CGEP Progress

Publications

2013

  • Ponzielli R., Tu W.B., Jurisica I., Penn L.Z., Identifying myc interactors. Methods Mol Biol. 1012:51-64. 2013.
  • Norel, R., Bilal, E., Conrad-Chemineau, N., Bonneau, R., de la Fuente, A., Jurisica, I., Marbach, D., Meyer, P., Rice, J. J., Tuller, T. Stolovitzky, G. sbv IMPROVER Diagnostics Signature Challenge. Scoring strategies, Systems Biomedicine, 1(4):1.9, 2013.
  • Cirilo, P. D. R., Marchi, F. A., Filho, M. C. B., Rocha, R. M., Domingues, M. A. C., Jurisica, I., Pontes, A., Rogatto, S. R. An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas, PLoS One, (3):e57901, 2013.
  • Vafaee, F., Rosu, D., Broackes-Carter, F. and Jurisica, I. Novel semantic similarity measure improves an integrative approach to predicting gene functional associations, BMC Sys Biol, 7:22, 2013.
  • Goswami, R. S., Atenafu, E. G., Xuan, Y., Waldron, L., Pintor dos Reis, P., Sun, T., Datti, A., Xu, W., Kuruvilla, J., Good, D. J., Lai, R., Church, A. J., Lam, W., Baetz, T., LeBrun, D. P., Sehn, L. H., Farinha, P., Jurisica, I., Bailey, D. J., Gascoyne, R. D., Crump, M., and Kamel-Reid, S. A microRNA signature obtained from the comparison of aggressive to indolent non-Hodgkin lymphomas can be used in the prognosis of mantle cell lymphoma, J Clin Oncol, 31(23):2903-11, 2013.
  • Berger T, Ueda T, Arpaia E, Chio II, Shirdel EA, Jurisica I, Hamada K, You-Ten A, Haight J, Wakeham A, Cheung CC, Mak TW. Flotillin-2 deficiency leads to reduced lung metastases in a mouse breast cancer model. Oncogene, 32(41):4989-94, 2013. doi: 10.1038/onc.2012.499.
  • Pastrello, C., Otasek, D., Fortney, K., Agapito, G., Cannataro, M., Shirdel, E., Jurisica, I. Visual data mining of biological networks: one size does not fit all, PLoS Comp Biol, 9(1): e1002833. doi:10.1371/journal.pcbi.1002833, 2013.
  • Fortney, K., Xie, W., Kotlyar, M., Griesman, J., Kotseruba, J., Jurisica, I. NetwoRx: Connecting drugs to networks and phenotypes in S. Cerevisiae, Nucl Acids Res, 41(D1): D720-7, 2013.
  • Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q. Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med. 2013 Mar 28;5(3):29

2012

  • Starmans MH, Pintilie M, John T, Der SD, Shepherd FA, Jurisica I, Lambin P, Tsao MS, Boutros PC. Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies, Genome Med, 4(11):84, 2012.
  • Hammerman, P. S., et al., The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489, 519.525, 2012. doi:10.1038/nature11404,
  • McKee, C.M., Xu, D., Cao, Y., Kabraji, S., Allen, D., Kearsmans, V., Beech, J., Smart, S., Hamdy, F., Ishkanian, A., Sykes, J., Pintile, M., Milosevic, M., Kwast, T. van der, Zafarana, G., Ramnarine, R., Jurisica, I., Mallof, C., Lam, W., Bristow, R.G., Muschel, R.J. Protease Nexin 1 modulates prostate adenocarcinoma by regulating the Hedgehog pathway. J Clin Invest, 122(11):4025-36, 2012. doi: 10.1172/JCI59348
  • Kotlyar, M., Fortney, F. and Jurisica, I. Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods, 57(4): 477-485, 2012.
  • Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkmann, F.S.L., Cesareni, G., Chatr-aryamontri, A., Chautard, E., Chen, C., Dumousseau, M., Eisenberg, D., Goll, J., Hancock, R.E.W., Hannick, L.I., Jurisica, I., Khadake, J., Lynn, D.J., Mahadevan, U., Perfetto, L., Raghunath, A., Ricard-Blum, S., Roechert, B., Salwinski, L., Stmpflen, V., Tyers, M., Uetz, P., Xenarios, I., Hermjakob, H. Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx), Nat Methods, 9(4): 345-350, 2012.
