The following papers and publications have used I2D or its earlier version OPHID
1. Ponzielli R., Tu W.B., Jurisica I., Penn L.Z., Identifying myc interactors. Methods Mol Biol. 1012:51-64. 2013.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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
1. 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.
2. 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,
3. 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
4. Kotlyar, M., Fortney, F. and Jurisica, I. Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods, 57(4): 477-485, 2012.
5. 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., St�mpflen, 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.
6. 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.
7. 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
8. 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.
9. 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.
10. 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.
11. Zafarana, G., Ishkanian, A.S., Malloff, C.A., Locke, J.A., Sykes, J., Thoms, J., Lam, W.L., Squire, J.A., Yoshimoto, M., Ramnarine V.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, 118(16): 4053-4062, 2012.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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
17. Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in gwas. Pac Symp Biocomput. 2012:363-74.
18. Stegle O, Roth FP, Morris Q, Listgarten Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. J. Pac Symp Biocomput. 2012:323-6.
19. 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.
20. 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
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
22. 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
23. 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
24. 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
25. 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
26. 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
27. Wu G, Stein L. A network module-based method for identifying cancer prognostic signatures. Genome Biol. 2012 Dec 10;13(12):R112.
28. 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.
29. 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.
30. 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., St�mpflen, 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.
31. 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.
32. 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
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. 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
45. 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.
46. 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.
47. 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.
48. 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.
49. 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.
50. 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.
51. 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.
52. 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.
53. 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.
54. 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.
55. 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.
56. 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.
1. aldron, 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.
2. Hakem, A., Bohgaki, M., Lemmers, B., Tai, E., Salmena, L., Matysiak-Zablocki, E., L�pez B�hr, 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.
3. 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.
4. 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.
5. Yan, R., Boutros, P.C., Jurisica, I. A tree-based approach for motif discovery and sequence classification, Bioinformatics, 27(15): 2054-61, 2011.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. Fortney, K. and Jurisica, I. Integrative computational biology for cancer research. Human Genetics, 130(4): 465-481, 2011.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. Yakhini, Z and Jurisica, I. Cancer computational biology, BMC Bioinf. 12(1): 120, 2011.
19. 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.
20. 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.
21. 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.
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1. Motamed-Khorasani A, Jurisica I, Letarte M, Shaw PA, Parkes RK, Zhang X, Evangelou A, Rosen B, Murphy KJ, Brown TJ. Differentially androgen-modulated genes in ovarian epithelial cells from BRCA mutation carriers and control patients predict ovarian cancer survival and disease progression. Oncogene. 2007 Jan 11;26(2):198-214. Epub 2006 Jul 10. [ PubMed ]
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1. Seiden-Long IM, Brown KR, Shih W, Wigle DA, Radulovich N, Jurisica I, Tsao MS. Transcriptional targets of hepatocyte growth factor signaling and Ki-ras oncogene activation in colorectal cancer. Oncogene. 2006 Jan 5;25(1):91-102. [ PubMed ]
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