BUCHOFF, J., DAY, M., HANNAY, T. & BUETOW, K. H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Research, 37, D674-9.
SCHULZ, H., KOLDE, R., ADLER, P., AKSOY, I., ANASTASSIADIS, K., BADER, M., BILLON, N., BOEUF, H., BOURILLOT, P.-Y., BUCHHOLZ, F., DANI, C., DOSS, M. X., FORRESTER, L., GITTON, M., HENRIQUE, D., HESCHELER, J., HIMMELBAUER, H., HÜBNER, N., KARANTZALI, E., KRETSOVALI, A., LUBITZ, S., PRADIER, L., RAI, M., REIMAND, J., ROLLETSCHEK, A., SACHINIDIS, A., SAVATIER, P., STEWART, F., STORM, M. P., TROUILLAS, M., VILO, J., WELHAM, M. J., WINKLER, J., WOBUS, A. M. & HATZOPOULOS, A. K. (2009) The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS one, 4, e6804.
SENZEL, L., GNATENKO, D. V. & BAHOU, W. F. (2009) The platelet proteome. Current Opinion in Hematology, 16, 329-33.
SMEDLEY, D., HAIDER, S., BALLESTER, B., HOLLAND, R., LONDON, D., THORISSON, G. & KASPRZYK, A. (2009) BioMart--biological queries made easy. BMC Genomics, 10, 22.
STEIN, A., PACHE, R. A., BERNADÓ, P., PONS, M. & ALOY, P. (2009) Dynamic interactions of proteins in complex networks: a more structured view. The FEBS Journal, 276, 5390-405.
SUN, C.-H., KIM, M.-S., HAN, Y. & YI, G.-S. (2009) COFECO: composite function annotation enriched by protein complex data. Nucleic Acids Research, 37, W350-5.
SUPPER, J., SPANGENBERG, L., PLANATSCHER, H., DRÄGER, A., SCHRÖDER, A. & ZELL, A. (2009) BowTieBuilder: modeling signal transduction pathways. BMC Systems Biology, 3, 67.
SUZUKI, A., TAKAI-IGARASHI, T., NUMABE, Y. & TANAKA, H. (2009) Development of a database and ontology for pathogenic pathways in periodontitis. In Silico Biology, 9, 233-43.
TARCA, A. L., DRAGHICI, S., KHATRI, P., HASSAN, S. S., MITTAL, P., KIM, J.-S., KIM, C. J., KUSANOVIC, J. P. & ROMERO, R. (2009) A novel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
TARCEA, V. G., WEYMOUTH, T., ADE, A., BOOKVICH, A., GAO, J., MAHAVISNO, V., WRIGHT, Z., CHAPMAN, A., JAYAPANDIAN, M., OZGÜR, A., TIAN, Y., CAVALCOLI, J., MIREL, B., PATEL, J., RADEV, D., ATHEY, B., STATES, D. & JAGADISH, H. V. (2009) Michigan molecular interactions : from interacting proteins to pathways. Nucleic Acids Research, 37, D642-6.
TEBER, E. T., LIU, J. Y., BALLOUZ, S., FATKIN, D. & WOUTERS, M. A. (2009) Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. BMC Bioinformatics, 10 Suppl 1, S69.
TIFFIN, N., ANDRADE-NAVARRO, M. A. & PEREZ-IRATXETA, C. (2009) Linking genes to diseases: it's all in the data. Genome medicine, 1, 77.
TUN, K., RAO, R. K., SAMAVEDHAM, L., TANAKA, H. & DHAR, P. K. (2009) Rich can get poor: conversion of hub to non-hub proteins. Systems and Synthetic Biology, 2, 75-82.
URBACH, J. M., WEI, T., LIBERATI, N., GRENFELL-LEE, D., VILLANUEVA, J., WU, G. & AUSUBEL, F. M. (2009) Using PATIMDB to create bacterial transposon insertion mutant libraries. Current Protocols in Molecular Biology, Chapter 19, Unit 19.7.
VAN HAAGEN, H. H. H. B. M., 'T HOEN, P. A. C., BOTELHO BOVO, A., DE MORRÉE, A., VAN MULLIGEN, E. M., CHICHESTER, C., KORS, J. A., DEN DUNNEN, J. T., VAN OMMEN, G.-J. B., VAN DER MAAREL, S. M., KERN, V. M., MONS, B. & SCHUEMIE, M. J. (2009) Novel protein-protein interactions inferred from literature context. PLoS one, 4, e7894.
VAN VLIET, M. H., WESSELS, L. F. A. & REINDERS, M. J. T. (2009) Knowledge driven decomposition of tumor expression profiles. BMC Bioinformatics, 10 Suppl 1, S20.
VANDERVALK, B. P., MCCARTHY, E. L. & WILKINSON, M. D. (2009) Moby and Moby 2: creatures of the deep (web). Briefings in Bioinformatics, 10, 114-28.
VASKE, C. J., HOUSE, C., LUU, T., FRANK, B., YEANG, C.-H., LEE, N. H. & STUART, J. M. (2009) A factor graph nested effects model to identify networks from genetic perturbations. PLoS Computational Biology, 5, e1000274.
VIZCAÍNO, J. A., CÔTÉ, R., REISINGER, F., FOSTER, J. M., MUELLER, M., RAMESEDER, J., HERMJAKOB, H. & MARTENS, L. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics, 9, 4276-83.
VIZCAÍNO, J. A., MUELLER, M., HERMJAKOB, H. & MARTENS, L. (2009) Charting online OMICS resources: A navigational chart for clinical researchers. Proteomics – Clinical Applications, 3, 18-29.
WAAIJENBORG, S. & ZWINDERMAN, A. H. (2009) Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks. BMC Bioinformatics, 10, 315.
WANG, X.-S., PRENSNER, J. R., CHEN, G., CAO, Q., HAN, B., DHANASEKARAN, S. M., PONNALA, R., CAO, X., VARAMBALLY, S., THOMAS, D. G., GIORDANO, T. J., BEER, D. G., PALANISAMY, N., SARTOR, M. A., OMENN, G. S. & CHINNAIYAN, A. M. (2009) An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nature Biotechnology, 27, 1005-11.
WHITAKER, J. W., LETUNIC, I., MCCONKEY, G. A. & WESTHEAD, D. R. (2009) metaTIGER: a metabolic evolution resource. Nucleic Acids Research, 37, D531-8.
WHITAKER, J. W., MCCONKEY, G. A. & WESTHEAD, D. R. (2009) The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biology, 10, R36.
WICHAPONG, K., LINDNER, M., PIANWANIT, S., KOKPOL, S. & SIPPL, W. (2009) Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors. European journal of medicinal chemistry, 44, 1383-95.
WICHAPONG, K., LINDNER, M., PIANWANIT, S., KOKPOL, S. & SIPPL, W. (2009) Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors. European Journal of Medicinal Chemistry, 44, 1383-95.
WISHART, D. S. (2009) Bioinformatics for Systems Biology. Genomics, 581-599.
WISHART, D. S., KNOX, C., GUO, A. C., EISNER, R., YOUNG, N., GAUTAM, B., HAU, D. D., PSYCHOGIOS, N., DONG, E., BOUATRA, S., MANDAL, R., SINELNIKOV, I., XIA, J., JIA, L., CRUZ, J. A., LIM, E., SOBSEY, C. A., SHRIVASTAVA, S., HUANG, P., LIU, P., FANG, L., PENG, J., FRADETTE, R., CHENG, D., TZUR, D., CLEMENTS, M., LEWIS, A., DE SOUZA, A., ZUNIGA, A., DAWE, M., XIONG, Y., CLIVE, D., GREINER, R., NAZYROVA, A., SHAYKHUTDINOV, R., LI, L., VOGEL, H. J. & FORSYTHE, I. (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research, 37, D603-10.
WOHLERS, I., STACHELSCHEID, H., BORSTLAP, J., ZEILINGER, K. & GERLACH, J. C. (2009) The Characterization Tool: A knowledge-based stem cell, differentiated cell, and tissue database with a web-based analysis front-end. Stem Cell Research, 3, 88-95.
YAMADA, T. & BORK, P. (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nature Reviews Molecular Cell Biology, 10, 791-803.
YOSHIDA, Y., MAKITA, Y., HEIDA, N., ASANO, S., MATSUSHIMA, A., ISHII, M., MOCHIZUKI, Y., MASUYA, H., WAKANA, S., KOBAYASHI, N. & TOYODA, T. (2009) PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Research, 37, W147-52.
YU, J. & FINLEY, R. L. (2009) Combining multiple positive training sets to generate confidence scores for protein-protein interactions. Bioinformatics, 25, 105-11.

2008

ADLER, P., REIMAND, J., JÄNES, J., KOLDE, R., PETERSON, H. & VILO, J. (2008) KEGGanim: pathway animations for high-throughput data. Bioinformatics, 24, 588-90.
ADRIAENS, M. E., JAILLARD, M., WAAGMEESTER, A., COORT, S. L. M., PICO, A. R. & EVELO, C. T. A. (2008) The public road to high-quality curated biological pathways. Drug Discovery Today, 13, 856-62.
AGRAWAL, S., DIMITROVA, N., NATHAN, P., UDAYAKUMAR, K., LAKSHMI, S. S., SRIRAM, S., MANJUSHA, N. & SENGUPTA, U. (2008) T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics, 9, 320.
AIYAR, R. S., GAGNEUR, J. & STEINMETZ, L. M. (2008) Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods, 46, 248-55.
ALFIERI, R., MERELLI, I., MOSCA, E. & MILANESI, L. (2008) The cell cycle DB: a systems biology approach to cell cycle analysis. Nucleic Acids Research, 36, D641-5.
ALIBÉS, A., CAÑADA, A. & DÍAZ-URIARTE, R. (2008) PaLS: filtering common literature, biological terms and pathway information. Nucleic Acids Research, 36, W364-7.
ARAGUES, R., SANDER, C. & OLIVA, B. (2008) Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics, 9, 172.
BABUR, O., COLAK, R., DEMIR, E. & DOGRUSOZ, U. (2008) PATIKAmad: putting microarray data into pathway context. Proteomics, 8, 2196-8.
BELLEAU, F., NOLIN, M.-A., TOURIGNY, N., RIGAULT, P. & MORISSETTE, J. (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics, 41, 706-16.
BLINOV, M. L., RUEBENACKER, O. & MORARU, I. I. (2008) Complexity and Modularity of Intracellular Netwroks - A Systematic Approach for Modeling and Simulation. Systems Biology, IET, 2, 363-368.
BROMBERG, K. D., MA'AYAN, A., NEVES, S. R. & IYENGAR, R. (2008) Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science, 320, 903-9.
BRUFORD, E. A., LUSH, M. J., WRIGHT, M. W., SNEDDON, T. P., POVEY, S. & BIRNEY, E. (2008) The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Research, 36, D445-8.
CAI, Y.-D., QIAN, Z., LU, L., FENG, K.-Y., MENG, X., NIU, B., ZHAO, G.-D. & LU, W.-C. (2008) Prediction of compounds' biological function (metabolic pathways) based on functional group composition. Molecular Diversity, 12, 131-7.
