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Gary Bader - Publications

Affiliations: 
Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto, Toronto, ON, Canada 
Website:
http://baderlab.org/
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59/375 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
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  0.73
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  0.587
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  0.445
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  0.436
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  0.341
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  0.752
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  0.756
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  0.538
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  0.444
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  0.609
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  0.552
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
Low-probability matches (unlikely to be authored by this person)
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  0.3
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 : Amb. 10: 23. PMID 26157474 DOI: 10.1186/S13015-015-0054-4  0.299
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  0.292
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  0.291
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  0.291
2018 Hussain A, Voisin V, Poon S, Meens J, Dmytryshyn J, Bader G, Neel B, Ailles L. Abstract 140: A novel signature of mesenchymal stromal cells in high-grade serous ovarian carcinoma Cancer Research. 78: 140-140. DOI: 10.1158/1538-7445.Am2018-140  0.289
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  0.288
2021 Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH. scNetViz: from single cells to networks using Cytoscape. F1000research. 10. PMID 34912541 DOI: 10.12688/f1000research.52460.1  0.286
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  0.285
2014 Dolma S, So M, Voisin V, Zhu X, Head R, Clarke I, Bader G, Tyers M, Dirks P. SC-05 * DOPAMINE RECEPTOR ANTAGONISTS ARE SELECTIVE INHIBITORS OF GLIOBLASTOMA STEM CELLS THROUGH IMPAIRMENT OF AUTOPHAGY Neuro-Oncology. 16: v198-v198. DOI: 10.1093/Neuonc/Nou275.5  0.283
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  0.282
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  0.28
2020 Dobson SM, Garcia-Prat L, Vanner RJ, Wintersinger J, Waanders E, Gu Z, McLeod J, Gan OI, Grandal I, Payne-Turner D, Edmonson MN, Ma X, Fan Y, Voisin V, Chan-Seng-Yue M, ... ... Bader G, et al. Relapse fated latent diagnosis subclones in acute B lineage leukaemia are drug tolerant and possess distinct metabolic programs. Cancer Discovery. PMID 32086311 DOI: 10.1158/2159-8290.Cd-19-1059  0.279
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  0.275
2015 Remke M, Cavalli F, Morrissy A, Ramaswamy V, Jones D, Packer R, Bouffet E, Bader G, Borkhardt A, Pfister S, Jabado N, Marra M, Taylor MD. Integrated genomics elucidates relative spatial homogeneity of embryonal brain tumors Molecular and Cellular Pediatrics. 2: A10. DOI: 10.1186/2194-7791-2-S1-A10  0.271
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  0.268
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  0.267
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  0.266
2017 Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, ... ... Bader G, et al. ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells. Cell Stem Cell. PMID 28712938 DOI: 10.1016/J.Stem.2017.06.004  0.266
2015 Remke M, Cavalli F, Morrissy AS, Ramaswamy V, Jones D, Packer R, Bouffet E, Bader G, Pfister S, Jabado N, Marra M, Taylor M. MB-21 * INTEGRATED GENOMICS ELUCIDATES RELATIVE SPATIAL HOMOGENEITY OF EMBRYONAL BRAIN TUMORS Neuro-Oncology. 17: iii24-iii24. DOI: 10.1093/Neuonc/Nov061.97  0.265
2015 Law B, Bader GD. GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks. Scientific Reports. 5: 12074. PMID 26165520 DOI: 10.1038/srep12074  0.265
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  0.265
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  0.263
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  0.262
2017 Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, Bader G, Voisin V, Xu C, et al. Tracing the origins of relapse in acute myeloid leukaemia to stem cells. Nature. PMID 28658204 DOI: 10.1038/Nature22993  0.26
2003 Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends in Cell Biology. 13: 344-56. PMID 12837605 DOI: 10.1016/S0962-8924(03)00127-2  0.26
2022 Forster DT, Li SC, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas LAV, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B, Bader GD, Boone C. BIONIC: biological network integration using convolutions. Nature Methods. PMID 36192463 DOI: 10.1038/s41592-022-01616-x  0.258
2018 Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q. GeneMANIA update 2018. Nucleic Acids Research. PMID 29912392 DOI: 10.1093/nar/gky311  0.257
2013 Reimand J, Bader G, Margolin A, Gonzalez-Perez A, Tamborero D, Lopez-Bigas N, Weinstein J, Stuart J, Axton M. Thread 2: Network models Nature Genetics. 1-1. DOI: 10.1038/Ng.2787  0.257
2016 Jeyaraju DV, Voisin V, Ramakrishnan A, Hurren R, Maclean N, Gronda M, Minden M, Bader G, Schimmer AD. Abstract A87: Targeting the mitochondrial quality control machinery in acute myeloid leukemia Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Metca15-A87  0.257
2020 Selvadurai HJ, Luis E, Desai K, Lan X, Vladoiu MC, Whitley O, Galvin C, Vanner RJ, Lee L, Whetstone H, Kushida M, Nowakowski T, Diamandis P, Hawkins C, Bader G, et al. Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2 Granule Neuron Precursor. Cell Reports. 31: 107511. PMID 32294450 DOI: 10.1016/J.Celrep.2020.03.075  0.254
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  0.251
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  0.251
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  0.25
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  0.25
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  0.249
2010 Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics (Oxford, England). 26: 2347-8. PMID 20656902 DOI: 10.1093/bioinformatics/btq430  0.248
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  0.248
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  0.248
2018 Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000research. 7: 800. PMID 29983926 DOI: 10.12688/F1000Research.15355.1  0.247
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  0.247
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  0.245
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  0.243
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  0.24
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  0.239
2013 Samplaski M, Zhu Y, Hou H, Savio A, Bapat B, Bader G, McKerlie C, Jarvi K, Lo K. 2035 EPIGENETIC REGULATION OF GENE EXPRESSION PATTERNS IN HUMAN TESTIS XENOTRANSPLANTS AFTER TREATMENT WITH CYCLOPHOSPHAMIDE Journal of Urology. 189. DOI: 10.1016/J.Juro.2013.02.2454  0.239
2019 Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A. EPIC: software toolkit for elution profile-based inference of protein complexes. Nature Methods. PMID 31308550 DOI: 10.1038/S41592-019-0461-4  0.236
