• Publications

Last updated at 2023-06-01 02:43:55

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Peer-reviewed Articles

2023

1. Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities
   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, Meng Y, Karimi S, Wei Q, Nassiri F, Pugh TJ, Bader GD, Aldape KD, Largaespada DA, Zadeh G
   Nat Commun. 2023 May 10;14(1):2696
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2. Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition
   Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler AL, Bader GD
   Cereb Cortex. 2023 Apr 27
   PubMed Abstract - PDF
   PRECISION MEDICINE
   
   

3. Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels
   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
   Anal Chem. 2023 Apr 11;95(14):5877-5885
   PubMed Abstract - PDF
   COVID-19
   
   

4. Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics
   Franz M, Lopes CT, Fong D, Kucera M, Cheung M, Siper MC, Huck G, Dong Y, Sumer O, Bader GD
   Bioinformatics 2023 Jan 1;39(1)
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2022

1. Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity
   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, Finelli A, Wang B, MacParland SA, Bader GD, Konvalinka A, Crome SQ
   Nat Commun. 2022 Dec 10;13(1):7634
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

2. Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer
   Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D
   Cancer Discov. 2022 Dec 2;12(12):2930-2953
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

3. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies
   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, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK
   Cell Rep. 2022 Nov 22;41(8):111678
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

4. Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner
   Schwab N, Taskina D, Leung E, Innes BT, Bader GD, Hazrati LN
   Front Neurosci. 2022 Nov 3;16:1027116
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

5. BIONIC: biological network integration using convolutions
   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
   Nat Methods. 2022 Oct;19(10):1250-1261
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

6. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates
   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, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, MacParland S, Bader G, McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L
   Nat Cell Biol. 2022 Oct;24(10):1487-1498
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

7. Loss of epigenetic regulation disrupts lineage integrity, induces aberrant alveogenesis and promotes breast cancer
   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, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sorlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D
   Cancer Discov. 2022 Sep 15
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

8. PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal
   Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, Voisin V, Krivdova G, Lechman E, Marhon SA, De Carvalho DD, Dick JE, Bader GD, Hope KJ
   Blood. 2022 Sep 1;140(9):992-1008
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. Modeling human multi-lineage heart field development with pluripotent stem cells
   Yang D, Gomez-Garcia J, Funakoshi S, Tran T, Fernandes I, Bader GD, Laflamme MA, Keller GM
   Cell Stem Cell. 2022 Sep 1;29(9):1382-1401
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

10. Unraveling the Complexity of Liver Disease One Cell at a Time
    Atif J, Thoeni C, Bader GD, McGilvray ID, MacParland SA
    Semin Liver Dis. 2022 Aug;42(3):250-270
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    
    

11. 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
    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, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J
    Cancers (Basel). 2022 Jul 11;14(14)
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

12. Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity
    Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Khatri P, Dos Santos CC
    Sci Rep. 2022 Jul 4;12(1):11260
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data
    Helmy M, Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, Bader GD
    J Mol Biol. 2022 Jun 15;434(11):167603
    PubMed Abstract - PDF
    PROTEIN INTERACTION
    
    

14. The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness
    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, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, Bader GD, Hakem R, Kornblau S, Dick JE, Schimmer AD
    Nat Cell Biol. 2022 Jun 6
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

15. A sequence-to-sequence approach for document-level relation extraction
    Giorgi, John and Bader, Gary and Wang, Bo
    BioNLP @ ACL May 2022
    ACL Anthology - PDF
    NATURAL LANGUAGE PROCESSING
    
    

16. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML
    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, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER
    Cell Rep. 2022 Mar 8;38(10)
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

17. IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells
    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, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, Bader GD, Schimmer AD
    Leukemia. 2022 Feb 12
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

18. A Shared Transcriptional Identity for Forebrain and Dentate Gyrus Neural Stem Cells from Embryogenesis to Adulthood
    Borrett MJ, Tahmasian N, Innes BT, Bader GD, Kaplan DR, Miller FD
    eNeuro. 2022 Jan 13:ENEURO.0271-21.2021
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    
    

19. Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes
    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, Dick FA, Bader GD, Bremner R, Woo M, Zacksenhaus E
    EMBO J. 2022 Jan 13
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

2021

1. Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence
   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, Tatari N, Tran D, Seyfrid M, Hope K, Bock NA, Venugopal C, Bader GD, Singh SK
   Sci Adv. 2021 Dec 10;7(50)
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2. Author-sourced capture of pathway knowledge in computable form using Biofactoid
   Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C
   Elife. 2021 Dec 3;10
   PubMed Abstract - PDF
   SOFTWARE
   
   

3. Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
   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, Rozenblatt-Rosen O, Regev A, McGilvray ID, Bader GD, MacParland SA
   Hepatol Commun. 2021 Nov 18
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

4. The Reactome pathway knowledgebase 2022
   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, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P
   Nucleic Acids Res. 2021 Nov 12
   PubMed Abstract - PDF
   PATHWAY DATABASE
   
   

5. A flexible search system for high-accuracy identification of biological entities and molecules
   Franz M, Wong JV, Siper MC, Dallago C,Giorgi J, Demir E, Chris Sander C, Bader GD
   Journal of Open Source Software, 6(67), 3756
   PubMed Abstract - PDF
   SOFTWARE
   
   

6. A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells
   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
   Lab Chip. 2021 Oct 15
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

7. A roadmap for the Human Developmental Cell Atlas
   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, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S
   Nature. 2021 Sep;597(7875):196-205
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

8. A clinically applicable integrative molecular classification of meningiomas
   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, Mehani B, Suppiah S, Gao A, Workewych AM, Tabatabai G, Boutros PC, Bader GD, de Carvalho DD, Kislinger T, Aldape K, Zadeh G
   Nature. 2021 Aug 25
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

9. DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations
   John Giorgi, Osvald Nitski, Bo Wang, Gary Bader
   ACL/IJCNLP. 2021 Aug 1
   ACL Anthology - PDF
   NATURAL LANGUAGE PROCESSING
   
   

10. TFEB-mediated endolysosomal activity controls human hematopoietic stem cell fate
    García-Prat L, Kaufmann KB, Schneiter F, Voisin V, Murison A, Chen J, Chan-Seng-Yue M, Gan OI, McLeod JL, Smith SA, Shoong MC, Parris D, Pan K, Zeng AGX, Krivdova G, Gupta K, Takayanagi SI, Wagenblast E, Wang W, Lupien M, Schroeder T, Xie SZ, Dick JE
    Cell Stem Cell. 2021 Jul 28:S1934-5909(21)00288-5.
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

11. Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis
    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
    Cell Stem Cell. 2021 Jul 12:S1934-5909(21)
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Control of tissue development and cell diversity by cell cycle dependent transcriptional filtering
    Abou Chakra M, Isserlin R, Tran TN, Bader GD
    Elife. 2021 Jul 2;10:e64951
    PubMed Abstract - PDF
    MATHEMATICAL MODELLING
    
    

13. scNetViz: from single cells to networks using Cytoscape
    Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH
    F1000Res. 2021 Jun 7;10:ISCB Comm J-448
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    PATHWAY AND NETWORK ANALYSIS
    
    

14. Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device
    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, Chan WCW
    Nano Lett. 2021 Jun 10
    PubMed Abstract - PDF
    COVID-19
    
    

15. Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells
    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
    Nat Commun. 2021 May 26;12(1):3155
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

16. Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods
    Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, Bader GD
    Nat Protoc. 2021 May 24.
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    
    

17. SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
    Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, Bader GD, Blinov ML, Mazein A
    Brief Bioinform. 2021 Mar 24
    PubMed Abstract - PDF
    DATA STANDARDS
    
