| Year |
Citation |
Score |
| 2024 |
Clotet-Freixas S, Zaslaver O, Kotlyar M, Pastrello C, Quaile AT, McEvoy CM, Saha AD, Farkona S, Boshart A, Zorcic K, Neupane S, Manion K, Allen M, Chan M, Chen X, et al. Sex differences in kidney metabolism may reflect sex-dependent outcomes in human diabetic kidney disease. Science Translational Medicine. 16: eabm2090. PMID 38446901 DOI: 10.1126/scitranslmed.abm2090 |
0.378 |
|
| 2024 |
Koussiouris J, Looby N, Kotlyar M, Kulasingam V, Jurisica I, Chandran V. Classifying patients with psoriatic arthritis according to their disease activity status using serum metabolites and machine learning. Metabolomics : Official Journal of the Metabolomic Society. 20: 17. PMID 38267619 DOI: 10.1007/s11306-023-02079-7 |
0.387 |
|
| 2023 |
Khan S, Chakraborty M, Wu F, Chen N, Wang T, Chan YT, Sayad A, Vásquez JDS, Kotlyar M, Nguyen K, Huang Y, Alibhai FJ, Woo M, Li RK, Husain M, et al. B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters. Biorxiv : the Preprint Server For Biology. PMID 38529494 DOI: 10.1101/2023.09.12.556363 |
0.387 |
|
| 2023 |
Pastrello C, Kotlyar M, Abovsky M, Lu R, Jurisica I. PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. Nucleic Acids Research. PMID 37994706 DOI: 10.1093/nar/gkad1027 |
0.466 |
|
| 2023 |
Choksi H, Li S, Looby N, Kotlyar M, Jurisica I, Kulasingam V, Chandran V. Identifying Serum Metabolomic Markers Associated with Skin Disease Activity in Patients with Psoriatic Arthritis. International Journal of Molecular Sciences. 24. PMID 37894979 DOI: 10.3390/ijms242015299 |
0.402 |
|
| 2023 |
Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. USNAP: Fast unique dense region detection and its application to lung cancer. Bioinformatics (Oxford, England). PMID 37527019 DOI: 10.1093/bioinformatics/btad477 |
0.399 |
|
| 2023 |
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, et al. Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing. Arxiv. PMID 37332567 |
0.478 |
|
| 2022 |
Pastrello C, Abovsky M, Lu R, Ahmed Z, Kotlyar M, Veillette C, Jurisica I. Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database. Osteoarthritis and Cartilage Open. 4: 100237. PMID 36474475 DOI: 10.1016/j.ocarto.2022.100237 |
0.422 |
|
| 2022 |
Hauschild AC, Pastrello C, Ekaputeri GKA, Bethune-Waddell D, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I. MirDIP 5.2: tissue context annotation and novel microRNA curation. Nucleic Acids Research. PMID 36453996 DOI: 10.1093/nar/gkac1070 |
0.521 |
|
| 2022 |
Pathmanathan S, Yao Z, Coelho P, Valla R, Drecun L, Benz C, Snider J, Saraon P, Grozavu I, Kotlyar M, Jurisica I, Park M, Stagljar I. B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer. Iscience. 25: 105419. PMID 36388990 DOI: 10.1016/j.isci.2022.105419 |
0.503 |
|
| 2022 |
Lim SH, Snider J, Birimberg-Schwartz L, Ip W, Serralha JC, Botelho HM, Lopes-Pacheco M, Pinto MC, Moutaoufik MT, Zilocchi M, Laselva O, Esmaeili M, Kotlyar M, Lyakisheva A, Tang P, et al. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Molecular Systems Biology. 18: e10629. PMID 35156780 DOI: 10.15252/msb.202110629 |
0.461 |
|
| 2022 |
Kotlyar M, Wong SWH, Pastrello C, Jurisica I. Improving Analysis and Annotation of Microarray Data with Protein Interactions. Methods in Molecular Biology (Clifton, N.J.). 2401: 51-68. PMID 34902122 DOI: 10.1007/978-1-0716-1839-4_5 |
0.519 |
|
| 2022 |
Kotlyar M, Pastrello C, Ahmed Z, Chee J, Varyova Z, Jurisica I. IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. Nucleic Acids Research. 50: D640-D647. PMID 34755877 DOI: 10.1093/nar/gkab1034 |
0.522 |
|
| 2021 |
Bhat M, Pasini E, Pastrello C, Angeli M, Baciu C, Abovsky M, Coffee A, Adeyi O, Kotlyar M, Jurisica I. Estrogen Receptor 1 Inhibition of Wnt/β-Catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis. Frontiers in Oncology. 11: 777834. PMID 34881186 DOI: 10.3389/fonc.2021.777834 |