2021 Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, Bader GD, Blinov ML, Mazein A. SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings in Bioinformatics. PMID 33758926 DOI: 10.1093/bib/bbab049  0.235
2015 Rentas S, Holzapfel N, Belew M, Voisin V, Pratt G, Bader G, Yeo G, Hope K. Musashi-2 postranscriptionally attenuates aryl hydrocarbon receptor signaling to expand human hematopoietic stem cells Experimental Hematology. 43: S90. DOI: 10.1016/J.Exphem.2015.06.235  0.234
2011 Witt H, Mack S, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones D, Northcott P, Garzia L, Bertrand K, Wittmann A, ... ... Bader G, et al. Identification of Two Molecular and Clinical Distinct Entities of Posterior Fossa Ependymoma Klinische PäDiatrie. 223. DOI: 10.1055/S-0031-1292598  0.234
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  0.233
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  0.232
2022 Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, ... ... Bader GD, et al. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Cell Reports. 41: 111678. PMID 36417873 DOI: 10.1016/j.celrep.2022.111678  0.231
2017 Matan-Lithwick S, Cavalli FMG, Kijima N, Donovan L, Morrissy S, Garzia L, Bader G, Taylor M. Setting the stage for metastasis: changes in the activity of specific pathways in medulloblastoma primary tumours correlates with an increased frequency of metastasis F1000research. 6. DOI: 10.7490/F1000Research.1114252.1  0.23
2023 Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, et al. Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing. Arxiv. PMID 37332567  0.23
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  0.228
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  0.227
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  0.226
2007 Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D. NetMatch: a Cytoscape plugin for searching biological networks. Bioinformatics (Oxford, England). 23: 910-2. PMID 17277332 DOI: 10.1093/bioinformatics/btm032  0.226
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  0.226
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  0.225
2016 Jain S, Bader GD. Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. Bioinformatics (Oxford, England). PMID 26861823 DOI: 10.1093/bioinformatics/btw045  0.225
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  0.224
2021 Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, ... ... Bader GD, et al. The transcriptional landscape of Shh medulloblastoma. Nature Communications. 12: 1749. PMID 33741928 DOI: 10.1038/s41467-021-21883-0  0.224
2015 Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Bader GD, Goliaei B. Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. Algorithms For Molecular Biology : Amb. 10: 25. PMID 26265933 DOI: 10.1186/S13015-015-0055-3  0.223
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  0.223
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  0.222
2019 Newton D, Oh H, Shukla R, Fee C, Bader G, Banasr M, Sibille E. T120. Transcriptomic Analysis of Cortical Microcircuit Cell-Types Reveals Differential Cellular Vulnerabilities and Adaptations to Chronic Stress Biological Psychiatry. 85. DOI: 10.1016/J.Biopsych.2019.03.443  0.219
2013 Lechman ER, Gentner B, van Galen P, Wai-Kwong Ng S, Eppert K, Marke R, Slush L, Kennedy JA, Mitchell A, Chen WC, Voisin V, Bader G, Minden MD, Lu J, Wang JC, et al. Mir-126 Governs Human Leukemia Stem Cell Quiescence and Chemotherapy Resistance Blood. 122: 1647-1647. DOI: 10.1182/Blood.V122.21.1647.1647  0.217
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  0.217
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  0.217
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  0.217
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  0.216
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  0.215
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  0.211
2017 Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, ... ... Bader GD, et al. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling. Cell Systems. PMID 29128334 DOI: 10.1016/J.Cels.2017.10.010  0.211
2017 Tong J, Helmy M, Cavalli FM, Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD, Moran MF. Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia. Proteomics. PMID 28176486 DOI: 10.1002/pmic.201600361  0.211
2018 Wong A, Zamel R, Dos Santos C, Bader G, Keshavjee S, Liu M. Differential Gene Expression Profiling of Reperfusion During Ex Vivo Lung Perfusion and Lung Transplantation in Humans The Journal of Heart and Lung Transplantation. 37: S204. DOI: 10.1016/J.Healun.2018.01.497  0.21
2003 Sidhu SS, Bader GD, Boone C. Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Current Opinion in Chemical Biology. 7: 97-102. PMID 12547433 DOI: 10.1016/S1367-5931(02)00011-X  0.21
2003 Bader GD, Yan Tong AH, Cesareni G, Christopher W. H, Fields S, Boone C. Peptide Recognition Module Networks: Combining Phage Display with Two-Hybrid Analysis to Define Protein-Protein Interactions Handbook of Cell Signaling. 2: 311-315. DOI: 10.1016/B978-012124546-7/50536-2  0.21
2020 Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, ... ... Bader GD, et al. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Systems. 10: 333-350.e14. PMID 32325033 DOI: 10.1016/J.Cels.2020.03.003  0.21
2020 Tran TN, Bader GD. Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data. Plos Computational Biology. 16: e1008205. PMID 32903255 DOI: 10.1371/journal.pcbi.1008205  0.207
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  0.204
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: 1-3. PMID 29220957 DOI: 10.1515/jib-2015-258  0.203
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  0.203
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  0.203
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  0.202
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  0.198
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  0.197
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  0.197
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  0.196
2023 Li B, Rodrigo-Torres D, Pelz C, Innes B, Canaday P, Chai S, Zandstra P, Bader GD, Grompe M. Cell networks in the mouse liver during partial hepatectomy. Biorxiv : the Preprint Server For Biology. PMID 37503083 DOI: 10.1101/2023.07.16.549116  0.195
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  0.195
2018 Krivdova G, Lechman E, Schoof E, Voisin V, Gan O, Murison A, Hermans K, Trotman-Grant A, Bader G, Dick J. miR-130a Regulates Hematopoietic Stem Cell Self-Renewal by Repressing Several Chromatin Modifiers and Its Overexpression is Associated with Acute Myeloid Leukemia Experimental Hematology. 64: S48-S49. DOI: 10.1016/J.Exphem.2018.06.064  0.194
2016 Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG. Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance. Cell. 164: 293-309. PMID 26771497 DOI: 10.1016/J.Cell.2015.11.062  0.194
2021 Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, Bader GD. Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Nature Protocols. 16: 2749-2764. PMID 34031612 DOI: 10.1038/s41596-021-00534-0  0.193
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  0.193
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  0.192
