Journal Articles


2019

  • Holzinger A, Haibe-Kains B, Jurisica I. Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data, Eur J Nucl Med Mol Imaging. 2019 Jun 15. doi: 10.1007/s00259-019-04382-9.Holzinger A, Haibe-Kains B, Jurisica I. Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data, Eur J Nucl Med Mol Imaging. 2019 Jun 15. doi: 10.1007/s00259-019-04382-9.
  • Monette A, Bergeron D, Ben Amor A, Meunier L, Caron C, Mes-Masson AM, Kchir N, Hamzaoui K, Jurisica I, Lapointe R. Immune-enrichment of non-small cell lung cancer baseline biopsies for multiplex profiling define prognostic immune checkpoint combinations for patient stratification, J Immunother Cancer, 7(1):86, 2019. doi: 10.1186/s40425-019-0544-x
  • Monette A, Morou A, Al-Banna NA, Rousseau L, Lattouf JB, Rahmati S, Tokar T, Routy JP, Cailhier JF, Kaufmann DE, Jurisica I, Lapointe R. Failed immune responses across multiple pathologies share pan-tumor and circulating lymphocytic targets, J Clin Invest, 2019 Mar 26;130. pii: 125301. doi: 10.1172/JCI125301
  • Mohammed Ali Z, Tokar T, Batruch I, Reid S, Tavares-Brum A, Yip P, Cardinal H, Hébert MJ, Li Y, Kim SJ, Jurisica I, John R, Konvalinka A. Urine Angiotensin II Signature Proteins as Markers of Fibrosis in Kidney Transplant Recipients, Transplantation, 103(6):e146-e158, 2019. doi: 10.1097/TP.0000000000002676.
  • Kaufmann KB, Garcia-Prat L, Liu Q, Ng SWK, Takayanagi SI, Mitchell A, Wienholds E, van Galen P, Cumbaa CA, Tsay MJ, Pastrello C, Wagenblast E, Krivdova G, Minden MD, Lechman ER, Zandi S, Jurisica I, Wang JCY, Xie SZ, Dick JE. A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency, Blood, 133(20):2198-2211, 2019. doi: 10.1182/blood-2018-10-881441.
  • Mandilaras, V, Garg, S, Cabanero, M, Tan, Q, Pastrello, C, Burnier, J, Karakasis, K, Wang, L, Dhani, NC, Butler, MO, Bedard, PL, Siu, LL, Clarke, B, Shaw, PA, Stockley, T, Jurisica, I, Oza, AM. TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses. Int J Gyn Cancer, Jan 18. pii: ijgc-2018-000087. doi: 10.1136/ijgc-2018-000087.
  • del Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P. Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set." Nat Commun, 10(1): 10, 2019.
  • Li L, Guturi KKN, Gautreau B, Patel PS, Saad A, Morii M, Mateo F, Palomero L, Barbour H, Gomez A, Ng D, Kotlyar M, Pastrello C, Jackson HW, Khokha R, Jurisica I, Affar EB, Raught B, Sanchez O, Alaoui-Jamali M, Pujana MA, Hakem A, Hakem R., Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis, J Clin Invest, 128(10):4525-4542, 2018. doi: 10.1172/JCI120401
  • Kotlyar, M., Pastrello, C., Malik, Z., Jurisica, I., IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. Nucleic acids research, 47(D1):D581-D589, 2019.

    2018

  • Endisha, H., Rockel, J., Jurisica, I., Kapoor, M., The complex landscape of microRNAs in articular cartilage: biology, pathology, and therapeutic targets, JCI Insight. 3(17):e121630, 2018.
  • Singh, M., Venugopal, C., Tokar, T., McFarlane, N., Subapanditha, M. K., Qazi, M., Bakhshinyan, D., Vora, P., Murty, N., Jurisica, I., Singh, S. K., Therapeutic targeting of the pre-metastatic stage in human brain metastasis, Cancer Res, 2018. ePub 2018/07/11. DOI: 10.1158/0008-5472.CAN-18-1022.
  • Wen, B., Tokar, T., Taibi, A., Chen, J., Jurisica, I., Comelli, E. M. Citrobacter rodentium alters the mouse colonic miRNome, Genes and Immunity, 2018. In press. ePub 2018/05/08. Doi: 10.1038/s41435-018-0026-z
  • Jean-Quartier C, Jeanquartier F, Jurisica I, Holzinger A, In silico cancer research towards 3R. BMC Cancer, 18(1):408, 2018
  • Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1):134, 2018.
  • Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL., Large-scale discovery of previously undetected microRNAs specific to human liver. Hum Genomics, 12(1):16, 2018.
  • Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget. 9(10):9137-9155, 2018.
  • Paulitti A, Corallo D, Andreuzzi E, Bizzotto D, Marastoni S, Pellicani R, Tarticchio G, Pastrello C, Jurisica I, Ligresti G, Bucciotti F, Doliana R, Colladel R, Braghetta P, Di Silvestre A, Bressan G, Colombatti A, Bonaldo P, Mongiat M. The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth, Oncogene, 37(25): 3399-3414, 2018.
  • Tokar, T., Pastrello, C., Rossos, A., Abovsky, M., Hauschild, A.C., Tsay, M., Lu, R., Jurisica. I. mirDIP 4.1 – Integrative database of human microRNA target predictions, Nucl Acids Res, D1(46): D360-D370, 2018.

