Gary Bader - Publications

Affiliations: 
Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto, Toronto, ON, Canada 
Website:
http://baderlab.org/

153 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, ... ... Bader GD, et al. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Research. PMID 31647099 DOI: 10.1093/nar/gkz946  0.56
2019 Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, ... Bader GD, et al. Single-cell transcriptomic profiling of the aging mouse brain. Nature Neuroscience. 22: 1696-1708. PMID 31551601 DOI: 10.1038/s41593-019-0491-3  0.36
2019 Vora P, Seyfrid M, Venugopal C, Qazi MA, Salim S, Isserlin R, Subapanditha M, O'Farrell E, Mahendram S, Singh M, Bakhshinyan D, Chokshi C, McFarlane N, Dvorkin-Gheva A, Brown KR, ... ... Bader GD, et al. Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells. Journal of Neuro-Oncology. PMID 31115870 DOI: 10.1007/s11060-019-03192-1  0.36
2019 Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B. Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression. Clinical Epigenetics. 11: 54. PMID 30917865 DOI: 10.1186/s13148-019-0651-z  0.36
2019 Sun R, Hui S, Bader GD, Lin X, Kraft P. Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic. Plos Genetics. 15: e1007530. PMID 30875371 DOI: 10.1371/journal.pgen.1007530  0.92
2019 Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD. netDx: interpretable patient classification using integrated patient similarity networks. Molecular Systems Biology. 15: e8497. PMID 30872331 DOI: 10.15252/msb.20188497  0.92
2019 Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols. PMID 30664679 DOI: 10.1038/s41596-018-0103-9  0.36
2018 Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, Bader GD, Sibille E. The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety. Biological Psychiatry. PMID 30446205 DOI: 10.1016/j.biopsych.2018.09.019  0.36
2018 Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P, Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, ... ... Bader G, et al. Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. The Journal of Cell Biology. PMID 29921600 DOI: 10.1083/jcb.201804042  0.36
2018 Pai S, Bader GD. Patient Similarity Networks for Precision Medicine. Journal of Molecular Biology. PMID 29860027 DOI: 10.1016/j.jmb.2018.05.037  0.32
2017 Michailidou K, Lindström S, Dennis J, Beesley J, Hui S, Kar S, Lemaçon A, Soucy P, Glubb D, Rostamianfar A, Bolla MK, Wang Q, Tyrer J, Dicks E, Lee A, ... ... Bader GD, et al. Association analysis identifies 65 new breast cancer risk loci. Nature. PMID 29059683 DOI: 10.1038/nature24284  0.92
2017 Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, Hui S, Lemaçon A, Soucy P, Dennis J, Jiang X, Rostamianfar A, Finucane H, Bolla MK, McGuffog L, ... ... Bader GD, et al. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nature Genetics. PMID 29058716 DOI: 10.1038/ng.3785  0.92
2017 El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B. Integrative cancer pharmacogenomics to infer large-scale drug taxonomy. Cancer Research. PMID 28314784 DOI: 10.1158/0008-5472.CAN-17-0096  0.36
2016 Kucera M, Isserlin R, Arkhangorodsky A, Bader GD. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000research. 5: 1717. PMID 27830058 DOI: 10.12688/f1000research.9090.1  0.36
2016 Dumontier M, Gray AJ, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, et al. The health care and life sciences community profile for dataset descriptions. Peerj. 4: e2331. PMID 27602295 DOI: 10.7717/peerj.2331  0.36
2016 Jones RA, Robinson TJ, Liu JC, Shrestha M, Voisin V, Ju Y, Chung PE, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, ... Bader GD, et al. RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation. The Journal of Clinical Investigation. PMID 27571409 DOI: 10.1172/JCI81568  0.92
2016 Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, ... ... Bader GD, et al. Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors. Cell Stem Cell. PMID 27424784 DOI: 10.1016/j.stem.2016.06.008  0.92
2016 Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, Voisin V, Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, ... ... Bader G, et al. Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells. Cancer Cell. 29: 859-873. PMID 27300435 DOI: 10.1016/j.ccell.2016.05.002  0.92
