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Research using I2D

The following papers and publications have used I2D or its earlier version OPHID


Year 2013

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



Year 2012

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.



Year 2011

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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Year 2010

1. 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, 2010. In Press.

2. 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, 2010. In Press.

3. Malik, R., Dulla, K., Nigg, E.A., Körner, R. From proteome lists to biological impact--tools and strategies for the analysis of large MS data sets. Proteomics. 10(6):1270-83, 2010 Mar. [ PubMed ]

4. Radulovich, N., Pham, N. A., Strumpf, D., Leung, L., Xie, W., Jurisica, I., Tsao, M. S. Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma. Mol Cancer, 9(1): 24, 2010. [ PubMed ]

5. 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):111-119, 2010. Epub: 2009/10/24. [ PubMed ]

6. Clifton VL. Review: Sex and the human placenta: mediating differential strategies of fetal growth and survival. Placenta. Volume 31, Supplement 1, Pages S33-S39, 2010 Mar 31. Epub 2009 Dec 11. [ PubMed ]

7. Zhu, C.Q., Strumpf, D., Li, C.Y., Li, Q., Liu, N., Der, S., Shepherd, F.A., Tsao, M.S., Jurisica, I. Prognostic Gene Expression Signature for Squamous Cell Carcinoma of Lung. Clin Cancer Res. 2010 Aug 25. [Epub ahead of print] [ PubMed ]

8. Gefen, A., Cohen, R., Birk, O.S. Syndrome to gene (S2G): in-silico identification of candidate genes for human diseases. Hum Mutat. 2010 Mar;31(3):229-36. [ PubMed ]

9. Reis, P.P, Tomenson, M., Cervigne, N.K., Machado, J., Jurisica, I., Pintilie, M., Sukhai, M.A., Perez-Ordonez, B., Grenman, R., Gilbert, R.W., Gullane, P.J., Irish, J.C., 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. 2010 Sep 10;9(1):238. [Epub ahead of print] [ PubMed ]

10. Kerrigan, J.J, Xie, Q., Ames, R.S., Lu, Q. Production of protein complexes via co-expression. Protein Expr Purif. 2010 Aug 6. [Epub ahead of print] [ PubMed ]

11. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S.Biological process linkage networks. PLoS One. 2009;4(4):e5313. Epub 2009 Apr 23. [ PubMed ]

Year 2009

1. Deribe, Y.L., P. Wild, A. Chandrashaker, J. Curak, M. H.H. Schmidt, Y. Kalaidzidis, N. Milutinovic, I. Kratchmarova, L. Buerkle, M. J.Fetchko, P. Schmidt, S. Kittanakom, K. R. Brown, I. Jurisica, B. Blagoev, M. Zerial, I. Stagljar, and I. Dikic. Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6. Sci Signal, 2(102): RA84, 2009. Epub: 2009/12/24.[ PubMed ]

2. Bernthaler A, Mühlberger I, Fechete R, Perco P, Lukas A, Mayer B. A dependency graph approach for the analysis of differential gene expression profiles. Mol Biosyst. 2009 Dec;5(12):1720-31. Epub 2009 Jun 3. [ PubMed ]

3. Agarwal R, Jurisica I, Mills GB, Cheng KW. The emerging role of the RAB25 small GTPase in cancer. Traffic. 2009 Nov;10(11):1561-8. Epub 2009 Jul 27. [ PubMed ]

4. Chen YX, Li Y, Wang WM, Zhang W, Chen XN, Xie YY, Lu J, Huang QH, Chen N. Phosphoproteomic Study of Human Tubular Epithelial Cell in Response to Transforming Growth Factor-Beta-1-Induced Epithelial-to-Mesenchymal Transition. Am J Nephrol. 2009 Oct 28;31(1):24-35. [Epub ahead of print] [ PubMed ]

5. Lee E, Jung H, Radivojac P, Kim JW, Lee D. Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S2. [ PubMed ]

6. 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. 2009 Sep 15;125(6):1257-65. [ PubMed ]

7. Mills GB, Jurisica I, Yarden Y, Norman JC. Genomic amplicons target vesicle recycling in breast cancer. J Clin Invest. 2009 Aug;119(8):2123-7. doi: 10.1172/JCI40256. Epub 2009 Jul 20. [ PubMed ]

8. Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics. 2009 Jul 7;10 Suppl 1:S16. [ PubMed ]

9. Li J, Zhu X, Chen JY. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol. 2009 Jul;5(7):e1000450. Epub 2009 Jul 31. [ PubMed ]

10. Chautard E, Thierry-Mieg N, Ricard-Blum S. Interaction networks: from protein functions to drug discovery. A review. Pathol Biol (Paris). 2009 Jun;57(4):324-33. Epub 2008 Dec 13. Review. [ PubMed ]