    2017

  • Kotlyar M., Pastrello, C., Rossos, A., Jurisica, I., Prediction of protein-protein interactions, Current Protocols in Bioinf, 60, 8.2.1–8.2.14., 2017.
  • Singh, M., Venugopal, C., Tokar, T., Brown, K.B., McFarlane, N., Bakhshinyan, D., Vijayakumar, T., Manoranjan, B., Mahendram, S., Vora, P., Qazi, M., Dhillon, M., Tong, A., Durrer, K., Murty, N., Hallet, R., Hassell, J.A., Kaplan, D., Jurisica, I., Cutz, J-C., Moffat, J., Singh, D.K., RNAi screen identifies essential regulators of human brain metastasis initiating cells, Acta Neuropathologica, 134(6):923-940, 2017.
  • Wong, S, W. H., Pastrello, C., Kotlyar, M., Faloutsos, C., Jurisica, I. Modeling tumor progression via the comparison of stage-specific graphs, Methods, 132(1): 34-41, 2018. Available online 3 July 2017.
  • Pastrello C, Tsay M, McQuaid R, Abovsky M, Pasini E, Shirdel E, Angeli M, Tokar T, Jamnik J, Kotlyar M, Jurisicova A, Kotsopoulos J, El-Sohemy A, Jurisica I. Retraction: Circulating plant miRNAs can regulate human gene expression in vitro. Sci Rep. 7:46826, 2017.
  • Wang, D, Pham, NA, Tong, JF, Sakashita, S, Allo, G, Kim, L, Yanagawa, N, Raghavan, V, Wei, YH, To, C, Trinh, QM, Starmans, MHW, Chan-Seng-Ye, MA, Chadwick, D, Li, L, Zhu, CQ, Liu, N, Li, M, Lee, S, Ignatchenko, V, Strumpf, D, Taylor, P, Moghal, N, Liu, G, Boutros, PC, Kislinger, T, Pintilie, M, Jurisica, I, Shepherd, FA, McPherson, J, Muthuswami, L, Moran, MF, Tsao, MS. Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors, Int J Cancer, 140(3): 662-673, 2017.
  • Posfai, E., Petropoulos, S., de Barros, F.S.O., Schell, J.P., Jurisica, I., Sandberg, R., Lanner, F., Rossant, J., Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo, eLife, pii: e22906. 2017.
  • Pinheiro, M., Drigo, S.A., Tonhosolo, R., Andrade, S.C.S., Marchi, F.A., Jurisica, I., Kowalski, L.P., Achatz, M.I., Rogatto, S.R., HABP2 p.G534E variant in patients with family history of thyroid and breast cancer, Oncotarget, 8(25):40896-40905, 2017.
  • Citron, F., Armenia, J., Barzan, L., Franchin, G., Polesel, J., Talamini, R., Sulfaro, S., Croce, C.M., Klement, W., Pastrello, C., Jurisica, I., Vecchione, A., Belletti, B., Baldassarre, G., A microRNA signature identifies SP1 and TGFbeta pathways as potential mediators of local recurrences in head and neck squamous carcinomas, Clin Cancer Res, 23(14):3769-3780, 2017
  • Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Riley L, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, and Stagljar I. Systematic protein-protein interaction mapping for clinically-relevant human GPCRs, Mol Sys Biol, 13(3): 918, 2017.
  • Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Babu M, Neel B, Gingras AC, and Stagljar I, A global analysis of the protein phosphatase interactome, Mol Cell, 65(2):347-360, 2017.
  • Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, and Ketteler R, Systematic identification of oncogenic EGFR interaction partners, J Mol Biol, 429(2): 280-294, 2017.
  • Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucl Acids Res, 45(D1): D419-D426, 2017.