2016 Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, ... ... Bader GD, et al. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell. 29: 602-606. PMID 27070706 DOI: 10.1016/j.ccell.2016.03.015  0.92
2016 Kamdar SN, Ho LT, Kron KJ, Isserlin R, van der Kwast T, Zlotta AR, Fleshner NE, Bader G, Bapat B. Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis. Clinical Epigenetics. 8: 32. PMID 26981160 DOI: 10.1186/s13148-016-0195-4  0.36
2016 Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, ... ... Bader GD, et al. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell. PMID 26832662 DOI: 10.1016/j.ccell.2015.12.011  0.36
2015 Kofia V, Isserlin R, Buchan AM, Bader GD. Social Network: a Cytoscape app for visualizing co-authorship networks. F1000research. 4: 481. PMID 26949516 DOI: 10.12688/f1000research.6804.3  0.36
2015 Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics. 12: 258. PMID 26528556 DOI: 10.2390/biecoll-jib-2015-258  0.92
2015 Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP. Systematic analysis of somatic mutations impacting gene expression in 12 tumour types. Nature Communications. 6: 8554. PMID 26436532 DOI: 10.1038/ncomms9554  0.92
2015 Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD. Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics (Oxford, England). PMID 26415722 DOI: 10.1093/bioinformatics/btv557  0.92
2015 Cuenca-López MD, Serrano-Heras G, Montero JC, Corrales-Sánchez V, Gomez-Juarez M, Gascón-Escribano MJ, Morales JC, Voisin V, Núñez LE, Morís F, Bader GD, Pandiella A, Ocaña A. Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer. Oncotarget. 6: 27923-37. PMID 26314846 DOI: 10.18632/oncotarget.4736  0.92
2015 Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA, Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, ... ... Bader GD, et al. EAG2 potassium channel with evolutionarily conserved function as a brain tumor target. Nature Neuroscience. PMID 26258683 DOI: 10.1038/nn.4088  0.92
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/nmeth.3440  0.56
2015 Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T, Li RK, Fish JE, Bader GD, Husain M. Cardioprotective Signature of Short-Term Caloric Restriction. Plos One. 10: e0130658. PMID 26098549 DOI: 10.1371/journal.pone.0130658  0.92
2015 Cole A, Wang Z, Coyaud E, Voisin V, Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, ... ... Bader GD, et al. Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia. Cancer Cell. 27: 864-76. PMID 26058080 DOI: 10.1016/j.ccell.2015.05.004  0.92
2015 Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, ... ... Bader G, et al. Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. Cancer Cell. 27: 728-43. PMID 25965575 DOI: 10.1016/j.ccell.2015.04.002  0.92
2015 Wagih O, Reimand J, Bader GD. MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. Nature Methods. 12: 531-3. PMID 25938373 DOI: 10.1038/nmeth.3396  0.92
2015 Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G. Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action. The Biochemical Journal. PMID 25915851 DOI: 10.1042/BJ20141455  0.92
2015 Lerner-Ellis J, Wang M, White S, Lebo MS. Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations. Journal of Medical Genetics. 52: 438-45. PMID 25904639 DOI: 10.1136/jmedgenet-2014-102933  0.92
2015 Ammar R, Paton TA, Torti D, Shlien A, Bader GD. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000research. 4: 17. PMID 25901276 DOI: 10.12688/f1000research.6037.1  0.92
2015 Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TS, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, ... ... Bader GD, et al. Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis. The Lancet. Oncology. 16: 569-82. PMID 25882982 DOI: 10.1016/S1470-2045(15)70114-2  0.92
2015 Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N. Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Frontiers in Bioengineering and Biotechnology. 3: 19. PMID 25759811 DOI: 10.3389/fbioe.2015.00019  0.56
2015 Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B, Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel MS, Guidos CJ. IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection. Nature Immunology. 16: 397-405. PMID 25729925 DOI: 10.1038/ni.3122  0.92
