• Title: CDX2 as a biomarker to guide use of autophagy inhibitors in ovarian cancer
    US62/952,724; Application Date: Dec 23, 2019
    Joint Holder Names: Andrea Jurisicova; Igor Jurisica
  • Title: Integration, visualization and analysis of human interactome
    Joint Holder Names: Pastrello, C, Pasini, E., Jurisica, I.
  • Title: Computationally repurposing drugs for lung cancer: Candidate therapeutics from an integrative meta-analysis of cancer gene signatures and chemogenomic data
    Joint Holder Names: Fortney, K., Kotlyar, M., Jurisica, I.
  • Title: Comprehensive In Silico prediction of physical protein interactions and characterization of interactome orphans
    Joint Holder Names: Kotlyar, M., Jurisica, I.
  • Title: Systematically characterizing human proteins without reported interactions
    Track Code: 2013-018
    Joint Holder Names: Kotlyar, M., Jurisica, I.
  • Title: Construction of new medicines via game proof search
    Track Code: 2013-019
    Joint Holder Names: Heifets, A., Jurisica, I.
  • Title: Protein interaction and gene association prediction: Filling the gap with integrative approach
    Track Code: 2013-020
    Joint Holder Names: Vafaee, F., Jurisica, I.
  • Title: In silico drug screen in mouse liver identifiescandidate calorie restriction mimetics
    Track Code: 2013-021
    Joint Holder Names: Fortney, K, Kotlyar, M., Jurisica, I.
  • Title: NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
    Track Code: 2013-022
    Joint Holder Names: Fortney, Jurisica, I.
  • Title: Novel prognostic markers in mantle cell lymphoma.
    March 2012.
    Joint Holder Names: Goswami, R., L. Waldron, Jurisica, I., M. Crump, S. K. Reid
  • Title: SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents.
    2012-006, January 2012.
    Joint Holder Names: Abraham Heifets, I. Jurisica
  • Title: A prognostic signature that predicts aggressiveness in B-cell non-Hodgkin lymphoma.
    2010-051, August, 2010
    Joint Holder Names: Goswami, R., L. Waldron, M. Crump, Jurisica, I., S. K. Reid.
  • Title: 14-gene prognostic signature for ovarian cancer.
    March 2010
    Joint Holder Names: Jurisica, I., L. Waldron.
  • Title: A robust 4-gene prognostic signature for oral squamous cell carcinoma
    TDC reference number: 2010-016-02. March, 2010. Application filed 2012-Jan-11. Expiry 2013-July-11
    Joint Holder Names: Jurisica, I., L. Waldron, P. Reis, S. K. Reid.
  • Title: LSC and HSC signatures for predicting survival of patients having hematological cancer.
    December 3, 2010 US13/513,268; US20120237488A1 US Provisional Patent #61/266,704, TDC reference number: 2009-114-01. Filed Dec. 4, 2009
    Joint Holder Names: Dick, J.; I. Jurisica; M. Minden; K. Eppert; E. Lechman; L. D. Waldron; B. Nilsson; B. L. Ebert; J. S. Danska; K. Takenaka.
  • Title: Compositions and methods for classifying lung cancer and prognosing lung cancer survival.
    June 5, 2009; July 2008 PCT/CA2009/000774; WO02009146545, TDC #2007-020-02. USP 61-059085. September 15 2011 US 2011/0224313 A1
    Joint Holder Names: Zhu, C.Q., Jurisica, I., Aviel-Ronen, S., Coe, B., Lam, W., Tsao, M.-S., D. Der, S.
  • Title: Methods and compositions for lung cancer prognosis.
    October 29, 2010. US61-171687, TDC# 2009-043-02, Filed 2009-04-21. PTC filed on 2010-04-21; TDC# 2009-043-03. WO 2010/121380A1
    Joint Holder Names: Tsao, M.-S., Craddock, K., Lam, W., Buys, T., Jurisica, I., Shepherd, F.A.
  • Title: Prognostic gene expression signature for squamous cell carcinoma of the lung.
    October 28, 2010. US61170743, TDC # 2009-007-02. Filed 2009-04-20. PCT filed 2010-04-20; WO 2010/121370 A1
    Joint Holder Names: Tsao, M.-S., Shepherd, F. A., Jurisica, I., Der, S.D., Zhu, C.Q.