    2016

  • Chehade, R., R. Pettapiece-Phillips, Salmena, L., Kotlyar, M., Jurisica, I., Narod, S. A., Akbari, M. R., Kotsopoulos, J. Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific, Breast Cancer Res, 18(1): 87, 2016.
  • Cierna, Z., Mego, M., Jurisica, I., Machalekova, K., Chovanec, M., Miskovska, V., Svetlovska, D., Hainova, K., Kajo, K., Mardiak, J., Babal, P. Fibrillin-1 (FBN-1) a new marker of germ cell neoplasia in situ, BMC Cancer, 16: 597, 2016.
  • Nakamura, A., Rampersaud, R., Sharma, A., Lewis, S.J., Wu, B., Datta,P., Sundararajan, K., Endisha, H., Rossomacha, E., Rockel, J.S., Jurisica, I., Kapoor, M., Identification of microRNA-181a-5p and microRNA-4454 as mediators of facet cartilage degeneration, JCI Insight, 1(12):e86820, 2016.
  • Becker-Santos, D.D., Thu, K.L, English, J.C., Pikor, L.A., Chari, R., Lonergan, K.M., Martinez, V.D., Zhang, M., Vucic, E.A., Luk, M.T.Y., Carraro, A., Korbelik, J., Piga, D., Lhomme, N.M., Tsay, M.J., Yee, J., MacAulay, C.E., Lockwood, W.W., Robinson, W.P., Jurisica, I., Lam, W.L., Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma, J Pathology, 240(2):161-72, 2016.
  • Konvalinka, A., Batruch, I., Tokar, T., Dimitromanolakis, A., Reid, R., Song, X., Pei, Y., Drabovich, A.P.,PhD; Diamandis, E. P., Jurisica, I., Scholey, J.W. Quantification of Angiotensin II-Regulated Proteins in Urine of Patients with Polycystic and Other Chronic Kidney Diseases by Selected Reaction Monitoring, Clinical Proteomics, 13: 16, 2016.
  • Stojanova, A, Tu, W.B., Ponzielli, R., Kotlyar, M., Chan, P.K., Boutros, P.C., Khosravi, F., Jurisica, I., Raught, B., Penn, L.Z. MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation, Cell Cycle, 15(13): 1693-705, 2016.
  • Li, Y-H, Tavallaee, G., Tokar, T., Nakamura, A., Sundararajan, K., Weston, A., Sharma, A., Mahomed, N. N., Gandhi, R., Jurisica, I., Kapoor, M. Identification of synovial fluid microRNA signature in knee osteoarthritis: Differentiating early- and late-stage knee Osteoarthritis. Osteoarthritis and Cartilage, 24(9): 1577-86, 2016.
  • Cinegaglia, N.C., Andrade, S.C.S., Tokar, T., Pinheiro, M., Severino, F. E., Oliveira, R. A., Hasimoto, E. N., Cataneo, D. C., Cataneo, A.J.M., Defaveri, J., Souza, C.P., Marques, M.M.C, Carvalho, R. F., Coutinho, L.L., Gross, J.L., Rogatto, S.R., Lam, W.L., Jurisica, I., Reis, P.P. Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung, adenocarcinoma, Oncotarget, 7(20): 28920-34, 2016.
  • Vargas, A., Angeli, M., Pastrello, C., McQuaid, R., Li, H., Jurisicova, A., Jurisica, I., Robust quantitative scratch assay, Bioinformatics, 32(9):1439-40, 2016.
  • Snider, J., Kotlyar, M., Saraon, P., Yao, Z., Jurisica, I., Stagljar, I. Fundamentals of protein interaction network mapping, Mol Sys Biol, 11(12):848, 2015.
  • Pettapiece-Phillips*, R., Kotlyar*, M., Chehade, R., Salmena, L., Narod, S. A., Akbari, M., Jurisica, I., Kotsopoulos, J. Uninterrupted sedentary behavior downregulates BRCA1 gene expression, Cancer Prevention Res, 9(1): 83-8, 2016.
  • Benleulmi-Chaachoua, A., Chen, L., Sokolina, K., Wong, V., Jurisica, I., Emerit, M.B., Darmon, M., Espin, A., Stagljar, I., Tafelmeyer, P., Zamponi, G.W., Delagrange, P., Maurice, P., Jockers, R. Protein interactome mining defines melatonin MT1 receptors as integral component of presynaptic protein complexes of neurons, J Pineal Res, 60(1):95-108, 2016.
  • Kotlyar, M., Pastrello, C., Sheahan, N., Jurisica, I. Integrated Interactions Database: Tissue-specific view of the human and model organism interactomes, Nucleic Acids Res, 44(D1): D536-41, 2016.
  • Navab R, Strumpf D, To C, Pasko E, Kim KS, Park CJ, Hai J, Liu J, Jonkman J, Barczyk M, Bandarchi B, Wang YH, Venkat K, Ibrahimov E, Pham NA, Ng C, Radulovich N, Zhu CQ, Pintilie M, Wang D, Lu A, Jurisica I, Walker GC, Gullberg D, Tsao MS. Integrin a11b1 regulates cancer stromal stiffness and promotes tumorigenecity in non-small cell lung cancer, Oncogene, 35(15):1899-908, 2016.