2015 Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, Bader GD, Lydon JP, Waterhouse PD, Boutros PC, Khokha R. A progesterone-CXCR4 axis controls mammary progenitor cell fate in the adult gland. Stem Cell Reports. 4: 313-22. PMID 25702641 DOI: 10.1016/j.stemcr.2015.01.011  0.92
2015 Reimand J, Wagih O, Bader GD. Evolutionary constraint and disease associations of post-translational modification sites in human genomes. Plos Genetics. 11: e1004919. PMID 25611800 DOI: 10.1371/journal.pgen.1004919  0.92
2015 Meyer M, Reimand J, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, ... Bader GD, et al. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proceedings of the National Academy of Sciences of the United States of America. 112: 851-6. PMID 25561528 DOI: 10.1073/pnas.1320611111  0.92
2015 Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. Molecular Biosystems. 11: 239-51. PMID 25361207 DOI: 10.1039/c4mb00265b  0.92
2015 Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, ... ... Bader G, et al. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics (Oxford, England). 31: 306-10. PMID 25316676 DOI: 10.1093/bioinformatics/btu671  0.92
2015 Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Goliaei B, Bader GD. Inferring interaction type in gene regulatory networks using co-expression data Algorithms For Molecular Biology. 10. DOI: 10.1186/s13015-015-0054-4  0.92
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes Nature Methods. 12: 615-621. DOI: 10.1038/nmeth.3440  0.92
2015 Khosravi P, Gazestani VH, Law B, Bader GD, Sadeghi M. Comparative analysis of co-expression networks reveals molecular changes during the cancer progression Ifmbe Proceedings. 51: 1481-1487. DOI: 10.1007/978-3-319-19387-8_360  0.92
2014 Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000research. 3: 138. PMID 25580224 DOI: 10.12688/f1000research.4642.1  0.92
2014 Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E. Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K. Embo Molecular Medicine. 6: 1542-60. PMID 25330770 DOI: 10.15252/emmm.201404402  0.92
2014 Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q. GeneMANIA: Fast gene network construction and function prediction for Cytoscape. F1000research. 3: 153. PMID 25254104 DOI: 10.12688/f1000research.4572.1  0.92
2014 Pizzoferrato AC, Fermaut M, El Assal A, Fauconnier A, Bader G. [Urinary incontinence in nulliparous women: prevalence and evaluation of self-perineal reeducation]. ProgrèS En Urologie : Journal De L'Association FrançAise D'Urologie Et De La SociéTé FrançAise D'Urologie. 24: 646-50. PMID 25214294 DOI: 10.1016/j.purol.2014.03.007  0.01
2014 Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with cytoscape 3. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 47: 8.13.1-8.13.24. PMID 25199793 DOI: 10.1002/0471250953.bi0813s47  0.92
2014 Isserlin R, Merico D, Voisin V, Bader GD. Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. F1000research. 3: 141. PMID 25075306 DOI: 10.12688/f1000research.4536.1  0.92
2014 Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, ... Bader GD, et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature. 511: 428-34. PMID 25043047 DOI: 10.1038/nature13379  0.92
2014 Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW. Intercellular network structure and regulatory motifs in the human hematopoietic system. Molecular Systems Biology. 10: 741. PMID 25028490 DOI: 10.15252/msb.20145141  0.92
2014 Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, ... ... Bader G, et al. Quiescent sox2(+) cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma. Cancer Cell. 26: 33-47. PMID 24954133 DOI: 10.1016/j.ccr.2014.05.005  0.92
2014 Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q. Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Frontiers in Genetics. 5: 123. PMID 24904632 DOI: 10.3389/fgene.2014.00123  0.92
2014 Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, ... ... Bader GD, et al. A draft map of the human proteome. Nature. 509: 575-81. PMID 24870542 DOI: 10.1038/nature13302  0.92