0.383 |
|
| 2021 |
Aboualizadeh F, Yao Z, Guan J, Drecun L, Pathmanathan S, Snider J, Umapathy G, Kotlyar M, Jurisica I, Palmer R, Stagljar I. Mapping the Phospho-dependent ALK Interactome to Identify Novel Components in ALK Signaling. Journal of Molecular Biology. 433: 167283. PMID 34606829 DOI: 10.1016/j.jmb.2021.167283 |
0.491 |
|
| 2021 |
Clotet-Freixas S, Kotlyar M, McEvoy CM, Pastrello C, Rodríguez-Ramírez S, Farkona S, Cardinal H, Dieudé M, Hébert MJ, Li Y, Famure O, Chen P, Kim SJ, Chan E, Jurisica I, et al. Increased Autoantibodies Against Ro/SS-A, CENP-B, and La/SS-B in Patients With Kidney Allograft Antibody-mediated Rejection. Transplantation Direct. 7: e768. PMID 34557585 DOI: 10.1097/TXD.0000000000001215 |
0.368 |
|
| 2021 |
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, et al. Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis. The Journal of Clinical Investigation. 131. PMID 34196309 DOI: 10.1172/JCI152424 |
0.405 |
|
| 2021 |
Berra G, Farkona S, Mohammed-Ali Z, Kotlyar M, Levy L, Clotet-Freixas S, Ly P, Renaud-Picard B, Zehong G, Daigneault T, Duong A, Batruch I, Jurisica I, Konvalinka A, Martinu T. Association between renin-angiotensin system and chronic lung allograft dysfunction. The European Respiratory Journal. PMID 33863738 DOI: 10.1183/13993003.02975-2020 |
0.404 |
|
| 2021 |
Bhat M, Pasini E, Pastrello C, Rahmati S, Angeli M, Kotlyar M, Ghanekar A, Jurisica I. Integrative analysis of layers of data in hepatocellular carcinoma reveals pathway dependencies. World Journal of Hepatology. 13: 94-108. PMID 33584989 DOI: 10.4254/wjh.v13.i1.94 |
0.373 |
|
| 2021 |
Chakraborty M, Chu K, Shrestha A, Revelo XS, Zhang X, Gold MJ, Khan S, Lee M, Huang C, Akbari M, Barrow F, Chan YT, Lei H, Kotoulas NK, Jovel J, ... ... Kotlyar M, et al. Mechanical Stiffness Controls Dendritic Cell Metabolism and Function. Cell Reports. 34: 108609. PMID 33440149 DOI: 10.1016/j.celrep.2020.108609 |
0.389 |
|
| 2020 |
Nakamura A, Rampersaud YR, Sundararajan K, Nakamura S, Wu B, Matip E, Haroon N, Krawetz RJ, Rossomacha E, Gandhi R, Kotlyar M, Rockel JS, Jurisica I, Kapoor M. Zinc finger protein-440 promotes cartilage degenerative mechanisms in human facet and knee osteoarthritis chondrocytes. Osteoarthritis and Cartilage. PMID 33347923 DOI: 10.1016/j.joca.2020.12.004 |
0.4 |
|
| 2020 |
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, et al. Towards a unified open access dataset of molecular interactions. Nature Communications. 11: 6144. PMID 33262342 DOI: 10.1038/s41467-020-19942-z |
0.461 |
|
| 2020 |
Clotet-Freixas S, McEvoy CM, Batruch I, Pastrello C, Kotlyar M, Van JAD, Arambewela M, Boshart A, Farkona S, Niu Y, Li Y, Famure O, Bozovic A, Kulasingam V, Chen P, et al. Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection: A Proteomics Study. Journal of the American Society of Nephrology : Jasn. PMID 32900843 DOI: 10.1681/Asn.2020030286 |
0.437 |
|
| 2020 |
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, et al. The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. Biorxiv : the Preprint Server For Biology. PMID 32587962 DOI: 10.1101/2020.06.16.153817 |
0.454 |
|
| 2020 |
Yao Z, Aboualizadeh F, Kroll J, Akula I, Snider J, Lyakisheva A, Tang P, Kotlyar M, Jurisica I, Boxem M, Stagljar I. Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition. Nature Communications. 11: 2440. PMID 32415080 DOI: 10.1038/S41467-020-16299-1 |
0.518 |
|
| 2020 |
Sinsky J, Majerova P, Kovac A, Kotlyar M, Jurisica I, Hanes J. Physiological Tau Interactome in Brain and Its Link to Tauopathies. Journal of Proteome Research. 19: 2429-2442. PMID 32357304 DOI: 10.1021/Acs.Jproteome.0C00137 |
0.52 |
|
| 2020 |
Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, et al. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS. Nature Communications. 11: 499. PMID 31980649 DOI: 10.1038/S41467-019-14224-9 |