    

18. Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer
    Peter MR, Bilenky M, Davies A, Isserlin R, Bader GD, Fleshner NE, Hirst M, Zoubeidi A, Bapat B
    Sci Rep. 2021 Mar 23;11(1):6630
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

19. The transcriptional landscape of Shh medulloblastoma
    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, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD
    Nat Commun. 2021 Mar 19;12(1):1749
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

20. Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
    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, Guidos CJ, Lupien M, Dick JE, Minden MD, Schimmer AD, Haibe-Kains B
    Nat Commun. 2021 Feb 16;12(1):1054
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

21. PRMT5 inhibition disrupts splicing and stemness in glioblastoma
    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, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB
    Nat Commun. 2021 Feb 12;12(1):979
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

22. Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation
    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, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE
    Blood Cancer Discov. 2021 Jan 1;2(1):32-53
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

23. Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity
    Richards LM,Whitley OKN, MacLeod G, Cavalli FMG, Coutinho F, Jaramillo J, Svergun N, Riverin M, Croucher D, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti J, Bozek D, Li N, Lee L, Che C, Luis E, Park N, Xu Z, Ketela T, Moore R, Marra M, Spears, Cusimano M, Das S, Bernstein M, Haibe-Kains B, Lupien M, Luchman H, Weiss S, Angers S, Dirks PB, Bader GD, Pugh TJ.
    Nature Cancer 2021 Feb;2(2):157-173
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    
    

2020

1. Large-scale survey and database of high affinity ligands for peptide recognition modules
   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
   Mol Syst Biol. 2020 Dec;16(12)
   PubMed Abstract - PDF
   PROTEIN INTERACTION PREDICTION
   
   

2. CD200 expression marks leukemia stem cells in human AML
   Ho JM, Dobson SM, Voisin V, McLeod J, Kennedy JA, Mitchell A, Jin L, Eppert K, Bader G, Minden MD, Dick JE, Wang JCY
   Blood Adv. 2020 Nov 10;4(21):5402-5413
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
   Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD
   F1000Res. 2020 Oct 15;9:1239
   PubMed Abstract - PDF
   PRECISION MEDICINE
   
   

4. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells
   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, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J
   Nature. 2020 Sep 23
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
   Tran TN, Bader GD
   PLoS Comput Biol. 2020 Sep 9;16(9)
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

6. Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment
   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
   Epigenomics. 2020 Sep 1.
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

7. Wnt activation as a therapeutic strategy in medulloblastoma
   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, Provias JP, Yarascavitch B, Ajani O, Fleming A, Bader GD, Pugh TJ, Doble BW, Singh SK
   Nat Commun. 2020 Aug 28;11(1):4323
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis
   Borrett MJ, Innes BT, Jeong D, Tahmasian N, Storer MA, Bader GD, Kaplan DR, Miller FD
   Cell Rep. 2020 Aug 11;32(6):108022
   PubMed Abstract - PDF
   SINGLE CELL GENOMICS
   
   

9. Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
   Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader GD
   Comput Struct Biotechnol J. 2020;18:1735-1745
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts
    Gage BK, Liu JC, Innes BT, MacParland SA, McGilvray ID, Bader GD, Keller GM
    Cell Stem Cell. 2020;S1934-5909(20)30274-5
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS
    
    

11. Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21
    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
    J Exp Med. 2020 Aug 3;217(8)
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Disrupting Mitochondrial Copper Distribution Inhibits Leukemic Stem Cell Self-Renewal
    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, Mirali S, Borenstein A, Thomas GE, Soriano J, Orouji E, Minden MD, Arruda A, Chan SM, Bader GD, Lupien M, Schimmer AD
    Cell Stem Cell. 2020 May 12
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain
    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, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A.
    Cell Syst. 2020 Apr 22;10(4):333-350
    PubMed Abstract - PDF
    PROTEIN INTERACTION
    
    

14. Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival
    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, Marhon SA, Carvalho DD, Minden MD, Gross A, Schimmer AD
    Blood. 2020 Apr 16
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

15. Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2(+) Granule Neuron Precursor
    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, Kriegstein A, Taylor MD, Dirks PB
    Cell Rep. 2020 Apr 14;31(2):107511
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

16. A reference map of the human binary protein interactome
    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, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA
    Nature.2020 Apr;580(7803):402-408
    PubMed Abstract - PDF
    PROTEIN INTERACTION
    
    

17. The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplexformation and is necessary for AML viability
    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, Minden MD, Horton TM, Kornblau SM, Chan SM, Bader GD, Raught B, Schimmer AD
    Sci Transl Med. 2020 Apr 8;12(538)
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

18. Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model
    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, Cheng M, Sekhon M, Zagorovsky K, Abdou Mohamed MA, Thoeni C, Atif J, Echeverri J, Kollmann D, Fischer S, Bader GD, Chan WCW, Michalak TI, McGilvray ID, MacParland SA
    ACS Nano. 2020 Apr 7
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

19. Relapse fated latent diagnosis subclones in acute B lineage leukaemia are drug tolerant and possess distinct metabolic programs
    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, Xie SZ, Hosseini M, Abelson S, Gupta P, Rusch M, Shao Y, Olsen SR, Neale G, Chan SM, Bader G, Easton J, Guidos CJ, Danska JS, Zhang J, Minden MD, Morris Q, Mullighan CG, Dick JE
    Cancer Discov. 2020 Feb 21
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

20. Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion
    Wong A, Zamel R, Yeung J, Bader GD, Dos Santos CC, Bai X, Wang Y, Keshavjee S, Liu M
    Eur Respir J. 2020 Feb 14
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

21. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.
    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, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK
    Nat Commun. 2020 Jan 16;11(1):312
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

22. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
    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, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C
    Nucleic Acids Res. 2020 Jan 8
    PubMed Abstract - PDF
    PATHWAY DATABASE
    
    

2019

1. End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models
   John Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang
   arXiv. 2019 Dec 20
   arXiv - PDF
   NATURAL LANGUAGE PROCESSING
   
   

2. Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
   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, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE
   Cell Stem Cell. 2019 Oct 11
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. Single-cell transcriptomic profiling of the aging mouse brain
   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, Levin JZ, Rubin LL
   Nat Neurosci. 2019 Oct;22(10):1696-1708
   PubMed Abstract - PDF
   
   SINGLE CELL GENOMICS
   
   

4. Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis
   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, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M
   iScience. 2019 Sep 4;19:1114-1132
   PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE
   
   

5. Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture
   Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS
   Adv Mater. 2019 Jul 19;31(36)
   PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE
   
   

6. EPIC: software toolkit for elution profile-based inference of protein complexes
   Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A
   Nat Methods. 2019 July 15
   PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE
   
   

7. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
   Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. J
   Integr Bioinform. 2019 Jul 13
   PubMed Abstract - PDF
   DATA STANDARDS
   
   

8. Towards reliable named entity recognition in the biomedical domain
   Giorgi JM, Bader GD
   Bioinformatics. 2019 Jun 20
   PubMed Abstract - PDF
   TEXT MINING
   
   

9. Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells
   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, Murty N, Moffat J, Bader GD, Singh SK
   J Neurooncol. 2019 May 21
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids
    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, Mullokandov M, Sharon D, Thomas G, Chouinard-Watkins R, Hawley JR, Schafer C, Yau HL, Khuchua Z, Aman A, Al-Awar R, Gross A, Claypool SM, Bazinet R, Lupien M, Chan S, De Carvalho DD, Minden MD, Bader GD, Stark KD, LeBlanc P, Schimmer AD
    Cell Stem Cell. 2019 Mar 19
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

11. Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
    Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B
    Clin Epigenetics. 2019 Mar 27;11(1):54
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. netDx: interpretable patient classification using integrated patient similarity networks
    Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD
    Mol Syst Biol. 2019 Mar 14;15(3):e8497
    PubMed Abstract -PDF
    
    PRECISION MEDICINE
    
    

13. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.
    Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH
    F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296
    PubMed Abstract -PDF
    SINGLE CELL GENOMICS
    
    

14. Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
    Sun R, Hui S, Bader GD, Lin X, Kraft P
    PLoS Genet. 2019 Mar 15;15(3)
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

15. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
    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
    Nat Protoc. 2019 Feb;14(2):482-517
    PubMed Abstract -PDF
    
    PATHWAY AND NETWORK ANALYSIS
    
    

16. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
    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, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL
    Nucleic Acids Res. 2019 Jan 30
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

2018

1. Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells
   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
   Stem Cell Res. 2018 Nov 13;33:215-227
   PubMed Abstract -PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2. The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety
   Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, Bader GD, Sibille E
   Biol Psychiatry. 2018 Oct 5
   PubMed Abstract -PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
   MacParland SA, Liu, JC, Ma X, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID
   Nat Commun. 2018 Oct 22;9(1):4383
   PubMed Abstract -PDF
   SINGLE CELL GENOMICS
   
   

4. scClustViz - Single-cell RNAseq cluster assessment and visualization
   Innes BT, Bader GD
   F1000Res. 2018 Sep 21;7
   PubMed Abstract -PDF
   SINGLE CELL GENOMICS
   
   

5. The Human Cell Atlas White Paper
   Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee
   -PDF
   SINGLE CELL GENOMICS, PREPRINT
   
   

6. Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics
   Dasgupta S, Bader GD, Goyal S
   Biophys J. 2018 Aug 7;115(3):429-435
   PubMed Abstract -PDF
   SINGLE CELL GENOMICS
   
   

7. The Cytoscape Automation app article collection.
   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.
   F1000Res. 2018 Jun 20;7:800
   PubMed Abstract -PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities
   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, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R
   J Cell Biol. 2018 Jun 19
   PubMed Abstract -PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. GeneMANIA update 2018
   Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q
   Nucleic Acids Res. 2018 Jun 15
   PubMed Abstract -PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. Transfer learning for biomedical named entity recognition with neural networks
    Giorgi JM, Bader GD
    Bioinformatics. 2018 Jun 1
    PubMed Abstract -PDF
    
    
    

11. Patient Similarity Networks for Precision Medicine
    Pai S, Bader GD
    J Mol Biol. 2018 May 31
    PubMed Abstract -PDF
    
    PRECISION MEDICINE
    
    

12. Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer
    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, Datti A, Zacksenhaus E
    Cell Rep. 2018 Apr 3;23(1):112-126
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
    Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D
    J Integr Bioinform. 2018 Mar 29
    PubMed Abstract -PDF
    DATA STANDARDS
    
    

14. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection
    Zhang N, Bao YJ, Tong AH, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SM
    BMC Med Genomics. 2018 Feb 23;11(1):20
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

2017

1. Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling
   Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD
   Cell Rep. 2017 Dec 26;21(13):3970-3986
   PubMed Abstract -PDF
   SINGLE CELL GENOMICS
   
   

2. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling
   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, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M
   Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7
   PubMed Abstract -PDF
   
   

3. Association analysis identifies 65 new breast cancer risk loci
   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, Wang Z, Allen J, Keeman R, Eilber U, French JD, Qing Chen X, Fachal L, McCue K, McCart Reed AE, Ghoussaini M, Carroll JS, Jiang X, Finucane H, Adams M, Adank MA, Ahsan H, Aittomäki K, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Arun B, Auer PL, Bacot F, Barrdahl M, Baynes C, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Brinton L, Broberg P, Brock IW, Broeks A, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Butterbach K, Cai Q, Cai H, Caldés T, Canzian F, Carracedo A, Carter BD, Castelao JE, Chan TL, David Cheng TY, Seng Chia K, Choi JY, Christiansen H, Clarke CL; NBCS Collaborators, Collée M, Conroy DM, Cordina-Duverger E, Cornelissen S, Cox DG, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Elvira M, Engel C, Eriksson M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gaborieau V, Gabrielson M, Gago-Dominguez M, Gao YT, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hamel N, Hankinson S, Harrington P, Hart SN, Hartikainen JM, Hartman M, Hein A, Heyworth J, Hicks B, Hillemanns P, Ho DN, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Hou MF, Hsiung CN, Huang G, Humphreys K, Ishiguro J, Ito H, Iwasaki M, Iwata H, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kasuga Y, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Kosma VM, Kristensen VN, Krüger U, Kwong A, Lambrechts D, Le Marchand L, Lee E, Lee MH, Lee JW, Neng Lee C, Lejbkowicz F, Li J, Lilyquist J, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Lophatananon A, Lubinski J, Luccarini C, Lux MP, Ma ESK, MacInnis RJ, Maishman T, Makalic E, Malone KE, Kostovska IM, Mannermaa A, Manoukian S, Manson JE, Margolin S, Mariapun S, Martinez ME, Matsuo K, Mavroudis D, McKay J, McLean C, Meijers-Heijboer H, Meindl A, Menéndez P, Menon U, Meyer J, Miao H, Miller N,Taib NAM, Muir K, Mulligan AM, Mulot C, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Noh DY, Nordestgaard BG, Norman A, Olopade OI, Olson JE, Olsson H, Olswold C, Orr N, Pankratz VS, Park SK, Park-Simon TW, Lloyd R, Perez JIA, Peterlongo P, Peto J, Phillips KA, Pinchev M, Plaseska-Karanfilska D, Prentice R, Presneau N, Prokofyeva D, Pugh E, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Ruddy KJ, Rüdiger T, Rudolph A, Ruebner M, Rutgers EJT, Saloustros E, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Scott RJ, Scott C, Seal S, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng G, Sherman ME, Shrubsole MJ, Shu XO, Smeets A, Sohn C, Southey MC, Spinelli JJ, Stegmaier C, Stewart-Brown S, Stone J, Stram DO, Surowy H, Swerdlow A, Tamimi R, Taylor JA, Tengström M, Teo SH, Beth Terry M, Tessier DC, Thanasitthichai S, Thöne K, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Truong T, Tseng CC, Tsugane S, Ulmer HU, Ursin G, Untch M, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van der Kolk L, van der Luijt RB, Vincent D, Vollenweider J, Waisfisz Q, Wang-Gohrke S, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yamaji T, Yang XR, Har Yip C, Yoo KY, Yu JC, Zheng W, Zheng Y, Zhu B, Ziogas A, Ziv E; ABCTB Investigators; ConFab/AOCS Investigators, Lakhani SR, Antoniou AC, Droit A, Andrulis IL, Amos CI, Couch FJ, Pharoah PDP, Chang-Claude J, Hall P, Hunter DJ, Milne RL, García-Closas M, Schmidt MK, Chanock SJ, Dunning AM, Edwards SL, Bader GD, Chenevix-Trench G, Simard J, Kraft P, Easton DF
   Nature. 2017 Oct 23
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

4. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
   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, Wang Q, Aalfs CM; ABCTB Investigators, Adams M, Adlard J, Agata S, Ahmed S, Ahsan H, Aittomäki K, Al-Ejeh F, Allen J, Ambrosone CB, Amos CI, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Arnold N, Aronson KJ, Auber B, Auer PL, Ausems MGEM, Azzollini J, Bacot F, Balmaña J, Barile M, Barjhoux L, Barkardottir RB, Barrdahl M, Barnes D, Barrowdale D, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Bernstein L, Bignon YJ, Blazer KR, Blok MJ, Blomqvist C, Blot W, Bobolis K, Boeckx B, Bogdanova NV, Bojesen A, Bojesen SE, Bonanni B, Børresen-Dale AL, Bozsik A, Bradbury AR, Brand JS, Brauch H, Brenner H, Bressac-de Paillerets B, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Brunet J, Brüning T, Burwinkel B, Buys SS, Byun J, Cai Q, Caldés T, Caligo MA, Campbell I, Canzian F, Caron O, Carracedo A, Carter BD, Castelao JE, Castera L, Caux-Moncoutier V, Chan SB, Chang-Claude J, Chanock SJ, Chen X, Cheng TD, Chiquette J, Christiansen H, Claes KBM, Clarke CL, Conner T, Conroy DM, Cook J, Cordina-Duverger E, Cornelissen S, Coupier I, Cox A, Cox DG, Cross SS, Cuk K, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, Davidson R, De Leeneer K, Devilee P, Dicks E, Diez O, Ding YC, Ditsch N, Doheny KF, Domchek SM, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dubois S, Dugué PA, Dumont M, Dunning AM, Durcan L, Dwek M, Dworniczak B, Eccles D, Eeles R, Ehrencrona H, Eilber U, Ejlertsen B, Ekici AB, Eliassen AH; EMBRACE, Engel C, Eriksson M, Fachal L, Faivre L, Fasching PA, Faust U, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gaddam P, Gammon MD, Ganz PA, Gapstur SM, Garber J, Garcia-Barberan V, García-Sáenz JA, Gaudet MM, Gauthier-Villars M, Gehrig A; GEMO Study Collaborators, Georgoulias V, Gerdes AM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goodfellow P, Greene MH, Alnæs GIG, Grip M, Gronwald J, Grundy A, Gschwantler-Kaulich D, Guénel P, Guo Q, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hallberg E, Hamann U, Hamel N, Hankinson S, Hansen TVO, Harrington P, Hart SN, Hartikainen JM, Healey CS; HEBON, Hein A, Helbig S, Henderson A, Heyworth J, Hicks B, Hillemanns P, Hodgson S, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover B, Hopper JL, Hu C, Huang G, Hulick PJ, Humphreys K, Hunter DJ, Imyanitov EN, Isaacs C, Iwasaki M, Izatt L, Jakubowska A, James P, Janavicius R, Janni W, Jensen UB, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kast K; kConFab/AOCS Investigators, Keeman R, Kerin MJ, Kets CM, Keupers M, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Konstantopoulou I, Kosma VM, Kristensen VN, Kruse TA, Kwong A, Lænkholm AV, Laitman Y, Lalloo F, Lambrechts D, Landsman K, Lasset C, Lazaro C, Le Marchand L, Lecarpentier J, Lee A, Lee E, Lee JW, Lee MH, Lejbkowicz F, Lesueur F, Li J, Lilyquist J, Lincoln A, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Loud JT, Lubinski J, Luccarini C, Lush M, MacInnis RJ, Maishman T, Makalic E, Kostovska IM, Malone KE, Manoukian S, Manson JE, Margolin S, Martens JWM, Martinez ME, Matsuo K, Mavroudis D, Mazoyer S, McLean C, Meijers-Heijboer H, Menéndez P, Meyer J, Miao H, Miller A, Miller N, Mitchell G, Montagna M, Muir K, Mulligan AM, Mulot C, Nadesan S, Nathanson KL; NBSC Collaborators, Neuhausen SL, Nevanlinna H, Nevelsteen I, Niederacher D, Nielsen SF, Nordestgaard BG, Norman A, Nussbaum RL, Olah E, Olopade OI, Olson JE, Olswold C, Ong KR, Oosterwijk JC, Orr N, Osorio A, Pankratz VS, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Lloyd R,Pedersen IS, Peissel B, Peixoto A, Perez JIA, Peterlongo P, Peto J, Pfeiler G,Phelan CM, Pinchev M, Plaseska-Karanfilska D, Poppe B, Porteous ME, Prentice R, Presneau N, Prokofieva D, Pugh E, Pujana MA, Pylkäs K, Rack B, Radice P, Rahman N, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rennert HS, Rhenius V, Rhiem K, Richardson A, Rodriguez GC, Romero A, Romm J, Rookus MA, Rudolph A, Ruediger T,Saloustros E, Sanders J, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seal S, Senter L, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng X, Shimelis H,Shrubsole MJ, Shu XO, Side LE, Singer CF, Sohn C, Southey MC, Spinelli JJ, Spurdle AB, Stegmaier C, Stoppa-Lyonnet D, Sukiennicki G, Surowy H, Sutter C, Swerdlow A, Szabo CI, Tamimi RM, Tan YY, Taylor JA, Tejada MI, Tengström M, Teo SH, Terry MB, Tessier DC, Teulé A, Thöne K, Thull DL, Tibiletti MG, Tihomirova L, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Tranchant M, Truong T, Tucker K, Tung N, Tyrer J, Ulmer HU, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van Rensburg EJ, Varesco L, Varon-Mateeva R, Vega A, Viel A, Vijai J, Vincent D, Vollenweider J, Walker L, Wang Z, Wang-Gohrke S, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wesseling J, Whittemore AS, Wijnen JT, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yang XR, Yannoukakos D, Zaffaroni D, Zheng W, Zhu B, Ziogas A, Ziv E, Zorn KK, Gago-Dominguez M, Mannermaa A, Olsson H, Teixeira MR, Stone J, Offit K, Ottini L, Park SK, Thomassen M, Hall P, Meindl A, Schmutzler RK, Droit A, Bader GD, Pharoah PDP, Couch FJ, Easton DF, Kraft P, Chenevix-Trench G, García-Closas M, Schmidt MK, Antoniou AC, Simard J
   Nat Genet. 2017 Oct 23
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities
   Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS
   Structure. 2017 Aug 28. S0969-2126(17)30251-4
   PubMed Abstract - PDF
   PROTEIN INTERACTION
   
   

6. microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer
   Wang S, Liu JC, Ju Y, Pellecchia G, Voisin V, Wang DY, Leha L R, Ben-David Y, Bader GD, Zacksenhaus E
   JCI Insight. 2017 Aug 3;2(15)
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

7. ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells
   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, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB
   Cell Stem Cell. 2017 Aug 3;21(2):209-224
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Tracing the origins of relapse in acute myeloid leukaemia to stem cells
   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, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE
   Nature. 2017 Jul 6;547(7661):104-108
   PubMed Abstract - PDF
   
   
   

9. Intertumoral Heterogeneity within Medulloblastoma Subgroups
   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, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD
   Cancer Cell. 2017 Jun 12;31(6):737-754
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

10. Spatial heterogeneity in medulloblastoma
    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, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD
    Nat Genet. 2017 Apr 10
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

11. Integrative cancer pharmacogenomics to infer large-scale drug taxonomy
    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
    Cancer Res. 2017 Mar 17
    PubMed Abstract - PDF
    
    NETWORK ANALYSIS
    
    

12. Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML
    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, Laposa R, Schimmer AD
    Blood. 2017 Mar 10
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia
    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
    Proteomics. 2017 Feb 7.
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

2016

1. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
   Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D
   J Integr Bioinform. 2016 Dec 18;13(3):289
   PubMed Abstract - PDF
   DATA STANDARDS
   
   

2. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors
   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, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DM, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N,Huang A
   Cancer Cell. 2016 Dec 12;30(6):891-908
   PubMed Abstract - PDF
   
   