2014 Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, ... ... Bader GD, et al. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science (New York, N.Y.). 344: 208-11. PMID 24723613 DOI: 10.1126/science.1250217  0.92
2014 Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD. Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs. Plos One. 9: e94507. PMID 24722214 DOI: 10.1371/journal.pone.0094507  0.92
2014 Leung A, Bader GD, Reimand J. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Bioinformatics (Oxford, England). 30: 2230-2. PMID 24713437 DOI: 10.1093/bioinformatics/btu172  0.92
2014 Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, ... ... Bader GD, et al. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell. 25: 393-405. PMID 24651015 DOI: 10.1016/j.ccr.2014.02.004  0.92
2014 Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS. Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan. Proteomics. 14: 975-88. PMID 24596128 DOI: 10.1002/pmic.201400041  0.92
2013 Alshalalfa M, Bader GD, Bismar TA, Alhajj R. Coordinate microRNA-mediated regulation of protein complexes in prostate cancer. Plos One. 8: e84261. PMID 24391925 DOI: 10.1371/journal.pone.0084261  0.92
2013 Reimand J, Wagih O, Bader GD. The mutational landscape of phosphorylation signaling in cancer. Scientific Reports. 3: 2651. PMID 24089029 DOI: 10.1038/srep02651  0.92
2013 Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific Reports. 3: 2650. PMID 24084849 DOI: 10.1038/srep02650  0.92
2013 Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Using biological pathway data with paxtools. Plos Computational Biology. 9: e1003194. PMID 24068901 DOI: 10.1371/journal.pcbi.1003194  0.92
2013 Rodchenkov I, Demir E, Sander C, Bader GD. The BioPAX Validator. Bioinformatics (Oxford, England). 29: 2659-60. PMID 23918249 DOI: 10.1093/bioinformatics/btt452  0.92
2013 Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/nmeth.2562  0.92
2013 Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q. GeneMANIA prediction server 2013 update. Nucleic Acids Research. 41: W115-22. PMID 23794635 DOI: 10.1093/nar/gkt533  0.92
2013 Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Cytoscape app store. Bioinformatics (Oxford, England). 29: 1350-1. PMID 23595664 DOI: 10.1093/bioinformatics/btt138  0.92
2013 Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, ... ... Bader GD, et al. SH3 interactome conserves general function over specific form. Molecular Systems Biology. 9: 652. PMID 23549480 DOI: 10.1038/msb.2013.9  0.92
2013 Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD. Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells. Plos One. 8: e58367. PMID 23520503 DOI: 10.1371/journal.pone.0058367  0.92
2013 Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Molecular Systems Biology. 9: 637. PMID 23340843 DOI: 10.1038/msb.2012.68  0.92
2013 Hui S, Xing X, Bader GD. Predicting PDZ domain mediated protein interactions from structure. Bmc Bioinformatics. 14: 27. PMID 23336252 DOI: 10.1186/1471-2105-14-27  0.92
2013 Karagiannis GS, Weile J, Bader GD, Minta J. Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation. Bmc Cardiovascular Disorders. 13: 4. PMID 23324130 DOI: 10.1186/1471-2261-13-4  0.92
2013 Antoniotti M, Bader GD, Caravagna G, Crippa S, Graudenzi A, Mauri G. GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinformatics (Oxford, England). 29: 513-4. PMID 23292740 DOI: 10.1093/bioinformatics/bts726  0.92
2013 Lee AY, Bader GD, Nislow C, Giaever G. Chemogenomic Profiling: Understanding the Cellular Response to Drug Handbook of Systems Biology. 153-176. DOI: 10.1016/B978-0-12-385944-0.00008-3  0.92
2012 Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L. Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice. Oncogenesis. 1: e26. PMID 23552839 DOI: 10.1038/oncsis.2012.28  0.92
2012 Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C. Chromatin is an ancient innovation conserved between Archaea and Eukarya. Elife. 1: e00078. PMID 23240084 DOI: 10.7554/eLife.00078  0.92
2012 Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L. Attenuation of miR-126 activity expands HSC in vivo without exhaustion. Cell Stem Cell. 11: 799-811. PMID 23142521 DOI: 10.1016/j.stem.2012.09.001  0.92
2012 Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nature Methods. 9: 1069-76. PMID 23132118 DOI: 10.1038/nmeth.2212  0.92