CALZONE, L., GELAY, A., ZINOVYEV, A., RADVANYI, F. & BARILLOT, E. (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Molecular Systems Biology, 4, 173.
CESARENI, G., CHATR-ARYAMONTRI, A., LICATA, L. & CEOL, A. (2008) Searching the MINT database for protein interaction information. Current Protocols in Bioinformatics, Chapter 8, Unit 8.5.
CHATR-ARYAMONTRI, A., CEOL, A., LICATA, L. & CESARENI, G. (2008) Protein interactions: integration leads to belief. Trends in Biochemical Sciences, 33, 241-2; author reply 242-3.
CHATR-ARYAMONTRI, A., ZANZONI, A., CEOL, A. & CESARENI, G. (2008) Functional Searching the Protein Interaction Space Through the MINT Database. Methods in Molecular Biology, 484, 305-317.
DE CHASSEY, B., NAVRATIL, V., TAFFOREAU, L., HIET, M. S., AUBLIN-GEX, A., AGAUGUÉ, S., MEIFFREN, G., PRADEZYNSKI, F., FARIA, B. F., CHANTIER, T., LE BRETON, M., PELLET, J., DAVOUST, N., MANGEOT, P. E., CHABOUD, A., PENIN, F., JACOB, Y., VIDALAIN, P. O., VIDAL, M., ANDRÉ, P., RABOURDIN-COMBE, C. & LOTTEAU, V. (2008) Hepatitis C virus infection protein network. Molecular Systems Biology, 4, 230.
DIAZ-URIARTE, R. (2008) SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. BMC Bioinformatics, 9, 30.
DIELLA, F., GOULD, C. M., CHICA, C., VIA, A. & GIBSON, T. J. (2008) Phospho.ELM: a database of phosphorylation sites--update 2008. Nucleic Acids Research, 36, D240-4.
DIHAL, A., WOUDE, H. V. D. & HENDRIKSEN, P. (2008) Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis. Proteomics, 45-61.
DIMMER, E. C., HUNTLEY, R. P., BARRELL, D. G., BINNS, D., DRAGHICI, S., CAMON, E. B., HUBANK, M., TALMUD, P. J., APWEILER, R. & LOVERING, R. C. (2008) The Gene Ontology - Providing a Functional Role in Proteomic Studies. Proteomics, 2-11.
DÖNITZ, J., GOEMANN, B., LIZÉ, M., MICHAEL, H., SASSE, N., WINGENDER, E. & POTAPOV, A. P. (2008) EndoNet: an information resource about regulatory networks of cell-to-cell communication. Nucleic Acids Research, 36, D689-94.
DYER, M. D., MURALI, T. M. & SOBRAL, B. W. (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathogens, 4, e32.
EISENACHER, M., HARDT, T., MARTENS, L., HÄKKINEN, J., APWEILER, R., HAMACHER, M., MEYER, H. E. & STEPHAN, C. (2008) Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain. Proteomics, 8, 4163-7.
ELKON, R., VESTERMAN, R., AMIT, N., ULITSKY, I., ZOHAR, I., WEISZ, M., MASS, G., ORLEV, N., STERNBERG, G., BLEKHMAN, R., ASSA, J., SHILOH, Y. & SHAMIR, R. (2008) SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics, 9, 110.
ELLIOTT, B., KIRAC, M., CAKMAK, A., YAVAS, G., MAYES, S., CHENG, E., WANG, Y., GUPTA, C., OZSOYOGLU, G. & MERAL OZSOYOGLU, Z. (2008) PathCase: pathways database system. Bioinformatics, 24, 2526-33.
FERNÁNDEZ-SUÁREZ, X. M. & BIRNEY, E. (2008) Advanced genomic data mining. PLoS Computational Biology, 4, e1000121.
FERREIRA, G. B., OVERBERGH, L., VAN ETTEN, E., LAGE, K., D'HERTOG, W., HANSEN, D. A., MARIS, M., MOREAU, Y., WORKMAN, C. T., WAELKENS, E. & MATHIEU, C. (2008) Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach. Proteomics – Clinical Applications, 2, 1349-60.
FRANKE, L., KOVEL, C. G. F. D., AULCHENKO, Y. S., TRYNKA, G., ZHERNAKOVA, A., HUNT, K. A., BLAUW, H. M., BERG, L. H. V. D., OPHOFF, R., DELOUKAS, P., HEEL, D. A. V. & WIJMENGA, C. (2008) Detection , Imputation , and Association Analysis of Small Deletions and Null Alleles on Oligonucleotide Arrays. Journal of Human Genetics, 1316-1333.
GARRITY, G. M., FIELD, D., KYRPIDES, N., HIRSCHMAN, L., SANSONE, S.-A., ANGIUOLI, S., COLE, J. R., GLÖCKNER, F. O., KOLKER, E., KOWALCHUK, G., MORAN, M. A., USSERY, D. & WHITE, O. (2008) Toward a standards-compliant genomic and metagenomic publication record. Omics: A Journal of Integrative Biology, 12, 157-60.
GEBICKE-HAERTER, P. J. (2008) Systems biology in molecular psychiatry. Pharmacopsychiatry, 41 Suppl 1, S19-27.
GEORGES, S. A., BIERY, M. C., KIM, S.-Y., SCHELTER, J. M., GUO, J., CHANG, A. N., JACKSON, A. L., CARLETON, M. O., LINSLEY, P. S., CLEARY, M. A. & CHAU, B. N. (2008) Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215. Cancer Research, 68, 10105-12.
GRAFAHREND-BELAU, E., WEISE, S., KOSCHÜTZKI, D., SCHOLZ, U., JUNKER, B. H. & SCHREIBER, F. (2008) MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-8.
GUDIVADA, R. C., QU, X. A., CHEN, J., JEGGA, A. G., NEUMANN, E. K. & ARONOW, B. J. (2008) Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge. Journal of Biomedical Informatics, 41, 717-29.
HUANG, Y. J., HANG, D., LU, L. J., TONG, L., GERSTEIN, M. B. & MONTELIONE, G. T. (2008) Targeting the human cancer pathway protein interaction network by structural genomics. Molecular and Cellular Proteomics, 7, 2048-60.
JIANG, K., HUANG, Y. & ROBERTSON, J. (2008) A method of biological pathway similarity search using high performance computing. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 4933-6.
JIANG, K. & ROBERTSON, J. (2008) A system for exploring and visualizing biological pathways from large scale datasets. Proceedings of 30th Annual International IEEE EMBS Conference.
JIN, Y., MURALI, T. M. & RAMAKRISHNAN, N. (2008) Compositional mining of multirelational biological datasets. ACM Transactions on Knowledge Discovery from Data.
JONES, P., CÔTÉ, R. G., CHO, S. Y., KLIE, S., MARTENS, L., QUINN, A. F., THORNEYCROFT, D. & HERMJAKOB, H. (2008) PRIDE: new developments and new datasets. Nucleic Acids Research, 36, D878-83.
KRALLINGER, M., LEITNER, F., RODRIGUEZ-PENAGOS, C. & VALENCIA, A. (2008) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology, 9.
KRASNOGOR, N., SHAH, A. A., BARTHEL, D., LUKASIAK, P. & BLAZEWICZ, J. (2008) Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review. Current Bioinformatics, 3, 10-31.
KUHN, M., CAMPILLOS, M., GONZÁLEZ, P., JENSEN, L. J. & BORK, P. (2008) Large-scale prediction of drug-target relationships. FEBS Letters, 582, 1283-90.
KUHN, M., VON MERING, C., CAMPILLOS, M., JENSEN, L. J. & BORK, P. (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research, 36, D684-8.
LEE, I., LEHNER, B., CROMBIE, C., WONG, W., FRASER, A. G. & MARCOTTE, E. M. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nature Genetics, 40, 181-8.
LEHNER, B. & LEE, I. (2008) Network-guided genetic screening: building, testing and using gene networks to predict gene function. Briefings in Functional Genomics and Proteomics, 7, 217-27.
LEONELLI, S. (2008) Regulating Data Travel in the Life Sciences : The Impact of Commodification. The Commodification of Academic Research: Philosophical Perspectives.
LI, Y., AGARWAL, P. & RAJAGOPALAN, D. (2008) A global pathway crosstalk network. Bioinformatics, 24, 1442-7.
LIN, C.-Y., CHIN, C.-H., WU, H.-H., CHEN, S.-H., HO, C.-W. & KO, M.-T. (2008) Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Research, 36, W438-43.
LYNN, D. J., WINSOR, G. L., CHAN, C., RICHARD, N., LAIRD, M. R., BARSKY, A., GARDY, J. L., ROCHE, F. M., CHAN, T. H. W., SHAH, N., LO, R., NASEER, M., QUE, J., YAU, M., ACAB, M., TULPAN, D., WHITESIDE, M. D., CHIKATAMARLA, A., MAH, B., MUNZNER, T., HOKAMP, K., HANCOCK, R. E. W. & BRINKMAN, F. S. L. (2008) InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology, 4, 218.
MA'AYAN, A. (2008) Network integration and graph analysis in mammalian molecular systems biology. Systems Biology, IET, 2, 206-221.
MATHUR, S., VISVANATHAN, M., SVOJANOVSKY, S., YOO, B., SRINIVAS, A., LUSHINGTON, G. & SMITH, P. (2008) GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. Open Bioinformatics Journal, 22, 629-629.
MURALI, T. M. & RIVERA, C. G. (2008) Network legos: building blocks of cellular wiring diagrams. Journal of Computational Biology, 15, 829-44.
NEWMAN, A., HUNTER, J., LI, Y. F., BOUTON, C. & DAVIS, M. (2008) A scale-out RDF molecule store for distributed processing of biomedical data. Semantic Web for Health Care and Life Sciences Workshop (HCLS'08) at the 17th International Conference on World Wide Web (WWW'08). Citeseer.
NIELSEN, J. & JEWETT, M. C. (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Research, 8, 122-31.
NOEL, S., SHARMA, S., SHANKAR, R. & RATH, S. K. (2008) Identification of differentially expressed genes after acute exposure to bulaquine (CDRI 80/53) in mice liver. Basic and Clinical Pharmacology and Toxicology, 103, 522-9.
NOOKAEW, I., JEWETT, M. C., MEECHAI, A., THAMMARONGTHAM, C., LAOTENG, K., CHEEVADHANARAK, S., NIELSEN, J. & BHUMIRATANA, S. (2008) The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Systems Biology, 2, 71.
OKUDA, S., YAMADA, T., HAMAJIMA, M., ITOH, M., KATAYAMA, T., BORK, P., GOTO, S. & KANEHISA, M. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Research, 36, W423-6.
ORTON, R. J., STURM, O. E., GORMAND, A., WOLCH, W. & GILBERT, D. R. (2008) Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway. IET systems biology, 2, 173-83.
PACHE, R. A., ZANZONI, A., NAVAL, J., MAS, J. M. & ALOY, P. (2008) Towards a molecular characterisation of pathological pathways. FEBS Letters, 582, 1259-65.
PAN, W. (2008) Network-based model weighting to detect multiple loci influencing complex diseases. Human Genetics, 124, 225-34.
PANG, C. N. I. & WILKINS, M. R. (2008) Online resources for the molecular contextualization of disease. Methods in Molecular Medicine, 141, 287-308.
