| Year |
Citation |
Score |
| 2023 |
Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler AL, Bader GD. Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition. Cerebral Cortex (New York, N.Y. : 1991). PMID 37106565 DOI: 10.1093/cercor/bhad142 |
0.501 |
|
| 2022 |
Helmy M, Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, Bader GD. OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data. Journal of Molecular Biology. 434: 167603. PMID 35662469 DOI: 10.1016/j.jmb.2022.167603 |
0.309 |
|
| 2021 |
Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi JM, Rodchenkov I, Babur Ö, Bachman JA, Gyori B, Demir E, Bader GD, Sander C. Author-sourced capture of pathway knowledge in computable form using Biofactoid. Elife. 10. PMID 34860157 DOI: 10.7554/eLife.68292 |
0.731 |
|
| 2021 |
Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, ... ... Bader G, et al. The reactome pathway knowledgebase 2022. Nucleic Acids Research. PMID 34788843 DOI: 10.1093/nar/gkab1028 |
0.502 |
|
| 2020 |
Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD. netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000research. 9: 1239. PMID 33628435 DOI: 10.12688/f1000research.26429.1 |
0.552 |
|
| 2020 |
Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Ross C, Brown KR, Zid AA, Fan ZP, Hui S, Krall JA, Simons DM, ... ... Bader G, et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature. PMID 32968282 DOI: 10.1038/s41586-020-2746-2 |
0.531 |
|
| 2020 |
Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, ... ... Bader GD, et al. A reference map of the human binary protein interactome. Nature. 580: 402-408. PMID 32296183 DOI: 10.1038/S41586-020-2188-X |
0.316 |
|
| 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 |
0.784 |
|
| 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 |
0.53 |
|
| 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 |
0.534 |
|
| 2019 |
Richards LM, Whitley O, Cavalli FM, Safikhani Z, Coutinho F, Luchman HA, Haibe-Kains B, Weiss S, Dirks P, Bader G, Pugh TJ. Abstract 967: Single-cell transcriptomics uncovers clonal heterogeneity linked to drug response and cellular phenotype in adult brain tumor stem cells Cancer Research. 79: 967-967. DOI: 10.1158/1538-7445.Am2019-967 |
0.303 |
|
| 2018 |
Goebels F, Hu L, Bader G, Emili A. Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data. Methods in Molecular Biology (Clifton, N.J.). 1764: 391-399. PMID 29605929 DOI: 10.1007/978-1-4939-7759-8_25 |
0.374 |
|
| 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 |
0.479 |
|
| 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 |
0.463 |
|
| 2017 |
Wong JV, Luna A, Demir E, Rodchenkov I, Babur Ö, Sander C, Bader G. How can you interpret gene lists from -omics experiments? F1000research. 6. DOI: 10.7490/F1000Research.1115132.1 |
0.449 |
|
| 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 |
0.587 |
|
| 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 |
0.588 |
|
| 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 |
0.494 |
|
| 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 |
0.353 |
|
| 2015 |
Kamdar SN, Ho LT, Isserlin R, Kron KJ, Kwast Tvd, Zlotta AR, Fleshner NE, Bader G, Bapat B. Abstract B1-32: Genome-wide integrative analysis correlating locus-specific DNA methylation and hydroxymethylation to gene expression in normal prostate cells Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-32 |
0.336 |
|
| 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 |
0.569 |
|
| 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 |
0.769 |
|
| 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 |
0.446 |
|
| 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 |
0.539 |
|
| 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 |
0.51 |
|
| 2013 |
Lan X, Meyer M, Reimand J, Zhu X, Kushida M, Head R, Clarke I, Bader G, Dirks P. Abstract B29: Defining subclonal signaling heterogeneity in glioblastoma multiforme (GBM) Cancer Research. 73. DOI: 10.1158/1538-7445.Fbcr13-B29 |
0.304 |
|
| 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 |
0.474 |
|
| 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 |
0.574 |
|
| 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 |
0.437 |
|
| 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 |
0.342 |
|
| 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 |
0.754 |
|
| 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 |
0.549 |
|
| 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 |
0.758 |
|
| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Bader GD, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.539 |
|
| 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 |
0.445 |
|
| 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. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing Nature Biotechnology. 28: 1308-1308. DOI: 10.1038/Nbt1210-1308C |
0.431 |
|
| 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 |
0.503 |
|
| 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 |
0.423 |
|
| 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 |
0.484 |
|
| 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 |
0.63 |
|
| 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 |
0.61 |
|
| 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 |
0.48 |
|
| 2007 |
Hu P, Bader G, Wigle DA, Emili A. Computational prediction of cancer-gene function. Nature Reviews. Cancer. 7: 23-34. PMID 17167517 DOI: 10.1038/Nrc2036 |
0.339 |
|
| 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 |
0.553 |
|
| 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 |
0.558 |
|
| 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 |
0.462 |
|
| 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 |
0.475 |
|
| 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 |
0.715 |
|
| 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 DOI: 10.1186/1471-2105-4-11 |
0.62 |
|
| 2003 |
Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. Bmc Bioinformatics. 4: 2. PMID 12525261 DOI: 10.1186/1471-2105-4-2 |
0.613 |
|
| 2003 |
Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Research. 31: 248-50. PMID 12519993 DOI: 10.1093/Nar/Gkg056 |
0.624 |
|
| 2002 |
Fields S, Drees B, Hazbun TR, Tucker C, Tong AHY, Evangelista M, Boone C, Nardelli G, Castagnoli L, Zucconi A, Cesareni G, Bader G, Hogue C. Approaches to Analyze Protein Interactions. Thescientificworldjournal. 2: 93-94. PMID 29973818 DOI: 10.1100/Tsw.2002.44 |
0.558 |
|
| 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 DOI: 10.1186/1471-2105-3-32 |
0.666 |
|
| 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 |
0.608 |
|
| 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 |
0.61 |
|
| 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 |
0.608 |
|
| 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 |
0.571 |
|
| 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 |
0.62 |
|
| 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 DOI: 10.1093/Bioinformatics/16.5.465 |
0.636 |
|
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