2018 Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics. PMID 29596055 DOI: 10.1515/Jib-2018-0013  0.187
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  0.186
2017 Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L, Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, ... ... Bader GD, et al. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 31: 737-754.e6. PMID 28609654 DOI: 10.1016/J.Ccell.2017.05.005  0.186
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  0.186
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  0.186
2020 Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Blot W, ... ... Bader GD, et al. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. Nature Communications. 11: 312. PMID 31949161 DOI: 10.1038/S41467-019-14100-6  0.185
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 CWV. PreBIND and textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine Bmc Bioinformatics. 4. DOI: 10.1186/1471-2105-4-11  0.184
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.5279417  0.184
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  0.179
2016 Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ. Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells. Nature. 532: 508-11. PMID 27121842 DOI: 10.1038/Nature17665  0.179
2009 Merico D, Gfeller D, Bader GD. How to visually interpret biological data using networks. Nature Biotechnology. 27: 921-4. PMID 19816451 DOI: 10.1038/nbt.1567  0.178
2016 Narayan S, Bader GD, Reimand J. Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. Genome Medicine. 8: 55. PMID 27175787 DOI: 10.1186/s13073-016-0311-2  0.178
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  0.176
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  0.176
2024 Boccacino JM, Dos Santos Peixoto R, Fernandes CFL, Cangiano G, Sola PR, Coelho BP, Prado MB, Melo-Escobar MI, de Sousa BP, Ayyadhury S, Bader GD, Shinjo SMO, Marie SKN, da Rocha EL, Lopes MH. Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas. Bmc Cancer. 24: 199. PMID 38347462 DOI: 10.1186/s12885-024-11914-6  0.175
2016 Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, ... ... Bader GD, et al. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell. 30: 891-908. PMID 27960086 DOI: 10.1016/J.Ccell.2016.11.003  0.175
2023 Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, ... ... Bader GD, et al. Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer. Nature Communications. 14: 4313. PMID 37463901 DOI: 10.1038/s41467-023-39935-y  0.175
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  0.173
2003 Andrews BJ, Bader GD, Boone C. Playing tag with the yeast proteome. Nature Biotechnology. 21: 1297-9. PMID 14595360 DOI: 10.1038/Nbt1103-1297  0.172
2018 Giorgi JM, Bader GD. Transfer learning for biomedical named entity recognition with neural networks. Bioinformatics (Oxford, England). PMID 29868832 DOI: 10.1093/bioinformatics/bty449  0.172
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  0.17
2017 Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS. Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities. Structure (London, England : 1993). PMID 28890361 DOI: 10.1016/j.str.2017.07.017  0.17
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  0.17
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  0.169
2015 Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R. NetMatchStar: an enhanced Cytoscape network querying app. F1000research. 4: 479. PMID 26594341 DOI: 10.12688/F1000Research.6656.2  0.169
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  0.167
2022 Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, Voisin V, Krivdova G, Lechman ER, Marhon SA, De Carvalho D, Dick JE, Bader GD, Hope K. PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal. Blood. PMID 35639948 DOI: 10.1182/blood.2021014698  0.166
2018 Innes BT, Bader GD. scClustViz - Single-cell RNAseq cluster assessment and visualization. F1000research. 7. PMID 31016009 DOI: 10.12688/f1000research.16198.2  0.165
2018 Liu Q, Subedi A, Xu C, Voisin V, Bader GD, Chan SM, Wang JC. Identification of Compounds That Target Acute Myeloid Leukemia Stem Cells Using a Scalable Next-Generation Screening Platform Blood. 132: 259-259. DOI: 10.1182/blood-2018-99-115323  0.164
2015 Meyn M, Monfared N, Marshall CR, Merico D, Stavropoulos DJ, Hayeems RZ, Szego M, Jobling R, Girdea M, Bader GD, Brudno M, Cohn RD, Scherer SW, Shaul RZ, Shuman C, et al. MG-108 Beyond the ACMG 56: Parental choices and initial results from a comprehensive whole genome sequencing-based search for predictive genomic variants in children Journal of Medical Genetics. 52: A3.2-A4. DOI: 10.1136/Jmedgenet-2015-103578.8  0.164
2019 Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. Journal of Integrative Bioinformatics. PMID 31301675 DOI: 10.1515/Jib-2019-0035  0.164
2022 Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, ... ... Bader GD, et al. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. Cancers. 14. PMID 35884425 DOI: 10.3390/cancers14143363  0.164
2014 Laporte D, Huot JL, Bader G, Enkler L, Senger B, Becker HD. Exploring the evolutionary diversity and assembly modes of multi-aminoacyl-tRNA synthetase complexes: lessons from unicellular organisms. Febs Letters. 588: 4268-78. PMID 25315413 DOI: 10.1016/j.febslet.2014.10.007  0.163
2015 Kofia V, Isserlin R, Buchan AM, Bader GD. Social Network: a Cytoscape app for visualizing co-publication networks F1000research. 4: 481. DOI: 10.12688/F1000Research.6804.1  0.162
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  0.162
2019 Nachmias B, Voisin V, Hurren R, Wang X, Maclean N, Xu GW, Seneviratne AK, Xu C, Bader GD, Shlush LI, Schimmer AD. IPO11 Is Upregulated in Relapsed AML and Supports Survival of Leukemic Stem Cells Blood. 134: 2530-2530. DOI: 10.1182/blood-2019-122284  0.161
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  0.161
2013 Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. Journal of Proteome Research. 12: 23-7. PMID 23259511 DOI: 10.1021/Pr301151M  0.158
2020 Teyra J, Kelil A, Jain S, Helmy M, Jajodia R, Hooda Y, Gu J, D'Cruz AA, Nicholson SE, Min J, Sudol M, Kim PM, Bader GD, Sidhu SS. Large-scale survey and database of high affinity ligands for peptide recognition modules. Molecular Systems Biology. 16: e9310. PMID 33438817 DOI: 10.15252/msb.20199310  0.157
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  0.156
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  0.156
2018 Xie SZ, Garcia Prat L, Voisin V, Murison A, Gan OI, Ferrari R, Takayama N, Kaufmann KB, Patel I, Lee E, Holmes G, Medina T, Vedi A, Luberto C, Bader GD, et al. Sphingolipid Perturbation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal Blood. 132: 170-170. DOI: 10.1182/Blood-2018-170  0.155
2022 Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, ... ... Bader G, et al. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates. Nature Cell Biology. PMID 36109670 DOI: 10.1038/s41556-022-00989-7  0.155
2021 Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R, Macklin AM, Khan S, Singh O, Karimi S, Corona RI, Liu LY, Chen CY, Chakravarthy A, Wei Q, ... ... Bader GD, et al. A clinically applicable integrative molecular classification of meningiomas. Nature. PMID 34433969 DOI: 10.1038/s41586-021-03850-3  0.154
