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Gary Bader
Gary Bader
Professor of Molecular Genetics and Computer Science, The Donnelly Centre, University of Toronto
Verified email at utoronto.ca - Homepage
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Cited by
Year
An automated method for finding molecular complexes in large protein interaction networks
GD Bader, CWV Hogue
BMC bioinformatics 4, 1-27, 2003
59282003
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Y Ho, A Gruhler, A Heilbut, GD Bader, L Moore, SL Adams, A Millar, ...
Nature 415 (6868), 180-183, 2002
46222002
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
D Warde-Farley, SL Donaldson, O Comes, K Zuberi, R Badrawi, P Chao, ...
Nucleic acids research 38 (suppl_2), W214-W220, 2010
40792010
Integration of biological networks and gene expression data using Cytoscape
MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, ...
Nature protocols 2 (10), 2366-2382, 2007
27452007
Systematic genetic analysis with ordered arrays of yeast deletion mutants
AHY Tong, M Evangelista, AB Parsons, H Xu, GD Bader, N Pagé, ...
Science 294 (5550), 2364-2368, 2001
26102001
Global mapping of the yeast genetic interaction network
AHY Tong, G Lesage, GD Bader, H Ding, H Xu, X Xin, J Young, GF Berriz, ...
science 303 (5659), 808-813, 2004
25492004
The genetic landscape of a cell
M Costanzo, A Baryshnikova, J Bellay, Y Kim, ED Spear, CS Sevier, ...
science 327 (5964), 425-431, 2010
25022010
A draft map of the human proteome
MS Kim, SM Pinto, D Getnet, RS Nirujogi, SS Manda, R Chaerkady, ...
Nature 509 (7502), 575-581, 2014
24642014
Functional impact of global rare copy number variation in autism spectrum disorders
D Pinto, AT Pagnamenta, L Klei, R Anney, D Merico, R Regan, J Conroy, ...
Nature 466 (7304), 368-372, 2010
23302010
International network of cancer genome projects
Data coordination centre Kasprzyk (Leader) Arek 1 Stein (Leader) Lincoln D ...
Nature 464 (7291), 993-998, 2010
22752010
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation
D Merico, R Isserlin, O Stueker, A Emili, GD Bader
PloS one 5 (11), e13984, 2010
21832010
Pan-cancer analysis of whole genomes
Nature 578 (7793), 82-93, 2020
1726*2020
BIND: the biomolecular interaction network database
GD Bader, D Betel, CWV Hogue
Nucleic acids research 31 (1), 248-250, 2003
15822003
A travel guide to Cytoscape plugins
R Saito, ME Smoot, K Ono, J Ruscheinski, PL Wang, S Lotia, AR Pico, ...
Nature methods 9 (11), 1069-1076, 2012
14992012
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Nature Protocols 14, 482–517, 2019
14622019
Association analysis identifies 65 new breast cancer risk loci
K Michailidou, S Lindström, J Dennis, J Beesley, S Hui, S Kar, A Lemaçon, ...
Nature 551 (7678), 92-94, 2017
13602017
Pathway Commons, a web resource for biological pathway data
EG Cerami, BE Gross, E Demir, I Rodchenkov, Ö Babur, N Anwar, ...
Nucleic acids research 39 (suppl_1), D685-D690, 2010
12702010
The reactome pathway knowledgebase 2022
M Gillespie, B Jassal, R Stephan, M Milacic, K Rothfels, A Senff-Ribeiro, ...
Nucleic acids research 50 (D1), D687-D692, 2022
12202022
Bioinformatics
AD Baxevanis, GD Bader, DS Wishart
John Wiley & Sons, 2020
11272020
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
SA MacParland, JC Liu, XZ Ma, BT Innes, AM Bartczak, BK Gage, ...
Nature communications 9 (1), 4383, 2018
11042018
Molecular classification of ependymal tumors across all CNS compartments, histopathological grades, and age groups
KW Pajtler, H Witt, M Sill, DTW Jones, V Hovestadt, F Kratochwil, K Wani, ...
Cancer cell 27 (5), 728-743, 2015
11002015
Intertumoral heterogeneity within medulloblastoma subgroups
FMG Cavalli, M Remke, L Rampasek, J Peacock, DJH Shih, B Luu, ...
Cancer cell 31 (6), 737-754. e6, 2017
10662017
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
PA Northcott, DJH Shih, J Peacock, L Garzia, A Sorana Morrissy, ...
Nature 488 (7409), 49-56, 2012
9722012
A reference map of the human binary protein interactome
K Luck, DK Kim, L Lambourne, K Spirohn, BE Begg, W Bian, R Brignall, ...