  • Hai, J., Zhu, C. Q., Bandarchi-Chamkhaleh, B., Wang, Y. H., Navab, R., Shepherd, F. A., Jurisica, I., Tsao, M. S., L1 Cell Adhesion Molecule promotes tumorigenicity and metastatic potential in non-small-cell lung cancer, Clin Cancer Res, 18(7):1914-1924, 2012.
  • Kotseruba, Y., Cumbaa, C. A., Jurisica, I., High.throughput protein crystallization on the World Community Grid and the GPU. J Physics: Conference Series, 341, 2012. doi:10.1088/1742-6596/341/1/012027
  • Arneson, N., Moreno, Iakovlev, J.V., Ghazani, A., Warren. K., McCready, D., Jurisica, I. and Done, S.J. Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue, ISRN Oncology, v. 2012, Article ID 710692. doi:10.5402/2012/710692.
  • Locke, J. A., Zafarana, G., Malloff, C.A., Lam, W. L., Sykes, J., Pintilie, M., Ramnarine, V.R., Jurisica, I., Guns. E. T., van der Kwast, T., Milosevic, M., Bristow, R.G. Allelic loss of the loci containing StAR is prognostic for relapse in intermediate-risk prostate cancer, Prostate, 18(1): 308-316, 2012.
  • Singh, N., Shirdel, E. A., Waldron, L., Zhang, R.-H., Jurisica, I., Comelli, E.M., The murine caecal microRNA signature depends on the presence of the endogenous microbiota, Int J Bio Sci, 8(2):171-86, 2012.
  • Singh, N., Shirdel, E. A., Waldron, L., Zhang, R.-H., Jurisica, I., Comelli, E.M., The murine caecal microRNA signature depends on the presence of the endogenous microbiota, Int J Bio Sci, 8(2):171-86, 2012.
  • Fortney, K., Morgen, E. K., Kotlyar, M., Jurisica, I. In silico drug screen in mouse liver identifies candidate calorie restriction mimetics. Rejuvenation Res, 15(2): 148-152, 2012.
  • Locke, J.A., Zafarana, G., Ishkanian, A.S., Milosevic, M., Thoms, J., Have, C.L., Malloff, C.A., Lam, W.L., Squire, J.A., Pintilie, M., Sykes, J., Ramnarine, V.R., Meng, A., Ahmed, O., Jurisica, I., van der Kwast, T., Bristow, R.G. NKX3.1 haploinsufficiency is prognostic for prostate cancer relapse following image-guided radiotherapy, Clinical Cancer Research, 18(1): p. 308-16, 2012.
  • Heifets, A. and Jurisica, I. SCRIPDB: A portal for easy access to syntheses, chemicals, and reactions in patents. Nucl Acid Res, 40(Database issue): D428-33, 2012.
  • Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of propagation. PLoS One. 2012;7(12):e51947. doi:10.1371/journal.pone.0051947.
  • Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol. 2012 Aug 28;6:112
  • Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in gwas. Pac Symp Biocomput. 2012:363-74.
  • Stegle O, Roth FP, Morris Q, Listgarten Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. J. Pac Symp Biocomput. 2012:323-6.
  • Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics. 2012 May;12(10):1687-96. doi: 10.1002/pmic.201100607.
  • 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. doi: 10.1021/pr301151m. Epub 2012 Dec 21
  • 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. doi: 10.1038/nmeth.2212. Epub 2012
  • 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. doi: 10.1186/1752-0509-6-112
  • 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) 1, e26; doi:10.1038/oncsis.2012.28
  • Subgroup-specific structural variation across 1,000 medulloblastoma genomes Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Statz 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
  • 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
  • Wu G, Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 2012 Dec 10;13(12):R112.
  • Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P and Stein L. (2012) Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome. Cancers. 4, 1180-1211.
  • Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, Lance RS, Gramolini AO, Troyer DA,Stein LD, Boutros PC, Medin JA, Semmes OJ, Drake RR, Kislinger T. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer.
  • Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkmann, F.S.L., Cesareni, G., Chatr-aryamontri, A., Chautard, E., Chen, C., Dumousseau, M., Eisenberg, D., Goll, J., Hancock, R.E.W., Hannick, L.I., Jurisica, I., Khadake, J., Lynn, D.J., Mahadevan, U., Perfetto, L., Raghunath, A., Ricard-Blum, S., Roechert, B., Salwinski, L., Stmpflen, V., Tyers, M., Uetz, P., Xenarios, I., Hermjakob, H.Protein Interaction Data Curation - The International Molecular ExchangeConsortium (IMEx), Nat Methods, 9(4): 345-350, 2012.
  • Hai, J., Zhu, C. Q., Bandarchi-Chamkhaleh, B., Wang, Y. H., Navab, R., Shepherd, F. A., Jurisica, I., Tsao, M. S., L1 Cell Adhesion Molecule promotes tumorigenicity and metastatic potential in non-small-cell lung cancer, Clin Cancer Res, 18(7):1914-1924, 2012.
  • Kotseruba, Y., Cumbaa, C. A., Jurisica, I., High.throughput protein crystallization on the World Community Grid and the GPU. J Physics: Conference Series, 341, 2012.doi:10.1088/1742-6596/341/1/012027
  • Arneson, N., Moreno, Iakovlev, J.V., Ghazani, A., Warren. K., McCready, D., Jurisica, I. and Done, S.J. Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue, ISRN Oncology, v. 2012, Article ID 710692. doi:10.5402/2012/710692.
  • Locke, J. A., Zafarana, G., Malloff, C.A., Lam, W. L., Sykes, J., Pintilie, M., Ramnarine, .R.,Jurisica, I., Guns. E. T., van der Kwast, T., Milosevic, M., Bristow, R.G. Allelic loss of the loci containing StAR is prognostic for relapse in intermediate-risk prostate cancer, Prostate, 18(1): 308-316, 2012.
  • Singh, N., Shirdel, E. A., Waldron, L., Zhang, R.-H., Jurisica, I., Comelli, E.M., The murine caecal microRNA signature depends on the presence of the endogenous microbiota, Int J Bio Sci, 8(2):171-86, 2012.
  • Zafarana, G., Ishkanian, A.S., Malloff, C.A., Locke, J.A., Sykes, J., Thoms, J., Lam, W.L., Squire, J.A., Yoshimoto, M., RamnarineV.R.,Jurisica, I., Milosevic, M., Pintilie, M., van der Kwast, T., Bristow, R.G. Copy number alterations of c-MYC and PTEN are prognostic factors for relapse following prostate cancer radiotherapy, Cancer, 2012, In press.
  • Fortney, K., Morgen, E. K., Kotlyar, M.,Jurisica, I.In silico drug screen in mouse liver identifies candidate calorie restriction mimetics. Rejuvenation Res, 2012.In press.
  • Locke, J.A., Zafarana, G., Ishkanian, A.S., Milosevic, M., Thoms, J., Have, C.L., Malloff, C.A., Lam, W.L., Squire, J.A., Pintilie, M., Sykes, J., Ramnarine, V.R., Meng, A., Ahmed, O., Jurisica, I., van der Kwast, T., Bristow, R.G. NKX3.1 haploinsufficiency is prognostic for prostate cancer relapse following image-guided radiotherapy, Clinical Cancer Research, 18(1): p. 308-16, 2012.
  • Heifets, A.and Jurisica, I. SCRIPDB: A portal for easy access to syntheses, chemicals, and reactions in patents. Nucl Acid Res,40(Database issue): D428-33, 2012.
  • Heifets,A.,Jurisica, I. Construction of new medicines via game proof search.26th American Association for Artificial Intelligence Conference on Artificial Intelligence (AAAI-12), AAAI Press, Menlo Park, 2012.In press.
  • Wong, S., Cercone,N., Jurisica, I. Characterizing healthy and disease states by systematically comparing differential correlation networks in lung. Advances in Health Informatics Conference, 2012.In press.
  • Otasek, D., Pastrello, C., Jurisica, I. Scalable, integrative analysis and visualization of protein interactions, Protein-Protein Interactions - Computational and Experimental Tools, INTECH, 2012. In press.