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  0.154
2018 Dasgupta S, Bader GD, Goyal S. Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics. Biophysical Journal. PMID 30033145 DOI: 10.1016/J.Bpj.2018.07.003  0.153
2021 Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, et al. A roadmap for the Human Developmental Cell Atlas. Nature. 597: 196-205. PMID 34497388 DOI: 10.1038/s41586-021-03620-1  0.153
2016 Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. Journal of Integrative Bioinformatics. 13: 1-7. PMID 29215991 DOI: 10.1515/jib-2016-289  0.153
2016 Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. Journal of Integrative Bioinformatics. 13: 289. PMID 28187405 DOI: 10.2390/Biecoll-Jib-2016-289  0.153
2021 Richards LM, Whitley OKN, MacLeod G, Cavalli FMG, Coutinho FJ, Jaramillo JE, Svergun N, Riverin M, Croucher DC, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti JK, ... ... Bader GD, et al. Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity. Nature Cancer. 2: 157-173. PMID 35122077 DOI: 10.1038/s43018-020-00154-9  0.15
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  0.147
2019 Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. F1000research. 8. PMID 31508207 DOI: 10.12688/F1000Research.18490.3  0.147
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  0.147
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  0.146
2023 Sadria M, Layton A, Bader GD. Adversarial training improves model interpretability in single-cell RNA-seq analysis. Bioinformatics Advances. 3: vbad166. PMID 38099262 DOI: 10.1093/bioadv/vbad166  0.146
2021 Abou Chakra M, Isserlin R, Tran TN, Bader GD. Control of tissue development and cell diversity by cell cycle dependent transcriptional filtering. Elife. 10. PMID 34212855 DOI: 10.7554/eLife.64951  0.145
2020 Manoranjan B, Venugopal C, Bakhshinyan D, Adile AA, Richards L, Kameda-Smith MM, Whitley O, Dvorkin-Gheva A, Subapanditha M, Savage N, Tatari N, McKenna D, Bassey-Archibong B, Winegarden N, Hallett R, ... ... Bader GD, et al. Wnt activation as a therapeutic strategy in medulloblastoma. Nature Communications. 11: 4323. PMID 32859895 DOI: 10.1038/S41467-020-17953-4  0.143
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  0.143
2022 Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lu Y, ... ... Bader GD, et al. Loss of epigenetic regulation disrupts lineage integrity, induces aberrant alveogenesis and promotes breast cancer. Cancer Discovery. PMID 36108220 DOI: 10.1158/2159-8290.CD-21-0865  0.143
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  0.143
2021 Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, ... ... Bader GD, et al. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. Nature Communications. 12: 979. PMID 33579912 DOI: 10.1038/s41467-021-21204-5  0.141
2019 Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, et al. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Research. PMID 30698747 DOI: 10.1093/Nar/Gkz010  0.141
2016 Helmy M, Crits-Christoph A, Bader GD. Ten Simple Rules for Developing Public Biological Databases. Plos Computational Biology. 12: e1005128. PMID 27832061 DOI: 10.1371/journal.pcbi.1005128  0.141
2023 Suppiah S, Mansouri S, Mamatjan Y, Liu JC, Bhunia MM, Patil V, Rath P, Mehani B, Heir P, Bunda S, Velez-Reyes GL, Singh O, Ijad N, Pirouzmand N, Dalcourt T, ... ... Bader GD, et al. Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities. Nature Communications. 14: 2696. PMID 37164978 DOI: 10.1038/s41467-023-38432-6  0.141
2021 Coles BLK, Labib M, Poudineh M, Innes BT, Belair-Hickey J, Gomis S, Wang Z, Bader GD, Sargent EH, Kelley SO, van der Kooy D. A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells. Lab On a Chip. PMID 34651637 DOI: 10.1039/d1lc00790d  0.138
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  0.137
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  0.137
2021 Subedi A, Liu Q, Ayyathan DM, Sharon D, Cathelin S, Hosseini M, Xu C, Voisin V, Bader GD, D'Alessandro A, Lechman ER, Dick JE, Minden MD, Wang JCY, Chan SM. Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis. Cell Stem Cell. PMID 34293334 DOI: 10.1016/j.stem.2021.06.004  0.136
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  0.136
2023 McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, ... ... Bader GD, et al. Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms. Biorxiv : the Preprint Server For Biology. PMID 38187588 DOI: 10.1101/2023.12.22.573083  0.134
2021 Peter MR, Bilenky M, Davies A, Isserlin R, Bader GD, Fleshner NE, Hirst M, Zoubeidi A, Bapat B. Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer. Scientific Reports. 11: 6630. PMID 33758253 DOI: 10.1038/s41598-021-85812-3  0.133
2018 Singh RP, Jeyaraju DV, Voisin V, Xu C, Barghout SH, Khan DH, Hurren R, Gronda M, Wang X, Jitkova Y, Sharon D, Liyanage SU, Soriano J, Lechman, ER, ... ... Bader GD, et al. Targeting the Mitochondrial Metallochaperone Cox17 Reduces DNA Methylation and Promotes AML Differentiation through a Copper Dependent Mechanism Blood. 132: 1339-1339. DOI: 10.1182/Blood-2018-99-111015  0.132
2020 Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE. Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21. The Journal of Experimental Medicine. 217. PMID 32434219 DOI: 10.1084/jem.20191094  0.131
2021 Mer AS, Heath EM, Madani Tonekaboni SA, Dogan-Artun N, Nair SK, Murison A, Garcia-Prat L, Shlush L, Hurren R, Voisin V, Bader GD, Nislow C, Rantalainen M, Lehmann S, Gower M, et al. Biological and therapeutic implications of a unique subtype of NPM1 mutated AML. Nature Communications. 12: 1054. PMID 33594052 DOI: 10.1038/s41467-021-21233-0  0.13
2019 Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, ... ... Bader GD, et al. Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. Iscience. 19: 1114-1132. PMID 31536960 DOI: 10.1016/J.Isci.2019.08.057  0.129
2019 Mirali S, Aaron B, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Xu GW, Nachmias B, MacLean N, Wang X, ... ... Bader GD, et al. The Mitochondrial Protease, Neurolysin (NLN), Regulates Respiratory Chain Complex and Supercomplex Formation and Is Necessary for AML Viability Blood. 134: 729-729. DOI: 10.1182/Blood-2019-122784  0.128
2019 Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS. Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture. Advanced Materials (Deerfield Beach, Fla.). e1901166. PMID 31322299 DOI: 10.1002/adma.201901166  0.128
2021 Andrews TS, Atif J, Liu JC, Perciani CT, Ma XZ, Thoeni C, Slyper M, Eraslan G, Segerstolpe A, Manuel J, Chung S, Winter E, Cirlan I, Khuu N, Fischer S, ... ... Bader GD, et al. Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity. Hepatology Communications. PMID 34792289 DOI: 10.1002/hep4.1854  0.127
2018 Liu JC, Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, Bader GD, et al. Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer. Cell Reports. 23: 112-126. PMID 29617654 DOI: 10.1016/J.Celrep.2018.03.039  0.127
2022 Atif J, Thoeni C, Bader GD, McGilvray ID, MacParland SA. Unraveling the Complexity of Liver Disease One Cell at a Time. Seminars in Liver Disease. 42: 250-270. PMID 36008091 DOI: 10.1055/s-0042-1755272  0.126