Nature 580 (7803), 402-408, 2020
9512020
Biological network exploration with Cytoscape 3
G Su, JH Morris, B Demchak, GD Bader
Current protocols in bioinformatics 47 (1), 8.13. 1-8.13. 24, 2014
9482014
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
AHY Tong, B Drees, G Nardelli, GD Bader, B Brannetti, L Castagnoli, ...
Science 295 (5553), 321-324, 2002
9162002
GeneMANIA update 2018
M Franz, H Rodriguez, C Lopes, K Zuberi, J Montojo, GD Bader, Q Morris
Nucleic acids research 46 (W1), W60-W64, 2018
8542018
Cytoscape Web: an interactive web-based network browser
CT Lopes, M Franz, F Kazi, SL Donaldson, Q Morris, GD Bader
Bioinformatics 26 (18), 2347-2348, 2010
8192010
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition
M Kool, DTW Jones, N Jäger, PA Northcott, TJ Pugh, V Hovestadt, ...
Cancer cell 25 (3), 393-405, 2014
8152014
BIND—the biomolecular interaction network database
GD Bader, I Donaldson, C Wolting, BFF Ouellette, T Pawson, CWV Hogue
Nucleic acids research 29 (1), 242-245, 2001
7932001
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
7892010
The HUPO PSI's molecular interaction format—a community standard for the representation of protein interaction data
H Hermjakob, L Montecchi-Palazzi, G Bader, J Wojcik, L Salwinski, ...
Nature biotechnology 22 (2), 177-183, 2004
7572004
Cytoscape. js: a graph theory library for visualisation and analysis
M Franz, CT Lopes, G Huck, Y Dong, O Sumer, GD Bader
Bioinformatics 32 (2), 309-311, 2016
7262016
Analyzing yeast protein–protein interaction data obtained from different sources
GD Bader, CWV Hogue
Nature biotechnology 20 (10), 991-997, 2002
6992002
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
PA Northcott, C Lee, T Zichner, AM Stütz, S Erkek, D Kawauchi, DJH Shih, ...
Nature 511 (7510), 428-434, 2014
6782014
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
J Montojo, K Zuberi, H Rodriguez, F Kazi, G Wright, SL Donaldson, ...
Bioinformatics 26 (22), 2927, 2010
6542010
Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
SC Mack, H Witt, RM Piro, L Gu, S Zuyderduyn, AM Stütz, X Wang, ...
Nature 506 (7489), 445-450, 2014
6352014
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
JH Morris, L Apeltsin, AM Newman, J Baumbach, T Wittkop, G Su, ...
BMC bioinformatics 12, 1-14, 2011
6102011
Tracing the origins of relapse in acute myeloid leukaemia to stem cells
LI Shlush, A Mitchell, L Heisler, S Abelson, SWK Ng, A Trotman-Grant, ...
Nature 547 (7661), 104-108, 2017
5682017
Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
H Witt, SC Mack, M Ryzhova, S Bender, M Sill, R Isserlin, A Benner, ...
Cancer Cell 20 (2), 143-157, 2011
5642011
A specificity map for the PDZ domain family
R Tonikian, Y Zhang, SL Sazinsky, B Currell, JH Yeh, B Reva, HA Held, ...
PLoS biology 6 (9), e239, 2008
5642008
Comprehensive identification of mutational cancer driver genes across 12 tumor types
D Tamborero, A Gonzalez-Perez, C Perez-Llamas, J Deu-Pons, ...
Scientific reports 3 (1), 2650, 2013
5392013
NetPath: a public resource of curated signal transduction pathways
K Kandasamy, SS Mohan, R Raju, S Keerthikumar, GSS Kumar, ...
Genome biology 11 (1), R3, 2010
5322010
Pathguide: a pathway resource list
GD Bader, MP Cary, C Sander
Nucleic acids research 34 (suppl_1), D504-D506, 2006
5322006
Single-cell transcriptomic profiling of the aging mouse brain
M Ximerakis, SL Lipnick, BT Innes, SK Simmons, X Adiconis, D Dionne, ...
Nature neuroscience 22 (10), 1696-1708, 2019
5142019
Declutr: Deep contrastive learning for unsupervised textual representations
J Giorgi, O Nitski, B Wang, G Bader
arXiv preprint arXiv:2006.03659, 2020
4702020
PreBIND and Textomy–mining the biomedical literature for protein-protein interactions using a support vector machine
I Donaldson, J Martin, B De Bruijn, C Wolting, V Lay, B Tuekam, S Zhang, ...
BMC bioinformatics 4, 1-13, 2003
4612003
Functional genomic landscape of human breast cancer drivers, vulnerabilities, and resistance
R Marcotte, A Sayad, KR Brown, F Sanchez-Garcia, J Reimand, M Haider, ...
Cell 164 (1), 293-309, 2016
4602016
Too many roads not taken
AM Edwards, R Isserlin, GD Bader, SV Frye, TM Willson, FH Yu
Nature 470 (7333), 163-165, 2011
4412011
GeneMANIA prediction server 2013 update
K Zuberi, M Franz, H Rodriguez, J Montojo, CT Lopes, GD Bader, ...