  • King, A. D., 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, Vol. 804, 297-312, 2012.
  • 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, Vol. 804, 219-244, 2012
  • Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5832-7. Epub 2012 Mar 28. PubMed PMID: 22460789; PubMed Central PMCID: PMC3326451.
  • Tan CS, Bader GD. Phosphorylation sites of higher stoichiometry are more conserved. Nat Methods. 2012 Mar 27;9(4):317. doi: 10.1038/nmeth.1941. PubMed PMID: 22453906.
  • Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE. Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry. PLoS Genet. 2012 Mar;8(3):e1002562. Epub 2012 Mar 15. PubMed PMID: 22438817; PubMed Central PMCID: PMC3305360.
  • Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Res. 2012 Mar 1;40(6):e47. Epub 2011 Dec 30. PubMed PMID: 22210894; PubMed Central PMCID: PMC3315295.
  • Siddiqui NU, Li X, Luo H, Karaiskakis A, Hou H, Kislinger T, Westwood JT, Morris Q, Lipshitz HD. Genome-wide analysis of the maternal-to-zygotic transitio in Drosophila primordial germ cells. Genome Biol. 2012 Feb 20;13(2):R11. [Epub ahead of print] PubMed PMID: 22348290.
  • Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in gwas. Pac Symp Biocomput. 2012:363-74. PubMed PMID: 22174291.
  • Stegle O, Roth FP, Morris Q, Listgarten J. Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. Pac Symp Biocomput. 2012:323-6. PubMed PMID: 22174287.
  • Wu G, Stein L. Network Module Based Approaches in Cancer Data Analysis. Invited Chapter. Statistical Diagnostics of Cancer: Analyzing High Dimensional Genetics and Genomics Data, Wiley-Blackwell, (Frank Emmert-Streib and Matthias Dehmer, co-eds.), 2012.
  • Tran B, Dancey JE, Kamel-Reid S, McPherson JD, Bedard PL, Brown AM, Zhang T, Shaw P, Onetto N, Stein L, Hudson TJ, Neel BG, Siu LL. Cancer Genomics: Technology, Discovery, and Translation. J Clin Oncol. 2012 Jan 23.
  • Sprowl JA, Reed K, Armstrong S, Lanner C, Guo B, Kalatskaya I, Stein L, Hembruff SL, Parissenti AM. Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. Breast Cancer Res. 2012 Jan 6;14(1):R2.
  • Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G. modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012 Jan;40 (Database issue):D1082-8.
  • Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW. WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 2012 Jan 1;40(D1):D735-D741.

2011

  • Waldron, L., Pintilie, M., Tsao, M.S., Shepherd, F.A., Huttenhower, C., and Jurisica, I. Optimized application of penalized regression methods to diverse genomic data, Bioinformatics, 27(24): 3399-3406, 2011.
  • Hakem, A., Bohgaki, M., Lemmers, B., Tai, E., Salmena, L., Matysiak-Zablocki, E., Lpez Bhr, W. I., 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. Role of Pirh2 in mediating the regulation of p53 and c-Myc, PLoS Genetics, 7(11): e1002360, 2011.
  • Reis, P.P., Waldron, L., Perez-Ordonez, B., Pintilie, M., Galloni, N., Xuan, Y., Cervigne, N.K., Warner, G.C., Makitie, A.A., Simpson, C., GoldStein, D., Brown, D., Gilbert, R., Gullane, P., Irish, J., Jurisica, I., and 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, K. H., Greenblatt, E., Jurisica, I., Casper, R.F., Sun, Y., Jurisicova, A. Automated microinjection of recombinant BCL-X into mouse zygotes enhances embryo development, PLoS One, 6(7): e21687, 2011.
  • Yan, R., Boutros, P.C., Jurisica, I. A tree-based approach for motif discovery and sequence classification, Bioinformatics, 27(15): 2054-61, 2011.
  • Djebbari, A., Ali, M., Otasek, D., Kotlyar. M., Fortney, K., Wong, S., Hrvojic, A. and Jurisica, I. NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs. Internet Mathematics, 7(4): 314-347, 2011.
