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Peer-reviewed Articles

2024

  1. Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas
    Boccacino JM, Dos Santos Peixoto R, Fernandes CFL, Cangiano G, Sola PR, Coelho BP, Prado MB, Melo-Escobar MI, de Sousa BP, Ayyadhury S, Bader GD, Shinjo SMO, Marie SKN, da Rocha EL, Lopes MH
    BMC Cancer. 2024 Feb 13;24(1):199
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

  2. Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver
    Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S
    J Hepatol. 2024 Jan 4:S0168-8278(24)00003-5
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

2023

  1. Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms
    McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J
    bioRxiv [Preprint]. 2023 Dec 23,2023
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

  2. Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning
    Xie R, Pang K, Chung SW, Perciani C, MacParland S, Wang B, Bader GD
    Proceedings of the Thirty-seventh Conference on Neural Information Processing Systems
    arXiv -PDF
    Poster
    SPATIAL TRANSCRIPTOMICS

  3. Adversarial training improves model interpretability in single-cell RNA-seq analysis
    Sadria M, Layton A, Bader GD
    Bioinform Adv. 2023 Nov 23;3(1)
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

  4. Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval
    Giorgi J, Soldaini L, Wang B, Bader G, Lo K, Wang L, and Cohan A
    Findings of the Association for Computational Linguistics: EMNLP Dec 2023, pages 8177–8199
    arXiv. 2022 Dec 20
    PDF
    NATURAL LANGUAGE PROCESSING

  5. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity
    Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD
    iScience. 2023 Oct 14;26(11):108213
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

  6. Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution
    Yammine S, Burns I, Gosio J, Peluso A, Merritt D, Innes B, Coles B, Yan WR, Bader GD, Morshead C, van der Kooy D
    Stem Cells Dev. 2023 Oct;32(19-20):606-621
    PubMed Abstract - PDF
    SINGLE CELL GENOMICS

  7. Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer
    Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E
    Nat Commun. 2023 Jul 18;14(1):4313
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  8. Robust segregation of donor and recipient cells from single-cell RNA-sequencing of transplant samples
    Wilson GW, Duong A, Moshkelgosha S, Bader G, Keshavjee S, Martinu T, Juvet SC, Yeung JC
    Front. Transplant., 12 June 2023 Volume 2 - 2023
    PDF
    SINGLE CELL GENOMICS

  9. MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition
    Xie R, Pang K, Bader GD, Wang B
    Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2023, pp. 3292-3301
    PDF
    COMPUTER VISION

  10. 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

  11. 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

  12. 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

  13. 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
    https://www.biorxiv.org/content/10.1101/440032v1
    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
    https://www.biorxiv.org/content/10.1101/084418v4
    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
    https://www.biorxiv.org/content/early/2017/12/12/232835
    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
    https://arxiv.org/abs/1810.05192-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
    https://www.biorxiv.org/content/early/2018/02/12/262790

  11. Patient Similarity Networks for Precision Medicine
    Pai S, Bader GD
    J Mol Biol. 2018 May 31
    PubMed Abstract -PDF
    https://www.biorxiv.org/content/early/2018/05/25/084418
    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
    https://www.biorxiv.org/content/early/2017/01/05/046219
    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

2024

  1. Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state
    Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM
    Preprint 2024 Feb 6
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS, SINGLE CELL GENOMICS

2023

  1. Cell networks in the mouse liver during partial hepatectomy
    Li B, Rodrigo-Torres D, Pelz C, Innes B, Canaday P, Chai S, Zandstra P, Bader GD, Grompe M
    bioRxiv [Preprint]. 2023 Jul
    PubMed Abstract - PDF

  2. Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing
    Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sakar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J
    ArXiv [Preprint]. 2023 May 24
    PubMed Abstract - PDF

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. 2023 Brendan Innes - Intercellular Signaling Networks of a Tissue from Single-Cell Transcriptomics - PDF, University of Toronto, Department of Molecular Genetics

  2. 2019 Brian Law - Protein-Protein Interaction Network Alignment and Evolution - PDF, University of Toronto, Department of Computer Science

  3. 2018 Shobhit Jain - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Computer Science

  4. 2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - PDF, University of Toronto, Department of Computer Science

  5. 2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Molecular Genetics

  6. 2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - PDF, University of Toronto, Department of Molecular Genetics

  7. 2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - PDF, University of Toronto, Department of Molecular Genetics

  8. 2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - PDF, University of Toronto, Department of Molecular Genetics

  9. 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

Publications (last edited 2024-03-05 13:55:45 by RuthIsserlin)

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