PATTIN, K. A. & MOORE, J. H. (2008) Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. Human Genetics, 124, 19-29.
PAVLOPOULOS, G. A., WEGENER, A. L. & SCHNEIDER, R. (2008) A survey of visualization tools for biological network analysis. BioData Mining, 1.
PICO, A. R., KELDER, T., VAN IERSEL, M. P., HANSPERS, K., CONKLIN, B. R. & EVELO, C. (2008) WikiPathways: pathway editing for the people. PLoS Biology, 6, e184.
PIERONI, E., DE LA FUENTE VAN BENTEM, S., MANCOSU, G., CAPOBIANCO, E., HIRT, H. & DE LA FUENTE, A. (2008) Protein networking: insights into global functional organization of proteomes. Proteomics, 8, 799-816.
PITKÄNEN, E., AKERLUND, A., RANTANEN, A., JOUHTEN, P. & UKKONEN, E. (2008) ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. Journal of Integrative Bioinformatics, 5, 1-13.
RAMANI, A. K., LI, Z., HART, G. T., CARLSON, M. W., BOUTZ, D. R. & MARCOTTE, E. M. (2008) A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Molecular Systems Biology, 4, 180.
RASCHE, A., AL-HASANI, H. & HERWIG, R. (2008) Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics, 9, 310.
REIMAND, J., TOOMING, L., PETERSON, H., ADLER, P. & VILO, J. (2008) GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Research, 36, W452-9.
REVERTER, A. & CHAN, E. K. F. (2008) Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics, 24, 2491-7.
REVERTER, A., INGHAM, A. & DALRYMPLE, B. P. (2008) Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes. BioData mining, 1, 8.
REYAL, F., VAN VLIET, M. H., ARMSTRONG, N. J., HORLINGS, H. M., DE VISSER, K. E., KOK, M., TESCHENDORFF, A. E., MOOK, S., VAN 'T VEER, L., CALDAS, C., SALMON, R. J., VAN DE VIJVER, M. J. & WESSELS, L. F. A. (2008) A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer. Breast Cancer Research, 10, R93.
RUBIN, D. L., SHAH, N. H. & NOY, N. F. (2008) Biomedical ontologies: a functional perspective. Briefings in Bioinformatics, 9, 75-90.
SACCONE, S. F., SACCONE, N. L., SWAN, G. E., MADDEN, P. A. F., GOATE, A. M., RICE, J. P. & BIERUT, L. J. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics, 24, 1805-11.
SAHOO, S. S., BODENREIDER, O., RUTTER, J. L., SKINNER, K. J. & SHETH, A. P. (2008) An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence. Journal of Biomedical Informatics, 41, 752-65.
SCHMIDT, C. J., ROMANOV, M., RYDER, O., MAGRINI, V., HICKENBOTHAM, M., GLASSCOCK, J., MCGRATH, S., MARDIS, E. & STEIN, L. D. (2008) Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Research, 36, D719-23.
SKRABANEK, L., SAINI, H. K., BADER, G. D. & ENRIGHT, A. J. (2008) Computational prediction of protein-protein interactions. Molecular Biotechnology, 38, 1-17.
SPLENDIANI, A. (2008) RDFScape: Semantic Web meets systems biology. BMC Bioinformatics, 9 Suppl 4, S6.
SQUIRES, B., MACKEN, C., GARCIA-SASTRE, A., GODBOLE, S., NORONHA, J., HUNT, V., CHANG, R., LARSEN, C. N., KLEM, E., BIERSACK, K. & SCHEUERMANN, R. H. (2008) BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Research, 36, D497-503.
SUNDARAMOORTHY, E., MAITI, S., BRAHMACHARI, S. K. & SENGUPTA, S. (2008) Predicting protein homocysteinylation targets based on dihedral strain energy and pKa of cysteines. Proteins, 71, 1475-83.
TAUBNER, C. & ECKSTEIN, S. (2008) Modellierung und Simulation biologischer Prozesse mit diskreten Modellierungssprachen: ein MDE-Ansatz. Lecture Notes in Informatics, 149-164.
TELEFONT, M. & LIU, Y. (2008) Bioinformation OntoSlug : a dynamic visual front-end program for ontologies. Bioinformatician, 438-440.
TIFFIN, N., OKPECHI, I., PEREZ-IRATXETA, C., ANDRADE-NAVARRO, M. A. & RAMESAR, R. (2008) Prioritization of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypes. Physiological Genomics, 35, 55-64.
TÖPEL, T., KORMEIER, B., KLASSEN, A. & HOFESTÄDT, R. (2008) BioDWH: a data warehouse kit for life science data integration. Journal of Integrative Bioinformatics, 5, 1-9.
TSESMETZIS, N., COUCHMAN, M., HIGGINS, J., SMITH, A., DOONAN, J. H., SEIFERT, G. J., SCHMIDT, E. E., VASTRIK, I., BIRNEY, E., WU, G., D'EUSTACHIO, P., STEIN, L. D., MORRIS, R. J., BEVAN, M. W. & WALSH, S. V. (2008) Arabidopsis reactome: a foundation knowledgebase for plant systems biology. The Plant cell, 20, 1426-36.
ULITSKY, I., GAT-VIKS, I. & SHAMIR, R. (2008) MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biology, 9, R1.
VAN DAM, T. J. P. & SNEL, B. (2008) Protein complex evolution does not involve extensive network rewiring. PLoS Computational Biology, 4, e1000132.
VILLANUEVA-ROSALES, N. & DUMONTIER, M. (2008) yOWL: an ontology-driven knowledge base for yeast biologists. Journal of Biomedical Informatics, 41, 779-89.
VISVANATHAN, M., BREIT, M., PFEIFER, B., BAUMGARTNER, C., MODRE-OSPRIAN, R. & TILG, B. (2008) DMSP – Database for Modeling Signaling Pathways. Methods of Information in Medicine, 140-148.
VISWANATHAN, G. A., SETO, J., PATIL, S., NUDELMAN, G. & SEALFON, S. C. (2008) Getting started in biological pathway construction and analysis. PLoS Computational Biology, 4, e16.
VIVEKANANDAN, P. & SINGH, O. V. (2008) High-dimensional biology to comprehend hepatocellular carcinoma. Expert Review of Proteomics, 5, 45-60.
WILLEMSEN, A. M., JANSEN, G. A., KOMEN, J. C., VAN HOOFF, S., WATERHAM, H. R., BRITES, P. M. T., WANDERS, R. J. A. & VAN KAMPEN, A. H. C. (2008) Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. Bioinformatics, 24, i21-7.
XIONG, B., LIU, K., WU, J., BURK, D. L., JIANG, H. & SHEN, J. (2008) DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks. Bioinformatics, 24, 2117-8.
YANG, W., STEEN, H. & FREEMAN, M. R. (2008) Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics, 8, 832-51.
YELLABOINA, S., DUDEKULA, D. B. & KO, M. S. (2008) Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics, 9, 465.
YEUNG, N., CLINE, M. S., KUCHINSKY, A., SMOOT, M. E. & BADER, G. D. (2008) Exploring biological networks with Cytoscape software. Current Protocols in Bioinformatics, Chapter 8, Unit 8.13.
YOSHIDA, Y., MIYAMOTO, M., BO, X., YAOITA, E. & YAMAMOTO, T. (2008) Overview of kidney and urine proteome databases. Contributions to Nephrology, 160, 186-97.
YU, J., PACIFICO, S., LIU, G. & FINLEY, R. L. (2008) DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics, 9, 461.
ZHU, J., HE, F., SONG, S., WANG, J. & YU, J. (2008) How many human genes can be defined as housekeeping with current expression data? BMC Genomics, 9, 172.
ZINOVYEV, A., VIARA, E., CALZONE, L. & BARILLOT, E. (2008) BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics, 24, 876-7.

2007

ALFIERI, R., MERELLI, I., MOSCA, E. & MILANESI, L. (2007) A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Systems Biology, 1, 35.
ALIBÉS, A., YANKILEVICH, P., CAÑADA, A. & DÍAZ-URIARTE, R. (2007) IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC Bioinformatics, 8, 9.
ALVES, J. M. P. & BUCK, G. A. (2007) Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases. Chemistry and Biodiversity, 4, 2593-602.
ANATSKAYA, O. V. & VINOGRADOV, A. E. (2007) Genome multiplication as adaptation to tissue survival: evidence from gene expression in mammalian heart and liver. Genomics, 89, 70-80.
ANTOSHECHKIN, I. & STERNBERG, P. W. (2007) The versatile worm: genetic and genomic resources for Caenorhabditis elegans research. Nature Reviews Genetics, 8, 518-32.
BAI, X., WU, J., ZHANG, Q., ALESCI, S., MANOLI, I., BLACKMAN, M., CHROUSOS, G., GOLDSTEIN, A., RENNERT, O. & SU, Y. (2007) Third-generation human mitochondria-focused cDNA microarray and its bioinformatic tools for analysis of gene expression. BioTechniques, 42, 365-375.
BERGHOLDT, R., STØRLING, Z. M., LAGE, K., KARLBERG, E. O., OLASON, P. I., AALUND, M., NERUP, J., BRUNAK, S., WORKMAN, C. T. & POCIOT, F. (2007) Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biology, 8, 53.
BOURQUI, R., COTTRET, L., LACROIX, V., AUBER, D., MARY, P., SAGOT, M.-F. & JOURDAN, F. (2007) Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Systems Biology, 1, 29.
CAKMAK, A. & OZSOYOGLU, G. (2007) Mining biological networks for unknown pathways. Bioinformatics, 23, 2775-83.
CAVALIERI, D., CASTAGNINI, C., TOTI, S., MACIAG, K., KELDER, T., GAMBINERI, L., ANGIOLI, S. & DOLARA, P. (2007) Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics, 23, 2631-2.
CHAURASIA, G., IQBAL, Y., HÄNIG, C. & HERZEL, H. (2007) Flexible web-based integration of distributed large-scale human protein interaction maps. Journal of Integrative Bioinformatics, 6-10.
CHEN, J., XU, H., ARONOW, B. J. & JEGGA, A. G. (2007) Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics, 8, 392.
CHUANG, H.-Y., LEE, E., LIU, Y.-T., LEE, D. & IDEKER, T. (2007) Network-based classification of breast cancer metastasis. Molecular Systems Biology, 3, 140.
CLINE, M. S., SMOOT, M., CERAMI, E., KUCHINSKY, A., LANDYS, N., WORKMAN, C., CHRISTMAS, R., AVILA-CAMPILO, I., CREECH, M., GROSS, B., HANSPERS, K., ISSERLIN, R., KELLEY, R., KILLCOYNE, S., LOTIA, S., MAERE, S., MORRIS, J., ONO, K., PAVLOVIC, V., PICO, A. R., VAILAYA, A., WANG, P.-L., ADLER, A., CONKLIN, B. R., HOOD, L., KUIPER, M., SANDER, C., SCHMULEVICH, I., SCHWIKOWSKI, B., WARNER, G. J., IDEKER, T. & BADER, G. D. (2007) Integration of biological networks and gene expression data using Cytoscape. Nature Protocols, 2, 2366-82.