  • Title:NAViGaTOR: A scalable tool for protein-protein interaction network analysis and visualization
    Invention Disclosure, March 25, 2009. 2009-032
    Joint Holder Names: D. Otasek, M. Ali, W. Xie, M. McGuffin, B. Devani, K. R. Brown, I. Jurisica.
  • Title: Prognostic and predictive gene signature for non-small cell lung cancer and adjuvant chemotherapy
    July 22, 2010 US12/465,954; US12/684,370; PCT/CA2009/000650; WO0200913 July 3, 2012 US 8,211,643 B2; US 20090291448
    Joint Holder Names: M.-S. Tsao, F. A. Shepherd, I. Jurisica, S. D. Der, C. Q. Zhu, D. Strumpf, L. Seymour, K. Ding.
  • Title: A 12-gene prognostic gene signature for squamous cell carcinoma of lung.
    January 2009. PCT/CA2010
    Joint Holder Names: M.-S. Tsao, C.-Q. Zhu, I. Jurisica, S. D. Der, F. A. Shepherd.
  • June 10, 2010 Title: Methods for biomarker identification and biomarker for non-small cell lung cancer.
    US61119936, TDC #2008-024-01, December 4, 2008. PCT/CA2009/001775 filed on 2 December 2009; WO 2010/063121 A1
    Joint Holder Names: M.-S. Tsao, P. C. Boutros, S. Lau, F. A. Shepherd, L. Z. Penn, I. Jurisica, S. D. Der.
  • Title: A method to find all prognostic signatures from a microarray dataset.
    Invention Disclosure. July 2008.
    Joint Holder Names: P. C. Boutros, S. Lau, F. A. Shepherd, S. D. Der, M.-S. Tsao, L. Z. Penn, I. Jurisica
  • Title: 2048 Novel Six-Gene Prognostic Markers for Non-Small Cell Lung Cancer.
    Invention Disclosure. July 2008.
    Joint Holder Names: P. C. Boutros, S. K. Lau, F. A. Shepherd, S. D. Der, M.-S. Tsao, L. Z. Penn, I. Jurisica.
  • Title: Gene markers of invasive cancer in lung bronchiole-alveolar carcinoma.
    IPD 2007-020-02.INV 08-011, US61/059,085, B&P 10723-271, filed June 5, 2008.
    Joint Holder Names: M.-S. Tsao, S. A.-Ronen, I. Jurisica, C.-Q. Zhu, W. Lam, B. P. Coe.
  • Title: A 15-gene prognostic signature for non-small cell lung cancer.
    June 2008.
    Joint Holder Names: M.-S. Tsao, F. A. Shepherd, I. Jurisica, C.-Q. Zhu, D. Strumpf, K. Ding, L. Seymour.
  • Title: Interologous interaction database
    Invention Disclosure, June 18, 2007. 2007-034
    Joint Holder Names: K. R. Brown and I. Jurisica.
  • May 22, 2007 Title: Detection of ovarian cancer biomarkers by proteomics and bioinformatics
    US Provisional Patent 60/929, 861
    Joint Holder Names: T. Kislinger and I. Jurisica.
  • Title: A minimal set of prognostic marker genes for early stage Non-small cell lung cancer - Materials and Methods for Prognosing Lung Cancer - 6-gene classifier
    Joint Holder Names: M. Sound-Tsao, S. Der, P. Boutros, S. Lau, M. Pintilie, F. Shepherd, I. Jurisica.
  • September 27, 2011 Title: A minimal set of prognostic marker genes for early stage Non-small cell lung cancer - Materials and Methods for Prognosing Lung Cancer - 3-gene classifier
    US 11/940,707, 2007. Patent No: US8026055B2, US20080176236, Sept 27, 2011
    Joint Holder Names: M. Sound-Tsao, S. Der, P. Boutros, S. Lau, M. Pintilie, F. Shepherd, I. Jurisica, L. Penn.
  • Nov 12, 2009 Title: Scalable Scheduling of Tasks in Heterogeneous Systems.
    IBM Invention Disclosure, IP&L Disclosure Evaluation: CA8-2007-0054, 2007. Patent filed February 21, 2008; CA9-2008-0019. US2009/0282413 A1, November 12, 2009
    Joint Holder Names: E. Xia., I. Jurisica, J. Waterhouse, E. Cialini. April 30, 2013 US-8434085
  • Title: Dynamic selection of scheduling heuristics in heterogeneous systems.
    IBM Invention Disclosure, 2006.
    Joint Holder Names: E. Xia, I. Jurisica, J. Waterhouse, V. Sloan.
