Citing Reactome Biology

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This is a list of peer-reviewed research articles citing the use of Reactome pathway data by biologists, clinicians, geneticists and bioinformaticians to answer important biological questions.

Press this link to see a complete listing of all peer-reviewed articles and reviews citing Reactome Publications.


Research Topic Reference Paper
Cystic Fibrosis 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.
Human Proteome 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.
Periodontitis 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.
Gliomas 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.
Type-2-Diabetes 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.
Plant Cell Cycle 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.
Chemical carcinogens 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.
Yeast Chemical Genetics 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.
Macrophage 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, 185, 605-14.
Allergy 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.
Platlets 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.
Diet 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.
Influenza Infection 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.
Cardiomyopathy 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.
Tumour Biology 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.
Cancer Theraputics 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.
Dengue 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.
Organogenesis 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.
Host-Bacterial Protein Interactions PPI 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.
Microbiology 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.
Human Embryonic Stem Cell 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.
Migratory Locust Phase Traits 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.
Arrhythmias BERGER, S. I., MA\'AYAN, A. & IYENGAR, R. (2010) Systems pharmacology of arrhythmias. Science Signaling, 3, ra30.
Williams-Beuren syndrome 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.
Innate Immunology and Inflammatory Signals 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.
Human Proteome SAHA, S., HARRISON, S. H. & CHEN, J. Y. (2009) Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics, 9, 470-84.
Renal Carcinoma 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.
Diabetic Kidney Disease 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.
Neuronal Synapse Function 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.
Selenium Uptake 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.
Human Leucocytes 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.
Neural Dysfunction 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.
Influenza Virus 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.
Hypoxia 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.
Human Cell Cycle 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.
Structural Biology 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.
Toxicology 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.
miRNA and Cell Cycle 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.
GWAS 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.
Human Dendritic Cells FERREIRA, G.B., VAN ETTEN, E., LAGE, K., HANSEN, D.A., MOREAU, Y., WORKMAN, C.T., WAER, M., VERSTUYF, A., WAELKINS, E., OVERBERGH, L. & MATHIEU, C. (2009) Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D. Proteomics, 9, 3752-64.
Neurite Growth 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.
Hepatology 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.
Cancer Genomics 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.
Proteomics 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.
Human Miochondrion 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.
Tissue Survival 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.
Infective Disease 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.
Human Genetics CHEUNG, V. G. & EWENS, W. J. (2006) Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype. Genome Research, 16, 973-9.
Human Proteome Map 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.