0.547 |
|
| 2020 |
Pastrello C, Kotlyar M, Jurisica I. Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). Methods in Molecular Biology (Clifton, N.J.). 2074: 125-134. PMID 31583635 DOI: 10.1007/978-1-4939-9873-9_10 |
0.533 |
|
| 2019 |
Rahmati S, 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. Nucleic Acids Research. PMID 31733064 DOI: 10.1093/Nar/Gkz989 |
0.536 |
|
| 2019 |
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, et al. Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications. 10: 1098. PMID 30833551 DOI: 10.1038/S41467-019-08814-W |
0.396 |
|
| 2019 |
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, et al. Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications. 10: 10. PMID 30602777 DOI: 10.1038/S41467-018-07709-6 |
0.522 |
|
| 2018 |
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. PMID 30407591 DOI: 10.1093/Nar/Gky1037 |
0.556 |
|
| 2018 |
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, et al. Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis. The Journal of Clinical Investigation. PMID 30222135 DOI: 10.1172/Jci120401 |
0.495 |
|
| 2017 |
Kotlyar M, Rossos AEM, Jurisica I. Prediction of Protein-Protein Interactions. Current Protocols in Bioinformatics. 60: 8.2.1-8.2.14. PMID 29220074 DOI: 10.1002/Cpbi.38 |
0.513 |
|
| 2017 |
Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. Modeling tumor progression via the comparison of stage-specific graphs. Methods (San Diego, Calif.). PMID 28684340 DOI: 10.1016/J.Ymeth.2017.06.033 |
0.513 |
|
| 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. Scientific Reports. 7: 46826. PMID 28530244 DOI: 10.1038/Srep46826 |
0.722 |
|
| 2017 |
Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Oishi A, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Yao Z, et al. Systematic protein-protein interaction mapping for clinically relevant human GPCRs. Molecular Systems Biology. 13: 918. PMID 28298427 DOI: 10.15252/Msb.20167430 |
0.544 |
|
| 2016 |
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, et al. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. Molecular Cell. PMID 28065597 DOI: 10.1016/J.Molcel.2016.12.004 |
0.523 |
|
| 2016 |
Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, Ketteler R. Systematic Identification of Oncogenic EGFR Interaction Partners. Journal of Molecular Biology. PMID 27956147 DOI: 10.1016/J.Jmb.2016.12.006 |
0.532 |
|
| 2016 |
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. Circulating plant miRNAs can regulate human gene expression in vitro. Scientific Reports. 6: 32773. PMID 27604570 DOI: 10.1038/Srep32773 |
0.739 |
|
| 2016 |
Chehade R, Pettapiece-Phillips R, Salmena L, Kotlyar M, Jurisica I, Narod SA, Akbari MR, Kotsopoulos J. Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific. Breast Cancer Research : Bcr. 18: 87. PMID 27534398 DOI: 10.1186/S13058-016-0739-8 |
0.475 |
|
| 2016 |
Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. MYC interaction with the tumour suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. Cell Cycle (Georgetown, Tex.). 0. PMID 27267444 DOI: 10.1080/15384101.2016.1146836 |
0.557 |
|
| 2016 |
Pettapiece-Phillips R, Kotlyar M, Chehade R, Salmena L, Narod SA, Akbari M, Jurisica I, Kotsopoulos J. Uninterrupted Sedentary Behavior Downregulates BRCA1 Gene Expression. Cancer Prevention Research (Philadelphia, Pa.). 9: 83-8. PMID 26526989 DOI: 10.1158/1940-6207.Capr-15-0291 |
0.48 |
|
| 2016 |
Kotlyar M, Pastrello C, Sheahan N, Jurisica I. Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Research. 44: D536-41. PMID 26516188 DOI: 10.1093/Nar/Gkv1115 |
0.546 |
|
| 2015 |
Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. Fundamentals of protein interaction network mapping. Molecular Systems Biology. 11: 848. PMID 26681426 DOI: 10.15252/Msb.20156351 |