3. Global neuroscience and mental health research: a bibliometrics case study
   Buchan AMJ, Jurczyk E, Isserlin R, Bader GD
   Scientometrics 109 (1), 515-531
   PDF
   NETWORK ANALYSIS SOFTWARE
   
   

4. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
   Kucera M, Isserlin R, Arkhangorodsky A, Bader GD
   F1000Res. 2016 Jul 15;5:1717
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. Ten Simple Rules for Developing Public Biological Databases
   Helmy M, Crits-Christoph A, Bader GD
   PLoS Comput Biol. 2016 Nov 10;12(11)
   PubMed Abstract -PDF
   
   

6. RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation
   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, Schimmer A, Zacksenhaus E
   J Clin Invest. 2016 Aug 29
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

7. Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors
   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, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G
   Cell Stem Cell. 2016 Jul 12. pii: S1934-5909(16)30158-8
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
   Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Dos Santos CC
   Sci Rep. 2016 Jul 14;6:29334
   PubMed Abstract - PDF
   
   

9. Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells
   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, Clarke ID, Bader G, Harrington L, Brumell JH, Tyers M, Dirks PB
   Cancer Cell. 2016 Jun 13;29(6):859-73
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
    Narayan S, Bader GD, Reimand J
    Genome Med. 2016 May 12;8(1):55
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

11. Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
    Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ
    Nature. 2016 Apr 28;532(7600):508-11
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. HOX gene complement and expression in the planarian Schmidtea mediterranea
    Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ
    Evodevo. 2016 Mar 30;7:7
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. Social Network: a Cytoscape app for visualizing co-authorship networks
    Kofia V, Isserlin R, Buchan AM, Bader GD
    F1000Res. 2015 Aug 5;4:481
    PubMed Abstract - PDF
    NETWORK ANALYSIS SOFTWARE
    
    

14. Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast
    Jain S, Bader GD
    Bioinformatics. 2016 Feb 9
    PubMed Abstract - PDF
    PROTEIN INTERACTION PREDICTION
    
    

15. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells
    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, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE
    Cancer Cell. 2016 Apr 11;29(4):602-606
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

16. Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance
    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
    Cell. 2016 Jan 14;164(1-2):293-309
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

17. Divergent clonal selection dominates medulloblastoma at recurrence
    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, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD
    Nature. 2016 Jan 13. doi: 10.1038/nature16478
    PubMed Abstract - PDF
    CANCER MUTATIONS

2015

1. NetMatchStar: an enhanced Cytoscape network querying app
   Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A,Giugno R F1000Res.2015 Aug 5;4:479
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2. Specifications of Standards in Systems and Synthetic Biology
   Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S
   J Integr Bioinform. 2015 Sep 4;12(2):258
   PubMed Abstract - PDF
   DATA STANDARDS
   
   

3. Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma
   Wei Q, Tang YJ, Voisin V, Sato S, Hirata M, Whetstone H, Han I, Ailles L, Bader GD, Wunder J, Alman BA
   Oncotarget. 2015 Oct 26.
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

4. Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer
   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
   Oncotarget. 2015 Sep 29;6(29):27923-37
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. Systematic analysis of somatic mutations impacting gene expression in 12 tumour types
   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
   Nat Commun. 2015 Oct 5;6:8554
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

6. Cytoscape.js: a graph theory library for visualisation and analysis
   Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD
   Bioinformatics 2015 Sep 28
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

7. EAG2 potassium channel with evolutionarily conserved function as a brain tumor target
   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, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY
   Nat Neurosci 2015 Aug 10
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

8. GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks
   Law B, Bader GD
   Sci Rep 2015 Jul 13;5:12074
   PubMed Abstract - PDF
   PROTEIN INTERACTIONS
   
   

9. Inferring interaction type in gene regulatory networks using co-expression data
   Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Bader GD,Goliaei B
   Algorithms Mol Biol 2015 Jul 8;10:23
   PubMed Abstract - PDF
   GENE REGULATORY INTERACTIONS
   
   

10. Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations
    Lerner-Ellis J, Wang M, White S, Lebo MS; Canadian Open Genetics Repository Group
    J Med Genet 2015 Jul;52(7):438-45
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

11. Pathway and network analysis of cancer genomes
    Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium
    Nat Methods 2015 Jun 30;12(7):615-21
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Cardioprotective Signature of Short-Term Caloric Restriction
    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
    PLoS One 2015 Jun 22;10(6)
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

13. Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia
    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, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, Bader GD, Hao Z, Kornblau SM, Raught B, Schimmer AD
    Cancer Cell 2015 Jun 8;27(6):864-76
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

14. MIMP: predicting the impact of mutations on kinase-substrate phosphorylation
    Wagih O, Reimand J, Bader GD
    Nat Methods 2015 Jun;12(6):531-3
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

15. Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups
    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, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM
    Cancer Cell 2015 May 11;27(5):728-43
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

16. Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action
    Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G
    Biochem J 2015 Jul 1;469(1):71-82
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

17. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
    Ammar R, Paton TA, Torti D, Shlien A, Bader GD
    F1000Res 2015 Jan 21;4:17
    PubMed Abstract - PDF
    DNA SEQUENCING
    
    

18. Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis
    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, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S,Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, Bader GD, Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A
    Lancet Oncol 2015 May;16(5):569-82
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

19. Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative
    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
    Front Bioeng Biotechnol 2015 Feb 24;3:19
    PubMed Abstract - PDF
    DATA STANDARDS
    
    

20. IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection
    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
    Nat Immunol 2015 Apr;16(4):397-405
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

21. A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.
    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
    Stem Cell Reports. 2015 Mar 10;4(3):313-322
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

22. Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes
    Reimand J, Wagih O, Bader GD
    PLoS Genet 2015 Jan 22;11(1)
    PubMed Abstract - PDF
    CANCER MUTATIONS
    
    

23. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity
    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, Dirks PB
    Proc Natl Acad Sci U S A 2015 Jan 20;112(3):851-6
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

2014

1. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy
   Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A
   Mol Biosyst 2015 Jan;11(1):239-51
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

2. Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K
   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
   EMBO Mol Med 2014 Oct 20;6(12):1542-60
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
   James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu
   Bioinformatics 2015 Feb 1;31(3):306-10
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

4. The Cytoscape app article collection
   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.
   F1000Res 2014 Jul 1;3:138.
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. GeneMANIA: Fast gene network construction and function prediction for Cytoscape
   Jason Montojo,Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
   F1000Res 2014 Jul 1;3:153
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

6. Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results
   Isserlin R, Merico D, Voisin V, Bader GD
   F1000Res 2014 Jul 1;3:141
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

7. Intercellular network structure and regulatory motifs in the human hematopoietic system
   Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW
   Mol Syst Biol 2014 Jul 15;10(7):741
   Pubmed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
   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, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM
   Nature 2014 Jul 24;511(7510):428-34
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
   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, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB
   Cancer Cell 2014 Jul 14;26(1):33-47
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction
    Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q
    Front Genet 2014 May 16;5:123
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

11. A draft map of the human proteome
    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, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A
    Nature 2014 May 29;509(7502):575-81
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Mapping the cellular response to small molecules using chemogenomic fitness signatures
    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, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G
    Science 2014 Apr 11;344(6180):208-11
    PubMed Abstract - PDF
    CHEMICAL GENOMICS
    
    

13. Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs
    Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD
    PLoS One 2014 Apr 10;9(4):e94507
    PubMed Abstract - PDF
    FUNCTIONAL MUTATION ANALYSIS
    
    

14. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
    Leung A, Bader GD, Reimand J
    Bioinformatics 2014 Apr 8
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

15. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition
    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, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project
    Cancer Cell 2014 Mar 17;25(3):393-405
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

16. Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics
    Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS
    Proteomics 2014 May;14(9):975-88
    PubMed Abstract - PDF
    PROTEOMICS
    
    

17. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
    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, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD
    Nature 2014 Feb 27;506(7489):445-50
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

2013

1. TCGA pan-cancer project, thread 2: Network models
   Reimand J, Bader GD, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton
   Nature Genetics (2013) doi:10.1038/ng.2787
   CANCER MUTATIONS, NETWORKS
   
   

2. Coordinate microRNA-mediated regulation of protein complexes in prostate cancer
   Alshalalfa M, Bader GD, Bismar TA, Alhajj R
   PLoS One 2013 Dec 31;8(12):e84261
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. Comprehensive identification of mutational cancer driver genes across 12 tumor types
   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
   Sci Rep 2013 Oct 2;3:2650
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

4. The mutational landscape of phosphorylation signaling in cancer
   Reimand J, Wagih O, Bader GD
   Sci Rep 2013 Oct 2;3:2651
   PubMed Abstract - PDF
   CANCER MUTATIONS, NETWORKS
   
   

5. Using biological pathway data with paxtools
   Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.
   PLoS Comput Biol 2013;9(9):e1003194
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

6. The BioPAX Validator
   Rodchenkov I, Demir E, Sander C, Bader GD
   Bioinformatics 2013 Oct 15;29(20):2659-60
   PubMed Abstract - PDF
   DATA STANDARD
   
   

7. Computational approaches to identify functional genetic variants in cancer genomes
   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, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group
   Nature Methods 2013 Aug;10(8):723-9
   PubMed Abstract - PDF
   CANCER MUTATIONS
   
   

8. GeneMANIA prediction server 2013 update
   Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q
   Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. Cytoscape App Store
   Lotia S, Montojo J, Dong Y, Bader GD, Pico AR
   Bioinformatics 2013 May 15;29(10):1350-1
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

10. SH3 interactome conserves general function over specific form
    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, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD
    Mol Syst Biol 2013 Apr 2;9:652
    Pubmed Abstract - PDF
    Interactions in Intact Database
    PROTEIN INTERACTION PREDICTION
    
    

11. Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells
    Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.
    PLoS One 2013;8(3):e58367
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
    Reimand J, Bader GD
    Mol Syst Biol 2013;9:637
    PubMed Abstract - PDF
    Research Highlight in Genome Medicine (2013)
    CANCER MUTATIONS, SIGNALING NETWORKS
    
    

13. Predicting PDZ domain mediated protein interactions from structure
    Hui S, Xing X, Bader GD
    BMC Bioinformatics 2013 Jan 21;14:27
    PubMed Abstract - PDF
    PROTEIN INTERACTION PREDICTION
    
    

14. Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation
    Karagiannis GS, Weile J, Bader GD, Minta J.
    BMC Cardiovasc Disord 2013 Jan 16;13:4
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

15. GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process
    Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri
    Bioinformatics 2013 Feb 15;29(4):513-4
    PubMed Abstract - PDF
    NETWORK SIMULATION

2012

1. The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community
   Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS
   J Proteome Res 2013 Jan 4;12(1):23-7
   PubMed Abstract - PDF
   PROTEOMICS
   
   

2. Chromatin is an ancient innovation conserved between Archaea and Eukarya
   Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C
   Elife 2012 Dec 13;1:e00078
   PubMed Abstract - PDF
   ANALYSIS OF ARCHAEAL CHROMATIN
   
   

3. Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion
   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
   Cell Stem Cell 2012 Nov 7
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

4. A travel guide to Cytoscape plugins
   Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T
   Nat Methods 2012 Nov;9(11):1069-76
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

5. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
   Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R
   BMC Syst Biol 2012 Aug 28;6:112
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

6. Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice
   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
   Oncogenesis 2012 Sep 3;1:e26
   PubMed Abstract - PDF
   CANCER GENOMICS
   
   

7. Subgroup-specific structural variation across 1,000 medulloblastoma genomes
   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, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD
   Nature 2012 Aug 2;488(7409):49-56
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
   Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ
   Stem Cells 2012 Jun 13
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
   Michaut M, Bader GD
   PLoS Comput Biol 8(6): e1002559
   PubMed Abstract - PDF
   GENETIC INTERACTIONS
   
   

10. Domain-mediated protein interaction prediction: From genome to network
    Reimand J, Hui S, Jain S, Law B, Bader GD
    FEBS Lett 2012 May 3
    PubMed Abstract - PDF
    PROTEIN INTERACTIONS
    
    

11. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer
    Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E
    Proc Natl Acad Sci U S A 2012 Mar 28
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

12. Phosphorylation sites of higher stoichiometry are more conserved
    Tan CS, Bader GD
    Nat Methods 2012 Mar 27;9(4):317
    PubMed Abstract -PDF
    PHOSPHOPROTEOMICS
    
    

13. Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry
    Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE
    PLoS Genet 2012 Mar;8(3):e1002562
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

2011

1. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
   Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM
   Nucleic Acids Res 2011 Dec 30
   PubMed Abstract - PDF
   DOMAIN SPECIFICITY SOFTWARE
   
   

2. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
   Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A
   Stand Genomic Sci 2011 Nov 30;5(2):230-42
   PubMed Abstract - PDF
   DATA STANDARD
   
   

3. clusterMaker: a multi-algorithm clustering plugin for Cytoscape
   Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
   BMC Bioinformatics 2011 Nov 9;12(1):436
   PubMed Abstract -PDF
   NETWORK ANALYSIS SOFTWARE
   
   

4. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms
   Iain M. Wallace, Malene L. Urbanus, Genna M. Luciani,Andrew R. Burns,Mitchell K.L. Han, Hao Wang, Kriti Arora, Lawrence E. Heisler, Michael Proctor, Robert P. St. Onge, Terry Roemer, Peter J. Roy,Carolyn L. Cummins, Gary D. Bader, Corey Nislow, Guri Giaever
   Cell Chemistry & Biology 2011 18, 1273–1283
   PubMed Abstract - PDF
   Chemistry & Biology 2011 18:10, 1204-1205 Commentary on paper
   CHEMICAL GENOMICS
   
   

5. NetSlim: high-confidence curated signaling maps
   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, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Sameer Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A
   Database (Oxford) 2011 Sep 29;2011(0):bar032
   PubMed Abstract - PDF
   PATHWAY DATABASE
   
   

6. Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
   Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM
   Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
   PubMed Abstract - PDF
   PATHWAY ANALYSIS
   
   

7. A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
   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, Pandey A
   Database (Oxford) 2011 Jul 8;2011
   PubMed Abstract -PDF
   PATHWAY DATABASE
   
   

8. PSICQUIC and PSISCORE: accessing and scoring molecular interactions
   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, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H
   Nature Methods 2011 Jun 29;8(7):528-9
   Pubmed Abstract - PDF
   PROTEIN INTERACTIONS
   
   

9. Response to Comment on Positive Selection of Tyrosine Loss in Metazoan Evolution,
   Tan CS, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD and Linding R
   Science 332(6032):917, 20 May 2011
   PDF
   NETWORK EVOLUTION
   
   

10. The multiple-specificity landscape of modular peptide recognition domains
    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
    Molecular Systems Biology 7:484, 26 April 2011
    PubMed Abstract - PDF
    PROTEIN INTERACTION PREDICTION
    
    

11. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
    Oesper L, Merico D, Isserlin R, Bader GD
    Source Code for Biology and Medicine 2011, 6:7, 7 April 2011
    PubMed Abstract -PDF
    NETWORK ANALYSIS SOFTWARE
    
    

