CGEP Progress

Publications

2011

  • Heifets A and Jurisica I. SCRIPDB: A portal for easy access to syntheses, chemicals, and reactions in patents. Nucl Acid Res, In press.
  • Fortney K, Morgen EK, Kotlyar M, Jurisica I. In silico drug screen in mouse liver identifies candidate calorie restriction mimetics. Rejuvenation Res, 2011. In press.
  • Hakem A, Bohgaki M, Lemmers B, Tai E, Salmena L, Matysiak-Zablocki E, Lpez Bhr WI, Karaskova J, Boutros P, Sheng Y, Arrowsmith C, Chesi M, Bergsagel L, Perez-Ordonez B, Squire J, Jurisica I, Penn L, Sanchez O, Benchimol S, Hakem R. PIRH2, a novel tumour suppressor that negatively regulates c-Myc protein stability, PLoS Genetics, 2011. In press.
  • Reis PP, Waldron L, Perez-Ordonez B, Pintilie M, Galloni N, Xuan Y, Cervigne NK, Warner GC, Makitie AA, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S. A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. BMC Cancer, 11:437, 2011.
  • Liu X, Fernandes R, Gertsenstein M, Perumalsamy A, Lai I, Chi M, Moley KH, Greenblatt E, Jurisica I, Casper RF, Sun Y, Jurisicova A. Automated microinjection of recombinant BCL-X into mouse zygotes enhances embryo development, PLoS One, 6(7): e21687, 2011.
  • Cumbaa CA, Kotseruba Y, Jurisica I. High.throughput protein crystallization on the World Community Grid and the GPU. J Physics: Conference Series, High Performance Computing Symposium (HPCS 2011: HPC in Medical Science), 2011. In press.
  • Eppert K, Takenaka K, Lechman ER, Waldron L, Nilsson B, van Galen P, Metzeler K, Poeppl A, Ling V, Beyene J, Canty AJ, Danska JS, Bohlander SK, Buske C, Minden MD, Golub TR, Jurisica I, Ebert BL, Dick JE. Stem Cell Gene Expression Programs Influence Clinical Outcome in Human Leukemia, Nat Medicine, 2011. Advanced online publication, August 28: 10.1038/nm.2415.
  • Notta F, Doulatov S, Laurenti E, Poeppl A, Jurisica I, Dick JE. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment, Science, 333, 218.221, 2011.
  • Djebbari A, Ali M, Otasek D, Kotlyar M, Fortney K, Wong S, Hrvojic A, Jurisica I. NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs. Internet Mathematics, 7(4), 2011. In press.
  • Yan R, Boutros PC, Jurisica I. A tree-based approach for motif discovery and sequence classification, Bioinformatics, 27(15): 2054-61, 2011.
  • Osei-Kumah A, Smith R, Jurisica I, Caniggia I, Clifton VL. Sex-specific differences in placental global gene expression in pregnancies complicated by asthma. Placenta, 32(8): 570-8, 2011.
  • Reis PP, Waldron L, Goswami RS, Xu W, Xuan Y, Perez-Ordonez B, Gullane P, Irish J, Jurisica I, Kamel-Reid S. mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnology, 11:46, 2011.
  • Yakhini Z and Jurisica I. Cancer computational biology, BMC Bioinf. 12(1): 120, 2011. (editorial)
  • Fortney K and Jurisica I. Integrative computational biology for cancer research. Human Genetics, 130(4): 465-481, 2011. (peer-reviewed review)
  • Navab R, Strumpf D, Bandarchi B, Zhu CQ, Pintilie M, Ramnarine VR, Ibrahimov E, Radulovich N, Leung L, Barczyk M, Panchal D, To C, Yun JJ, Der S, Shepherd FA, Jurisica I, Tsao MS. Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer. PNAS, 108(17):7160-7165, 2011.
  • Elschenbroich S, Ignatchenko V, Clarke B, Kalloger S, Boutros P, Gramolini A, Shaw P, Jurisica I, Kislinger T. In-depth proteomics of ovarian cancer ascites: Combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res, 2011. In press.
  • Chang Q, Jurisica I, Do T, Hedley DW. Hypoxia predicts for aggressive growth and spontaneous metastasis formation from othotopically-grown primary xenografts of human pancreatic cancer. Cancer Res, 71(8):3110-3120, 2011.
  • Shirdel EA, Xie W, Mak TW, Jurisica I. NAViGaTing the micronome: Using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS ONE, 6(2): e17429, 2011.
  • Arshadi N, Jurisica I. Ensembles of Case-Based Reasoning Classifiers in High-Dimensional Biological Domains. WIRE.s Data Mining and Knowledge Discovery, Wiley-Blackwell, 1(2):164-171, 2011. DOI:10.1002/widm.22
  • D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol. 2011;694:49-61.
  • Gillespie M, Shamovsky V, D'Eustachio P. Human and chicken TLR pathways: manual curation and computer-based orthology analysis. Mammalian Genome. 2011 Feb;22(1-2):130-8.
  • Dall'olio GM, Jassal B, Montanucci L, Gagneux P, Bertranpetit J, Laayouni H. The annotation of the Asparagine N-linked Glycosylation pathway in the Reactome Database. Glycobiology. 2011 Jan 2. [Epub ahead of print].
  • Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7.
  • Wei Y, Tong J, Taylor P, Strumpf D, Ignatchenko V, Pham NA, Yanagawa N, Liu G, Jurisica I, Shepherd FA, Tsao MS, Kislinger T, Moran MF. Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures. J Proteome Res, 10(1):161-174, 2011.
  • Geraci J, Liu G, Jurisica I. Algorithms for systematic identification of small sub-graphs. Bacterial Molecular Networks, Series: Methods in Molecular Biology, Editors: Jacques van Helden, Ariane Toussaint, Denis Thieffry, Humana Press, 2011. In press.
  • King AD, Przulj N, Jurisica I. Protein Complex Prediction with RNSC. Bacterial Molecular Networks, Series: Methods in Molecular Biology, Editors: Jacques van Helden, Ariane Toussaint, Denis Thieffry, Humana Press, 2011. In Press.
  • Arshadi N, Jurisica I. Ensembles of Case-Based Reasoning Classifiers in High-Dimensional Biological Domains. WIRE.s Data Mining and Knowledge Discovery, Wiley-Blackwell, 2011. In press.
  • Shirdel EA, Xie W, Mak TW, Jurisica I. NAViGaTing the micronome: Using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS ONE. In press.
  • Isserlin R, El-Badrawi RA, Bader GD. The Biomolecular Interaction Network Database in PSI-MI 2.5. Database 2011; doi: 10.1093/database/baq037.