COGBURN, L. A., PORTER, T. E., DUCLOS, M. J., SIMON, J., BURGESS, S. C., ZHU, J. J., CHENG, H. H., DODGSON, J. B. & BURNSIDE, J. (2007) Functional genomics of the chicken--a model organism. Poultry Science, 86, 2059-94.
COOK, D., GENNARI, J. & WILEY, J. (2007) Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms. Pacific Symposium on Biocomputing. Citeseer.
DAWELBAIT, G., WINTER, C., ZHANG, Y., PILARSKY, C., GRÜTZMANN, R., HEINRICH, J.-C. & SCHROEDER, M. (2007) Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data. Bioinformatics, 23, i115-24.
DE JONG, E., FRANKE, L., SIEBES, A., SIEBES, A. P. J. M., BERTHOLD, M. R., GLEN, R. C. & FEELDERS, A. J. (2007) On the Measurement of Genetic Interactions. AIP Conference Proceedings. Aip.
DEGENHARDT, J., HAUBROCK, M., DÖNITZ, J., WINGENDER, E. & CRASS, T. (2007) DEEP--a tool for differential expression effector prediction. Nucleic Acids Research, 35, W619-24.
DIAZ-URIARTE, R. (2007) GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. BMC Bioinformatics, 8, 328.
DÍAZ-URIARTE, R., ALIBÉS, A., MORRISSEY, E. R., CAÑADA, A., RUEDA, O. M. & NEVES, M. L. (2007) Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Nucleic Acids Research, 35, W75-80.
DÍAZ-URIARTE, R. & RUEDA, O. M. (2007) ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data. PLoS one, 2, e737.
DRAGHICI, S., KHATRI, P., TARCA, A. L., AMIN, K., DONE, A., VOICHITA, C., GEORGESCU, C. & ROMERO, R. (2007) A systems biology approach for pathway level analysis. Genome Research, 17, 1537-45.
DYER, M. D., MURALI, T. M. & SOBRAL, B. W. (2007) Computational prediction of host-pathogen protein-protein interactions. Bioinformatics, 23, i159-66.
EISENACHER, M., HARDT, T., HAMACHER, M., MARTENS, L., HÄKKINEN, J., LEVANDER, F., APWEILER, R., MEYER, H. E. & STEPHAN, C. (2007) Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. Proteomics, 8, 1326-30.
FATO, M., GIUNCHIGLIA, E., PORRO, I. & VASSALLI, L. (2007) On the integration of biomedical knowledge bases: problems and solutions. Proceedings of Workshop on A Semantic Web for Bioinformatics (NETTAB 2007). Citeseer.
FRISHMAN, D. (2007) Protein annotation at genomic scale: the current status. Chemical Reviews, 107, 3448-66.
GAJ, S., VAN ERK, A., VAN HAAFTEN, R. I. M. & EVELO, C. T. A. (2007) Linking microarray reporters with protein functions. BMC Bioinformatics, 8, 360.
GAT-VIKS, I. & SHAMIR, R. (2007) Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Research, 17, 358-67.
GILLE, C., HOFFMANN, S. & HOLZHÜTTER, H.-G. (2007) METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. BMC Systems Biology, 1, 5.
GONG, Y. & ZHANG, Z. (2007) CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks. Annals of the New York Academy of Sciences, 1115, 249-66.
GREENE, J. M., COLLINS, F., LEFKOWITZ, E. J., ROOS, D., SCHEUERMANN, R. H., SOBRAL, B., STEVENS, R., WHITE, O. & DI FRANCESCO, V. (2007) National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infection and Immunity, 75, 3212-9.
GREENMAN, C., STEPHENS, P., SMITH, R., DALGLIESH, G. L., HUNTER, C., BIGNELL, G., DAVIES, H., TEAGUE, J., BUTLER, A., STEVENS, C., EDKINS, S., O'MEARA, S., VASTRIK, I., SCHMIDT, E. E., AVIS, T., BARTHORPE, S., BHAMRA, G., BUCK, G., CHOUDHURY, B., CLEMENTS, J., COLE, J., DICKS, E., FORBES, S., GRAY, K., HALLIDAY, K., HARRISON, R., HILLS, K., HINTON, J., JENKINSON, A., JONES, D., MENZIES, A., MIRONENKO, T., PERRY, J., RAINE, K., RICHARDSON, D., SHEPHERD, R., SMALL, A., TOFTS, C., VARIAN, J., WEBB, T., WEST, S., WIDAA, S., YATES, A., CAHILL, D. P., LOUIS, D. N., GOLDSTRAW, P., NICHOLSON, A. G., BRASSEUR, F., LOOIJENGA, L., WEBER, B. L., CHIEW, Y.-E., DEFAZIO, A., GREAVES, M. F., GREEN, A. R., CAMPBELL, P., BIRNEY, E., EASTON, D. F., CHENEVIX-TRENCH, G., TAN, M.-H., KHOO, S. K., TEH, B. T., YUEN, S. T., LEUNG, S. Y., WOOSTER, R., FUTREAL, P. A. & STRATTON, M. R. (2007) Patterns of somatic mutation in human cancer genomes. Nature, 446, 153-8.
HEDELER, C., WONG, H. M., CORNELL, M. J., ALAM, I., SOANES, D. M., RATTRAY, M., HUBBARD, S. J., TALBOT, N. J., OLIVER, S. G. & PATON, N. W. (2007) e-Fungi: a data resource for comparative analysis of fungal genomes. BMC Genomics, 8, 426.
HETHERINGTON, J., BOGLE, I., SAFFREY, P., MARGONINSKI, O., LI, L., REY, M., YAMAJI, S., BAIGENT, S., ASHMORE, J. & PAGE, K. (2007) Addressing the challenges of multiscale model management in systems biology. Computers and Chemical Engineering, 31, 962-979.
HU, Z., MELLOR, J., WU, J., KANEHISA, M., STUART, J. M. & DELISI, C. (2007) Towards zoomable multidimensional maps of the cell. Nature Biotechnology, 25, 547-554.
HU, Z., NG, D. M., YAMADA, T., CHEN, C., KAWASHIMA, S., MELLOR, J., LINGHU, B., KANEHISA, M., STUART, J. M. & DELISI, C. (2007) VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research, 35, W625-32.
HUBER, W., CAREY, V. J., LONG, L., FALCON, S. & GENTLEMAN, R. (2007) Graphs in molecular biology. BMC Bioinformatics, 8 Suppl 6, S8.
HULBERT, E. M., SMINK, L. J., ADLEM, E. C., ALLEN, J. E., BURDICK, D. B., BURREN, O. S., CASSEN, V. M., CAVNOR, C. C., DOLMAN, G. E., FLAMEZ, D., FRIERY, K. F., HEALY, B. C., KILLCOYNE, S. A., KUTLU, B., SCHUILENBURG, H., WALKER, N. M., MYCHALECKYJ, J., EIZIRIK, D. L., WICKER, L. S., TODD, J. A. & GOODMAN, N. (2007) T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Research, 35, D742-6.
IOANNIS, K., ARISTOTELIS, C., ILIAS, M. & FRAGISKOS, K. (2007) SBML-Bridge: An XML Pathway Converting Tool. Proceedings of 11th Panhellenic Conference in Informatics. Citeseer.
ISSERLIN, R. & EMILI, A. (2007) Nine steps to proteomic wisdom: A practical guide to using protein-protein interaction networks and molecular pathways as a framework for interpreting disease proteomic profiles. Proteomics – Clinical Applications, 1, 1156-1168.
JAYAPANDIAN, M., CHAPMAN, A., TARCEA, V. G., YU, C., ELKISS, A., IANNI, A., LIU, B., NANDI, A., SANTOS, C., ANDREWS, P., ATHEY, B., STATES, D. & JAGADISH, H. V. (2007) Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Research, 35, D566-71.
JEGGA, A. G., GOWRISANKAR, S., CHEN, J. & ARONOW, B. J. (2007) PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Research, 35, D700-6.
JEONG, E., NAGASAKI, M. & MIYANO, S. (2007) Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Informatics, 18, 225-36.
KAHLEM, P. & BIRNEY, E. (2007) ENFIN a network to enhance integrative systems biology. Annals of the New York Academy of Sciences, 1115, 23-31.
KERRIEN, S., ALAM-FARUQUE, Y., ARANDA, B., BANCARZ, I., BRIDGE, A., DEROW, C., DIMMER, E., FEUERMANN, M., FRIEDRICHSEN, A., HUNTLEY, R., KOHLER, C., KHADAKE, J., LEROY, C., LIBAN, A., LIEFTINK, C., MONTECCHI-PALAZZI, L., ORCHARD, S., RISSE, J., ROBBE, K., ROECHERT, B., THORNEYCROFT, D., ZHANG, Y., APWEILER, R. & HERMJAKOB, H. (2007) IntAct--open source resource for molecular interaction data. Nucleic Acids Research, 35, D561-5.
KHATRI, P., VOICHITA, C., KATTAN, K., ANSARI, N., KHATRI, A., GEORGESCU, C., TARCA, A. L. & DRAGHICI, S. (2007) Onto-Tools: new additions and improvements in 2006. Nucleic Acids Research, 35, W206-11.
LAGE, K., KARLBERG, E. O., STØRLING, Z. M., OLASON, P. I., PEDERSEN, A. G., RIGINA, O., HINSBY, A. M., TÜMER, Z., POCIOT, F., TOMMERUP, N., MOREAU, Y. & BRUNAK, S. (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnology, 25, 309-16.
LANGE, M. C., LEMAY, D. G. & GERMAN, J. B. (2007) A multi-ontology framework to guide agriculture and food towards diet and health. Interface, 87, 1427-1434.
LEE, B., KIM, T., KIM, S.-K., LEE, K. H. & LEE, D. (2007) Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. Nucleic Acids Research, 35, D47-50.
LEE, D., REDFERN, O. & ORENGO, C. (2007) Predicting protein function from sequence and structure. Nature Reviews Molecular Cell Biology, 8, 995-1005.
LIANG, M. (2007) Integrative pathway knowledge bases as a tool for systems molecular medicine. Physiological Genomics, 30, 209-12.
LIN, J. & QIAN, J. (2007) Systems biology approach to integrative comparative genomics. Expert Review of Proteomics, 4, 107-19.
LISACEK, F., HOOGLAND, C., LESCUYER, P., HOCHSTRASSER, D. F. & APPEL, R. D. (2007) Using bioinformatic resources in the proteomic analysis of biological fluids. Proteomics – Clinical Applications, 1, 900-15.
LU, L. J., SBONER, A., HUANG, Y. J., LU, H. X., GIANOULIS, T. A., YIP, K. Y., KIM, P. M., MONTELIONE, G. T. & GERSTEIN, M. B. (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends in Biochemical Sciences, 32, 320-31.
LYNE, R., SMITH, R., RUTHERFORD, K., WAKELING, M., VARLEY, A., GUILLIER, F., JANSSENS, H., JI, W., MCLAREN, P., NORTH, P., RANA, D., RILEY, T., SULLIVAN, J., WATKINS, X., WOODBRIDGE, M., LILLEY, K., RUSSELL, S., ASHBURNER, M., MIZUGUCHI, K. & MICKLEM, G. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biology, 8, R129.