    2015

  • Agostini M, Janssen KP, Kim LJ, D'Angelo E, Pizzini S, Zangrando A, Zanon C, Pastrello C, Maretto I, Digito M, Bedin C, Jurisica I, Rizzolio F, Giordano A, Bortoluzzi S, Nitti D, Pucciarelli S. An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer. Oncotarget, 6(32): 32561-74, 2015.
  • Singh M, Garg N, Venugopal C, Hallett RM, Tokar T, McFarlane N, Arpin C, Page B, Haftchenary S, Todic A, Rosa DA, Lai P, Gómez-Biagi R, Ali AM, Lewis A, Geletu M, Mahendram S, Bakhshinyan D, Manoranjan B, Vora P, Qazi M, Murty NK, Hassell JA, Jurisica I, Gunning P, Singh SK. STAT3 pathway regulates lung-derived brain metastasis initiating cell capacity through miR-21 activation. Oncotarget, 6(29): 27461-77, 2015.
  • Agostini M, Zangrando A, Pastrello C, D'Angelo E, Romano G, Giovannoni R, Giordan M, Maretto I, Bedin C, Zanon C, Digito M, Esposito G, Mescoli C, Lavitrano M, Rizzolio F, Jurisica I, Giordano A, Pucciarelli S, Nitti D. A functional biological network centered on XRCC3: a new possible marker of chemoradiotherapy resistance in rectal cancer patients, Cancer Biol Ther, 16(8):1160-71, 2015.
  • Stewart, E.L., Mascaux, C., Pham, N-A, Sakashita, S., Sykes, J., Kim, L., Yanagawa, N., Allo, G., Ishizawa, K., Wang, D., Zhu, C.Q., Li, M., Ng, C., Liu, N., Pintilie, M., Martin, P., John, T., Jurisica, I., Leighl, N.B., Neel, B.G., Waddell, T.K., Shepherd, F.A., Liu, G., Tsao, M-S. Clinical Utility of Patient Derived Xenografts to Determine Biomarkers of Prognosis and Map Resistance Pathways in EGFR-Mutant Lung Adenocarcinoma, J Clin Oncol, 33(22):2472-80, 2015.
  • Camargo, J. F., Resende, M., Zamel, R., Klement, W., Bhimji, A., Huibner, S., Kumar, D., Humar, A., Jurisica, I., Keshavjee, S., Kaul, R., Husain, S. Potential role of CC chemokine receptor 6 (CCR6) in prediction of late-onset CMV infection following solid organ transplant. Clin Transplant, 29(6):492-8, 2015.
  • Fortney, K., Griesman, G., Kotlyar, M., Pastrello, C., Angeli, M., Tsao, M.S., Jurisica, I. Prioritizing therapeutics for lung cancer: An integrative meta-analysis of cancer gene signatures and chemogenomic data, PLoS Comp Biol, 11(3): e1004068, 2015.
  • Starmans, M.H., Pintilie, M., Chan-Seng-Yue, M., Moon, N.C., Haider, S., Nguyen, F., Lau, S.K., Liu, N., Kasprzyk, A., Wouters, B.G., Der, S.D., Shepherd, F.A., Jurisica, I., Penn, L.Z., Tsao, M.S., Lambin, P., Boutros, P.C. Integrating RAS status into prognostic signatures for adenocarcinomas of the lung. Clin Cancer Res, 21(6): 1477-86, 2015.
  • Tu, W.B., Helander, S., Pilstål, R., Hickman, K.A., Lourenco, C., Jurisica, I., Raught, B., Wallner, B., Sunnerhagen, M., Penn, L.Z. Myc and its interactors take shape. Biochim Biophys Acta, 1849(5): 469-483, 2015.
  • Dingar, D., Kalkat, M., Chan, M. P-K, Bailey, S.D., Srikumar, T., Tu, W.B., Ponzielli, R., Kotlyar, M., Jurisica, I., Huang, A., Lupien, M., Penn, L.Z., Raught, B. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors, J Proteomics, 118:95-111, 2015.
  • Wong, S. W. H., Cercone, N., Jurisica, I. Comparative network analysis via differential graphlet communities, Special Issue of Proteomics dedicated to Signal Transduction, Proteomics, 15(2-3):608-17, 2015.

    2014

  • Vucic, E. A., Thu, K. T., Pikor, L. A., Enfield, K. S. S., Yee, J., English, J. C., MacAulay, C. E., Lam, S., Jurisica, I., Lam, W. L. Smoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology, BMC Cancer, 14: 778, 2014.
  • Lalonde, E., Ishkanian, A. S., Sykes, J., Fraser, M., Ross-Adam, H., Erho, N., Dunning, M., Lamb, A.D., Moon, N.C., Zafarana, G., Warren, A.Y., Meng, A., Thoms, J., Grzadkowski, M.R., Berlin, A., Halim, S., Have, C.L., Ramnarine, V.R., Yao, C.Q., Malloff, C.A., Lam, L. L., Xie, H., Harding, N.J., Mak, D.Y.F., Chu1, K. C., Chong, L.C., Sendorek, D.H., P’ng, C., Collins, C.C., Squire, J.A., Jurisica, I., Cooper, C., Eeles, R., Pintilie, M., Pra, A.D., Davicioni, E., Lam, W. L., Milosevic, M., Neal, D.E., van der Kwast, T., Boutros, P.C., Bristow, R.G., Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncology. 15(13):1521-32, 2014.
  • Berlin, A., Lalonde, E., Sykes, J., Zafarana, G., Chu, K.C., Ramnarine, V.R., Ishkanian, A., Sendorek, D.H.S., Pasic, I., Lam, W.L., Jurisica, I., van der Kwast, T., Milosevic, M., Boutros, P.C., Bristow, R.G.. NBN Gain Is Predictive for Adverse Outcome Following Image-Guided Radiotherapy for Localized Prostate Cancer, Oncotarget, 5(22): 11081–11090, 2014.
  • Lapin, V., Shirdel, E., Wei, X., Mason, J., Jurisica, I., Mak, T.W., Kinome-wide screening of HER2+ breast cancer cells for molecules that mediate cell proliferation or sensitize cells to trastuzumab therapy, Oncogenesis, 3(12): e133; doi:10.1038/oncsis.2014.45, 2014.
  • Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma, Nature, 511(7511):543-50, 2014. doi: 10.1038/nature13385. Epub 2014 Jul 9.
  • Kotlyar M., Pastrello C., Pivetta, F., Lo Sardo A., Cumbaa, C., Li, H., Naranian, T., Niu Y., Ding Z., Vafaee F., Broackes-Carter F., Petschnigg, J., Mills, G.B., Jurisicova, A., Stagljar, I., Maestro, R., & Jurisica, I. In silico prediction of physical protein interactions and characterization of interactome orphans, Nat Methods, 12(1):79-84, 2015. E-pub 2014/11/18.
  • Kittanakom, S., Barrios-Rodiles, M., Petschnigg, J., Arnoldo, A., Wong, V., Heisler, L., Kotlyar, M., Jurisica, I., Wrana, J.L., Nislow, C., Stagljar, I. CHIP-MYTH: A novel interactive proteomics method for the assessment of agonist-dependent interactions of the human ß2-adrenergic receptor, J Biochemical & Biophysical Research Communications, 445(4):746-56, 2014. doi: 10.1016/j.bbrc.2014.02.033
  • Pastrello, C., Pasini, E., Kotlyar, M., Otasek, D., Wong, S., Sangrar, W., Rahmati, S., Jurisica, I., Integration, visualization and analysis of human interactome, J Biochemical & Biophysical Research Communications, 445(4):757-73, 2014. doi: 10.1016/j.bbrc.2014.01.151
  • Cervigne, N.K., Machado, J. Goswami, R. S., Sadikovic, B., Bradley, G., Perez-Ordonez, B., Galloni, N.N., Gilbert, R., Gullane, P., Irish, J.C., Jurisica, I., Reis, P.P., Kamel-Reid, S. Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis? Hum Mol Genet, 23(10):2618-28, 2014; doi: 10.1093/hmg/ddt657
  • Petschnigg, J., Groisman, B., Kotlyar, M., Taipale, M., Zheng, Y., Kurat, C., Sayad, A., Sierra, J., Mattiazzi Usaj, M., Snider, J., Nachman, A., Krykbaeva, I., Tsao, M.S., Moffat, J., Pawson, T., Lindquist, S., Jurisica, I., Stagljar, I. Mammalian Membrane Two-Hybrid assay (MaMTH): a novel split-ubiquitin two-hybrid tool for functional investigation of signaling pathways in human cells; Nat Methods, 11(5):585-92, 2014; doi: 10.1038/nmeth.2895
  • Der S.D., Sykes J., Pintilie M., Zhu C.Q., Strumpf D., Liu N., Jurisica I., Shepherd F.A., Tsao M.S. Validation of a histology-independent prognostic gene signature for early-stage, non-small-cell lung cancer including stage IA patients. J Thorac Oncol, 9(1):59-64, 2014. doi: 10.1097/JTO.0000000000000042