0.532 |
|
| 2015 |
Fortney K, Griesman J, Kotlyar M, Pastrello C, Angeli M, Sound-Tsao M, Jurisica I. Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic data. Plos Computational Biology. 11: e1004068. PMID 25786242 DOI: 10.1371/Journal.Pcbi.1004068 |
0.695 |
|
| 2015 |
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 GB, Jurisicova A, Stagljar I, et al. In silico prediction of physical protein interactions and characterization of interactome orphans. Nature Methods. 12: 79-84. PMID 25402006 DOI: 10.1038/Nmeth.3178 |
0.546 |
|
| 2015 |
Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. Fundamentals of protein interaction network mapping Molecular Systems Biology. 11. DOI: 10.15252/msb.20156351 |
0.455 |
|
| 2015 |
Tu WB, Stojanova A, Ponzielli R, Kotlyar M, Chan P, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. Abstract A36: Interaction of the MYC oncoprotein with the tumor suppressive SWI/SNF complex member INI1 Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-A36 |
0.544 |
|
| 2015 |
Poloz Y, Sheikh MZE, Petschnigg J, Groisman B, Kotlyar M, Jurisica I, Stagljar I, Stambolic V. Abstract A20: Insulin receptor signaling in mammary epithelial cells Molecular Cancer Therapeutics. 14. DOI: 10.1158/1538-8514.Pi3K14-A20 |
0.491 |
|
| 2014 |
Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, et al. The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Nature Methods. 11: 585-92. PMID 24658140 DOI: 10.1038/Nmeth.2895 |
0.536 |
|
| 2014 |
Kittanakom S, Barrios-Rodiles M, Petschnigg J, Arnoldo A, Wong V, Kotlyar M, Heisler LE, Jurisica I, Wrana JL, Nislow C, Stagljar I. CHIP-MYTH: a novel interactive proteomics method for the assessment of agonist-dependent interactions of the human β₂-adrenergic receptor. Biochemical and Biophysical Research Communications. 445: 746-56. PMID 24561123 DOI: 10.1016/J.Bbrc.2014.02.033 |
0.567 |
|
| 2014 |
Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I. Integration, visualization and analysis of human interactome. Biochemical and Biophysical Research Communications. 445: 757-73. PMID 24491561 DOI: 10.1016/J.Bbrc.2014.01.151 |
0.52 |
|
| 2013 |
Fortney K, Xie W, Kotlyar M, Griesman J, Kotseruba Y, Jurisica I. NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. Nucleic Acids Research. 41: D720-7. PMID 23203867 DOI: 10.1093/Nar/Gks1106 |
0.688 |
|
| 2012 |
Kotlyar M, Fortney K, Jurisica I. Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods (San Diego, Calif.). 57: 499-507. PMID 22749929 DOI: 10.1016/J.Ymeth.2012.06.003 |
0.702 |
|
| 2012 |
Fortney K, Morgen EK, Kotlyar M, Jurisica I. In silico drug screen in mouse liver identifies candidate calorie restriction mimetics. Rejuvenation Research. 15: 148-52. PMID 22533420 DOI: 10.1089/Rej.2011.1263 |
0.69 |
|
| 2012 |
Wong S, Kotlyar M, Strumpf D, Cercone N, Shepherd FA, Tsao M, Jurisica I. Abstract 4912: Systematic, comparative network analysis on non-small cell lung cancer Cancer Research. 72: 4912-4912. DOI: 10.1158/1538-7445.Am2012-4912 |
0.547 |
|
| 2011 |
Djebbari A, Ali M, Otasek D, Kotlyar M, Fortney K, Wong S, Hrvojic A, Jurisica I. Navigator: Large scalable and interactive navigation and analysis of large graphs Internet Mathematics. 7: 314-347. DOI: 10.1080/15427951.2011.604289 |
0.666 |
|
| 2010 |
Fortney K, Kotlyar M, Jurisica I. Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biology. 11: R13. PMID 20128910 DOI: 10.1186/Gb-2010-11-2-R13 |
0.678 |
|
| 2009 |
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. Molecular Systems Biology. 5: 279. PMID 19536202 DOI: 10.1038/Msb.2009.37 |
0.551 |
|
| 2006 |
Kotlyar M, Jurisica I. Predicting protein-protein interactions by association mining Information Systems Frontiers. 8: 37-47. DOI: 10.1007/S10796-005-6102-8 |
0.547 |
|
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