  • Eppert, K., Takenaka, K., Lechman, E.R., Waldron, L., Nilsson, B., van Galen, P., Metzeler, K., Poeppl, A., Ling, V., Beyene, J., Canty, A.J., Danska, J.S., Bohlander, S.K., Buske, C., Minden, M.D., Golub, T.R., Jurisica, I., Ebert, B.L., Dick, J.E. Stem cell gene expression programs influence clinical outcome in human leukemia, Nat Medicine, 17(9): 1086-1093, 2011.
  • Notta, F., Doulatov, S., Laurenti, E., Poeppl, A., Jurisica, I. and Dick, J.E. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment, Science, 333, 218-221, 2011.
  • Reis, P.P., Waldron, L., Goswami, R.S., Xu, W., Xuan, Y., Ordonez, B.P., Patrick Gullane, P., Irish, J., Jurisica, I. and Kamel-Reid mRNA, S. mRNA transcript quantification in archival samples using multiplexed, color-coded probes, BMC Biotechnology, 11:46, 2011.
  • Navab R., Strumpf D., Bandarchi B., Zhu C.Q., Pintilie M., Ramnarine V.R., Ibrahimov E., Radulovich N., Leung L., Barczyk M., Panchal, D., To, C., Yun, J. J., Der, S., Shepherd, F. A., Jurisica, I., Tsao, M. S. Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer. PNAS, 108(17):7160-7165, 2011.
  • Elschenbroich, S., V. Ignatchenko, B. Clarke, S.E. Kalloger, P.C. Boutros, A.O. Gramolini, P. Shaw, I. Jurisica, and T. Kislinger, In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res, 10(5): p. 2286-99, 2011.
  • Fortney, K. and Jurisica, I. Integrative computational biology for cancer research. Human Genetics, 130(4): 465-481, 2011.
  • Chang, Q., Jurisica, I., Do, T., Hedley, D.W. 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, E.A., Xie, W., Mak, T.W., Jurisica, I. NAViGaTing the micronome: Using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS ONE, 6(2): e17429, 2011.
  • Osei-Kumah, A., R. Smith, I. Jurisica, I. Caniggia, and V.L. Clifton, Sex-specific differences in placental global gene expression in pregnancies complicated by asthma. Placenta, 32(8): 570-8, 2011.
  • Arshadi, N., Jurisica, I., Ensembles of Case-Based Reasoning Classifiers in High-Dimentional DIological Domains, WIRE.s Data Mining and Knowledge Discovery, Wiley-Blackwell, 1(2):164-171, 2011.
  • Wei, Y.; Tong, J.; Taylor, P.; Strumpf, D.; Ignatchenko, V.; Pham, N. A.; Yanagawa, N.; Liu, G.; Jurisica, I.; Shepherd, F. A.; Tsao, M. S.; Kislinger, T.; Moran, M. F., Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures. J Proteome Res, 10(1):161-174, 2011.
  • Yakhini, Z and Jurisica, I. Cancer computational biology, BMC Bioinf. 12(1): 120, 2011.
  • Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics. 2011 Nov 15;27(22):3166-72. Epub 2011 Sep 28. PubMed PMID: 21965819.
  • Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nat Biotechnol. 2011 Jun 7;29(6):483-4. doi: 10.1038/nbt.1892. PubMed PMID: 21654663.
  • Schimmer BP, Tsao J, Cordova M, Mostafavi S, Morris Q, Scheys JO. Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells. Mol Cell Endocrinol. 2011 Apr 10;336(1-2):85-91. Epub 2010 Nov 25. PubMed PMID: 21111771; PubMed Central PMCID PMC3057232.
  • Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res. 2011 Feb;21(2):342-8. Epub 2010 Dec 22. PubMed PMID: 21177968; PubMed Central PMCID: PMC3032936.
  • Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods Mol Biol. 2011;781:399-414. PubMed PMID: 21877293.
  • Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 2011 Jan;39(Database issue):D301-8 Epub 2010 Oct 29. PubMed PMID: 21036867; PubMed Central PMCID: PMC3013675.
  • Radfar MH, Wong W, Morris Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One 2011;6(6):e19312. Epub 2011 Jun 9. PubMed PMID: 21694770; PubMed Central PMCID: PMC3111417.