2023 Yammine S, Burns I, Gosio J, Peluso A, Merritt D, Innes B, Coles B, Yan WR, Bader GD, Morshead C, van der Kooy D. Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution. Stem Cells and Development. PMID 37551982 DOI: 10.1089/scd.2023.0038  0.126
2022 McEvoy CM, Murphy JM, Zhang L, Clotet-Freixas S, Mathews JA, An J, Karimzadeh M, Pouyabahar D, Su S, Zaslaver O, Röst H, Arambewela R, Liu LY, Zhang S, Lawson KA, ... ... Bader GD, et al. Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity. Nature Communications. 13: 7634. PMID 36496458 DOI: 10.1038/s41467-022-35297-z  0.125
2012 Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, ... ... Bader GD, et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 488: 49-56. PMID 22832581 DOI: 10.1038/Nature11327  0.125
2017 Wang S, Liu JC, Ju Y, Pellecchia G, Voisin V, Wang DY, Leha L R, Ben-David Y, Bader GD, Zacksenhaus E. microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer. Jci Insight. 2. PMID 28768903 DOI: 10.1172/jci.insight.93313  0.125
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  0.124
2023 Franz M, Lopes CT, Fong D, Kucera M, Cheung M, Siper MC, Huck G, Dong Y, Sumer O, Bader GD. Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics (Oxford, England). PMID 36645249 DOI: 10.1093/bioinformatics/btad031  0.123
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  0.122
2016 Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, ... ... Bader GD, et al. Divergent clonal selection dominates medulloblastoma at recurrence. Nature. PMID 26760213 DOI: 10.1038/Nature16478  0.121
2012 Wong PPC, Merico D, Matei I, Ling V, Bashir S, Chang SG, Cheung QCK, Haw RA, Stueker O, Montpellier B, Bader GD, Beyene J, Danska JS, Guidos CJ. Kruppel-Like Factor, Klf9, Promotes Proliferation of Notch-Independent Precursor T-Cell Lymphoblastic Lymphomas Blood. 120: 3496-3496. DOI: 10.1182/Blood.V120.21.3496.3496  0.12
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  0.12
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  0.119
2012 Solca F, Dahl G, Zoephel A, Bader G, Sanderson M, Klein C, Kraemer O, Himmelsbach F, Haaksma E, Adolf GR. Target binding properties and cellular activity of afatinib (BIBW 2992), an irreversible ErbB family blocker. The Journal of Pharmacology and Experimental Therapeutics. 343: 342-50. PMID 22888144 DOI: 10.1124/jpet.112.197756  0.118
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  0.118
2022 Nachmias B, Khan DH, Voisin V, Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, ... ... Bader GD, et al. IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells. Leukemia. PMID 35152270 DOI: 10.1038/s41375-022-01513-4  0.117
2014 Will M, Bader GD, Conard NJ. Characterizing the Late Pleistocene MSA Lithic Technology of Sibudu, KwaZulu-Natal, South Africa. Plos One. 9: e98359. PMID 24878544 DOI: 10.1371/journal.pone.0098359  0.117
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  0.117
2017 Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, ... ... Bader GD, et al. Spatial heterogeneity in medulloblastoma. Nature Genetics. PMID 28394352 DOI: 10.1038/Ng.3838  0.117
2016 Buchan AMJ, Jurczyk E, Isserlin R, Bader GD. Global neuroscience and mental health research: a bibliometrics case study Scientometrics. 109: 515-531. DOI: 10.1007/S11192-016-2094-Z  0.116
2019 Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, ... ... Bader GD, et al. Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal. Cell Stem Cell. PMID 31631013 DOI: 10.1016/j.stem.2019.09.008  0.115
2014 Frechin M, Enkler L, Tetaud E, Laporte D, Senger B, Blancard C, Hammann P, Bader G, Clauder-Münster S, Steinmetz LM, Martin RP, di Rago JP, Becker HD. Expression of nuclear and mitochondrial genes encoding ATP synthase is synchronized by disassembly of a multisynthetase complex. Molecular Cell. 56: 763-76. PMID 25453761 DOI: 10.1016/J.Molcel.2014.10.015  0.115
2012 Bozhena J, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Wang X, Laister RC, Bader GD, Minden MD, Schimmer AD. Chronic Inhibition of Mitochondrial Translation Alters Metabolism and Stemness in AML Blood. 120: 1364-1364. DOI: 10.1182/Blood.V120.21.1364.1364  0.114
2014 Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, ... ... Bader GD, et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature. 506: 445-50. PMID 24553142 DOI: 10.1038/Nature13108  0.114
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  0.113
2016 Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ. HOX gene complement and expression in the planarian Schmidtea mediterranea. Evodevo. 7: 7. PMID 27034770 DOI: 10.1186/S13227-016-0044-8  0.113
2022 Borrett MJ, Tahmasian N, Innes BT, Bader GD, Kaplan DR, Miller FD. A Shared Transcriptional Identity for Forebrain and Dentate Gyrus Neural Stem Cells from Embryogenesis to Adulthood. Eneuro. PMID 35027446 DOI: 10.1523/ENEURO.0271-21.2021  0.112
2015 Wei Q, Tang YJ, Voisin V, Sato S, Hirata M, Whetstone H, Han I, Ailles L, Bader GD, Wunder J, Alman BA. Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma. Oncotarget. PMID 26517673 DOI: 10.18632/Oncotarget.5375  0.112
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  0.111
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  0.111
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  0.111
2020 Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader GD. Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities. Computational and Structural Biotechnology Journal. 18: 1735-1745. PMID 32695266 DOI: 10.1016/j.csbj.2020.06.023  0.11
2018 Khalili S, Ballios BG, Belair-Hickey J, Donaldson L, Liu J, Coles BLK, Grisé KN, Baakdhah T, Bader GD, Wallace VA, Bernier G, Shoichet MS, van der Kooy D. Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells. Stem Cell Research. 33: 215-227. PMID 30453152 DOI: 10.1016/J.Scr.2018.11.005  0.108
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  0.108
2022 Yang D, Gomez-Garcia J, Funakoshi S, Tran T, Fernandes I, Bader GD, Laflamme MA, Keller GM. Modeling human multi-lineage heart field development with pluripotent stem cells. Cell Stem Cell. 29: 1382-1401.e8. PMID 36055193 DOI: 10.1016/j.stem.2022.08.007  0.107
2020 Mirali S, Botham A, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Nachmias B, MacLean N, Wang X, Arruda A, ... ... Bader GD, et al. The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability. Science Translational Medicine. 12. PMID 32269163 DOI: 10.1126/Scitranslmed.Aaz8264  0.106
2018 Mirali S, Aaron B, Voisin V, Qiu Y, Hoff FW, Hurren R, Gronda M, Jitkova Y, Xu GW, MacLean N, Wang X, Horton TM, Kornblau SM, Chan SM, Bader GD, et al. The Mitochondrial Protease, Neurolysin (NLN), Regulates Respiratory Chain Supercomplex Formation and Represents a New Therapeutic Target for AML Blood. 132: 1335-1335. DOI: 10.1182/Blood-2018-99-110869  0.105
2023 Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. Iscience. 26: 108213. PMID 38026201 DOI: 10.1016/j.isci.2023.108213  0.103
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  0.103
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  0.103
2017 Liyanage SU, Hurren R, Voisin V, Bridon G, Wang X, Xu C, MacLean N, Siriwardena TP, Gronda M, Yehudai D, Sriskanthadevan S, Avizonis D, Shamas-Din A, Minden MD, Bader GD, et al. Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML. Blood. PMID 28283480 DOI: 10.1182/Blood-2016-10-741207  0.102