2012 Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. Bmc Systems Biology. 6: 112. PMID 22929553 DOI: 10.1186/1752-0509-6-112  0.92
2012 Michaut M, Bader GD. Multiple genetic interaction experiments provide complementary information useful for gene function prediction. Plos Computational Biology. 8: e1002559. PMID 22737063 DOI: 10.1371/journal.pcbi.1002559  0.92
2012 Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells (Dayton, Ohio). 30: 1734-45. PMID 22696458 DOI: 10.1002/stem.1144  0.92
2012 Reimand J, Hui S, Jain S, Law B, Bader GD. Domain-mediated protein interaction prediction: From genome to network. Febs Letters. 586: 2751-63. PMID 22561014 DOI: 10.1016/j.febslet.2012.04.027  0.92
2012 Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 5832-7. PMID 22460789 DOI: 10.1073/pnas.1201105109  0.92
2012 Tan CS, Bader GD. Phosphorylation sites of higher stoichiometry are more conserved. Nature Methods. 9: 317; author reply 31. PMID 22453906 DOI: 10.1038/nmeth.1941  0.92
2012 Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE. Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry. Plos Genetics. 8: e1002562. PMID 22438817 DOI: 10.1371/journal.pgen.1002562  0.92
2012 Pan C, Xing X, Han P, Zheng S, Ma J, Liu J, Lv X, Lu J, Bader G. Efficacy and tolerability of vildagliptin as add-on therapy to metformin in Chinese patients with type 2 diabetes mellitus. Diabetes, Obesity & Metabolism. 14: 737-44. PMID 22369287 DOI: 10.1111/j.1463-1326.2012.01593.x  0.44
2012 Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Research. 40: e47. PMID 22210894 DOI: 10.1093/nar/gkr1294  0.92
2012 Demir E, Cary MP, 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, ... ... Bader GD, et al. The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) Nature Biotechnology. 30: 365. DOI: 10.1038/nbt0412-365c  0.92
2011 Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences. 5: 230-42. PMID 22180826 DOI: 10.4056/sigs.2034671  0.92
2011 Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. Bmc Bioinformatics. 12: 436. PMID 22070249 DOI: 10.1186/1471-2105-12-436  0.92
2011 Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MK, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, et al. Compound prioritization methods increase rates of chemical probe discovery in model organisms. Chemistry & Biology. 18: 1273-83. PMID 22035796 DOI: 10.1016/j.chembiol.2011.07.018  0.92
2011 Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, ... ... Bader GD, et al. NetSlim: high-confidence curated signaling maps. Database : the Journal of Biological Databases and Curation. 2011: bar032. PMID 21959865 DOI: 10.1093/database/bar032  0.92
2011 Wallace IM, Bader GD, Giaever G, Nislow C. Displaying chemical information on a biological network using Cytoscape. Methods in Molecular Biology (Clifton, N.J.). 781: 363-76. PMID 21877291 DOI: 10.1007/978-1-61779-276-2_18  0.92
2011 Merico D, Isserlin R, Bader GD. Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods in Molecular Biology (Clifton, N.J.). 781: 257-77. PMID 21877285 DOI: 10.1007/978-1-61779-276-2_12  0.92
2011 Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DT, Northcott PA, Garzia L, Bertrand KC, Wittmann A, ... ... Bader GD, et al. Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell. 20: 143-57. PMID 21840481 DOI: 10.1016/j.ccr.2011.07.007  0.92
2011 Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, et al. A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database : the Journal of Biological Databases and Curation. 2011: bar021. PMID 21742767 DOI: 10.1093/database/bar021  0.92
2011 Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, ... ... Bader GD, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods. 8: 528-9. PMID 21716279 DOI: 10.1038/nmeth.1637  0.92
2011 Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM. The multiple-specificity landscape of modular peptide recognition domains. Molecular Systems Biology. 7: 484. PMID 21525870 DOI: 10.1038/msb.2011.18  0.92
2011 Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code For Biology and Medicine. 6: 7. PMID 21473782 DOI: 10.1186/1751-0473-6-7  0.92