  • Title: Run time estimation using TA3 case-based reasoning system for scheduling in a grid environment.
    IBM Invention Disclosure, /IPCOM//000148769D, 2006.
    Joint Holder Names: E. Xia, I. Jurisica, J. Waterhouse, V. Sloan.
  • Title: Potential new markers for colorectal cancer diagnosis and targeting.
    Invention Disclosure, 2005.
    Joint Holder Names: M. Sound-Tsao, I. Jurisica, I. Seiden-Long, K. Brown.
  • Title: Dynamic semi-structured repository for mining software and software-related information.
    January 15, 2002 US Patent US 6,339,776 B2, January 15, 2002; October 14, 2003 Canadian Patent 2,284,949, October 14, 2003.
    Joint Holder Names: H. Dayani-Fard, I. Jurisica.
Cancer Informatics in Post Genomic Era
Jurisica, I., D. A. Wigle, and B. Wong. Cancer Informatics in the Post Genomic Era; Toward Information-Based Medicine Series: Cancer Treatment and Research, Volume 137, Springer Verlag, July 2007.
Less than 50% of diagnosed cancers are cured using current treatment modalities. Many common cancers can already be fractionated into such therapeutic subsets with unique prognostic outcomes based on characteristic molecular phenotypes. It is widely expected that treatment approaches of complex cancer will soon be revolutionized by combining molecular profiling and computational analysis, which will result in the introduction of novel therapeutics and treatment decision algorithms that target the underlying molecular mechanisms of cancer.

The sequencing of the human genome was the first step in understanding the ways in which we are wired; However, this genetic blueprint provides only a "parts list", and neither information about how the human organism is actually working, nor insight into function or interactions among the ~30 thousand constitutive parts that comprise our genome. Considering that the 30 years of worldwide molecular biology efforts have only annotated about 10% of this gene set, and we know even less about proteins, it is comforting to know that high-throughput data generation and analysis is now widely available.

By arraying tens of thousands of genes and analyzing abundance of and interaction among proteins, it is now possible to measure the relative activity of genes and proteins in normal and diseased tissue. The technology and datasets of such profiling-based analyses will be described along with the mathematical challenges that face the mining of the resulting datasets; We describe the issues related to using this information in the clinical setting, and the future steps that will lead to drug design and development to cure complex diseases such as cancer.
Knowledge Discovery in Proteomics
Jurisica, I.and D. Wigle. Knowledge Discovery in Proteomics. Mathematical, Computational Biology Series, Volume 8, Chapman; Hall/CRC Press, 2006.
"He who knows useful things, not many things, is wise." Aeschylus (ca. 525-456 BC)

The nascent fields of bioinformatics and computational biology are currently an odd amalgam of everything from biologists with a computational bent, through physicists and mathematicians, to computer scientists and engineers sifting through the myriad of data and grappling with biological questions. Much of the excitement comes from a collective sense that there is something truly new evolving. Hardware and software limitations are declaring themselves as major challenges to managing and interpreting the avalanche of data from high-throughput biological platforms. This drinking from the fire hydrant'' sensation continues to spark interest and draw technical skill from other domains. As we move forward to true systems biology experimentation, it is increasingly obvious that experts in robotics, engineering, mathematics, physics, and computer science have become key players alongside traditional molecular biology.

Life sciences applications are typically characterized by multimodal representations, lack of complete and consistent domain theories, rapid evolution of domain knowledge, high dimensionality, and large amounts of missing information. Data in these domains require robust approaches to deal with missing and noisy information. Modern proteomics is no exception. As our understanding of protein structure and function becomes ever more complicated, we have reached a point in time where the actual management of data is a major hurdle to knowledge discovery. Many of the browse-through applications of yesterday are clearly not useful for computational manipulation. If the data was not created having data mining and decision support in mind, how well can it serve that purpose?

We felt this book was a timely discussion of some of the key issues in the field. In subsequent chapters we discuss a number of examples from our own experience that represent some of the challenges of knowledge discovery in high-throughput proteomics. This discussion is by no means comprehensive, and does not attempt to highlight all relevant domains. However, we hope to provide the reader with an overview of what we envision as an important and emerging field in its own right by discussing the challenges and potential solutions to the problems presented. We have selected five specific domains to discuss: (1) Mass spectrometry based protein analysis; (2) Protein--protein interaction network analysis; (3) Systematic high-throughput protein crystallization; (4) A systematic and integrated analysis of multiple data repositories using a diverse set of algorithms and tools; and (5) Systems biology. In each of these areas, we describe the challenges created by the type of data produced, and potential solutions to the problem of data mining within the domain. We hope this stimulates even more discussion, and newer and better ways to deal with the problems at hand.