2020 Peter MR, Bilenky M, Isserlin R, Bader GD, Shen SY, De Carvalho DD, Hansen AR, Hu P, Fleshner NE, Joshua AM, Hirst M, Bapat B. Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment. Epigenomics. PMID 32867540 DOI: 10.2217/Epi-2020-0173  0.102
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  0.102
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  0.101
2016 Jeyaraju DV, Voisin V, Xu C, Hurren R, Gronda M, Wang X, Jitkova Y, Soriano J, MacLean N, Bader GD, Schimmer AD. Inhibition of the Mitochondrial Protein Import Machinery Is Selectively Cytotoxic to Acute Myeloid Leukemia (AML) Cells and Stem Cells Blood. 128: 1572-1572. DOI: 10.1182/BLOOD.V128.22.1572.1572  0.1
2016 Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Dos Santos CC. Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness. Scientific Reports. 6: 29334. PMID 27411715 DOI: 10.1038/Srep29334  0.098
2020 Singh RP, Jeyaraju DV, Voisin V, Hurren R, Xu C, Hawley JR, Barghout SH, Khan DH, Gronda M, Wang X, Jitkova Y, Sharon D, Liyanagae S, MacLean N, Seneviratene AK, ... ... Bader GD, et al. Disrupting Mitochondrial Copper Distribution Inhibits Leukemic Stem Cell Self-Renewal. Cell Stem Cell. PMID 32416059 DOI: 10.1016/J.Stem.2020.04.010  0.097
2022 Schwab N, Taskina D, Leung E, Innes BT, Bader GD, Hazrati LN. Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner. Frontiers in Neuroscience. 16: 1027116. PMID 36408415 DOI: 10.3389/fnins.2022.1027116  0.097
2022 Thomas GE, Egan G, García-Prat L, Botham A, Voisin V, Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, MacLean N, ... ... Bader GD, et al. The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness. Nature Cell Biology. PMID 35668135 DOI: 10.1038/s41556-022-00925-9  0.096
2020 Khan DH, Mullokandov M, Wu Y, Voisin V, Gronda MV, Hurren R, Wang X, MacLean N, Jeyaraju DV, Jitkova Y, Xu GW, Laister RC, Seneviratne A, Blatman Z, Ketala T, ... Bader GD, et al. Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival. Blood. PMID 32299104 DOI: 10.1182/Blood.2019000106  0.096
2012 Bader G, Anjomshoaa A, Tjoa AM. A context-aware mashup integration guideline for Enterprise 2.0 Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7465: 17-30. DOI: 10.1007/978-3-642-32498-7_2  0.096
2022 Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, ... ... Bader GD, et al. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. Cell Reports. 38: 110481. PMID 35263585 DOI: 10.1016/j.celrep.2022.110481  0.095
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  0.094
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  0.094
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: 313-322. PMID 28447939 DOI: 10.1016/J.Stemcr.2015.01.011  0.093
2016 Liyanage SU, Hurren R, Voisin V, Xiaoming W, Bridon G, Xu C, MacLean N, Siriwardena T, Shamas-Din A, Sriskanthadevan S, Minden MD, Bader GD, Laposa R, Schimmer AD. Leveraging Increased Nucleoside Kinase Activity to Selectively Deplete Mitochondrial DNA (mtDNA), Impair Oxidative Phosphorylation, and Target AML Cells Blood. 128: 1573-1573. DOI: 10.1182/Blood.V128.22.1573.1573  0.093
2024 Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, ... ... Bader GD, et al. Metformin reduces the clonal fitness of hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state. Research Square. PMID 38405837 DOI: 10.21203/rs.3.rs-3874821/v1  0.091
2017 Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD. Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling. Cell Reports. 21: 3970-3986. PMID 29281841 DOI: 10.1016/j.celrep.2017.12.017  0.089
2021 Funakoshi S, Fernandes I, Mastikhina O, Wilkinson D, Tran T, Dhahri W, Mazine A, Yang D, Burnett B, Lee J, Protze S, Bader GD, Nunes SS, Laflamme M, Keller G. Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells. Nature Communications. 12: 3155. PMID 34039977 DOI: 10.1038/s41467-021-23329-z  0.089
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  0.087
2022 Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, ... ... Bader GD, et al. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. Biorxiv : the Preprint Server For Biology. PMID 36324805 DOI: 10.1101/2022.10.27.514070  0.086
2019 Giorgi JM, Bader GD. Towards reliable named entity recognition in the biomedical domain. Bioinformatics (Oxford, England). PMID 31218364 DOI: 10.1093/bioinformatics/btz504  0.086
2018 MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, ... ... Bader GD, et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nature Communications. 9: 4383. PMID 30348985 DOI: 10.1038/S41467-018-06318-7  0.086
2023 Kozlowski HN, Malekjahani A, Li VYC, Lekuti AA, Perusini S, Bell NG, Voisin V, Pouyabahar D, Pai S, Bader GD, Mubareka S, Gubbay JB, Chan WCW. Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels. Analytical Chemistry. PMID 37000033 DOI: 10.1021/acs.analchem.2c04630  0.085
2013 Klimaszewski C, Bader GE, Nyce JM. Hierarchy, complicity and culture in the library and information science preservation agenda: Observations from Romania Journal of Librarianship and Information Science. 45: 38-52. DOI: 10.1177/0961000611434998  0.085
2024 Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, ... ... Bader GD, et al. The multimodality cell segmentation challenge: toward universal solutions. Nature Methods. PMID 38532015 DOI: 10.1038/s41592-024-02233-6  0.084
2021 Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, McLeod J, Wagenblast E, Mitchell A, ... ... Bader GD, et al. Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation. Blood Cancer Discovery. 2: 32-53. PMID 33458693 DOI: 10.1158/2643-3230.BCD-20-0155  0.084
2019 Seneviratne AK, Xu M, Henao JJA, Fajardo VA, Hao Z, Voisin V, Xu GW, Hurren R, Kim S, MacLean N, Wang X, Gronda M, Jeyaraju D, Jitkova Y, Ketela T, ... ... Bader GD, et al. The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids. Cell Stem Cell. PMID 30930145 DOI: 10.1016/J.Stem.2019.02.020  0.083
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  0.08
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  0.08
2021 Bakhshinyan D, Adile AA, Liu J, Gwynne WD, Suk Y, Custers S, Burns I, Singh M, McFarlane N, Subapanditha MK, Qazi MA, Vora P, Kameda-Smith MM, Savage N, Desmond KL, ... ... Bader GD, et al. Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence. Science Advances. 7: eabi5568. PMID 34878832 DOI: 10.1126/sciadv.abi5568  0.077
2020 Liu LY, Ma XZ, Ouyang B, Ings DP, Marwah S, Liu J, Chen AY, Gupta R, Manuel J, Chen XC, Gage BK, Cirlan I, Khuu N, Chung S, Camat D, ... ... Bader GD, et al. Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model. Acs Nano. PMID 32255624 DOI: 10.1021/Acsnano.0C00468  0.077
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  0.077
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  0.074
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  0.072
2018 Subedi A, Liu Q, Sharon D, Xu C, Voisin V, Bader GD, Wang J, Chan SM. Inhibition of Nicotinamide Phosphoribosyltransferase (NAMPT) Activity Selectively Targets Human Acute Myeloid Leukemia Stem Cells Blood. 132: 3932-3932. DOI: 10.1182/blood-2018-99-120258  0.071
2014 Detweiler MB, Kenneth A, Bader G, Sullivan K, Murphy PF, Halling M, Kalafat N, Detweiler JG. Can improved intra- and inter-team communication reduce missed delirium? The Psychiatric Quarterly. 85: 211-24. PMID 24310243 DOI: 10.1007/s11126-013-9284-0  0.069