2011 Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD. Protein complexes are central in the yeast genetic landscape. Plos Computational Biology. 7: e1001092. PMID 21390331 DOI: 10.1371/journal.pcbi.1001092  0.92
2011 Bellay J, Han S, Michaut M, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM. Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biology. 12: R14. PMID 21324131 DOI: 10.1186/gb-2011-12-2-r14  0.92
2011 Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH. Too many roads not taken. Nature. 470: 163-5. PMID 21307913 DOI: 10.1038/470163a  0.92
2011 Isserlin R, El-Badrawi RA, Bader GD. The Biomolecular Interaction Network Database in PSI-MI 2.5. Database : the Journal of Biological Databases and Curation. 2011: baq037. PMID 21233089 DOI: 10.1093/database/baq037  0.36
2011 Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD. A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics (Oxford, England). 27: 383-90. PMID 21127034 DOI: 10.1093/bioinformatics/btq657  0.92
2011 Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Research. 39: D685-90. PMID 21071392 DOI: 10.1093/nar/gkq1039  0.92
2011 Tan CSH, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R. Response to comment on "positive selection of tyrosine loss in metazoan evolution" Science. 332: 917-b. DOI: 10.1126/science.1188535  0.92
2010 Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. Plos One. 5: e13984. PMID 21085593 DOI: 10.1371/journal.pone.0013984  0.92
2010 Jain S, Bader GD. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. Bmc Bioinformatics. 11: 562. PMID 21078182 DOI: 10.1186/1471-2105-11-562  0.92
2010 Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, et al. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nature Methods. 7: 1017-24. PMID 21076421 DOI: 10.1038/nmeth.1534  0.92
2010 Hui S, Bader GD. Proteome scanning to predict PDZ domain interactions using support vector machines. Bmc Bioinformatics. 11: 507. PMID 20939902 DOI: 10.1186/1471-2105-11-507  0.92
2010 Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics (Oxford, England). 26: 2927-8. PMID 20926419 DOI: 10.1093/bioinformatics/btq562  0.92
2010 Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW. Dynamic interaction networks in a hierarchically organized tissue. Molecular Systems Biology. 6: 417. PMID 20924352 DOI: 10.1038/msb.2010.71  0.92
2010 Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader GD, Sidhu SS, Vandekerckhove J, Gettemans J, Sudol M. Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling. The Biochemical Journal. 432: 461-72. PMID 20868367 DOI: 10.1042/BJ20100870  0.92
2010 Demir E, Cary MP, 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, ... ... Bader GD, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/nbt.1666  0.92
2010 Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Molecular Biosystems. 6: 1782-90. PMID 20714644 DOI: 10.1039/c0mb00061b  0.92
2010 Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, ... Bader GD, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research. 38: W214-20. PMID 20576703 DOI: 10.1093/nar/gkq537  0.92
2010 Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature. 466: 368-72. PMID 20531469 DOI: 10.1038/nature09146  0.92
2010 Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans. Nature Chemical Biology. 6: 549-57. PMID 20512140 DOI: 10.1038/nchembio.380  0.92
2010 Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics. 10: 1316-27. PMID 20127684 DOI: 10.1002/pmic.200900412  0.36
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Bader GD, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/science.1180823  0.92
2010 Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, ... ... Bader GD, et al. NetPath: a public resource of curated signal transduction pathways. Genome Biology. 11: R3. PMID 20067622 DOI: 10.1186/gb-2010-11-1-r3  0.92
2010 Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Research. 38: D502-7. PMID 19880385 DOI: 10.1093/nar/gkp820  0.92
2009 Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. Plos Biology. 7: e1000218. PMID 19841731 DOI: 10.1371/journal.pbio.1000218  0.92
2009 Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS. Rapid evolution of functional complexity in a domain family. Science Signaling. 2: ra50. PMID 19738200 DOI: 10.1126/scisignal.2000416  0.92