11. Cox B, Kotlyar M, Evangelou AI, Ignatchenko V, Ignatchenko A, Whiteley K, Jurisica I, Adamson SL, Rossant J, Kislinger T. Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology. Mol Syst Biol. 2009;5:279. Epub 2009 Jun 16. [ PubMed ]

12. Blankenburg H, Finn RD, Prlić A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M. DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics. 2009 May 15;25(10):1321-8. [ PubMed ]

13. Hauser PV, Perco P, Mühlberger I, Pippin J, Blonski M, Mayer B, Alpers CE, Oberbauer R, Shankland SJ. Microarray and bioinformatics analysis of gene expression in experimental membranous nephropathy. Nephron Exp Nephrol. 2009;112(2):e43-58. Epub 2009 Apr 18. [ PubMed ]

14. Wilflingseder J, Kainz A, Perco P, Korbély R, Mayer B, Oberbauer R. Molecular predictors for anaemia after kidney transplantation. Nephrol Dial Transplant. 2009 Mar;24(3):1015-23. Epub 2008 Dec 18. [ PubMed ]

15. Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol. 2009 Feb;27(2):199-204. Epub 2009 Feb 1. [ PubMed ]

16. Dong J, Kislinger T, Jurisica I, Wigle DA. Lung cancer: developmental networks gone awry? Cancer Biol Ther. 2009 Feb;8(4):312-8. Epub 2009 Feb 1. Review. [ PubMed ]

17. Teber ET, Liu JY, Ballouz S, Fatkin D, Wouters MA. Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S69. [ PubMed ]

18. McDowall MD, Scott MS, Barton GJ. PIPs: human protein-protein interaction prediction database. Nucleic Acids Res. 2009 Jan;37(Database issue):D651-6. Epub 2008 Nov 6. [ PubMed ]

19. Plewczyński D, Ginalski K. The interactome: predicting the protein-protein interactions in cells. Cell Mol Biol Lett. 2009;14(1):1-22. Epub 2008 Oct 6. Review. [ PubMed ]

20. Chen JY, Youn E, Mooney SD. Connecting protein interaction data, mutations, and disease using bioinformatics. Methods Mol Biol. 2009;541:449-61. Review. [ PubMed ]

21. Wu X, Huan T, Pandey R, Zhou T, Chen JY. Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease. Int J Comput Biol Drug Des. 2009;2(4):340-52. doi: 10.1504/IJCBDD.2009.030765. Epub 2009 Jan 4. [ PubMed ]



Year 2008

1. Lee SA, Chan CH, Tsai CH, Lai JM, Wang FS, Kao CY, Huang CY. Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S11. [ PubMed ]

2. Skalnikova H, Vodicka P, Pelech S, Motlik J, Gadher SJ, Kovarova H. Protein signaling pathways in differentiation of neural stem cells. Proteomics. 2008 Nov;8(21):4547-59. [ PubMed ]

3. Wang Y, Chen G, Yang Y, Hu Z, Chen X. A systems biology analysis of protein-protein interactions in the APOBEC family. Life Sci. 2008 Oct 10;83(15-16):521-30. Epub 2008 Aug 8. [ PubMed ]

4. Tomasini R, Tsuchihara K, Wilhelm M, Fujitani M, Rufini A, Cheung CC, Khan F, Itie-Youten A, Wakeham A, Tsao MS, Iovanna JL, Squire J, Jurisica I, Kaplan D, Melino G, Jurisicova A, Mak TW. TAp73 knockout shows genomic instability with infertility and tumor suppressor functions. Genes Dev. 2008 Oct 1;22(19):2677-91. Epub 2008 Sep 19. [ PubMed ]

5. Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics. 2008 Sep 30;9:405. [ PubMed ]

6. Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 2008 Sep 26;4(9):e1000165. [ PubMed ]

7. Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol. 2008 Sep;2(5):206-21. Review. [ PubMed ]

8. Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD. An integrated approach to inferring gene-disease associations in humans. Proteins. 2008 Aug 15;72(3):1030-7. [ PubMed ]

9. Huan T, Sivachenko AY, Harrison SH, Chen JY. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. [ PubMed ]

10. Jurisicova A, Jurisica I, Kislinger T. Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions. Expert Rev Proteomics. 2008 Aug;5(4):551-60. Review. [ PubMed ]

11. Perco P, Wilflingseder J, Bernthaler A, Wiesinger M, Rudnicki M, Wimmer B, Mayer B, Oberbauer R. Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: a systems biology perspective. J Cell Mol Med. 2008 Aug;12(4):1177-87. Epub 2008 Feb 8. Review. [ PubMed ]

12. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. InteroPORC: automated inference of highly conserved protein interaction networks. Bioinformatics. 2008 Jul 15;24(14):1625-31. Epub 2008 May 28. [ PubMed ]

13. Ozgür A, Vu T, Erkan G, Radev DR. Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics. 2008 Jul 1;24(13):i277-85. [ PubMed ]

14. Tone AA, Begley H, Sharma M, Murphy J, Rosen B, Brown TJ, Shaw PA. Gene expression profiles of luteal phase fallopian tube epithelium from BRCA mutation carriers resemble high-grade serous carcinoma. Clin Cancer Res. 2008 Jul 1;14(13):4067-78. [ PubMed ]

15. Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T. Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT). Mol Biosyst. 2008 Jul;4(7):762-73. Epub 2008 Apr 17. [ PubMed ]

16. Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Front Biosci. 2008 May 1;13:3391-407. Review. [ PubMed ]

17. Kasabov N, Jain V, Benuskova L. Integrating evolving brain-gene ontology and connectionist-based system for modeling and knowledge discovery. Neural Netw. 2008 Mar-Apr;21(2-3):266-75. Epub 2007 Dec 31. Erratum in: Neural Netw. 2008 May;21(4):698. [ PubMed ]

18. Viswanathan GA, Seto J, Patil S, Nudelman G, Sealfon SC. Getting started in biological pathway construction and analysis. PLoS Comput Biol. 2008 Feb;4(2):e16. Review. [ PubMed ]

19. Rapberger R, Perco P, Sax C, Pangerl T, Siehs C, Pils D, Bernthaler A, Lukas A, Mayer B, Krainer M. Linking the ovarian cancer transcriptome and immunome. BMC Syst Biol. 2008 Jan 3;2:2. [ PubMed ]

20. Taşan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP. An en masse phenotype and function prediction system for Mus musculus. Genome Biol. 2008;9 Suppl 1:S8. Epub 2008 Jun 27. [ PubMed ]

21. Kim WK, Krumpelman C, Marcotte EM. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol. 2008;9 Suppl 1:S5. Epub 2008 Jun 27. [ PubMed ]

22. Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 2008;9 Suppl 1:S2. Epub 2008 Jun 27. [ PubMed ]

23. Gortzak-Uzan L, Ignatchenko A, Evangelou AI, Agochiya M, Brown KA, St Onge P, Kireeva I, Schmitt-Ulms G, Brown TJ, Murphy J, Rosen B, Shaw P, Jurisica I, Kislinger T. A proteome resource of ovarian cancer ascites: integrated proteomic and bioinformatic analyses to identify putative biomarkers. J Proteome Res. 2008 Jan;7(1):339-51. Epub 2007 Dec 13. [ PubMed ]



Year 2007

1. Loganantharaj R, Chung J. Integrating diverse information to gain more insight into microarray analysis. J Biomed Biotechnol. 2009;2009:648987. Epub 2009 Oct 12. [ PubMed ]

2. Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica I, Der SD, Tsao MS. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol. 2007 Dec 10;25(35):5562-9. [ PubMed ]

3. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol. 2007 Nov 27;1:56. [ PubMed ]

4. Berger SI, Posner JM, Ma'ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics. 2007 Oct 4;8:372. [ PubMed ]

5. Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007 Sep;17(9):1304-18. Epub 2007 Aug 10. [ PubMed ]

6. Scott MS, Barton GJ. Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics. 2007 Jul 5;8:239. [ PubMed ]

7. Platzer A, Perco P, Lukas A, Mayer B. Characterization of protein-interaction networks in tumors. BMC Bioinformatics. 2007 Jun 27;8:224. [ PubMed ]

8. Wu C, Ma MH, Brown KR, Geisler M, Li L, Tzeng E, Jia CY, Jurisica I, Li SS. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Proteomics. 2007 Jun;7(11):1775-85. [ PubMed ]

9. Huang TW, Lin CY, Kao CY. Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics. 2007 May 10;8:152. [ PubMed ]

10. Schlicker A, Huthmacher C, Ramírez F, Lengauer T, Albrecht M. Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics. 2007 Apr 1;23(7):859-65. [ PubMed ]

11. Futschik ME, Chaurasia G, Herzel H. Comparison of human protein-protein interaction maps. Bioinformatics. 2007 Mar 1;23(5):605-11. Epub 2007 Jan 19. [ PubMed ]

12. Przulj N. Biological network comparison using graphlet degree distribution. Bioinformatics. 2007 Jan 15;23(2):e177-83. [ PubMed ]

13. Brown KR, Jurisica I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol. 2007;8(5):R95. [ PubMed ]

14. Futschik ME, Tschaut A, Chaurasia G, Herzel H. Graph-theoretical comparison reveals structural divergence of human protein interaction networks. Genome Inform. 2007;18:141-51. [ PubMed ]