2010

  • Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD. A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence. Bioinformatics 2010 Dec 2.
  • Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation. PLoS One. 2010 Nov 15;5(11):e13984.
  • Jain S, Bader GD. An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. BMC Bioinformatics. 2010 Nov 15;11(1):562.
  • 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. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods. 2010 Nov 14
  • Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2010 Nov 10.
  • Hui S, Bader GD. Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinformatics. 2010 Oct 12;11(1):50.
  • Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD. GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop. Bioinformatics. 2010 Oct 5.
  • Wei Y, Tong J, Taylor P, Strumpf D, Ignatchenko V, Pham NA, Yanagawa N, Liu G, Jurisica I, Shepherd FA, Tsao MS, Kislinger T, Moran MF. Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures. J Proteome Res, 2010.
  • Viau C, McGuffin MJ, Chiricota Y, and Jurisica I. The FlowVizMenu and parallel scatterplot matrix: Hybrid multidimensional visualizations for network exploration. IEEE Trans Vis Comput Graph, 16(6):1100-8, 2010.
  • Zhu CQ, Strumpf D, Li CY, Li Q, Liu N, Der S, Shepherd FA, Tsao MS, and Jurisica I. Prognostic gene expression signature for squamous cell carcinoma of lung. Clin Cancer Res, 16(20):5038-47, 2010.
  • Reis PR, Tomenson M, Cervigne NK, Machado J, Jurisica I, Pintilie M, Sukhai MA, Perez-Ordonez B, Grenman R, Gilbert RW, Gullane PJ, Irish JC, Kamel-Reid S. Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma. Mol Cancer, 9(1):238, 2010.
  • Boutros PC, Pintilie M, John T, Starmans MHW, Der SD, Shepherd FA, Tsao MS, Jurisica I. Re: Gene expression-based prognostic signatures in lung cancer: Ready for clinical use? J Nat Cancer Inst, 102(21): 1677-8, 2010, 2010.
  • Zhu CQ, Ding K, Strumpf D, Weir BA, Meyerson M, Pennell N, Thomas RK, Naoki K, Ladd-Acosta C, Liu N, Pintilie M, Der S, Seymour L, Jurisica I, Shepherd FA, and Tsao MS. Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer. J Clin Oncol, 28(29):4417-24, 2010.
  • Radfar M, Wong W, Morris QD. Predicting the target genes of intronic microRNAs using large-scale gene expression data. Conf Proc IEEE Eng Med Biol Soc. 2010;1:791-4.PMID: 21096111.
  • Clendening JW, Pandyra A, Boutros PC, El Ghamrasni S, Khosravi F, Trentin GA, Martirosyan A, Hakem A; Hakem R, Jurisica I, Penn LZ. Dysregulation of the mevalonate pathway promotes transformation. Proc Natl Acad Sci USA, 107(34):15051-6, 2010.
  • Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, 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, Novčre NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep;28(9):935-42.
  • Wong WW, Boutros PC, Wasylishen AR, Guckert KD, O'Brien EM, Griffiths R, Martirosyan AR, Bros C, Jurisica I, Langler RF, and Penn LZ. Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer, 10: 351, 2010. ePub: 2010/07/06.
  • Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P. (2010) The systematic annotation of the three main GPCR families in Reactome. Database:baq018.
  • Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics. 2010 Jul 23.
  • Mostafavi S, Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics. 2010 Jul 15;26(14):1759-65. Epub 2010 May 27.
  • Goswami RS, Waldron L, Machado J, Cervigne NK, Xu W, Reis PP, Bailey DJ, Jurisica I, Crump MR, and Kamel-Reid S. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples. BMC Biotechnol, 10:47, 2010. ePub: 2010/06/25.
  • Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. Jun 2. [Epub ahead of print].
  • Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11(5):R53.
  • 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. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W214-20.
  • International Cancer Genome Consortium. International network of cancer genome projects. Nature 2010 Apr 15;464(7291):993-8.
  • Clendening JW, Pandyra A, Li Z, Boutros PC, Martirosyan A, Lehner R, Jurisica I, Trudel S, and Penn LZ. Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma. Blood, 115:4787-4797, 2010. ePub: 2010/04/03.
  • Radulovich N, Pham NA, Strumpf D, Leung L, Xie W, Jurisica I, Tsao MS. Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma. Mol Cancer, 9(1): 24, 2010.
  • Fortney K, Kotlyar M and Jurisica I. Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol, 11(2): R13, 2010. [Supplementary Data]
  • Cumbaa CA and Jurisica I. Protein crystallization analysis on the World Community Grid. J Struct Funct Genomics, 11(2): 61-69, 2010.
  • Hui ABY, Lenarduzzi M, Krushel T, Waldron L, Pintilie M, Shi W, Perez-Ordonez BP, Jurisica I, O'Sullivan B, Waldron J, Gullane P, Cummings B, Liu FF. Comprehensive microRNA profiling for head & neck squamous cell carcinomas. Clin Cancer Res, 16(4): 1129-39, 2010.
  • Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, 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. The genetic landscape of a cell. Science. 2010 Jan 22;327(5964):425-31.
  • 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. NetPath: a public resource of curated signal transduction pathways. Genome Biology 2010 Jan 12;11(1):R3.
  • Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub 2009 Oct 30.
  • Niu Y, Otasek D, Jurisica I. Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics, 26(1): 111-9, 2010. Epub 2009 Oct 24. [Supplementary Data]