Interactive Knowledge Discovery and Data Mining
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.
Biomedical research is drowning in data, yet starving for knowledge. Current challenges in biomedical research and clinical practice include information overload - the need to combine vast amounts of structured, semi-structured, weakly structured data and vast amounts of unstructured information - and the need to optimize workflows, processes and guidelines, to increase capacity while reducing costs and improving efficiencies. In this paper we provide a very short overview on interactive and integrative solutions for knowledge discovery and data mining. In particular, we emphasize the benefits of including the end user into the .interactive. knowledge discovery process. We describe some of the most important challenges, including the need to develop and apply novel methods, algorithms and tools for the integration, fusion, pre-processing, mapping, analysis and interpretation of complex biomedical data with the aim to identify testable hypotheses, and build realistic models. The HCI-KDD approach, which is a synergistic combination of methodologies and approaches of two areas, Human-Computer Interaction (HCI) and Knowledge Discovery & Data Mining (KDD), offer ideal conditions towards solving these challenges: with the goal of supporting human intelligence with machine intelligence. There is an urgent need for integrative and interactive machine learning solutions, because no medical doctor or biomedical researcher can keep pace today with the increasingly large and complex data sets -- often called "Big Data".
Data Integration in the Life Sciences
Baker, C.J.O., Butler, G., Jurisica, I. Data Integration in the Life Sciences, 9th International Conference, DILS 2013, Montreal, QC, Canada, July 11-12, 2013. Lecture Notes in Computer Science, Volume 7970 2013, DOI: 10.1007/978-3-642-39437-9, Springer Berlin Heidelberg, 2013.
  • Goncalves LCO, Magalhaes-Neto AM, Bassini A, Prado ES, Muniz-Santos R, Verli MVA, Jurisica L, Lopes JSS, Jurisica I, Andrade CMB, Cameron LC, Sportomics suggests that albuminuria is a sensitive biomarker of hydration in cross combat, Sci Reports, 12:8150, 2022.
  • Ali SA, Espin-Garcia O, Wong AK, Potla P, Pastrello C, McIntyre M, Lively S, Jurisica I, Gandhi R, Kapoor M. Circulating microRNAs differentiate fast-progressing from slow-progressing and non-progressing knee osteoarthritis in the Osteoarthritis Initiative cohort, Ther Adv Musculoskelet Dis, 14:1759720X221082917, 2022.
  • Sandmo SB, Matyasova K, Filipcik P, Cente M, Koerte IK, Pasternak O, Andersen TE, Straume-Naesheim TM, Bahr R, Jurisica I. Changes in circulating microRNAs following head impacts in soccer, Brain Inj. 2022 Feb 16:1-12. doi: 10.1080/02699052.2022.2034042. Online ahead of print.
  • Cabral-Marques O, Halpert G, Schimke LF, Ostrinski Y, Vojdani A, Baiocchi GC, Freire PP, Filgueiras IS, Zyskind I, Lattin MT, Tran F, Schreiber S, Marques AHC, Placa DR, Fonseca DLM, Humrich JY, Mueller A, Giil LM, Grasshoff H, Schumann A, Hackel A, Junker J, Meyer C, Ochs HD, Lavi YB, Scheibenbogen C, Dechend R, Jurisica I, Schulze-Forster K, Silverberg JI, Amital H, Zimmerman J, Heidecke H, Rosenberg AZ, Riemekasten G, Shoenfeld Y, Autoantibodies targeting GPCRs and RAS-related molecules associate with COVID-19 severity, Nat Commun, 13(1):1220, 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(1): 100237, 2022.
  • Lena F. Schimke, Alexandre H.C. Marques, Gabriela Crispim Baiocchi, Caroline Aliane de Souza Prado, Dennyson Leandro M. Fonseca, Paula Paccielli Freire, Desiree Rodrigues Placa, Igor Salerno Filgueiras, Ranieri Coelho Salgado, Gabriel Jansen-Marques, Antonio Edson Rocha Oliveira, Jean Pierre Schatzmann Peron, Gustavo Cabral-Miranda, Jose Alexandre Marzagao Barbuto, Niels Olsen Saraiva Camara, Vera Lucia Garcia Calich, Hans D. Ochs, Antonio Condino-Neto, Joseph Balnis, Ariel Jaitovich, Jonas Schulte-Schrepping, Thomas Ulas, Joachim L. Schultze, Helder I. Nakaya, Igor Jurisica and Otavio Cabral-Marques, Severe COVID-19 shares a common neutrophil activation signature with other acute inflammatory states, Cells, 11(5):847, 2022.