12. Protein Complexes are Central in the Yeast Genetic Landscape
    Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD
    PLoS Computational Biology 7(2): e1001092 Feb 24 2011
    February 2011 Issue Cover
    PubMed Abstract - PDF
    GENETIC INTERACTION NETWORK ANALYSIS
    
    

13. Bringing order to protein disorder through comparative genomics and genetic interactions
    Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM
    Genome Biology 12(2):R14 Feb 15 2011
    PubMed Abstract - PDF
    PROTEIN DISORDER AND COMPARATIVE GENOMICS
    
    

14. Too Many Roads Not Taken
    Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH
    Nature. (470) 163-165 Feb 9 2011
    PubMed Abstract - PDF
    Full Paper on arxiv.org
    BIBLIOMETRIC ANALYSIS
    
    

15. The Biomolecular Interaction Network Database in PSI-MI 2.5
    Isserlin R, El-Badrawi RA, Bader GD
    Database 2011 Jan 12;2011:baq037
    PubMed Abstract - PDF
    PROTEIN INTERACTION DATABASE

2010

1. A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence
   Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD
   Bioinformatics 2010 Dec 2
   PubMed Abstract - PDF
   PROTEIN INTERACTION PREDICTION
   
   

2. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
   Merico D, Isserlin R, Stueker O, Emili A, Bader GD
   PLoS One 2010 Nov 15;5(11):e13984
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

3. An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
   Jain S, Bader GD
   BMC Bioinformatics 2010 Nov 15;11(1):562
   PubMed Abstract -PDF
   PROTEIN INTERACTION PREDICTION
   
   

4. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
   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, Brown GW, Andrews B, Boone C, Myers CL
   Nat Methods 2010 Nov 14
   PubMed Abstract -PDF
   GENETIC INTERACTION NETWORK ANALYSIS
   
   

5. Pathway Commons, a web resource for biological pathway data
   Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C
   Nucleic Acids Res 2010 Nov 10
   PubMed Abstract - PDF
   PATHWAY DATABASE
   
   

6. Proteome scanning to predict PDZ domain interactions using support vector machines
   Hui S, Bader GD
   BMC Bioinformatics 2010 Oct 12;11(1):50
   PubMed Abstract - PDF
   PROTEIN INTERACTION PREDICTION
   
   

7. GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop
   Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD
   Bioinformatics 2010 Nov 15;26(22):2927-8
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

8. Dynamic interaction networks in a hierarchically organized tissue
   Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW
   Mol Syst Biol 2010 Oct 5;6:417
   PubMed Abstract - PDF
   PATHWAY AND NETWORK ANALYSIS
   
   

9. Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling
   Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader GD, Sidhu S, Vandekerckhove J, Gettemans J, Sudol M
   Biochem J 2010 Sep 24
   PubMed Abstract - PDF
   PROTEIN INTERACTION PREDICTION
   
   

10. The BioPAX community standard for pathway data sharing
    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, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD
    Nat Biotechnol 2010 Sep;28(9):935-42
    PubMed Abstract - PDF
    DATA STANDARD
    
    

11. Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
    Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS
    Mol. BioSyst., 2010, Advance Article
    PubMed Abstract - PDF
    PROTEIN INTERACTION NETWORK EVOLUTION
    
    

12. Cytoscape Web: an interactive web-based network browser
    Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD
    Bioinformatics 2010 Jul 23
    PubMed Abstract - PDF
    NETWORK VISUALIZATION
    
    

13. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
    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, Morris Q
    Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS
    
    

14. Functional impact of global rare copy number variation in autism spectrum disorders
    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, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C
    Nature 2010 Jul 15;466(7304):368-72
    PubMed Abstract - PDF
    Nature Blogs - In the news (The Globe and Mail)
    PATHWAY AND NETWORK ANALYSIS
    
    

15. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans
    Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ
    Nat Chem Biol 2010 May 30
    PubMed Abstract - PDF
    NCB_News&Views.pdf
    CHEMICAL GENOMICS
    
    

16. International network of cancer genome projects
    International Cancer Genome Consortium
    Nature 2010 Apr 15;464(7291):993-8
    PubMed Abstract - PDF
    CANCER GENOMICS
    
    

17. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
    Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A
    Proteomics 2010, March 10(6):1316-27
    Pubmed Abstract - PDF
    PATHWAY ANALYSIS
    
    

18. The Genetic Landscape of a Cell
    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, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C
    Science 2010 Jan 22;327(5964):425-31
    PubMed Abstract - PDF
    GENETIC INTERACTION NETWORK ANALYSIS
    
    

19. NetPath: a public resource of curated signal transduction pathways
    Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A
    Genome Biology 2010 Jan 12;11(1):R3
    PubMed Abstract - PDF
    PATHWAY DATABASE
    
    

20. DRYGIN: a database of quantitative genetic interaction networks in yeast
    Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C
    Nucleic Acids Res 2010 Jan;38(Database issue):D502-7
    PubMed Abstract - PDF
    GENETIC INTERACTION NETWORK DATABASE

2009

1. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
   Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C
   PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218
   PubMed Abstract - PDF
   PROTEIN-PROTEIN INTERACTION ANALYSIS
   
   

2. How to visually interpret biological data using networks
   Merico D, Gfeller D, Bader GD
   Nature Biotechnology 2009 Oct 27, 921-924
   PubMed Abstract - PDF
   Data: http://www.baderlab.org/NetworkPrimerNBT
   NETWORK PRIMER
   
   

3. Rapid evolution of functional complexity in a domain family
   Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS
   Science Signaling 2009 Sep 8;2(87):ra50
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION
   
   

4. Positive Selection of Tyrosine Loss in Metazoan Evolution
   Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
   Science. Sep 25;325(5948):1686-8
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION
   
   

5. Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases
   Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R
   Science Signaling 2(81):r39 (2009)
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION

2008

1. A Specificity Map for the PDZ Domain Family
   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, Boone C, Bader GD, Sidhu SS
   PLoS Biology Vol. 6, No. 9, e239
   PubMed Abstract - PDF
   PROTEIN-PROTEIN INTERACTION ANALYSIS
   
   

2. Cytoscape ESP: simple search of complex biological networks
   Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ
   Bioinformatics 2008 Jun 15;24(12):1465-6
   PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE
   
   

3. Computational prediction of protein-protein interactions
   Skrabanek L, Saini HK, Bader GD, Enright AJ
   Molecular Biotechnology 2008 Jan;38(1):1-17
   PubMed Abstract - PDF
   REVIEW

2007

1. Integration of biological networks and gene expression data using Cytoscape
   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, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
   Nature Protocols 2007;2(10):2366-82
   PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE
   
   

2. Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions
   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, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H
   BMC Biology 2007 Oct 9;5(1):44
   PubMed Abstract - PDF
   DATA STANDARD
   
   

3. The minimum information required for reporting a molecular interaction experiment (MIMIx)
   Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H
   Nat Biotechnol 2007 Aug;25(8):894-8
   PubMed Abstract - PDF
   DATA STANDARD
   
   

4. Germ-line DNA copy number variation frequencies in a large North American population
   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
   Hum Genet 2007 Nov;122(3-4):345-53
   PubMed Abstract - PDF
   GENOMICS
   
   

5. From bytes to bedside: data integration and computational biology for translational cancer research
   Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B
   PLoS Comput Biol 2007 Feb 23;3(2):e12
   PubMed Abstract - PDF
   CANCER REVIEW
   
   

6. NetMatch: a Cytoscape Plugin for Searching Biological Networks
   Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D
   Bioinformatics 2007 Apr 1;23(7):910-2
   PubMed Abstract - PDF
   Download software
   NETWORK ANALYSIS SOFTWARE
   
   