MAK, H. C., DALY, M., GRUEBEL, B. & IDEKER, T. (2007) CellCircuits: a database of protein network models. Nucleic Acids Research, 35, D538-45.
MATHEW, J. P., TAYLOR, B. S., BADER, G. D., PYARAJAN, S., ANTONIOTTI, M., CHINNAIYAN, A. M., SANDER, C., BURAKOFF, S. J. & MISHRA, B. (2007) From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Computational Biology, 3, e12.
MATSUZAWA, N., TAKAMURA, T., KURITA, S., MISU, H., OTA, T., ANDO, H., YOKOYAMA, M., HONDA, M., ZEN, Y., NAKANUMA, Y., MIYAMOTO, K.-I. & KANEKO, S. (2007) Lipid-induced oxidative stress causes steatohepatitis in mice fed an atherogenic diet. Hepatology, 46, 1392-403.
MAZIERE, P., PARISEY, N., BEURTON-AIMAR, M. & MOLINA, F. (2007) Formal TCA cycle description based on elementary actions. Journal of Biosciences, 32, 145-55.
MAZZA, T. (2007) Towards a complete covering of SBML functionalities. Membrane Computing, 353-366.
MCGARY, K. L., LEE, I. & MARCOTTE, E. M. (2007) Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biology, 8, 58.
MI, H., GUO, N., KEJARIWAL, A. & THOMAS, P. D. (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Research, 35, D247-52.
NATALE, D. A., ARIGHI, C. N., BARKER, W. C., BLAKE, J., CHANG, T.-C., HU, Z., LIU, H., SMITH, B. & WU, C. H. (2007) Framework for a protein ontology. BMC Bioinformatics, 8 Suppl 9, S1.
RAPAPORT, F., ZINOVYEV, A., DUTREIX, M., BARILLOT, E. & VERT, J.-P. (2007) Classification of microarray data using gene networks. BMC Bioinformatics, 8, 35.
REIMAND, J., KULL, M., PETERSON, H., HANSEN, J. & VILO, J. (2007) g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research, 35, W193-200.
RUTTENBERG, A., CLARK, T., BUG, W., SAMWALD, M., BODENREIDER, O., CHEN, H., DOHERTY, D., FORSBERG, K., GAO, Y., KASHYAP, V., KINOSHITA, J., LUCIANO, J., MARSHALL, M. S., OGBUJI, C., REES, J., STEPHENS, S., WONG, G. T., WU, E., ZACCAGNINI, D., HONGSERMEIER, T., NEUMANN, E., HERMAN, I. & CHEUNG, K.-H. (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics, 8 Suppl 3, S2.
SALOMONIS, N., HANSPERS, K., ZAMBON, A. C., VRANIZAN, K., LAWLOR, S. C., DAHLQUIST, K. D., DONIGER, S. W., STUART, J., CONKLIN, B. R. & PICO, A. R. (2007) GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics, 8, 217.
SALWINSKI, L. & EISENBERG, D. (2007) The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. Bioinformatics, 23, 2193-5.
SAM, L., LUI, Y., JIANRONG, L., FRIEDMAN, C. & LUSSIER, Y. (2007) Discovery of protein interaction networks shared by diseases. Pacific Symposium on Biocomputing, 76-87.
SCARIA, V. & JADHAV, V. (2007) microRNAs in viral oncogenesis. Retrovirology, 4, 82.
SIVACHENKO, A. Y. & YURYEV, A. (2007) Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism. Expert Opinion on Therapeutic Targets, 11, 411-21.
SRINIVASAN, B. S., SHAH, N. H., FLANNICK, J. A., ABELIUK, E., NOVAK, A. F. & BATZOGLOU, S. (2007) Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics, 8, 318-32.
STRÖMBÄCK, L., HALL, D. & LAMBRIX, P. (2007) A review of standards for data exchange within systems biology. Proteomics, 7, 857-67.
THOMAS, P. D., MI, H. & LEWIS, S. (2007) Ontology annotation: mapping genomic regions to biological function. Current Opinion in Chemical Biology, 11, 4-11.
THORN, C. F., WHIRL-CARRILLO, M., KLEIN, T. E. & ALTMAN, R. B. (2007) Pathway-based Approaches to Pharmacogenomics. Current Pharmacogenomics, 5, 79-86.
TIAN, Y., MCEACHIN, R. C., SANTOS, C., STATES, D. J. & PATEL, J. M. (2007) SAGA: a subgraph matching tool for biological graphs. Bioinformatics, 23, 232-9.
TSUI, I. F. L., CHARI, R., BUYS, T. P. H. & LAM, W. L. (2007) Public databases and software for the pathway analysis of cancer genomes. Cancer Informatics, 3, 379-97.
VINOGRADOV, A. E. & ANATSKAYA, O. V. (2007) Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Research, 35, 6350-6.
VISWANATHAN, G. A., NUDELMAN, G., PATIL, S. & SEALFON, S. C. (2007) BioPP: a tool for web-publication of biological networks. BMC Bioinformatics, 8, 168.
VON MERING, C., JENSEN, L. J., KUHN, M., CHAFFRON, S., DOERKS, T., KRÜGER, B., SNEL, B. & BORK, P. (2007) STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35, D358-62.
WANG, K. & XIAO, X. (2007) Endogenous myocardial protection: present questions and prospects. Sheng Li Xue Bao Acta Physiologica Sinica, 59, 635.
WIERLING, C., HERWIG, R. & LEHRACH, H. (2007) Resources, standards and tools for systems biology. Briefings in Functional Genomics and Proteomics, 6, 240-51.
WISHART, C. (2007) Metabolism and Metabolic Disease Resources on the Web. OMMBID.
WISHART, D. S. (2007) Introduction to cheminformatics. Current Protocols in Bioinformatics, Chapter 14, Unit 14.1.
WISHART, D. S. (2007) Current progress in computational metabolomics. Briefings in Bioinformatics, 8, 279-93.
WISHART, D. S., TZUR, D., KNOX, C., EISNER, R., GUO, A. C., YOUNG, N., CHENG, D., JEWELL, K., ARNDT, D., SAWHNEY, S., FUNG, C., NIKOLAI, L., LEWIS, M., COUTOULY, M.-A., FORSYTHE, I., TANG, P., SHRIVASTAVA, S., JERONCIC, K., STOTHARD, P., AMEGBEY, G., BLOCK, D., HAU, D. D., WAGNER, J., MINIACI, J., CLEMENTS, M., GEBREMEDHIN, M., GUO, N., ZHANG, Y., DUGGAN, G. E., MACINNIS, G. D., WELJIE, A. M., DOWLATABADI, R., BAMFORTH, F., CLIVE, D., GREINER, R., LI, L., MARRIE, T., SYKES, B. D., VOGEL, H. J. & QUERENGESSER, L. (2007) HMDB: the Human Metabolome Database. Nucleic Acids Research, 35, D521-6.
WORTH, C. L., BICKERTON, G. R. J., SCHREYER, A., FORMAN, J. R., CHENG, T. M. K., LEE, S., GONG, S., BURKE, D. F. & BLUNDELL, T. L. (2007) A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease. Journal of Bioinformatics and Computational Biology, 5, 1297-318.
YANG, M. Q. & ELNITSKI, L. L. (2007) A computational study of bidirectional promoters in the human genome. Lecture notes in Computer Science, 4463, 361-371.
ZHANG, S., JIN, G., ZHANG, X.-S. & CHEN, L. (2007) Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics, 7, 2856-69.

2006

ALOY, P. & RUSSELL, R. B. (2006) Structural systems biology: modelling protein interactions. Nature Reviews Molecular Cell Biology, 7, 188-97.
ANTEZANA, E., TSIPORKOVA, E., MIRONOV, V. & KUIPER, M. (2006) A cell-cycle knowledge integration framework. Data Integration in the Life Sciences. Springer.
ARISI, I., CATTANEO, A. & ROSATO, V. (2006) Parameter estimate of signal transduction pathways. BMC Neuroscience, 7 Suppl 1, S6.
BRAZMA, A., KRESTYANINOVA, M. & SARKANS, U. (2006) Standards for systems biology. Nature Reviews Genetics, 7, 593-605.
CERAMI, E. G., BADER, G. D., GROSS, B. E. & SANDER, C. (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics, 7, 497.
CHEUNG, K.-H., QI, P., TUCK, D. & KRAUTHAMMER, M. (2006) A semantic web approach to biological pathway data reasoning and integration. Journal of Web Semantics, 4, 207-215.
CHEUNG, V. G. & EWENS, W. J. (2006) Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype. Genome Research, 16, 973-9.
CONSORTIUM, T. G. O. (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Research, 34, D322-6.
DINAKARPANDIAN, D., LEE, Y., VISHWANATH, K. & LINGAMBHOTLA, R. (2006) MachineProse: an ontological framework for scientific assertions. Journal of the American Medical Informatics Association, 13, 220-232.
DOGRUSOZ, U., ERSON, E. Z., GIRAL, E., DEMIR, E., BABUR, O., CETINTAS, A. & COLAK, R. (2006) PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics, 22, 374-5.
EBENHOH, O. & LIEBERMEISTER, W. (2006) Structural Analysis of Expressed Metabolic Subnetworks. Genome Informatics, 17, 163.
FRANKE, L., VAN BAKEL, H., FOKKENS, L., DE JONG, E. D., EGMONT-PETERSEN, M. & WIJMENGA, C. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. American Journal of Human Genetics, 78, 1011-25.
HAMACHER, M., STEPHAN, C., BLÜGGEL, M., CHAMRAD, D., KÖRTING, G., MARTENS, L., MÜLLER, M., HERMJAKOB, H., PARKINSON, D., DOWSEY, A., REIDEGELD, K. A., MARCUS, K., DUNN, M. J., MEYER, H. E. & APWEILER, R. (2006) The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics, 6, 1719-21.
HART, G. T., RAMANI, A. K. & MARCOTTE, E. M. (2006) How complete are current yeast and human protein-interaction networks? Genome Biology, 7, 120.
HINRICHS, A. S., KAROLCHIK, D., BAERTSCH, R., BARBER, G. P., BEJERANO, G., CLAWSON, H., DIEKHANS, M., FUREY, T. S., HARTE, R. A., HSU, F., HILLMAN-JACKSON, J., KUHN, R. M., PEDERSEN, J. S., POHL, A., RANEY, B. J., ROSENBLOOM, K. R., SIEPEL, A., SMITH, K. E., SUGNET, C. W., SULTAN-QURRAIE, A., THOMAS, D. J., TRUMBOWER, H., WEBER, R. J., WEIRAUCH, M., ZWEIG, A. S., HAUSSLER, D. & KENT, W. J. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Research, 34, D590-8.
HSING, M., BELLENSON, J. L., SHANKEY, C. & CHERKASOV, A. (2006) Modeling of cell signaling pathways in macrophages by semantic networks. BMC Bioinformatics, 5, 156.
HYLAND, C., PINNEY, J. W., MCCONKEY, G. A. & …, D. R. (2006) metaSHARK: a WWW platform for interactive exploration of metabolic networks. Nucleic Acids Research, 34, W725-W728.