2009

  • Deribe YL, Wild P, Chandrashaker A, Curak J, Schmidt MHH, Kalaidzidis Y, Milutinovic N, Kratchmarova I, Buerkle L, Fetchko MJ, Schmidt P, Kittanakom S, Brown KR, Jurisica I, Blagoev B, Zerial M, Stagljar I, and Dikic I. Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6. Sci Signal, 2(102): RA84, 2009. Epub: 2009/12/24. [Supplementary Data]
  • Brown KR, Otasek D, Ali M, McGuffin M, Xie W, Devani B, Van Toch IL, Jurisica I. NAViGaTOR: Network analysis, visualization & graphing Toronto. Bioinformatics, 25(24):3327-9, 2009. epub 2009/10/20. [Supplementary Data]
  • McGuffin M and Jurisica I. Interaction techniques for selecting and manipulating subgraphs in network visualizations. IEEE Transactions on Visualization and Computer Graphics (TVCG), 15 (6): 937-944, 2009. [Honorable Mention at InfoVis'09]
  • Cervigne NK, Reis PP, Machado J, Sadikovic B, Bradley G, Galloni NN, Pintilie M, Jurisica I, Gilbert R, Gullane P, Irish J, and Kamel-Reid S. Identification of a microRNA signature associated with progression of leukoplakia to oral carcinoma. Hum Mol Genet, 18(24): 4818-29, 2009.
  • Mills GB, Jurisica I, Yarden Y, Norman JC. Genomic amplicons target vesicle recycling in breast cancer. J Clin Invest, 119, 2123-7, 2009.
  • Agarwal R, Jurisica I, Cheng KW, Mills GB. The emerging role of the RAB25 small GTPase in cancer. Traffic, 10(11): 1561-8, 2009.
  • Cox B, Kotlyar M, Evangelou A, Ignatchenko V, Ignatchenko A, Whiteley K, Jurisica I, Adamson L, Rossant J, Kislinger T. Comparative systems biology of human and mouse as a tool for modeling human placental pathology. Mol Syst Biol 5, 279, 2009.
  • Hui AB, Shi W, Boutros PC, Miller N, Pintilie M, Fyles T, McCready D, Wong D, Gerster K, Waldron L, Jurisica I, Penn LZ, Liu FF. Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab Invest 89, 597-606, 2009.
  • Savas S, Geraci J, Jurisica I, Liu G. A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research. Int J Cancer 125, 1257-65, 2009.
  • Boutros PC, Lau SK, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small cell lung cancer. PNAS, 106(8): 2824-8, 2009. [Supplementary Data]
  • Zhu CQ, Pintilie M, John T, Strumpf D, Shepherd FA, Der SD, Jurisica I, Tsao MS. Understanding Prognostic Gene Expression Signatures in Lung Cancer. Clin Lung Cancer, 10(4), 2009.
  • Dong J, Kislinger T, Jurisica I, Wigle DA. Lung cancer: Developmental networks gone awry? Cancer Biol Ther, 8(4), 2009.