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  0.069
2020 Gage BK, Liu JC, Innes BT, MacParland SA, McGilvray ID, Bader GD, Keller GM. Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts. Cell Stem Cell. PMID 32640183 DOI: 10.1016/J.Stem.2020.06.007  0.069
2014 Pizzoferrato AC, Nyangoh Timoh K, Fritel X, Zareski E, Bader G, Fauconnier A. Dynamic Magnetic Resonance Imaging and pelvic floor disorders: how and when? European Journal of Obstetrics, Gynecology, and Reproductive Biology. 181: 259-66. PMID 25212114 DOI: 10.1016/j.ejogrb.2014.07.025  0.064
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  0.063
2020 Ho JM, Dobson SM, Voisin V, McLeod J, Kennedy JA, Mitchell A, Jin L, Eppert K, Bader G, Minden MD, Dick JE, Wang JCY. CD200 expression marks leukemia stem cells in human AML. Blood Advances. 4: 5402-5413. PMID 33147339 DOI: 10.1182/bloodadvances.2020001802  0.062
2020 Borrett MJ, Innes BT, Jeong D, Tahmasian N, Storer MA, Bader GD, Kaplan DR, Miller FD. Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis. Cell Reports. 32: 108022. PMID 32783944 DOI: 10.1016/j.celrep.2020.108022  0.06
2013 Nyce JM, Bader GE, Klimaszewski C. "Lose your time in a useful way": Digital inclusion of the elderly at a pensioners' club in Romania Information Access and Library User Needs in Developing Countries. 173-189. DOI: 10.4018/978-1-4666-4353-6.ch012  0.059
2021 Zhang Y, Malekjahani A, Udugama BN, Kadhiresan P, Chen H, Osborne M, Franz M, Kucera M, Plenderleith S, Yip L, Bader GD, Tran V, Gubbay JB, McGeer A, Mubareka S, et al. Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device. Nano Letters. PMID 34110166 DOI: 10.1021/acs.nanolett.1c01280  0.057
2012 Helal R, Bader G, Melzig MF. Stimulation of lysozyme release by selected microbial preparations. Die Pharmazie. 67: 564-6. PMID 22822548 DOI: 10.1691/ph.2012.1785  0.056
2014 Ahrén B, Mathieu C, Bader G, Schweizer A, Foley JE. Efficacy of vildagliptin versus sulfonylureas as add-on therapy to metformin: comparison of results from randomised controlled and observational studies. Diabetologia. 57: 1304-7. PMID 24682379 DOI: 10.1007/s00125-014-3222-z  0.055
2011 Bader G. Navn og parallelism Dansk Teologisk Tidsskrift. 74: 196-216.  0.054
2015 Saab C, Al-Saber FA, Haddad J, Jallo MK, Steitieh H, Bader G, Ibrahim M. Effectiveness and tolerability of second-line treatment with vildagliptin versus other oral drugs for type 2 diabetes in a real-world setting in the Middle East: results from the EDGE study. Vascular Health and Risk Management. 11: 149-55. PMID 25750538 DOI: 10.2147/VHRM.S73703  0.051
2019 Seneviratne AK, Xu M, Aristizabal Henao JJ, Fajardo VA, Hao Z, Voisin V, Xu GW, Hurren R, Kim S, MacLean N, Wang X, Gronda M, Jeyaraju D, Jitkova Y, Ketela T, ... ... Bader GD, et al. The Mitochondrial Transacylase, Tafazzin, Regulates AML Stemness by Modulating Intracellular Levels of Phospholipids. Cell Stem Cell. 24: 1007. PMID 31173706 DOI: 10.1016/J.Stem.2019.04.020  0.051
2013 Mathieu C, Barnett AH, Brath H, Conget I, de Castro JJ, Göke R, Márquez Rodriguez E, Nilsson PM, Pagkalos E, Penfornis A, Schaper NC, Wangnoo SK, Kothny W, Bader G. Effectiveness and tolerability of second-line therapy with vildagliptin vs. other oral agents in type 2 diabetes: a real-life worldwide observational study (EDGE). International Journal of Clinical Practice. 67: 947-56. PMID 23961850 DOI: 10.1111/ijcp.12252  0.05
2012 Bader G, He W, Anjomshoaa A, Tjoa AM. Proposing a context-aware enterprise mashup readiness assessment framework Information Technology and Management. 13: 377-387. DOI: 10.1007/s10799-012-0134-9  0.049
2013 Rathmann W, Kostev K, Gruenberger JB, Dworak M, Bader G, Giani G. Treatment persistence, hypoglycaemia and clinical outcomes in type 2 diabetes patients with dipeptidyl peptidase-4 inhibitors and sulphonylureas: a primary care database analysis. Diabetes, Obesity & Metabolism. 15: 55-61. PMID 22862879 DOI: 10.1111/j.1463-1326.2012.01674.x  0.049
2020 Wong A, Zamel R, Yeung J, Bader GD, Dos Santos CC, Bai X, Wang Y, Keshavjee S, Liu M. Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion. The European Respiratory Journal. PMID 32060066 DOI: 10.1183/13993003.02222-2019  0.049
2022 Jiang Z, Li H, Schroer SA, Voisin V, Ju Y, Pacal M, Erdmann N, Shi W, Chung PED, Deng T, Chen NJ, Ciavarra G, Datti A, Mak TW, Harrington L, ... ... Bader GD, et al. Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes. The Embo Journal. e106825. PMID 35023164 DOI: 10.15252/embj.2020106825  0.049
2017 Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, ... ... Bader G, et al. ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells. Cell Stem Cell. 21: 411. PMID 28886368 DOI: 10.1016/j.stem.2017.08.008  0.049
2024 Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, ... ... Bader GD, et al. Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver. Journal of Hepatology. PMID 38199298 DOI: 10.1016/j.jhep.2023.12.023  0.048
2018 Zhang N, Bao YJ, Tong AH, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SM. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection. Bmc Medical Genomics. 11: 20. PMID 29475453 DOI: 10.1186/s12920-018-0335-0  0.048
2013 Lucot JP, Fritel X, Debodinance P, Bader G, Cosson M, Giraudet G, Collinet P, Rubod C, Fernandez H, Fournet S, Lesavre M, Deffieux X, Faivre E, Trichot C, Demoulin G, et al. [PROSPERE randomized controlled trial: laparoscopic sacropexy versus vaginal mesh for cystocele POP repair]. Journal De Gynã©Cologie, Obstã©Trique Et Biologie De La Reproduction. 42: 334-41. PMID 23618743 DOI: 10.1016/j.jgyn.2013.03.012  0.045
2014 Göke R, Bader G, Dworak M. Real-life effectiveness and tolerability of vildagliptin and other oral glucose-lowering therapies in patients with type 2 diabetes in Germany. Diabetes Therapy : Research, Treatment and Education of Diabetes and Related Disorders. 5: 183-91. PMID 24643724 DOI: 10.1007/s13300-014-0060-4  0.043
2014 Willecocq C, Pizzoferrato AC, Fauconnier A, Bader G. [Use of glue in laparoscopic sacrocolpopexy. A comparative study about 32 cases]. GynéCologie, ObstéTrique & Fertilité. 42: 822-6. PMID 25456490 DOI: 10.1016/j.gyobfe.2014.10.008  0.043
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  0.042
2020 Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, ... ... Bader GD, et al. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Systems. 11: 208. PMID 32853540 DOI: 10.1016/j.cels.2020.08.006  0.042
2015 Nyangoh Timoh K, Bader G, Fauconnier A, Barrau V, Delmas V, Touboul C. Determination of a Central Avascular Triangle within the Obturator Foramen: A Radioanatomic Study. Plos One. 10: e0143642. PMID 26624993 DOI: 10.1371/journal.pone.0143642  0.04
2014 Blüher M, Schweizer A, Bader G, Foley JE. Changes in body weight after 24 weeks of vildagliptin therapy as a function of fasting glucose levels in patients with type 2 diabetes. Vascular Health and Risk Management. 10: 661-4. PMID 25429228 DOI: 10.2147/VHRM.S73608  0.037
2011 Rossi MC, Lucisano G, Comaschi M, Coscelli C, Cucinotta D, Di Blasi P, Bader G, Pellegrini F, Valentini U, Vespasiani G, Nicolucci A. Quality of diabetes care predicts the development of cardiovascular events: results of the AMD-QUASAR study. Diabetes Care. 34: 347-52. PMID 21270192 DOI: 10.2337/dc10-1709  0.037