JENSEN, L. J., JENSEN, T. S., DE LICHTENBERG, U., BRUNAK, S. & BORK, P. (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature, 443, 594-7.
KAHLEM, P. & BIRNEY, E. (2006) Dry work in a wet world: computation in systems biology. Molecular Systems Biology, 2, 40.
KIM, J. S., YUN, H., KIM, H. U., CHOI, H. S., KIM, T. Y., WOO, H. M., LEE, S. Y. & OTHERS (2006) Resources for Systems Biology Research. Journal of Microbiology and Biotechnology, 16, 832.
KONG, S. W., PU, W. T. & PARK, P. J. (2006) A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics, 22, 2373-80.
KONO, N., ARAKAWA, K. & TOMITA, M. (2006) MEGU: pathway mapping web-service based on KEGG and SVG. In Silico Biology, 6, 621-5.
KRULL, M., PISTOR, S., VOSS, N., KEL, A., REUTER, I., KRONENBERG, D., MICHAEL, H., SCHWARZER, K., POTAPOV, A., CHOI, C., KEL-MARGOULIS, O. & WINGENDER, E. (2006) TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Research, 34, D546-51.
KUSHIDA, T., TAKAGI, T. & FUKUDA, K. I. (2006) Event Ontology: A Pathway-Centric Ontology for Biological Process. Pacific Symposium on Biocomputing.
LAM, H. Y. K., MARENCO, L., CLARK, T., GAO, Y., KINOSHITA, J., SHEPHERD, G., MILLER, P., WU, E., WONG, G., LIU, N. & OTHERS (2006) Semantic Web Meets e-Neuroscience: an RDF use case. Proceedings of International Workshop on Semantic e-Science, ASWC. Citeseer.
LETUNIC, I., COPLEY, R. R., PILS, B., PINKERT, S., SCHULTZ, J. & BORK, P. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Research, 34, D257-60.
LIEBERMEISTER, W. & KLIPP, E. (2006) Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theoretical Biology and Medical Modelling, 3, 42.
LO, S. L., YOU, T., LIN, Q., JOSHI, S. B., CHUNG, M. C. M. & HEW, C. L. (2006) SPLASH: systematic proteomics laboratory analysis and storage hub. Proteomics, 6, 1758-69.
MARSHALL, K. W., ZHANG, H. & NOSSOVA, N. (2006) Chondrocyte genomics: implications for disease modification in osteoarthritis. Drug Discovery Today, 11, 825-32.
MATHIVANAN, S., PERIASWAMY, B., GANDHI, T. K. B., KANDASAMY, K., SURESH, S., MOHMOOD, R., RAMACHANDRA, Y. L. & PANDEY, A. (2006) An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics, 7 Suppl 5, S19.
MCCARTHY, F. M., WANG, N., MAGEE, G. B., NANDURI, B., LAWRENCE, M. L., CAMON, E. B., BARRELL, D. G., HILL, D. P., DOLAN, M. E., WILLIAMS, W. P., LUTHE, D. S., BRIDGES, S. M. & BURGESS, S. C. (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics, 7, 229.
MÖLLER, S., ZETTL, U. K., SERRANO-FERNÁNDEZ, P. & GOERTSCHES, R. (2006) Comparative genomics for the investigation of autoimmune diseases. Current Pharmaceutical Design, 12, 3707-22.
MUELLER, M., MARTENS, L., REIDEGELD, K. A., HAMACHER, M., STEPHAN, C., BLÜGGEL, M., KÖRTING, G., CHAMRAD, D., SCHEER, C., MARCUS, K., MEYER, H. E. & APWEILER, R. (2006) Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. Proteomics, 6, 5059-75.
NAIR, V. & ZAVOLAN, M. (2006) Virus-encoded microRNAs: novel regulators of gene expression. Trends in Microbiology, 14, 169-75.
NG, A., BURSTEINAS, B., GAO, Q., MOLLISON, E. & ZVELEBIL, M. (2006) Resources for integrative systems biology: from data through databases to networks and dynamic system models. Briefings in Bioinformatics, 7, 318-30.
NG, A., BURSTEINAS, B., GAO, Q., MOLLISON, E. & ZVELEBIL, M. (2006) pSTIING : a ‘ systems ’ approach towards integrating signalling pathways , interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Research, 34, D527.
OZSOYOGLU, Z. M., OZSOYOGLU, G. & NADEAU, J. (2006) Genomic pathways database and biological data management. Animal Genetics, 37 Suppl 1, 41-7.
PALEY, S. M. & KARP, P. D. (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Research, 34, 3771-8.
PERCO, P., RAPBERGER, R., SIEHS, C., LUKAS, A., OBERBAUER, R., MAYER, G. & MAYER, B. (2006) Transforming omics data into context: bioinformatics on genomics and proteomics raw data. Electrophoresis, 27, 2659-75.
RACUNAS, S. A., SHAH, N. H. & FEDOROFF, N. V. (2006) A case study in pathway knowledgebase verification. BMC Bioinformatics, 7, 196.
REGULY, T., BREITKREUTZ, A., BOUCHER, L., BREITKREUTZ, B. J., HON, G. C., MYERS, C. L., PARSONS, A., FRIESEN, H., OUGHTRED, R., TONG, A. & OTHERS (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology, 5, 11.
SPLENDIANI, A., BLAZEWICZ, J. & FREYTAG, J. (2006) Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)}. Managing and Mining Genome Information: Frontiers in Bioinformatics.
VAN DRIEL, M. A., BRUGGEMAN, J., VRIEND, G., BRUNNER, H. G. & LEUNISSEN, J. A. M. (2006) A text-mining analysis of the human phenome. European Journal of Human Genetics, 14, 535-42.
VERNON, S. D., WHISTLER, T., CAMERON, B., HICKIE, I. B., REEVES, W. C. & LLOYD, A. (2006) Preliminary evidence of mitochondrial dysfunction associated with post-infective fatigue after acute infection with Epstein Barr virus. BMC Infectious Diseases, 6, 15.
VINOGRADOV, A. E. (2006) 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Research, 34, 5906-14.
WEISE, S., GROSSE, I., KLUKAS, C., KOSCHÜTZKI, D., SCHOLZ, U., SCHREIBER, F. & JUNKER, B. H. (2006) Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics, 7, 465.
WU, C. H., APWEILER, R., BAIROCH, A., NATALE, D. A., BARKER, W. C., BOECKMANN, B., FERRO, S., GASTEIGER, E., HUANG, H., LOPEZ, R., MAGRANE, M., MARTIN, M. J., MAZUMDER, R., O'DONOVAN, C., REDASCHI, N. & SUZEK, B. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research, 34, D187-91.
YIP, K. Y., YU, H., KIM, P. M., SCHULTZ, M. & GERSTEIN, M. (2006) The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics, 22, 2968-70.

2005

ALOY, P. & RUSSELL, R. B. (2005) Structure-based systems biology: a zoom lens for the cell. FEBS Letters, 579, 1854-8.
BEVAN, M. & WALSH, S. (2005) The Arabidopsis genome: a foundation for plant research. Genome Research, 15, 1632-42.
BROOKSBANK, C., CAMERON, G. & THORNTON, J. (2005) The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Research, 33, D46-53.
CARY, M. P., BADER, G. D. & SANDER, C. (2005) Pathway information for systems biology. FEBS Letters, 579, 1815-20.
CONGREVE, M., MURRAY, C. W. & BLUNDELL, T. L. (2005) Structural biology and drug discovery. Drug Discovery Today, 10, 895-907.
DE LA CRUZ, N., BROMBERG, S., PASKO, D., SHIMOYAMA, M., TWIGGER, S., CHEN, J., CHEN, C.-F., FAN, C., FOOTE, C., GOPINATH, G. R., HARRIS, G., HUGHES, A., JI, Y., JIN, W., LI, D., MATHIS, J., NENASHEVA, N., NIE, J., NIGAM, R., PETRI, V., REILLY, D., WANG, W., WU, W., ZUNIGA-MEYER, A., ZHAO, L., KWITEK, A., TONELLATO, P. & JACOB, H. (2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Research, 33, D485-91.
JACKSON, D. & SCHNEIDER, R. (2005) Ensembl and UniProt (Swiss-Prot). Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 8.
KOKOCINSKI, F., DELHOMME, N., WROBEL, G., HUMMERICH, L., TOEDT, G. & LICHTER, P. (2005) FACT--a framework for the functional interpretation of high-throughput experiments. BMC Bioinformatics, 6, 161.
LESER, U. (2005) A query language for biological networks. Bioinformatics, 21 Suppl 2, ii33-9.
LOMAX, J. (2005) Get ready to GO! A biologist’s guide to the Gene Ontology. Briefings in Bioinformatics, 6, 298.
LUCIANO, J. S. (2005) PAX of mind for pathway researchers building and deploying the BioPAX data-exchange format for biological pathway data. Drug Discovery Today, 10, 973-42.
MACAULAY, I. C., CARR, P., GUSNANTO, A., OUWEHAND, W. H., FITZGERALD, D. & WATKINS, N. A. (2005) Platelet genomics and proteomics in human health and disease. Journal of Clinical Investigation, 115, 3370.
OTAKE, M. & TAKAGI, T. (2005) Reassembly and interfacing neural models registered on biological model databases. Genome Informatics, 16, 76-85.
PARSLOW, G. (2005) Multimedia in biochemistry and molecular biology education commentary: Molecular visualization tools are good teaching aids when used appropriately. Biochemistry and Molecular Biology Education, 30, 128-129.
PERSICO, M., CEOL, A., GAVRILA, C., HOFFMANN, R., FLORIO, A. & CESARENI, G. (2005) HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics, 6 Suppl 4, S21.
RAMANI, A. K., BUNESCU, R. C., MOONEY, R. J. & MARCOTTE, E. M. (2005) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biology, 6, R40.
RUAL, J.-F., VENKATESAN, K., HAO, T., HIROZANE-KISHIKAWA, T., DRICOT, A., LI, N., BERRIZ, G. F., GIBBONS, F. D., DREZE, M., AYIVI-GUEDEHOUSSOU, N., KLITGORD, N., SIMON, C., BOXEM, M., MILSTEIN, S., ROSENBERG, J., GOLDBERG, D. S., ZHANG, L. V., WONG, S. L., FRANKLIN, G., LI, S., ALBALA, J. S., LIM, J., FRAUGHTON, C., LLAMOSAS, E., CEVIK, S., BEX, C., LAMESCH, P., SIKORSKI, R. S., VANDENHAUTE, J., ZOGHBI, H. Y., SMOLYAR, A., BOSAK, S., SEQUERRA, R., DOUCETTE-STAMM, L., CUSICK, M. E., HILL, D. E., ROTH, F. P. & VIDAL, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-8.
SHIMOYAMA, M., PETRI, V., PASKO, D., BROMBERG, S., WU, W., CHEN, J., NENASHEVA, N., KWITEK, A., TWIGGER, S. & JACOB, H. (2005) Using multiple ontologies to integrate complex biological data. Comparative and Functional Genomics, 6, 373-8.
STRÖMBACK, L. & LAMBRIX, P. (2005) Modeling for simulation and data storage of cellular pathways: Similarities and differences. Proceedings of the Fourth Modeling and Simulation in Biology, Medicine and Biomedical Engineering Conference-BioMedSim, 2005.