    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.
  • Pastrello, C., Otasek, D.,Fortney, K.,Agapito, G., Cannataro, M., Shirdel, E.A., Jurisica, I. Visual data mining of biological networks: one size does not fit all, PLoS Comp Biol, 9(1): e1002833, 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.

    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.
  • 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.
  • 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., Stümpflen, 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.
  • 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.
  • 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.
  • 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.
  • 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.

    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., LópezBähr, 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 orthotopically-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-Dimensional Biological 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.

    2010

  • Clendening, J. W., Pandyra, A., Boutros, P. C., El Ghamrasni, S., Khosravi, F., Trentin, G. A., Martirosyan, A., Hakem, A., Hakem, R., Jurisica, I., Penn, L. Z., Dysregulation of the mevalonate pathway promotes transformation. PNAS, 107(34):15051-6, 2010.
  • Zhu, C.Q., Strumpf, D., Li, C.Y., Li, Q., Liu, N., Der, S., Shepherd, F.A., Tsao, M.S., and Jurisica, I., Prognostic gene expression signature for squamous cell carcinoma of lung. Clin Cancer Res, 16(20):5038-47, 2010.
  • Reis, P. R., 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, 9(1):238, 2010.
  • Viau, C., McGuffin, M J., 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.
  • Wong, W. W., P. C. Boutros, Wasylishen, A. R., Guckert, K. D., O'Brien, E. M., Griffiths, R., Martirosyan, A. R., Bros, C., Jurisica, I., Langler, R. F., Penn, L. Z. Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. BMC Cancer, 10(1): 351, 2010.
  • Goswami, R. S., L. Waldron, Machado, J., Cervigne, N. K., Xu, W., Reis, P. P., Bailey, D. J., Jurisica, I., Crump, M. R., 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.
  • Zhu, C. Q., Ding, K., Strumpf, D., Weir, B. A., Meyerson, M., Pennell, N., Thomas, R. K., Naoki, K., Ladd-Acosta, C., Liu, N., Pintilie, M., Der, S., Seymour, L., Jurisica, I., Shepherd, F. A., and Tsao, M. S. Prognostic and Predictive Gene Signature for Adjuvant Chemotherapy in Resected Non-Small Cell Lung cancer, J Clin Oncol, 28(29):4417-24, 2010.
  • Clendening, J.W., A. Pandyra, Z. Li, P.C. Boutros, A. Martirosyan, R. Lehner, I. Jurisica, S. Trudel, and L.Z. Penn, Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma. Blood, 115(23):4787-97, 2010.
  • 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.
  • Fortney, K., Kotlyar, M., Jurisica, I. Subnetworks containing known longevity genes are robust biomarkers of Caenorhabditis elegans aging, Genome Biol, 11(2): R13, 2010.
  • Cumbaa, C. A. and Jurisica, I. Protein crystallization analysis on the World Community Grid, J Struct Funct Genomics, 11(2): 61-69, 2010.
  • Hui, A.B.Y., M. Lenarduzzi, T. Krushel, L. Waldron, M. Pintilie, W. Shi, B. P.-Ordonez, I. Jurisica, B. O’Sullivan, J. Waldron, P. Gullane, B. Cummings, F-F. Liu, Comprehensive microRNA profiling for head & neck squamous cell carcinomas, Clin Cancer Res, 16(4): 1129-39,2010.
  • 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.