2003 Léger D, Guilleminault C, Bader G, Lévy E, Paillard M. Medical and socio-professional impact of insomnia. Sleep. 25: 625-9. PMID 12224841  0.036
2014 Göke R, Gruenberger JB, Bader G, Dworak M. Real-life efficacy and safety of vildagliptin compared with sulfonylureas as add-on to metformin in patients with type 2 diabetes mellitus in Germany. Current Medical Research and Opinion. 30: 785-9. PMID 24328429 DOI: 10.1185/03007995.2013.875464  0.035
2011 Chouillard EK, Al Khoury M, Bader G, Heitz D, Elrassi Z, Fauconnier A. Combined vaginal and abdominal approach to sleeve gastrectomy for morbid obesity in women: A preliminary experience Surgery For Obesity and Related Diseases. 7: 581-586. PMID 21126921 DOI: 10.1016/j.soard.2010.09.022  0.034
2014 Bruderer SG, Bodmer M, Jick SS, Bader G, Schlienger RG, Meier CR. Incidence of and risk factors for severe hypoglycaemia in treated type 2 diabetes mellitus patients in the UK--a nested case-control analysis. Diabetes, Obesity & Metabolism. 16: 801-11. PMID 24612200 DOI: 10.1111/Dom.12282  0.032
2016 Brath H, Paldánius PM, Bader G, Kolaczynski WM, Nilsson PM. Differences in glycemic control across world regions: a post-hoc analysis in patients with type 2 diabetes mellitus on dual antidiabetes drug therapy. Nutrition & Diabetes. 6: e217. PMID 27376699 DOI: 10.1038/nutd.2016.25  0.032
2011 Pizzoferrato AC, Fauconnier A, Bader G. [Value of ultrasonographic measurement of bladder neck mobility in the management of female stress urinary incontinence]. GynéCologie, ObstéTrique & Fertilité. 39: 42-8. PMID 21185762 DOI: 10.1016/j.gyobfe.2010.09.019  0.031
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  0.029
2013 Bader G, Geransar P, Schweizer A. Vildagliptin more effectively achieves a composite endpoint of HbA₁c < 7.0% without hypoglycaemia and weight gain compared with glimepiride after 2 years of treatment. Diabetes Research and Clinical Practice. 100: e78-81. PMID 23538267 DOI: 10.1016/j.diabres.2013.03.011  0.029
2014 Bader G. Previews: Three times a year Artforum looks ahead to the coming season. The following survey previews forty-five shows opening around the world between January and April Artforum International. 52: 109.  0.027
2013 Pizzoferrato AC, Bui C, Fauconnier A, Bader G. [Advanced uterine prolapse during pregnancy: pre- and postnatal management]. Gynã©Cologie, Obstã©Trique & Fertilitã©. 41: 467-70. PMID 23867760 DOI: 10.1016/j.gyobfe.2013.06.002  0.027
2015 Lacy PS, Brunel P, Bader G, Jones A, Baschiera F, Düsing R, Williams B. Effects of treatment withdrawal on brachial and central aortic pressure after direct renin inhibition or angiotensin receptor blockade. Journal of the Renin-Angiotensin-Aldosterone System : Jraas. PMID 25944854 DOI: 10.1177/1470320315579592  0.027
2015 Shebak SS, Bader G. Midazolam and Low Magnesium Associated With Myoclonic Jerks: A Case Report. The Primary Care Companion For Cns Disorders. 17. PMID 26445681 DOI: 10.4088/PCC.14l01724  0.025
2012 Poli D, Berenotto C, Blankenship S, Piatkowski B, Bader GA, Poore M. Bringing evolution to a technological generation: A case study with the video game SPORE American Biology Teacher. 74: 100-103. DOI: 10.1525/abt.2012.74.2.7  0.024
2012 Gilet H, Gruenberger JB, Bader G, Viala-Danten M. Demonstrating the burden of hypoglycemia on patients' quality of life in diabetes clinical trials: measurement considerations for hypoglycemia. Value in Health : the Journal of the International Society For Pharmacoeconomics and Outcomes Research. 15: 1036-41. PMID 23244805 DOI: 10.1016/j.jval.2012.06.002  0.024
2014 Pizzoferrato AC, Bader G, Nyangoh Timoh K, Andriamafidy-Berti C, Villefranque V. [Outpatient vaginal hysterectomy, feasibility and morbidity: an observational study on thirty patients]. GynéCologie, ObstéTrique & Fertilité. 42: 67-70. PMID 24468702 DOI: 10.1016/j.gyobfe.2013.12.004  0.023
2012 Sharma TR, Bader GM, Kline DB. "Holes in my head": a case of primary delusional parasitosis in a patient with end-stage renal disease. The Primary Care Companion For Cns Disorders. 14. PMID 23106015 DOI: 10.4088/PCC.11l01229  0.023
2011 Bader G. Rate of exchange Artforum International. 49: 198-203+243.  0.022
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  0.018
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  0.018
2013 Gatbonton P, Ko-De los Santos G, Domingo F, Bader G, Barangan G. Effectiveness and tolerability of vildagliptin versus other oral antidiabetic drugs in patients with type 2 diabetes mellitus in the Philippines: Results from one year observational study (EDGE) Phillippine Journal of Internal Medicine. 51.  0.018
2014 Bader GN. Antimicrobial studies of rhizome of Swertia petiolata Journal of Applied Pharmaceutical Science. 4: 128-130. DOI: 10.7324/JAPS.2014.41222  0.017
2014 Desforges J, Cheminot C, Laville N, Bader G. Rugate filters fabricated from dense and porous magnetron sputtered WO3 films. Applied Optics. 53: A110-3. PMID 24514201  0.017
2011 Bader G. Emptied gesture Artforum International. 49: 346-351.  0.017
2015 Fritel X, de Tayrac R, Bader G, Savary D, Gueye A, Deffieux X, Fernandez H, Richet C, Guilhot J, Fauconnier A. Preventing Urinary Incontinence With Supervised Prenatal Pelvic Floor Exercises: A Randomized Controlled Trial. Obstetrics and Gynecology. 126: 370-7. PMID 26241428 DOI: 10.1097/AOG.0000000000000972  0.016
2012 Klimaszewski C, Bader GE, Nyce JM. Studying up (and down) the cultural heritage preservation agenda: Observations from Romania European Journal of Cultural Studies. 15: 479-495. DOI: 10.1177/1367549412455495  0.015
2012 Bader G. Honored in the breach Artforum International. 50: 81-82.  0.013
2016 Pizzoferrato AC, Fauconnier A, Bader G, de Tayrac R, Fort J, Fritel X. Is prenatal urethral descent a risk factor for urinary incontinence during pregnancy and the postpartum period? International Urogynecology Journal and Pelvic Floor Dysfunction. 1-9. DOI: 10.1007/s00192-015-2918-z  0.01
2015 Pizzoferrato AC, Samie M, Rousseau A, Rozenberg P, Fauconnier A, Bader G. [Severe post-obstetric perineal tears: Medium-term consequences on women's quality of life]. Progres En Urologie : Journal De L'Association Francaise D'Urologie Et De La Societe Francaise D'Urologie. PMID 26032455 DOI: 10.1016/j.purol.2015.04.003  0.01
2015 Barman R, Bader G, Detweile MB. Sequelae of Hypoxia and Ventilation Psychiatric Annals. 45: 5-9. DOI: 10.3928/00485713-20150106-02  0.01
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 Desforges J, Cheminot C, Laville N, Bader G. Rugate filters fabricated from dense and porous magnetron sputtered WO3films Applied Optics. A110-A113. DOI: 10.1364/AO.53.00A110  0.01
2014 Madhuri KV, Bader G, Ashrit PV. Ellipsometry studies of electrochromic WO3 thin films International Journal of Applied Engineering Research. 9: 2061-2073.  0.01
2014 Bader G. The pairing of temptation and attentiveness | La tentation comme attention - l'attention comme tentation Revue De Theologie Et De Philosophie. 146: 137-153.  0.01
2013 Desforges J, Cheminot C, Bader G. Optical filters fabricated from dense and porous magnetron sputtered tungsten oxide films Optics Infobase Conference Papers.  0.01
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