  • Tokar T, Pastrello C, Abovsky M, Rahmati S, Jurisica I. miRAnno-network-based functional microRNA annotation, Bioinformatics, 2021 Jul 23:btab527
  • Eder L, Li Q, Rahmati S, Rahman P, Jurisica I, Chandran V. Defining Imaging Sub-phenotypes of Psoriatic Arthritis: Integrative Analysis of Imaging Data and Gene Expression in a PsA Patient Cohort. Rheumatology (Oxford). 2022 Feb 14:keac078. doi: 10.1093/rheumatology/keac078. Online ahead of print.
  • 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, Lopez Vazquez L, Akula I, Aboualizadeh F, Wong V, Grozavu I, Opacak-Bernardi T, Yao Z, Mendoza M, Babu M, Jurisica I, Gonska T, Bear CE, Amaral MD, Stagljar I. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Mol Syst Biol. 2022 Feb;18(2):e10629. doi: 10.15252/msb.202110629.
  • 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. Nucl Acids Res, 50(D1):D640-D647, 2022. doi: 10.1093/nar/gkab1034.
  • Holzinger A, Dehmer M, Emmert-Streib F, Cucchiara R, Augenstein I, Del Ser J, Samek W, Jurisica I, Diaz-Rodriguez N, Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence, Information Fusion, Volume 79, 2022, Pages 263-278, 2022.
  • Passalent L, Cyr A, Jurisica I, Mathur S, Inman RD, Haroon N, Motivators, barriers, and opportunity for e-health to encourage physical activity in axial spondyloarthritis: a qualitative descriptive study, Arthritis Care Res, 74(1):50-58, 2022.
  • 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/Beta-catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis, Frontiers in Oncology, section Molecular and Cellular Oncology, 11:777834. doi: 10.3389/fonc.2021.777834. eCollection 2021.
  • Ali SA, Pastrello C, Kaur N, Peffers MJ, Ormseth MJ, Jurisica I. A Network Biology Approach to Understanding the Tissue-Specific Roles of Non-Coding RNAs in Arthritis, Front Endocrinol, 12:744747. doi: 10.3389/fendo.2021.744747. eCollection 2021.
  • Matyasova K, Csicsatkova N, Filipcik P, Jurisica I, Cente M Peripheral microRNA alteration and pathway signaling after mild traumatic brain injury. Gen Physiol Biophys, 40(6):523-539. doi: 10.4149/gpb_2021038.
  • Salgado RC, Fonseca DLM, Marques AHC, da Silva Napoleao SM, Franca TT, Akashi KT, de Souza Prado CA, Baiocchi GC, Placa DR, Jansen-Marques G, Filgueiras IS, De Vito R, Freire PP, de Miranda GC, Camara NOS, Calich VLG, Ochs HD, Schimke LF, Jurisica I, Condino-Neto A, Cabral-Marques O. The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response, Sci Rep., 11(1):20281, 2021. doi: 10.1038/s41598-021-99838-0
  • Nakamura A, Zeng F, Nakamura S, Reid KT, Gracey E, Lim M, Leng L, Jo S, Park YS, Kusuda M, Machhar R, Boroojeni SF, Wu B, Rossomacha E, Kim TH, Ciccia F, Rockel JS, Kapoor M, Inman RD, Jurisica I, Crome SQ, Bucala R, Haroon N. Macrophage migration inhibitory factor drives the immunopathology of type 3 immunity-mediated arthritis, Sci Transl Med. 13(616):eabg1210, 2021. doi: 10.1126/scitranslmed.abg1210
  • 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, J Mol Biol. 433(23):167283, 2021. doi: 10.1016/j.jmb.2021.167283.
  • Shabana A. Ali, Mandy J. Peffers, Michelle J. Ormseth, Igor Jurisica & Mohit Kapoor. The non-coding RNA interactome in joint health and disease. Nat Rev Rheumatol, 17(11):692-705. doi: 10.1038/s41584-021-00687-y. Epub 2021 Sep 29.