7. Computational prediction of cancer-gene function
   Hu P, Bader G, Wigle DA, Emili A
   Nature Reviews Cancer 2007 Jan;7(1):23-34
   PubMed Abstract - PDF
   CANCER REVIEW

2006

1. cPath: open source software for collecting, storing, and querying biological pathways
   Cerami EG, Bader GD, Gross BE, Sander C
   BMC Bioinformatics 2006, 7:497
   PubMed Abstract - PDF
   PATHWAY SOFTWARE
   
   

2. Pathguide: a Pathway Resource List
   Bader GD, Cary MP, Sander C
   Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6
   PubMed Abstract - PDF
   PATHWAY WEBSITE

2005

1. Pathway information for systems biology
   Cary MP, Bader GD, Sander C
   FEBS Lett 2005 Mar 21;579(8):1815-20
   PubMed Abstract - PDF
   PATHWAY REVIEW

2004

1. Global Mapping of the Yeast Genetic Interaction Network
   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, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C
   Science 2004 Feb 6;303(5659):808-813
   PubMed Abstract - PDF
   Science Perspective PDF
   GENETIC INTERACTION NETWORK ANALYSIS
   
   

2. The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data
   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, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R
   Nature Biotechnology 2004 Feb;22(2):177-83
   PubMed Abstract - PDF
   DATA STANDARD

2003

1. Playing tag with the yeast proteome
   Andrews BJ, Bader GD, Boone C
   Nature Biotechnology Nov;21(11):1297-1299
   PubMed Abstract - PDF
   REVIEW
   
   

2. Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell
   Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C
   Trends in Cell Biology Jul, 2003 13(7):344-56
   PubMed Abstract - PDF
   REVIEW
   
   

3. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
   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
   BMC Bioinformatics Mar 27, 2003 4(1):11
   PubMed Abstract - PDF
   TEXT MINING SOFTWARE
   
   

4. Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
   Sidhu SS, Bader GD, Boone C
   Current Opinion in Chemical Biology 2003 Feb;7(1):97-102
   PubMed Abstract - PDF
   REVIEW
   
   

5. An automated method for finding molecular complexes in large protein interaction networks
   Bader GD, Hogue CWV
   BMC Bioinformatics 2003 Jan 13;4(1):2
   PubMed Abstract - PDF
   ALGORITHM
   
   

6. BIND-The Biomolecular Interaction Network Database
   Bader GD, Betel D, Hogue CWV
   Nucleic Acids Research Jan 1, 2003 31(1):248-250
   PubMed Abstract - PDF
   INTERACTION DATABASE

2002

1. SeqHound: biological sequence and structure database as a platform for bioinformatics research
   Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW
   BMC Bioinformatics 2002, 3:32 (25 October 2002)
   PubMed Abstract - PDF
   PROTEIN DATABASE
   
   

2. Analyzing yeast protein–protein interaction data obtained from different sources
   Bader GD, Hogue CW
   Nature Biotechnology 2002 Oct;20(10):991-997
   PubMed Abstract - PDF
   META-ANALYSIS
   
   

3. A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules
   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, Cesareni G
   Science 2002 Jan 11;295(5553):321-324
   PubMed Abstract - PDF
   Science Perspective PDF
   PROTEIN INTERACTION PREDICTION
   
   

4. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
   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, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M
   Nature 2002 Jan 10;415(6868): 180-183
   PubMed Abstract - PDF
   Nature News and Views PDF
   PROTEIN INTERACTION NETWORK ANALYSIS

2001

1. Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
   Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C
   Science 2001 Dec 14;294(5550):2364-8
   PubMed Abstract - PDF
   GENETIC INTERACTION NETWORK ANALYSIS
   
   

2. BIND - The Biomolecular Interaction Network Database
   Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW
   Nucleic Acids Research Jan 1, 2001 29(1):242-245
   PubMed Abstract - PDF
   INTERACTION DATABASE

2000

1. BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways
   Bader GD, Hogue CW
   Bioinformatics 2000 May;16(5):465-77
   PubMed Abstract - PDF
   INTERACTION DATABASE

Preprints

2022

1. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
   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, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS
   bioRxiv Preprint. 2022 Oct 28
   PubMed Abstract - PDF
   COVID-19
   
   

Textbook Chapters

2020

1. Biological Networks and Pathways
   Bader GD.
   in Bioinformatics 4th Eds. Andreas D. Baxevanis, Gary D. Bader, and David Wishart. John Wiley and Sons, New Jersey
   NETWORK ANALYSIS
   

2018

1. Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data
   Goebels F., Hu L., Bader G., Emili A.
   Methods Mol Bio 2018;1764:391-399 - PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE

2014

1. Biological network exploration with Cytoscape 3
   Su G, Morris JH, Demchak B, Bader GD
   Curr Protoc Bioinformatics 2014 Sep 8;47:8.13.1-8.13.24 - PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE

2011

1. Displaying chemical information on a biological network using cytoscape
   Wallace IM, Bader GD, Giaever G, Nislow C
   Methods Mol Biol 2011;781:363-76 - PubMed Abstract - PDF Supplemental Website
   NETWORK ANALYSIS SOFTWARE
   
   

2. Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
   Merico D, Isserlin R, Bader GD
   Methods Mol Biol 2011;781:257-77 - PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE

2008

1. Exploring Biological Networks with Cytoscape Software
   Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader
   Current Protocols in Bioinformatics - PubMed Abstract - PDF
   John Wiley & Sons, Inc.
   NETWORK ANALYSIS SOFTWARE

2006

1. BioPAX - Biological Pathway Data Exchange Format
   Gary D. Bader, Michael Cary, Chris Sander
   Encyclopedia of Genomics, Proteomics and Bioinformatics
   Humana Press, New Jersey
   DATA STANDARD

2005

1. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
   Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander
   Am Assoc Cancer Res Educ Book 2005: 12-16
   NETWORK ANALYSIS SOFTWARE
   
   

2. Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes
   Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone
   in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition
   Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA
   GENETIC INTERACTION NETWORK ANALYSIS

2004

1. Interaction Databases, in Genomics and Bioinformatics, 2nd Edition
   Gary D. Bader, Christopher W.V. Hogue
   in Volume 5B of the Series: Biotechnology, 2nd Edition
   Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany
   INTERACTION DATABASE
   
   

2. Intermolecular Interactions and Biological Pathways
   Gary D. Bader, Anton J. Enright
   in Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey
   INTERACTION DATABASE
   
   

3. Computational Prediction of Protein-Protein Interactions
   Anton J. Enright, Lucy Skrabanek, Gary D. Bader
   in The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)
   PROTEIN INTERACTION PREDICTION

2003

1. Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions
   Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone
   in Handbook of Cell Signaling
   Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)
   PDF
   PROTEIN INTERACTION PREDICTION

2002

1. Interaction Databases
   Gary D. Bader, Christopher W.V. Hogue
   Chapter 18, in Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)
   Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.
   Wiley-VCH, Germany
   INTERACTION DATABASE

Theses

1. 2019 Brian Law - Protein-Protein Interaction Network Alignment and Evolution - PDF, University of Toronto, Department of Computer Science
   
   

2. 2018 Shobhit Jain - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Computer Science
   
   

3. 2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - PDF, University of Toronto, Department of Computer Science
   
   

4. 2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Molecular Genetics
   
   

5. 2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - PDF, University of Toronto, Department of Molecular Genetics
   
   

6. 2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - PDF, University of Toronto, Department of Molecular Genetics
   
   

7. 2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - PDF, University of Toronto, Department of Molecular Genetics
   
   

8. 2011 Xiaojian Shao - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - PDF (in Mandarin), China Agricultural University and the University of Toronto