    2009

  • 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.
  • Cervigne, N. K., Reis, P. P., Machado, J., Sadikovic, B., Bradley, G., Galloni, N. N., 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.
  • Brown, K.R., Otasek, D., Ali, M., McGuffin, M., Xie, W., Devani, B., van Toch, I. L., Jurisica, I. NAViGaTOR: Network analysis, visualization & graphing Toronto. Bioinformatics, 25(24): 3327-3329, 2009.
  • McGuffin, M, and Jurisica, I. Interaction techniques for selecting and manipulating subgraphs in network visualizations. IEEE Trans Vis Comp Graphics, 15(6): 937-944, 2009. [Honorable Mention at InfoVis’09]
  • Agarwal R., Jurisica, I., Cheng K.W., Mills G.B. The emerging role of the Rab25 small GTPase in cancer, Traffic, 10(11):1561-1568, 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 Sys Bio, 5, 279, 2009.
  • Hui, A.B. Y., Shi, W., Boutros, P.C., Miller, N., Pintilie, M., Fyles, T., McCready, D., Wong, D., Gerster, K., Waldron, L.,Jurisica, I., Penn, L.Z., Liu, F.F. Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab Invest, 89(5):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(6): 1257-65, 2009.
  • Boutros, P.C., Lau, S.K., Liu, N., Shepherd, F.A., Der, S.D., Tsao, M.-S., Penn, L.Z., Jurisica, I. Prognostic gene signatures for non-small cell lung cancer. PNAS, 106(8): 2824-8, 2009.

    2008

  • Ponzielli, R., Boutros, P., Katz, S., Stojanova, A., Hanley, A., Khosravi, F., Bros, C., Jurisica, I., Penn, L. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies, Nucl Acid Res, 36(21): e144, 2008.
  • Tomasini, R., Tsuchihara, K., Wilhelm, M., Fujitani, M., Rufini, A., Cheung, C.C., Khan, F., Itie-Youten, A., Wakeham, A., Tsao, M.-S., Iovanna J. L., Squire, J., Jurisica, I., Kaplan, D., Melino, G., Jurisicova, A. and Mak, T. W., TAp73 knockout shows genomic instability with tumor suppressor, Genes Dev, 22(19): 2677-91, 2008.
  • Snell, E.H., Lauricella, A.M., Potter, S.A., Luft, J.R., Gulde, S.M, Collins, R.J., Franks, G., Malkowski, M.G., Cumbaa, C., Jurisica, I. and DeTitta, G. T., Establishing a training set through the visual analysis of crystallization trials part II: Crystal examples, Acta Crystallogr D Biol Crystallogr, 64(pt11): 1123-30, 2008.
  • Snell, E.H., Luft, J.R., Potter, S.A., Lauricella, A.M., Gulde, S.M, Malkowski, M.G., Koszelak-Rosenblum, M., Said, M.I., Smith, J.L., Veatch, C.K., Collins, R.J., Franks, G., Thayer, M., Cumbaa, C., Jurisica, I. and DeTitta, G. T., Establishing a training set through the visual analysis of crystallization trials part I: ~150,000 images. Acta Crystallogr D Biol Crystallogr, 64(pt11):1131-7, 2008.
  • Zavareh, R. B., Lau, K. S., Hurren, R., Datti, A., Ashline, D. J., Gronda, M., Cheung, P., Simpson, C. D., Liu, W., Wasylishen, A. R., Boutros, P. C., Shi, H., Vengopal, A., Jurisica, I., Penn, L. Z., Reinhold, V. N., Ezzat, S., Wrana, J., Rose, D. R., Schachter, H., Dennis, J. W., Schimmer, A. D. Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function, Cancer Res, 68(16): 6688-97, 2008.
  • Director’s Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma, Gene expression-based survival prediction in lung adenocarcinoma: A multi-site, blinded validation study, Nat Med, 14(8): 822-827, 2008.
  • Aviel-Ronen, S., Coe, B. P., Lau, S., Santos, G. C., Zhu, C. Q., Strumpf, D., Jurisica, I., Lam, W. L., Tsao, M.S. Genomic markers for malignant progression in pulmonary adenocarcinoma, PNAS, 105(29): 10155-10160, 2008.
  • Sodek K.L., Evangelou A.I., Ignatchenko A., Brown T.J., Ringuette M., Jurisica I., Kislinger T. Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT). Mol Biosystems, 4(7):762-773, 2008.
  • Gortzak-Uzan, L., Ignatchenko, A., Evangelou, A., Agochiya, M., Brown, K. R., St. Onge, P., Kireeva, I., Schmitt-Ulms, G., Brown, T., 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., 7(1): 339-351, 2008.

