OsteoDIP

Publications

Rahmati, S., O’Rielly, D.D., Li, Q. et al. Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. Sci Rep 10, 21703 (2020). doi: 10.1038/s41598-020-78866-2. Perfetto L, Pastrello C, Del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob HH, Porras P. The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions, Database, 2020. In press Ali SA, Gandhi R, Potla P, Keshavarzi S, Espin-Garcia O, Shestopaloff K, Pastrello C, Bethune-Waddell D, Lively S, Perruccio AV, Rampersaud YR, Veillette C, Rockel JS, Jurisica I, Appleton CT, Kapoor M. Sequencing identifies a distinct signature of circulating microRNAs in early radiographic knee osteoarthritis, Osteoarthritis Cartilage,S1063-4584(20)31081-5, 2020. doi: 10.1016/j.joca.2020.07.003. Epub ahead of print. Endisha H, Datta P, Sharma A, Nakamura S, Rossomacha E, Younan C, Ali SA, Tavallaee G, Lively S, Potla P, Shestopaloff K, Rockel JS, Krawetz R, Mahomed NN, Jurisica I, Gandhi R, Kapoor M. MicroRNA-34a-5p Promotes Joint Destruction during Osteoarthritis, Arthritis Rheumatol. 2020 Oct 8. doi: 10.1002/art.41552. Epub ahead of print. Poulami Datta, Rajiv Gandhi, Sayaka Nakamura, Starlee Lively, Evgeny Rossomacha, Pratibha Potla, Konstantin Shestopaloff, Helal Endisha, Chiara Pastrello, Igor Jurisica, Jason S. Rockel, Mohit Kapoor, Effect of autotaxin inhibition in a surgically-induced mouse model of osteoarthritis, Osteoarthritis and Cartilage Open, Volume 2, Issue 3, 2020, 100080, ISSN 2665-9131, https://doi.org/10.1016/j.ocarto.2020.100080. Tokar, T., Pastrello, C., Jurisica, I. GSOAP: A tool for visualization of gene set over-representation analysis, Bioinformatics, Bioinformatics, 36(9):2923-2925, 2020. doi: 10.1093/bioinformatics/btaa001 Rahmati R, Abovsky M, Pastrello C, Kotlyar M, Lu R, Cumbaa CA, Rahman P, Chandran V, Jurisica I, pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species, Nucl Acids Res, 48(D1): D479–D488, 2020, https://doi.org/10.1093/nar/gkz989 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, 46(13):2722-2730, 2019. doi: 10.1007/s00259-019-04382-9. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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.