  • Clotet-Freixas S, Kotlyar M, McEvoy CM, Pastrello C, Rodriguez-Ramirez S, Farkona S, Cardinal H, Dieude M, Hebert MJ, Li Y, Famure O, Chen P, Kim SJ, Chan E, Jurisica I, John R, Chruscinski A, Konvalinka A. Increased Autoantibodies Against Ro/SS-A, CENP-B, and La/SS-B in Patients With Kidney Allograft Antibody-mediated Rejection. Transplant Direct. 7(10):e768, 2021. doi: 10.1097/TXD.0000000000001215
  • Franca TT, Al-Sbiei A, Bashir G, Mohamed YA, Salgado RC, Barreiros LA, da Silva Napoleao SM, Weber CW, Ferreira JF, Aranda CS, Prando C, de Barros Dorna MB, Jurisica I, Fernandez-Cabezudo MJ, Ochs HD, Condino-Neto A, Al-Ramadi BK, Cabral-Marques O. CD40 ligand modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. JCI Insight. 6(16):e148652, 2021. doi: 10.1172/jci.insight.148652.
  • Cohn DE, Barros-Filho MC, Minatel BC, Pewarchuk ME, Marshall EA, Vucic EA, Sage AP, Telkar N, Stewart GL, Jurisica I, Reis PP, Robinson WP, Lam WL. Share, Reactivation of Multiple Fetal miRNAs in Lung Adenocarcinoma, Cancers, 13(11):2686, 2021.
  • McEvoy CM, Clotet-Freixas S, Tokar T, Pastrello C, Reid S, Batruch I, RaoPeters AAE, Kaths JM, Urbanellis P, Farkona S, Van JAD, Urquhart BL, John R, Jurisica I, Robinson LA, Selzner M, Konvalinka A., Normothermic Ex-vivo Kidney Perfusion in a Porcine Auto-Transplantation Model Preserves the Expression of Key Mitochondrial Proteins: An Unbiased Proteomics Analysis, Mol Cell Proteomics, 100101, 2021. doi: 10.1016/j.mcpro.2021.100101.
  • Freire PP, Marques AH, Baiocchi GC, Schimke LF, Fonseca DL, Salgado RC, Filgueiras IS, Napoleao SM, Placa DR, Akashi KT, Hirata TDC, El Khawanky N, Giil LM, Cabral-Miranda G, Carvalho RF, Ferreira LCS, Condino-Neto A, Nakaya HI, Jurisica I, Ochs HD, Camara NOS, Calich VLG, Cabral-Marques O., The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2-infected patients by sex and age, JCI Insight 6(10):147535, 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, Eur Respir J, 2002975, 2021. doi: 10.1183/13993003.02975-2020.
  • Agapito, G., Pastrello, C., Jurisica, I. Comprehensive pathway enrichment analysis workflows: Covid-19 case study, Briefings Bioinform, 22(2): 676-689, 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, Pastrello C, Kotlyar M, Goh C, Michelakis E, Clemente-Casares X, Ohashi PS, Engleman EG, Winer S, Jurisica I, Tsai S, Winer DA., Mechanical Stiffness Controls Dendritic Cell Metabolism and Function, Cell Reports, 34(2):108609, 2021.
  • Bhat, M. Elisa Pasini, Chiara Pastrello, Sarah Rahmati, Marc Angeli, Max Kotlyar, Anand Ghanekar and Igor Jurisica, Integrative Analysis of Layers of Data in Hepatocellular Carcinoma Reveals Pathway Dependencies, World J Hepatology, 13(1):94-108, 2021.
  • 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 Cartilage. 29(3):372-379, 2021. doi: 10.1016/j.joca.2020.12.004.
  • 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, 73(3):426-439, 2021
  • Rahmati S, O'Rielly DD, Li Q, Codner D, Dohey A, Jenkins K, Jurisica I, Gladman DD, Chandran V, Rahman P. Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. Sci Rep. 10(1):21703, 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, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Towards a unified open access dataset of molecular interactions. Nat Commun. 11(1):6144, 2020.