  • Le Novare N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2011 Nov 30;5(2):230-42. PubMed PMID: 22180826; PubMed Central PMCID: PMC3235518.
  • Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011 Nov 9;12:436. PubMed PMID: 22070249; PubMed Central PMCID: PMC3262844.
  • Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MK, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Compound prioritization methods increase rates of chemical probe discovery in model organisms. Chem Biol. 2011 Oct 28;18(10):1273-83. PubMed PMID: 22035796.
  • 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, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated signaling maps. Database (Oxford). 2011 Sep 29;2011:bar032. Print 2011. PubMed PMID: 21959865; PubMed Central PMCID: PMC3263596.
  • Wallace IM, Bader GD, Giaever G, Nislow C. Displaying chemical information on a biological network using Cytoscape. Methods Mol Biol. 2011;781:363-76. PubMed PMID: 21877291.
  • Merico D, Isserlin R, Bader GD. Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol. 2011;781:257-77. PubMed PMID: 21877285.
  • Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DT, Northcott PA, Garzia L, Bertrand KC, Wittmann A, 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. Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell. 2011 Aug 16;20(2):143-57. PubMed PMID: 21840481.
  • Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DT, Northcott PA, Garzia L, Bertrand KC, Wittmann A, 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. Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell. 2011 Aug 16;20(2):143-57. PubMed PMID: 21840481.
  • 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. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. PubMed PMID: 21716279; PubMed Central PMCID: PMC3246345.
  • Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM. The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol. 2011 Apr 26;7:484. PubMed PMID: 21525870; PubMed Central PMCID: PMC3097085.
  • Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med. 2011 Apr 7;6:7. PubMed PMID: 21473782; PubMed Central PMCID: PMC3083346.
  • Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD. Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol. 2011 Feb;7(2):e1001092. Epub 2011 Feb 24. PubMed PMID: 21390331; PubMed Central PMCID: PMC3044758.
  • Bellay J, Han S, Michaut M, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM. Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol. 2011;12(2):R14. Epub 2011 Feb 16. PubMed PMID: 21324131; PubMed Central PMCID: PMC3188796.
  • Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH. Too many roads not taken. Nature. 2011 Feb 10;470(7333):163-5. PubMed PMID: 21307913.
  • Isserlin R, El-Badrawi RA, Bader GD. The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford). 2011 Jan 12;2011:baq037. Print 2011. PubMed PMID: 21233089; PubMed Central PMCID: PMC3021793.
  • Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD. A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics. 2011 Feb 1;27(3):383-90. Epub 2010 Dec 2. PubMed PMID: 21127034; PubMed Central PMCID: PMC3031032.
  • 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. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659.
  • Stein LD. An introduction to the informatics of "next-generation" sequencing. Curr Protoc Bioinformatics. 2011 Dec; Chapter 11:Unit 11.1.
  • Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart. Database (Oxford) Oct 19; 2011.
  • Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE, Coin LJ, Deng G, Gieger C, Heard-Costa NL, Hottenga JJ, Kühnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Mateo Leach I, O'Reilly PF, Peden JF, Rahmioglu N, Soininen P, Speliotes EK, Yuan X, Thorleifsson G, Alizadeh BZ, Atwood LD, Borecki IB, Brown MJ, Charoen P, Cucca F, Das D, de Geus EJ, Dixon AL, Döring A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen AL, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppönen E, Janssen HL, Johnson T, Kangas AJ, Kema IP, Kühn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin JP, Loos RJ, Martin NG, Moffatt MF, Montgomery GW, Munroe PB, Musunuru K, Nakamura Y, O'Donnell CJ, Olafsson I, Penninx BW, Pouta A, Prins BP, Prokopenko I, Puls R, Ruokonen A, Savolainen MJ, Schlessinger D, Schouten JN, Seedorf U, Sen-Chowdhry S, Siminovitch KA, Smit JH, Spector TD, Tan W, Teslovich TM, Tukiainen T, Uitterlinden AG, Van der Klauw MM, Vasan RS, Wallace C, Wallaschofski H, Wichmann HE, Willemsen G, Würtz P, Xu C, Yerges-Armstrong LM; Alcohol Genome-wide Association (AlcGen) Consortium; Diabetes Genetics Replication and Meta-analyses (DIAGRAM+) Study; Genetic Investigation of Anthropometric Traits (GIANT) Consortium; Global Lipids Genetics Consortium; Genetics of Liver Disease (GOLD) Consortium; International Consortium for Blood Pressure (ICBP-GWAS); Meta-analyses of Glucose and Insulin-Related Traits Consortium (MAGIC), Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietiläinen KH, Schumann G, Snieder H, Sternberg MJ, Stolk RP, Thomas HC, ThorSteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JC, Wolffenbuttel BH, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, ölzke H, Schadt EE, Scott J, Järvelin MR, Elliott P, Kooner JS. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet. 2011 Oct 16;43(11):1131-8.