2009 Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling. 2: ra39. PMID 19638616 DOI: 10.1126/scisignal.2000316  0.92
2009 Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R. Positive selection of tyrosine loss in metazoan evolution. Science (New York, N.Y.). 325: 1686-8. PMID 19589966 DOI: 10.1126/science.1174301  0.92
2008 Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, ... ... Bader GD, et al. A specificity map for the PDZ domain family. Plos Biology. 6: e239. PMID 18828675 DOI: 10.1371/journal.pbio.0060239  0.92
2008 Yeung N, Cline MS, Kuchinsky A, Smoot ME, Bader GD. Exploring biological networks with Cytoscape software. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.13. PMID 18819078 DOI: 10.1002/0471250953.bi0813s23  0.92
2008 Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ. Cytoscape ESP: simple search of complex biological networks. Bioinformatics (Oxford, England). 24: 1465-6. PMID 18445605 DOI: 10.1093/bioinformatics/btn208  0.92
2008 Skrabanek L, Saini HK, Bader GD, Enright AJ. Computational prediction of protein-protein interactions. Molecular Biotechnology. 38: 1-17. PMID 18095187 DOI: 10.1007/s12033-007-0069-2  0.92
2007 Cline MS, 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, ... ... Bader GD, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/nprot.2007.324  0.92
2007 Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. Bmc Biology. 5: 44. PMID 17925023 DOI: 10.1186/1741-7007-5-44  0.92
2007 Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotechnology. 25: 894-8. PMID 17687370 DOI: 10.1038/nbt1324  0.92
2007 Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S. Germ-line DNA copy number variation frequencies in a large North American population. Human Genetics. 122: 345-53. PMID 17638019 DOI: 10.1007/s00439-007-0404-5  0.92
2007 Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B. From bytes to bedside: data integration and computational biology for translational cancer research. Plos Computational Biology. 3: e12. PMID 17319736 DOI: 10.1371/journal.pcbi.0030012  0.56
2006 Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. Bmc Bioinformatics. 7: 497. PMID 17101041 DOI: 10.1186/1471-2105-7-497  0.56
2006 Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Research. 34: D504-6. PMID 16381921 DOI: 10.1093/nar/gkj126  0.92
2005 Cary MP, Bader GD, Sander C. Pathway information for systems biology. Febs Letters. 579: 1815-20. PMID 15763557 DOI: 10.1016/j.febslet.2005.02.005  0.92
2004 Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, et al. Global mapping of the yeast genetic interaction network. Science (New York, N.Y.). 303: 808-13. PMID 14764870 DOI: 10.1126/science.1091317  0.92
2004 Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/nbt926  0.92
2003 Donaldson I, Martin J, de Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW. PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. Bmc Bioinformatics. 4: 11. PMID 12689350  0.92
2003 Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. Bmc Bioinformatics. 4: 2. PMID 12525261  0.8
2003 Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Research. 31: 248-50. PMID 12519993  0.8
2002 Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW. SeqHound: biological sequence and structure database as a platform for bioinformatics research. Bmc Bioinformatics. 3: 32. PMID 12401134  0.8
2002 Bader GD, Hogue CW. Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnology. 20: 991-7. PMID 12355115 DOI: 10.1038/nbt1002-991  0.8
2002 Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415: 180-3. PMID 11805837 DOI: 10.1038/415180a  0.92
2002 Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (New York, N.Y.). 295: 321-4. PMID 11743162 DOI: 10.1126/science.1064987  0.92
2001 Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (New York, N.Y.). 294: 2364-8. PMID 11743205 DOI: 10.1126/science.1065810  0.8
2001 Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Research. 29: 242-5. PMID 11125103  0.92
2000 Bader GD, Hogue CW. BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics (Oxford, England). 16: 465-77. PMID 10871269  0.8
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