  • Glaus Garzon JF, Pastrello C, Jurisica I, Hottiger MO, Wenger RH, Borsig L. Tumor cell endogenous HIF-1α activity induces aberrant angiogenesis and interacts with TRAF6 pathway required for colorectal cancer development. Neoplasia. 22(12):745-758, 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, Pellegrini M, Orchard S, Jurisica I, Hermjakob HH, Porras P. The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions, Database, 2020. baaa096. doi: 10.1093/database/baaa096
  • 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, 28(11):1471-1481, 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, Kim SJ, Chan E, Moshkelgosha S, Rahman SA, Das J, Martinu T, Juvet S, Jurisica I, Chruscinski A, John R, Konvalinka A. Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection: A Proteomics Study, J Am Soc Nephrol, 31(11):2705-2724, 2020.
  • Yao Z, Aboualizadeh F, Akula I, Snider J, Tang P, Kotlyar M, Jurisica I, Stagljar I. Split Intein-Mediated Protein Ligation, a Novel Method for Detecting Protein-Protein Interactions and Their Inhibition, Nat Commun, 11(1):2440, 2020.
  • Van JAD, Clotet-Freixas S, Hauschild AC, Batruch I, Jurisica I, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes, PLoS One, 15(5):e0233639, 2020. doi: 10.1371/journal.pone.0233639.
  • Sinsky J, Majerova P, Kovac A, Kotlyar M, Jurisica I, Hanes J. Physiological Tau Interactome in Brain and Its Link to Tauopathies, J Proteome Res, 19(6):2429-2442, 2020. doi: 10.1021/acs.jproteome.0c00137.
  • Agapito G, Pastrello C, Guzzi PH, Jurisica I, Cannataro M. BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways, Bioinformatics, 36(15):4377-4378, 2020. doi: 10.1093/bioinformatics/btaa529.
  • Pinheiro M, Lupinacci FCS, Santiago KM, Drigo SA, Marchi FA, Fonseca-Alves CE, Andrade SCDS, Aagaard MM, Basso TR, Dos Reis MB, Villacis RAR, Roffa M, Hajj GNM, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR. Cancers (Basel), 12(5):E1289, 2020. doi: 10.3390/cancers12051289.
  • Reis PP, Tokar T, Goswami RS, Xuan Y, Sukhai M, Seneda AL, Moz LES, Perez-Ordonez B, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S. A 4-gene signature from histologically normal surgical margins predicts local recurrence in patients with oral carcinoma: clinical validation, Scientific Reports, 10(1):1713, 2020. doi: 10.1038/s41598-020-58688-y.
  • 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,
  • Kennedy, S., Jarboui, M-A, 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, Stagljar, I, LeBihan, T, Imrie, L, Pillai, P, Lynn, M, Fasterius, E, Szigyarto, C. A-K, Breen, J, Kiel, C, Serrano, L, Rauch, N, Rukhlenko, O, Kholodenko, B, Iglesias-Martinez, L, Ryan, C, Pilkington, R, Cammareri, P, Sansom, O, Shave, S, Auer, M, Horn, N, Klose, F, Ueffing, M, Boldt, K, Lynn, D, Kolch, W, Extensive Rewiring of the EGFR Network in Colorectal Cancer Cells Expressing Transforming Levels of KRASG13D, Nat Commun, 11(1):499, 2020. doi: 10.1038/s41467-019-14224-9
  • Enfield, K.S.S., Marshall, E.A., Anderson, C., Ng, K.W., Rahmati, S, Xu, Z. Fuller, M., Milne, K., Lu, D., Shi, R., Rowbotham, D. A., Becker-Santos, D.D., Johnson, F.D., English, J.C., MacAulay, C.E., Lam, S., Lockwood, W.W., Chari, R., Karsan, A., Jurisica, I., Lam, W.L., Epithelial tumor suppressor ELF3 is a lineage-specific amplified oncogene in lung adenocarcinoma, Nat Commun, 10(1):5438, 2019. doi:10.1038/s41467-019-13295-y
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
Book Chapters
  • Kotlyar M, Wong SWH, Pastrello C, Jurisica I. Improving Analysis and Annotation of Microarray Data with Protein Interactions. Methods Mol Biol. 2022;2401:51-68. doi: 10.1007/978-1-0716-1839-4_5.
  • Pastrello C, Niu Y, Jurisica I. Pathway Enrichment Analysis of Microarray Data. Methods Mol Biol. 2022;2401:147-159. doi: 10.1007/978-1-0716-1839-4_10.
  • Pastrello C, Kotlyar M, Jurisica I., Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). Methods Mol Biol., 2074:125-134, 2020. doi: 10.1007/978-1-4939-9873-9_10.
  • 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.
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
  • 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.