STRÖMBÄCK, L. & LAMBRIX, P. (2005) Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics, 21, 4401-7.
TAKAI-IGARASHI, T. & MIZOGUCHI, R. (2005) An Integrative Model for Representation of Signaling Pathways on the Basis of Device Ontology. Transactions of the Japanese Society for Artificial Intelligence, 20, 406-416.
VALENCIA, A. (2005) Automatic annotation of protein function. Current opinion in Structural Biology, 15, 267-74.
VON MERING, C., JENSEN, L. J., SNEL, B., HOOPER, S. D., KRUPP, M., FOGLIERINI, M., JOUFFRE, N., HUYNEN, M. A. & BORK, P. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research, 33, D433-7.
WIERLING, C. (2005) PyBioS–ein Modellierungs-und Simulationssystem f"ur komplexe biologische Prozesse. Heinz-Billing Preis, 69, 53-71.
ZAMBON, A. C., ZHANG, L., MINOVITSKY, S., KANTER, J. R., PRABHAKAR, S., SALOMONIS, N., VRANIZAN, K., DUBCHAK, I., CONKLIN, B. R. & INSEL, P. A. (2005) Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proceedings of the National Academy of Sciences of the United States of America, 102, 8561-6.

2004

KOIKE, A. (2004) PRIME : automatically extracted PRotein Interactions and Molecular Information databasE. In Silico Biology, 0003.
ROBERTSON, M. (2004) Reactome: clear view of a starry sky. Drug Discovery Today, 9, 684-5.

Books

Book Title Authors ISBN Number
Computational systems biology Andres Kriete, Roland Eils ISBN:012088786X
Analysis of Complex Disease Association Studies: A Practical Guide Eleftheria Zeggini ISBN:012375142X
Bioinformatics: a concept-based introduction Venkatarajan Subramanian Mathura, Pandjassarame Kangueane ISBN:038784869X
Bioinformatics and Biomarker Discovery: Omic Data Analysis for Personalized Medicine Francisco Azuaje ISBN:047074460X
Biomacromolecules: introduction to structure, function and informatics C. Stan Tsai ISBN:047171397X
How Well Do Facts Travel?: The Dissemination of Reliable Knowledge Peter Howlett, Mary S. Morgan ISBN:052115958X
Analysis of growth factor signaling in embryos Malcolm Whitman, Amy Katherine Sater ISBN:084933165X
Genomic and Personalized Medicine Geoffrey S. Ginsburg ISBN:123694205
Structural Genomics Andrzej Joachimiak ISBN:123744369
Essentials of Genomic and Personalized Medicine Huntington F. Willard, Geoffrey S. Ginsburg ISBN:123749344
Desk Encyclopedia of General Virology Brian W. J. Mahy, Marc H. V. van Regenmortel ISBN:123751462
Molecular Biology of Cancer: Translation to the Clinic Raymond Ruddon ISBN:123850711
Human biochemistry and disease Gerald Litwack ISBN:124528155
Ultradian Rhythms from Molecules to Mind: A New Vision of Life David Lloyd, Ernest Lawrence Rossi ISBN:1402083513
Systems biology and biotechnology of Escherichia coli Sang Yup Lee ISBN:1402093934
Textbook of hepatology: from basic science to clinical practice Joan Rodes, Jean-Pierre Benhamou ISBN:1405127414
Plant systems biology Gloria Coruzzi ISBN:140516283X
Annual Plant Reviews, Biology of Plant Metabolomics Robert D. Hall ISBN:1405199547
Biological data mining Stefano Lonardi ISBN:1420086847
Pharmaceutical Perspectives of Cancer Therapeutics Ram I. Mahato, Yi Lu ISBN:1441901302
Lung Cancer Metastasis: Novel Biological Mechanisms and Impact on Clinical Practice Venkateshwar Keshamouni, Douglas Arenberg, Gregory Kalemkerian ISBN:1441907718
Computational Biology: Issues and Applications in Oncology Tuí¢n Pham ISBN:1441908102
Infectious Disease Informatics Vitali Sintchenko ISBN:1441913262
Biomedical Informatics in Cancer Research Michael F. Ochs ISBN:144195712X
Systems Biology of Signaling Networks Sangdun Choi ISBN:1441957960
Link Mining: Models, Algorithms, and Applications Philip S. Yu ISBN:1441965149
Frontiers of Statistical Decision Making and Bayesian Analysis: In Honor of James O. Berger Ming-Hui Chen ISBN:1441969438
Genetics and Genomics of the Brassicaceae Ian Bancroft ISBN:1441971173
Immunologic Signatures of Rejection Francesco M. Marincola ISBN:1441972188
Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology Werner Dubitzky ISBN:1441979638
Reverse engineering biological networks: opportunities and challenges in computational methods for pathway inference Gustavo Stolovitsky ISBN:157331689X
The challenges of systems biology: community efforts to harness biological complexity Gustavo Stolovitzky, Pascal Kahlem, Andrea Califano ISBN:1573317519
In silico technologies in drug target identification and validation Darryl Leon, Scott Markel ISBN:1574444786
MEDINFO 2007: Proceedings of the 12th World Congress on Health (Medical) Informatics Klaus A. Kuhn ISBN:1586037749
Introduction to systems biology Sangdun Choi ISBN:1588297063
Neuroinformatics Chiquito Joaquim Crasto ISBN:1588297209
Clinical bioinformatics R. J. Trent ISBN:1588297918
In silico genomics and proteomics: functional annotation of genomes and proteins Nicola Mulder ISBN:1594549958
Biological database modeling Jake Chen, Amandeep S. Sidhu ISBN:1596932589
Methods in bioengineering: systems analysis of biological networks Arul Jayaraman, Juergen Hahn ISBN:1596934069
Bioinformatics in the post-genomic era: the role of biophysics Ivan Y. Torshin ISBN:1600210481
Physiology and Medicine Ivan Y. Torshin ISBN:1600217524
Genome research advances Alberto P. Bellini ISBN:1600218059
Coumarin Anticoagulant Research Progress Joseph P. Edardes ISBN:160021990X
Bioinformatics methods in clinical research Rune Matthiesen ISBN:1603271937
Information retrieval in biomedicine: natural language processing for knowledge integration Violaine Prince, Mathieu Roche ISBN:1605662747
Open and Novel Issues in XML Database Applications: Future Directions and Advanced Technologies Eric Pardede ISBN:1605663085
Biological Data Mining in Protein Interaction Networks Xiao-Li Li, See-Kiong Ng ISBN:1605663980
Plant Stress Tolerance: Methods and Protocols Ramanjulu Sunkar ISBN:1607617013
Molecular Imaging: Principles and Practice Ralph Weissleder, Brian D. Ross, Alnawaz Rehemtulla, Sanjiv S Gambhir ISBN:1607950057
Genome informatics 2008: proceedings of the 19th International Conference, Gold Coast, Queensland, Australia, 1-3 December 2008 Jonathan Arthur, See-Kiong Ng ISBN:1848163312
Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano ISBN:1848820224
Modeling in Systems Biology: The Petri Net Approach Ina Koch ISBN:1849964734
Information processing and living systems Vladimir B. Bajic, Tin Wee Tan ISBN:1860945635
Computational systems bioinformatics: CSB2006 conference proceedings, Stanford CA, 14-18 August 2006 Peter Markstein, Life Sciences Society Computational Systems Bioinformatics Conference, Hewlett-Packard Company, Microsoft Research ISBN:186094700X
Computational methods for understanding bacterial and archaeal genomes Ying Xu, J. Peter Gogarten ISBN:1860949827
Genome informatics 2007: proceedings of the 18th International Conference, Biopolis, Singapore, 3-5 December 2007 See-Kiong Ng, Hiroshi Mamitsuka, Limsoon Wong ISBN:1860949843
Genome informatics 2007: proceedings of the 7th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2007) Satoru Miyano, Charles Delisi, Herman-Georg Holzhutter ISBN:1860949916
Aspergillus: molecular biology and genomics Masayuki Machida, Katsuya Gomi ISBN:1904455530
Metagenomics: Theory, Methods and Applications Diana Marco ISBN:1904455549
Expression Systems: Methods Express Michael R. Dyson, Yves Durocher ISBN:1904842453
Computational genomics: current methods Nikola Stojanovic ISBN:1904933300
Bioinformatics for Systems Biology Stephen A. Krawetz ISBN:1934115029
Foundations of systems biology Hiroaki Kitano ISBN:262112663
Advances in cryptology-CRYPTO87: proceedings Carl Pomerance ISBN:3029743
Modern genome annotation: the BioSapiens Network Dmitrij Frishman, Alfonso Valencia ISBN:321175122X
Systems biology in practice: concepts, implementation and application Edda Klipp ISBN:3527310789
Proteomics in Drug Research Michael Hamacher ISBN:3527312269
Industrial Biotechnology: Sustainable Growth and Economic Success Wim Soetaert, Erick J. Vandamme ISBN:3527314423
Systems biology: a textbook Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach ISBN:3527318747
The Dictionary of Genomics, Transcriptomics and Proteomics Gunter Kahl ISBN:3527320733
Systems Biology in Psychiatric Research: From High-Throughput Data to Mathematical Modeling Felix Tretter, Peter J. Gebicke-Haerter, Georg Winterer ISBN:3527325034
Medical Biostatistics for Complex Diseases Frank Emmert-Streib, Matthias Dehmer ISBN:3527325859
Molekulare Biotechnologie: Konzepte, Methoden und Anwendungen Michael Wink ISBN:3527326553
Methoden Der Bioinformatik Marc-Thorsten Hutt Manuel Dehnert ISBN:3540256873
Data integration in the life sciences: second international workshop, DILS 2005, San Diego, CA, USA, July 20-22, 2005 : proceedings Bertram Ludascher, Louiqa Raschid ISBN:3540279679
Tutorials in mathematical biosciences: Cell cycle, proliferation, and cancer Alla Borisyuk, Avner Friedman, Baltazar D. Aguda ISBN:3540291628
Data integration in the life sciences: third international workshop, DILS 2006, Hinxton, UK, July 20-22, 2006 : proceedings Ulf Leser, Felix Naumann, Barbara A. Eckman ISBN:3540365931
Principles and practice of semantic web reasoning: 4th international workshop, PPSWR 2006, Budva, Montenegro, June 10-11, 2006 ; revised selected papers Jose Julio Alferes ISBN:3540395865
Current trends in database technology - EDBT 2006: EDBT 2006 workshops Torsten Grust ISBN:3540467882
On the move to meaningful internet systems 2006: OTM 2006 workshops: OTM Confederated International Workshops and Posters R. Meersman, Zahir Tari, Herrero Martin Herrero ISBN:3540482695
Biological and medical data analysis: 7th international symposium, ISBMDA 2006, Thessaloniki, Greece, December 7-8, 2006 : proceedings Nicos Maglaveras ISBN:3540680632
Data mining and bioinformatics: first International Workshop, VDMB 2006, Seoul, Korea, September 11, 2006, revised selected papers Mehmet M. Dalkilic ISBN:3540689702
Grundlagen der Molekularen Medizin Detlev Ganten, Klaus Ruckpaul ISBN:3540694129
Data integration in the life sciences: 5th international workshop, DILS 2008, Evry, France, June 25-27, 2008 : proceedings Amos Bairoch, Christine Froidevaux ISBN:3540698272