  • Strawbridge RJ, Dupuis J, Prokopenko I, Barker A, Ahlqvist E, Rybin D, Petrie JR, Travers ME, Bouatia-Naji N, Dimas AS, Nica A, Wheeler E, Chen H, Voight BF, Taneera J, Kanoni S, Peden JF, Turrini F, Gustafsson S, Zabena C, Almgren P, Barker DJ, Barnes D, Dennison EM, Eriksson JG, Eriksson P, Eury E, Folkersen L, Fox CS, Frayling TM, Goel A, Gu HF, Horikoshi M, Isomaa B, Jackson AU, Jameson KA, Kajantie E, Kerr-Conte J, Kuulasmaa T, Kuusisto J, Loos RJ, Luan J, Makrilakis K, Manning AK, Martínez-Larrad MT, Narisu N, Nastase Mannila M, Ohrvik J, Osmond C, Pascoe L, Payne F, Sayer AA, Sennblad B, Silveira A, Stancáková A, Stirrups K, Swift AJ, Syvänen AC, Tuomi T, van 't Hooft FM, Walker M, Weedon MN, Xie W, Zethelius B; DIAGRAM Consortium; GIANT Consortium; MuTHER Consortium; CARDIoGRAM Consortium; C4D Consortium, Ongen H, Mälarstig A, Hopewell JC, Saleheen D, Chambers J, Parish S, Danesh J, Kooner J, Ostenson CG, Lind L, Cooper CC, Serrano-Ríos M, Ferrannini E, Forsen TJ, Clarke R, Franzosi MG, Seedorf U, Watkins H, Froguel P, Johnson P, Deloukas P, Collins FS, Laakso M, Dermitzakis ET, Boehnke M, McCarthy MI, Wareham NJ, Groop L, Pattou F, Gloyn AL, Dedoussis GV, Lyssenko V, Meigs JB, Barroso I, Watanabe RM, Ingelsson E, Langenberg C, Hamsten A, Florez JC. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes. 2011 Oct;60(10):2624-34.
  • Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG, Urbach A, Thornton JE, Triboulet R, Gregory RI; DIAGRAM Consortium; MAGIC Investigators, Altshuler D, Daley GQ. The Lin28/let-7 axis regulates glucose metabolism. Cell. 2011 Sep 30;147(1):81-94.
  • Haw R, Hermjakob H, D'Eustachio P, Stein L. Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics. 2011 Sep; 11(18):3598-613.
  • Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, Smith R, Zha Z, Lyne R, Carr A, Lloyd P, Kephart E, McKay SJ, Micklem G, Stein LD, Lewis SE. The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database (Oxford). 2011.
  • Ismail A, Bandla S, Reveiller M, Toia L, Zhou Z, Gooding WE, Kalatskaya I, Stein L, D'Souza M, Litle VR, Peters JH, Pennathur A, Luketich JD, Godfrey TE. Early G~B~A cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma. Clin Cancer Res. 2011 Jul 1;17(13):4513-22
  • Feng X, Grossman R, Stein L. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics. 2011 May 9;12:139.
  • Sawey ET, Chanrion M, Cai C, Wu G, Zhang J, Zender L, Zhao A, Busuttil RW, Yee H, Stein L, French DM, Finn RS, Lowe SW, Powers S. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell 2011 Mar 8;19(3): 347-58.
  • 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.

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, Novre 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, Pl 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.
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