15. Dhanapalan L, Chen JY. A case study of integrating protein interaction data using semantic web technology. Int J Bioinform Res Appl. 2007;3(3):286-302. [ PubMed ]

16. Cox B, Kislinger T, Wigle DA, Kannan A, Brown K, Okubo T, Hogan B, Jurisica I, Frey B, Rossant J, Emili A. Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol Syst Biol. 2007;3:109. Epub 2007 May 8. [ PubMed ]

17. Wigle D, Jurisica I. Cancer as a System Failure. Cancer Informatics 2007, 5:10.

18. Jurisica I. Integrative Computational Biology. Cancer Treatment and Research 2007, 137:129.

19. Jurisica I, Wigle DA, Wong B. Cancer Informatics in the Post-Genomics Era.. Implementing Information-Based Medicine, Series: Cancer Treatment and Research, Volume 137, Springer Verlag. 2007.



Year 2006

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 ]

2. Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE, Futschik ME. UniHI: an entry gate to the human protein interactome. Nucleic Acids Res. 2007 Jan;35(Database issue):D590-4. Epub 2006 Dec 7. [ PubMed ]

3. Gonzalez G, Uribe JC, Tari L, Brophy C, Baral C. Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. Pac Symp Biocomput. 2007:28-39. [ PubMed ]

4. Perco P, Pleban C, Kainz A, Lukas A, Mayer G, Mayer B, Oberbauer R. Protein biomarkers associated with acute renal failure and chronic kidney disease. Eur J Clin Invest. 2006 Nov;36(11):753-63. Review. [ PubMed ]

5. Przulj N, Higham DJ. Modelling protein-protein interaction networks via a stickiness index. J R Soc Interface. 2006 Oct 22;3(10):711-6. [ PubMed ]

6. Brierley MM, Marchington KL, Jurisica I, Fish EN. Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent. FEBS J. 2006 Apr;273(7):1569-81. [ PubMed ]

7. 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 ]

8. Chaurasia G, Herzel H, Wanker EE, Futschik ME. Systematic functional assessment of human protein-protein interaction maps. Genome Inform. 2006;17(1):36-45. [ PubMed ]

9. George RA, Liu JY, Feng LL, Bryson-Richardson RJ, Fatkin D, Wouters MA. Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res. 2006;34(19):e130. Epub 2006 Oct 4. [ PubMed ]

10. Chen JY, Shen C, Sivachenko AY. Mining Alzheimer disease relevant proteins from integrated protein interactome data. Pac Symp Biocomput. 2006:367-78. [ PubMed ]

11. Galloni NN, Bradley G, Gullane PJ, Irish JC, Perez-Ordonez B, Pintilie M, Reis PP, Kamel-Reid S. 10: 40 AM Biomarkers of Progression and Recurrence in Oral Carcinoma. Otolaryngology-Head and Neck Surgery 2006, 135:91–92.

12. Chen JY, Pinkerton SL, Shen C, Wang M. An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies. In Proceedings of the 2006 ACM symposium on Applied computing 2006:179.

13. Otasek D, Brown K, Jurisica I. Confirming protein-protein interactions by text mining. In Proceedings of the 6th SIAM Conference on Text Mining 2006.

14. Mamidipalli SR. HAPPI: A Bioinformatics Database Platform Enabling Network Biology Studies. 2006.

15. Haasl RJ, Fang J: Mining Protein-Protein Interaction Data. Current Bioinformatics 2006, 1:197205.

16. Kislinger T, Jurisica I. Proteomics and Bioinformatics in Biomedical Research. Cancer Genomics-Proteomics 2006, 3:11.

17. Piatetsky-Shapiro G, Djeraba C, Getoor L, Grossman R, Feldman R, Zaki M. What are the grand challenges for data mining? KDD-2006 panel report. ACM SIGKDD Explorations Newsletter 2006, 8:77.

18. Jurisica I, Wigle D A. Knowledge Discovery in Proteomics. Chapman & Hall/CRC Press 2006.



Year 2005

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 ]

2. Wachi S, Yoneda K, Wu R. Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics. 2005 Dec 1;21(23):4205-8. Epub 2005 Sep 27. [ PubMed ]

3. Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G. HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S21. [ PubMed ]

4. Neverov AD, Artamonova II, Nurtdinov RN, Frishman D, Gelfand MS, Mironov AA. Alternative splicing and protein function. BMC Bioinformatics. 2005 Nov 7;6:266. [ PubMed ]

5. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics. 2005 May 1;21(9):2076-82. Epub 2005 Jan 18. [ PubMed ]

6. Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana JL. High-throughput mapping of a dynamic signaling network in mammalian cells. Science. 2005 Mar 11;307(5715):1621-5. [ PubMed ]