Bioinformatics research and development: first international conference, BIRD 2007, Berlin, Germany, March 12-14, 2007 : proceedings Sepp Hochreiter, Roland R. Wagner ISBN:3540712321
Proteome Research: Concepts, Technology and Application Marc R. Wilkins ISBN:3540712410
Research in computational molecular biology: 11th annual international conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007 : proceedings Terry Speed, Haiyan Huang ISBN:3540716807
Bioinformatics research and applications: third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings Alexander Zelikovsky ISBN:3540720308
Applied bioinformatics: an introduction Paul M. Selzer, Richard J. Marhí_fer, Andreas Rohwer ISBN:354072799X
Data Integration in the Life Sciences: 4th international workshop, DILS 2007, Philadelphia, PA, USA, June 27-29, 2007 : proceedings Sarah Cohen-Boulakia, Val Tannen ISBN:3540732543
Advances in conceptual modeling: foundations and applications : ER 2007 workshops CMLSA, FP-UML, ONISW, QoIS, RIGiM, SeCoGIS, Auckland, New Zealand, November 5-9, 2007 : proceedings Jean-Luc Hainaut, Elke Al. Rundensteiner ISBN:3540762914
Membrane computing: 8th international workshop, WMC 2007, Thessaloniki, Greece, June 25-28, 2007 : revised, selected and invited papers George Eleftherakis, Petros Kefalas, Gheorghe Paun ISBN:3540773118
Bioinformatics and systems biology: collaborative research and resources Frederick B. Marcus ISBN:3540783520
Database and expert systems applications: 19th international conference, DEXA 2008, Turin, Italy, September 1-5, 2008 : proceedings Sourav S. Bhowmick ISBN:3540856536
Reasoning Web: 4th International Summer School 2008, Venice Italy, September 7-11, 2008, Tutorial Lectures Cristina Baroglio ISBN:3540856560
Pattern recognition in bioinformatics: third IAPR international conference, PRIB 2008, Melbourne, Australia, October 15-17, 2008 : proceedings Madhu Chetty, Alioune Ngom, Shandar Ahmad ISBN:3540884343
Bayesian Network Analysis Software Miroslawa Utzka ISBN:3639017498
BN++: A Biological Information System Jan Kuntzer ISBN:3639032837
Physiology and Genetics: Selected Basic and Applied Aspects Timm Anke, Daniela Weber ISBN:3642002854
Biomedical Data and Applications Amandeep S. Sidhu, Tharam Dillon, Matthew Bellgard ISBN:3642021921
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living Miguel P. Rocha ISBN:3642024807
Data Integration in the Life Sciences: 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009, Proceedings Norman W. Paton, Paolo Missier, Cornelia Hedeler ISBN:3642028780
Advances in Bioinformatics and Computational Biology: 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009, Proceedings Katia S. Guimaraes, Anna Panchenko, Teresa Przytycka ISBN:3642032222
Semantic Techniques for the Web: The REWERSE Perspective Franícois Bry, Jan Maluszynski ISBN:3642045804
Metadata and Semantic Research: Third International Conference, MTSR 2009, Milan, Italy, October 1-2, 2009. Proceedings Miguel-Angel Sicilia, Nikos Manouselis ISBN:3642045898
Knowledge-Based Intelligent Information and Engineering Systems: 13th International Conference, KES 2009, Santiago, Chile, September 28-30, 2009, Proceedings Sebastian A. Ríos, Robert J. Howlett ISBN:364204591X
Discovery Science: 12th International Conference, DS 2009, Porto, Portugal, October 3-5 2009 Joao Gama ISBN:3642047467
Flexible Query Answering Systems: 8th International Conference, FQAS 2009, Roskilde, Denmark, October 26-28, 2009, Proceedings Troels Andreasen, Ronald R. Yager, Henrik Bulskov ISBN:3642049567
Trends in Practical Applications of Agents and Multiagent Systems: 8th International Conference on Practical Applications of Agents and Multiagent Systems Pawel Pawlewski, Vicente J Julian, Florentino Ferníçndez-Riverola ISBN:3642124321
Bioinformatics Research and Applications: 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings Mark Borodovsky, Johann Peter Gogarten, Teresa Przytycka, Sanguthevar Rajasekaran ISBN:3642130771
Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010) Miguel P. Rocha, Florentino Ferníçndez Riverola, Hagit Shatkay ISBN:3642132138
The Semantic Web: Research and Applications: 7th European Semantic Web Conference, ESWC 2010 Lora Aroyo ISBN:3642134882
Biosystems Engineering I: Creating Superior Biocatalysts Christoph Wittmann ISBN:3642142303
Case-Based Reasoning: 18th International Conference, ICCBR 2010, Alessandria, Italy, July 19-22, 2010 Proceedings Isabelle Bichindaritz ISBN:3642142737
Information, Technology in Bio- and Medical Informatics, ITBAM 2010: First International Conference Sami Khuri ISBN:3642150195
Leveraging Applications of Formal Methods, Verification, and Validation: 4th International Symposium on Leveraging Applications, Isola 2010 Tiziana Margaria, Bernhard Steffen ISBN:3642165575
Kernel-based Data Fusion for Machine Learning: Methods and Applications in Bioinformatics and Text Mining Shi Yu, Leon-Charles Tranchevent, Bart Moor, Yves Moreau ISBN:3642194052
Database Systems for Advanced Applications: 16th International Conference, DASFAA 2011, Hong Kong, China, April 22-25, 2011, Proceedings Jeffrey Xu Yu, Myoung Ho Kim, Rainer Unland ISBN:3642201482
Bioinformatics Research and Application: 7th International Symposium, ISBRA 2011, Changsha, China, May 27-29, 2011, Proceedings Jianer Chen, Jianxin Wang, Alexander Zelikovsky ISBN:364221259X
Biowissenschaftlich recherchieren: íìber den Einsatz von Datenbanken und anderen Ressourcen der Bioinformatik Nicola Gaedeke ISBN:3764385251
Avian genomics in evolution, agriculture and health Jacqueline Smith, Indrajit Nanda ISBN:3805583389
Bioinformatics and computational biology solutions using R and Bioconductor Robert Gentleman ISBN:387251464
Semantic web: revolutionizing knowledge discovery in the life sciences Christopher J. O. Baker, Kei-Hoi Cheung ISBN:387484361
Cancer informatics in the post genomic era: toward information-based medicine Igor Jurisica, Dennis Wigle ISBN:387693203
Human blood plasma proteins: structure and function Johann Schaller, Simon Gerber, Urs Kaempfer ISBN:470016744
Analysis of biological networks Bjorn H. Junker, Falk Schreiber ISBN:470041447
Bioinformatics and functional genomics Jonathan Pevsner ISBN:470085851
Pathway analysis for drug discovery: computational infrastructure and applications Anton Yuryev ISBN:470107057
Machine learning in bioinformatics Yan-Qing Zhang, Jagath Chandana Rajapakse ISBN:470116625
Elements of Computational Systems Biology Huma M. Lodhi, Stephen H. Muggleton ISBN:470180935
Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools Sean Ekins, Jinghai J. Xu ISBN:470225556
Applications of Toxicogenomics in Safety Evaluation and Risk Assessment Darrell R. Boverhof, B. Bhaskar Gollapudi ISBN:470449829
Platelet Proteomics: Principles, Analysis, and Applications Angel Garcia-Alonso, Yotis Senis ISBN:470463376
Wiley encyclopedia of chemical biology Tadhg P. Begley ISBN:470470194
Advances in Chemical Physics Stuart A. Rice ISBN:470500255
Computational methods for mass spectrometry proteomics Ingvar Eidhammer ISBN:470512970
Batch Effects and Noise in Microarray Experiments: Sources and Solutions Andreas Scherer ISBN:470741384
Knowledge-Based Bioinformatics: From Analysis to Interpretation Gil Alterovitz, Marco Ramoni ISBN:470748311
Encyclopedia of genetics, genomics, proteomics, and bioinformatics: 8 volume set Lynn B. Jorde ISBN:470849746
Drug Discovery and Development: Drug discovery Mukund Shankar Chorghade ISBN:471398489
Aligning biological networks Andrew McKim ISBN:494497076
An introduction to genetic engineering Desmond S. T. Nicholl ISBN:521615216
Statistical mechanical approaches to informatics: Discovering motifs and clustering data David Anthony Hendrix, University of California, Berkeley ISBN:549168311
Semantic tuple space coordination for the Semantic Web with applications in life science Peishen Qi, Yale University ISBN:549372997
Beautiful Data: The Stories Behind Elegant Data Solutions Toby Segaran, Jeff Hammerbacher ISBN:596157118
因特网信息资源检索与利用 符绍宏 ISBN:7302114595
CompLife 2007: 3rd International Symposium on Computational Life Science, Utrecht, The Netherlands, 4-5 October 2007 Arno Siebes, Michael R. Berthold ISBN:735404526
Science in medicine: the JCI textbook of molecular medicine Andrew R. Marks, Ushma S. Neill ISBN:763750832
Semantic Web - Concepts and Applications B. Ravi Kumar Jain ISBN:8131411672
Nutrigenomics and proteomics in health and disease: food factors and gene interactions Yoshinori Mine, Kazuo Miyashita, Fereidoon Shahidi ISBN:813800331
Bioinformatics Prof. Vinay Sharma ISBN:8171339174
New therapeutic agents in thrombosis and thrombolysis Arthur Asao Sasahara, Joseph Loscalzo ISBN:824707958
Using the pharmaceutical literature Sharon Srodin ISBN:824729668
Genetic variation: a laboratory manual Michael P. Weiner ISBN:879697806
Genomes: perspectives from the 10th anniversary issue of Genome research Hillary E. Sussman, Maria Ann Smith ISBN:879698071
Plant hormone protocols Jeremy A. Roberts ISBN:896035778
An Omics Perspective on Cancer Research William C. S. Cho ISBN:9048126746
From fundamental genomics to systems biology: understanding the book of life Christina Kyriakopoulou ISBN:9279080040
Advanced Simulation and Verification of Electronic and Biological Systems Peng Li ISBN:9400701489
Biocomputing 2006: Proceedings of the Pacific Symposium; Hawaii, USA - 3-7 January 2006 Russ Altman, Russ B. Altman ISBN:9812564632
Pacific Symposium on Biocomputing 2007: Maui, Hawaii, 3-7 January 2007 Russ B. Altman, A. Keith Dunker, Lawrence Hunter ISBN:9812704175
Quantitative medical data analysis using mathematical tools and statistical techniques Don Hong, Yu Shyr ISBN:9812704612
Biological networks Francois Kepes ISBN:981270695X
Clustering challenges in biological networks W. Art Chaovalitwongse ISBN:9812771654
Biodata mining and visualization: novel approaches Ilkka Havukkala ISBN:9812790365
Pacific Symposium on Biocomputing 2009: Kohala Coast, Hawaii, USA, 5-9 January 2009 Russ B. Altman, A. Keith Dunker, Lawrence Hunter ISBN:9812836926