    2007

  • Ghavidel, A., T. Kislinger, O. Pogoutse, R. Sopko, I. Jurisica, and A. Emili. Regulated tRNA export mediates the execution of G1 checkpoint in response to DNA damage. Cell, 131(5):915-26, 2007.
  • Kim S.S., Shago M., Kaustov L., Boutros P.C., Clendening J.W., Sheng Y., Trentin G.A., Barsyte-Lovejoy D., Mao D.Y., Kay R., Jurisica I., Arrowsmith C., Penn L.Z. CUL7 is a novel anti-apoptotic oncogene, Cancer Res, 67(20): 9616-9622, 2007.
  • Lau, S.K., P. C. Boutros, M. Pintilie, F. H. Blackhall, C.-Q. Zhu, D. Strumpf, M. R. Johnston, G. Darling, S. Keshavjee, T. K. Waddell, N. Liu, D. Lau, L. Z. Penn, F. A. Shepherd, I. Jurisica, S. D. Der, M.-S. Tsao. A three-gene prognostic classifier for early stage non-small cell lung cancer. J Clin Oncol, 25(35): 5562-5569, 2007.
  • Zhu, C.Q., S. Popova, E. R S Brown, D. Barsyte-Lovejoy, R. Navab, W. Shih, M. Li, M. Lu, I. Jurisica, L. Penn, D. Gullberg and M.-S. Tsao. Integrin a11 regulates IGF-2 expression in fibroblasts to enhance tumorigenicity of human non-small cell lung cancer cells, PNAS, 104(28): 11754-9, 2007.
  • Brown, K. R. and I. Jurisica, Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol, 8(5):R95, 2007.
  • Wu, C., Ma, M. H., Brown, K. R.,Geisler, M., Li, L., Tzeng, E., Jia, C. Y., Jurisica, I., Li, S. S. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Proteomics, 7(11):1775-85, 2007.
  • Cox, B., T. Kislinger, D. A. Wigle, A. Kannan, K. R. Brown, T. Okubo, B. Hogan, I. Jurisica, B. Frey, J. Rossant and A. Emili. Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes, Mol Sys Biol, 3:109, 2007.
  • Wei-Lynn Wong, W., J. W. Clendening, A. Martirosyan, P. C. Boutros, C. Bros, F. Khosravi, I. Jurisica, K. Stewart, P. L. Bergsagel, and L. Z. Penn. Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma, Mol Cancer Therap, 6(6):1886-97, 2007.

  • Additional 62 peer-reviewed papers until 2007

  • Book Chapters


  • Hauschild, A-C, Pastrello, C, Kotlyar, M and Jurisica, I. Protein-protein interaction data, their quality, and major public databases. Ed. N. Przulj. Analyzing Network Data in Biology and Medicine, An Interdisciplinary Textbook for Biological, Medical and Computational Scientists, Cambridge University Press, Cambridge, UK, pp.151-192, 2019. ISBN 978-1-108-43223-8. DOI: 10.1017/978110837770
  • Wong, S., Pastrello, C., Kotlyar, M., Faloutsos, C., Jurisica, I. SDREGION: Fast spotting of changing communities in biological networks. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 867-875, 2018.
  • Kotlyar, M., Pastrello, C., Rossos, A., Jurisica, I. Protein-protein interaction databases. In: Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 1, pp. 988–996. Oxford: Elsevier, 2018.
  • Rahmati, S., Pastrello, C., Rossos, A., Jurisica, I. Two Decades of Biological Pathway Databases: Results and Challenges, In: Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 1, pp. 1071–1084. Oxford: Elsevier, 2018.
  • Hauschild, AC, Pastrello, C., Rossos, A., Jurisica, I. Visualization of Biomedical Networks, In: Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 1, pp. 1016–1035. Oxford: Elsevier, 2018.
  • Jeanquartier, F., Jean-Quartier, C., Kotlyar, M., Tokar, T., Hauschild, A.-C., Jurisica, I., Holzinger, A., Machine Learning for In Silico Modeling of Tumor Growth, Machine Learning for Health Informatics, State-of-the-Art and Future Challenges, LNAI 9605, Springer: 415-434, 2016.
  • Larsen, S.J., Alkaersig, F.G., Ditzel, L.J., Jurisica, I., Alcaraz, N., Baumbach, J. A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks, GECCO, ACM Press, 341-348, 2016.
  • Veillette, C. J. H. and I. Jurisica. Precision Medicine for Osteoarthritis. Osteoarthritis. Pathogenesis, Diagnosis, Available Treatments, Drug Safety, Regenerative and Precision Medicine. Eds. M. Kapoor and N. Mahomed, Springer: 257-270, 2015.
  • Holzinger, A., Dehmer M., Jurisica, I. Knowledge Discovery and Data Mining in Biomedical Informatics: The Future Is in Integrative, Interactive Machine Learning Solutions, Eds. Holzinger, A., Jurisica, I., Interactive Knowledge Discovery and Data Mining: State-of-the-Art and Future Challenges in Biomedical Informatics, Volume 8401, LNCS, SOTA, Springer, 1-18, 2014.
  • Otasek, D., Pastrello, C., Holzinger, A., Jurisica, I., Visual data mining: Effective exploration of the biological universe; Eds. Holzinger, A., Jurisica, I., Interactive Knowledge Discovery and Data Mining: State-of-the-Art and Future Challenges in Biomedical Informatics, Volume 8401, LNCS, SOTA, Springer, 19-33, 2014.
  • Ponzielli R., Tu W.B., Jurisica I., Penn L.Z., Identifying myc interactors. Methods Mol Biol. 1012:51-64. 2013.
  • Andritsos, P., Jurisica, I., and Glasgow, J. Case-Based Reasoning for Biomedical Informatics and Medicine, 2013.
  • 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, 1564-1570, 2012.
  • Wong, S., Cercone, N., Jurisica, I. Characterizing healthy and disease states by systematically comparing differential correlation networks in lung. Advances in Health Informatics, Toronto, ON, 2012. [Best student paper award]
  • Otasek, D., Pastrello, C., Jurisica, I. Scalable, integrative analysis and visualization of protein interactions, Protein-Protein Interactions - Computational and Experimental Tools, WeiboCai and Hao Hong (Ed.), ISBN: 978-953-51-0397-4, InTech, pp 457-472, 2012.
  • 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.
  • Xia, E., Jurisica, I., J. Waterhouse, V. Sloan. Runtime estimation using the case-based reasoning approach for scheduling in a grid environment. Eds. I. Bichindaritz and S. Montani, Case-Based Reasoning Research and Development, ICCBR-10, LNAI-6176, 525-539, 2010.
  • Chaudhri, V.K., Jurisica, I., Koubarakis, M., Plexousakis, D., Topaloglou, T.The KBMS project and beyond. In Borgida, A. T. et al., (Eds.), Conceptual Modeling: Foundations and Applications, LNCS 5600, Springer, 466-483, 2009
  • Niu, Y. and I. Jurisica, Detecting protein-protein interaction sentences using a mixture model, in Natural Language and Information Systems (NLDB'08), Lecture Notes in Computer Science, E. Kapetanios, V. Sugumaran, and M. Spiliopoulou, Editors, Springer Verlag, Berlin, 352-354, 2008.
  • Barrios-Rodiles, M., A. Viloria-Petit, K. R. Brown, I. Jurisica, and J. L. Wrana. High-throughput screening of protein interaction networks in the TGFb interactome: understanding the signaling mechanisms driving tumor progression. Cancer Drug Discovery and Development: Transforming Growth Factor-b in Cancer Therapy, Vol2: Cancer Treatment and Therapy, Edited by Sonia B. Jakowlew, Humana Press Inc., Totowa, N.J., pp. 265-285, 2007.
  • Yan, R., P. C. Boutros, L.Z. Penn, I. Jurisica. Comparison of machine learning and pattern discovery algorithms for the prediction of human single nucleotide polymorphisms. IEEE International Conference on Granular Computing, IEEE, 2007.
  • Xia, E., I. Jurisica, J. Waterhouse, V. Sloan. The impact of runtime estimation in accuracy on scheduler performance, IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS 2007), 351-356, November 19-21, Cambridge, MA, 2007.