Nucleic acids research 41 (W1), W115-W122, 2013
4202013
Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity
M Meyer, J Reimand, X Lan, R Head, X Zhu, M Kushida, J Bayani, ...
Proceedings of the National Academy of Sciences 112 (3), 851-856, 2015
4192015
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
A Baryshnikova, M Costanzo, Y Kim, H Ding, J Koh, K Toufighi, JY Youn, ...
Nature methods 7 (12), 1017-1024, 2010
4152010
Pathway and network analysis of cancer genomes
Nature methods 12 (7), 615-621, 2015
3762015
Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
RL Milne, KB Kuchenbaecker, K Michailidou, J Beesley, S Kar, ...
Nature genetics 49 (12), 1767-1778, 2017
3642017
Divergent clonal selection dominates medulloblastoma at recurrence
AS Morrissy, L Garzia, DJH Shih, S Zuyderduyn, X Huang, P Skowron, ...
Nature 529 (7586), 351-357, 2016
3482016
Inhibition of the mitochondrial protease ClpP as a therapeutic strategy for human acute myeloid leukemia
A Cole, Z Wang, E Coyaud, V Voisin, M Gronda, Y Jitkova, R Mattson, ...
Cancer cell 27 (6), 864-876, 2015
3342015
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
B Aranda, H Blankenburg, S Kerrien, FSL Brinkman, A Ceol, E Chautard, ...
Nature methods 8 (7), 528-529, 2011
3142011
Quiescent Sox2+ cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma
RJ Vanner, M Remke, M Gallo, HJ Selvadurai, F Coutinho, L Lee, ...
Cancer cell 26 (1), 33-47, 2014
3132014
Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions
S Kerrien, S Orchard, L Montecchi-Palazzi, B Aranda, A Quinn, N Vinod, ...
BMC biology 5 (1), 44, 2007
3092007
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
M Kucera, R Isserlin, A Arkhangorodsky, GD Bader
F1000Research 5, 2016
3062016
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
J Reimand, GD Bader
Molecular systems biology 9 (1), 637, 2013
3032013
miR-126 regulates distinct self-renewal outcomes in normal and malignant hematopoietic stem cells
ER Lechman, B Gentner, SWK Ng, EM Schoof, P van Galen, JA Kennedy, ...
Cancer cell 29 (2), 214-228, 2016
2892016
The minimum information required for reporting a molecular interaction experiment (MIMIx)
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, ...
Nature biotechnology 25 (8), 894-898, 2007
2882007
Functional genomic landscape of cancer-intrinsic evasion of killing by T cells
KA Lawson, CM Sousa, X Zhang, E Kim, R Akthar, JJ Caumanns, Y Yao, ...
Nature 586 (7827), 120-126, 2020
2832020
Computational Prediction of Protein-Protein Interactions
AJ Enright, L Skrabanek, GD Bader
The Proteomics Protocols Handbook, 629-652, 2005
280*2005
Computational prediction of protein–protein interactions
L Skrabanek, HK Saini, GD Bader, AJ Enright
Molecular biotechnology 38 (1), 1-17, 2008
2772008
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
J Montojo, K Zuberi, H Rodriguez, GD Bader, Q Morris
F1000Research 3, 2014
2762014
BIND—a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
GD Bader, CWV Hogue
Bioinformatics 16 (5), 465-477, 2000
2742000
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
I Rodchenkov, O Babur, A Luna, BA Aksoy, JV Wong, D Fong, M Franz, ...
Nucleic acids research 48 (D1), D489-D497, 2020
2722020
Mapping the cellular response to small molecules using chemogenomic fitness signatures
AY Lee, RP St. Onge, MJ Proctor, IM Wallace, AH Nile, PA Spagnuolo, ...
Science 344 (6180), 208-211, 2014
2662014
A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals
RM Labbé, M Irimia, KW Currie, A Lin, SJ Zhu, DDR Brown, EJ Ross, ...
Stem cells 30 (8), 1734-1745, 2012
2422012
A clinically applicable integrative molecular classification of meningiomas
F Nassiri, J Liu, V Patil, Y Mamatjan, JZ Wang, R Hugh-White, AM Macklin, ...
Nature 597 (7874), 119-125, 2021
2392021
Attenuation of miR-126 activity expands HSC in vivo without exhaustion
ER Lechman, B Gentner, P van Galen, A Giustacchini, M Saini, ...
Cell stem cell 11 (6), 799-811, 2012
2322012
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling
T Oka, E Remue, K Meerschaert, B Vanloo, C Boucherie, D Gfeller, ...