  • Other Publications


    Invited papers, reviews, correspondence

  • Zhu, C.Q., Pintilie, M., John, T., Strumpf, D., Shepherd, F.A., Der, S.D., Jurisica, I., Tsao, M.-S., Understanding Prognostic Gene Expression Signatures in Lung Cancer, Clin Lung Cancer, 10(5): 331-340, 2009
  • Dong, J., Kislinger, T., Jurisica, I., Wigle, D. A. Lung cancer: Developmental networks gone awry? Cancer BiolTher, 8(4), 2009.
  • Jurisicova, A., I. Jurisica, T. Kislinger. Advances in ovarian cancer proteomics: The quest for biomarkers and improved therapeutic interventions, Expert Review of Proteomics, 5(4): 551-560, 2008.
  • Wigle, D. A. and I. Jurisica. Cancer as a system failure. Cancer Informatics. Systems Biology Special Issue editorial, 3(2): 10-18, 2007
  • Evangelou, A., L. Gortzak-Uzan, I. Jurisica and T. Kislinger. Mass spectrometry, proteomics, data mining and their applications in infectious disease research, Anti-Infective Agents in Medicinal Chemistry, 6(2):89-105, 2007

  • Editorials

  • Hoeng J, Peitsch MC, Meyer, P. and Jurisica, I. Where are we at regarding species translation? A review of the sbv IMPROVER Challenge, Bioinformatics, 31(4):451-452, 2015.
  • Holzinger, A., Jurisica, I. Interactive Knowledge Discovery and Data Mining Methods in Biomedical Informatics: The future is in Integrative Machine Learning! Ed. Holzinger, A. and Jurisica, I. Interactive Knowledge Discovery and Data Mining: State-of-the-Art and Future Challenges in Biomedical Informatics, Volume 8401, LNCS, SOTA, Springer, 2014.
  • Holzinger, A., Dehmer, M. Jurisica, I. Interactive knowledge discovery and data mining in bioinformatics-State-of-the-art, future challenges and research directions, Special issue BMC Bioinf, 15 Suppl 6, I1, 2014.
  • Yakhini, Z. and Jurisica, I. Cancer computational biology, BMC Bioinf. 12(1): 120, 2011. Commentaries
  • Mills, G. B., Jurisica, I., Yarden, Y., Norman, J. C. Genomic amplicons target vesicle recycling in breast cancer. J Clin Invest, 19(8): 2123-7, 2009. Letters to Editor
  • Boutros, P.C., Pintilie, M., John, T., Starmans, M.H.W., Der, S.D., Shepherd, F.A., Tsao, M.S., Jurisica, I. Re: Gene expression-based prognostic signatures in lung cancer: Ready for clinical use?, J Nat Cancer Inst, 102(21): 1677-8, 2010.

  • All contents copyright Jurisica Lab, Krembil Research Institute, UHN. Last modified July 2019