Biochem. J 432, 461-472, 2010
2302010
Integrated (epi)-genomic analyses identify subgroup-specific therapeutic targets in CNS rhabdoid tumors
J Torchia, B Golbourn, S Feng, KC Ho, P Sin-Chan, A Vasiljevic, ...
Cancer cell 30 (6), 891-908, 2016
2282016
ASCL1 reorganizes chromatin to direct neuronal fate and suppress tumorigenicity of glioblastoma stem cells
NI Park, P Guilhamon, K Desai, RF McAdam, E Langille, M O’Connor, ...
Cell stem cell 21 (2), 209-224. e7, 2017
2202017
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, ...
PLoS biology 7 (10), e1000218, 2009
2132009
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology
S Jain, GD Bader
BMC bioinformatics 11, 1-14, 2010
2122010
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
2112020
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases.
CS Tan, B Bodenmiller, A Pasculescu, M Jovanovic, MO Hengartner, ...
Science signaling 2 (81), ra39, 2009
2072009
A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans
AR Burns, IM Wallace, J Wildenhain, M Tyers, G Giaever, GD Bader, ...
Nature chemical biology 6 (7), 549-557, 2010
2042010
The mutational landscape of phosphorylation signaling in cancer
J Reimand, O Wagih, GD Bader
Scientific reports 3 (1), 2651, 2013
1982013
Developmental emergence of adult neural stem cells as revealed by single-cell transcriptional profiling
SA Yuzwa, MJ Borrett, BT Innes, A Voronova, T Ketela, DR Kaplan, ...
Cell reports 21 (13), 3970-3986, 2017
1972017
Inhibition of dopamine receptor D4 impedes autophagic flux, proliferation, and survival of glioblastoma stem cells
S Dolma, HJ Selvadurai, X Lan, L Lee, M Kushida, V Voisin, H Whetstone, ...
Cancer cell 29 (6), 859-873, 2016
1962016
Computational approaches to identify functional genetic variants in cancer genomes
Nature methods 10 (8), 723-729, 2013
1882013
Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity
LM Richards, OKN Whitley, G MacLeod, FMG Cavalli, FJ Coutinho, ...
Nature Cancer, 1-17, 2021
1862021
Transfer learning for biomedical named entity recognition with neural networks
JM Giorgi, GD Bader
Bioinformatics 34 (23), 4087-4094, 2018
1842018
Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis
J Torchia, D Picard, L Lafay-Cousin, CE Hawkins, SK Kim, L Letourneau, ...
The lancet oncology 16 (5), 569-582, 2015
1822015
Cytoscape app store
S Lotia, J Montojo, Y Dong, GD Bader, AR Pico
Bioinformatics 29 (10), 1350-1351, 2013
1782013
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
L Oesper, D Merico, R Isserlin, GD Bader
Source Code for Biology and Medicine 6 (1), 7, 2011
1782011
Bringing order to protein disorder through comparative genomics and genetic interactions
J Bellay, S Han, M Michaut, TH Kim, M Costanzo, BJ Andrews, C Boone, ...
Genome biology 12, 1-15, 2011
1692011
Germ-line DNA copy number variation frequencies in a large North American population
G Zogopoulos, KCH Ha, F Naqib, S Moore, H Kim, A Montpetit, ...
Human genetics 122, 345-353, 2007
1612007
Functional genomics and proteomics: charting a multidimensional map of the yeast cell
GD Bader, A Heilbut, B Andrews, M Tyers, T Hughes, C Boone
Trends in cell biology 13 (7), 344-356, 2003
1612003
Pathway information for systems biology
MP Cary, GD Bader, C Sander
FEBS letters 579 (8), 1815-1820, 2005
1602005
Dynamic interaction networks in a hierarchically organized tissue
DC Kirouac, C Ito, E Csaszar, A Roch, M Yu, EA Sykes, GD Bader, ...
Molecular systems biology 6 (1), 417, 2010
1592010
cPath: open source software for collecting, storing, and querying biological pathways
EG Cerami, GD Bader, BE Gross, C Sander
BMC bioinformatics 7, 1-9, 2006
1502006
Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
A Ernst, D Gfeller, Z Kan, S Seshagiri, PM Kim, GD Bader, SS Sidhu
Molecular BioSystems 6 (10), 1782-1790, 2010
1492010
Spatial heterogeneity in medulloblastoma
AS Morrissy, FMG Cavalli, M Remke, V Ramaswamy, DJH Shih, ...
Nature genetics 49 (5), 780-788, 2017
1432017
How to visually interpret biological data using networks
D Merico, D Gfeller, GD Bader
Nature biotechnology 27 (10), 921-924, 2009
1432009
A roadmap for the human developmental cell atlas
M Haniffa, D Taylor, S Linnarsson, BJ Aronow, GD Bader, RA Barker, ...
Nature 597 (7875), 196-205, 2021
1412021
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