Yves Lussier, MD

Associate Professor of Medicine, Section of Genetic Medicine

Director, Center for Biomedical Informatics

Associate Director for Biomedical Informatics, The University of Chicago Comprehensive Cancer Center

Dr. Yves A. Lussier is the Associate Director for Informatics at the University of Chicago Comprehensive Cancer Center, co-Director for Biomedical Informatics of the University of Chicago Clinical and Translational Science Award (CTSA), and Director of the Department of Medicine (DOM) Center for Biomedical Informatics. He is an Associate Professor of Medicine in the Section of Genetic Medicine. From 2001-2006, Dr. Lussier was an Assistant Professor in the Departments of Biomedical Informatics and Medicine at Columbia University, where he mentored or co-mentored 26 graduate students. During his tenure at Columbia University, he was the first recipient of the “Columbia University Faculty Mentoring Award” for faculty members in the Biomedical Sciences, Graduate School of Arts and Sciences, and affiliated professional schools. Dr. Lussier has served or is serving on more than a dozen boards (governance, technology transfer, scientific and editorial). A member of the American Medical Informatics Association (AMIA) since 1990, he was inducted into the elected membership of the American College of Medical Informatics (ACMI) in 2005. He is credited with over 280 publications, communications and invited lectures.

Dr. Lussier chaired the 2009 AMIA Summit on Translational Bioinformatics. Indeed, he has established a track record in funding, building and leading teams that develop and “translate” valuable leading-edge informatics solutions to clinical problems (e.g., Purkinje.com’s Dossier, New York Presbyterian Hospital’s Vigilens, Greene Lab’s Panmicrobial Array). Dossier was the first pen-based (tablet-based) information system for physicians (1992) and the first commercial electronic medical record anchored on a substantial clinical terminology organized as a semantic network (60,000 entities). Later, during his tenure at Columbia University, he researched and developed Vigilens, a web-accessible, server-based and ontology-driven clinical decision support system that has been in operation since 2003 at the New York Presbyterian Hospital (Decision Supp Syst 43:1274-86, 2007). Every year, Vigilens monitors over 25 million laboratory results and sends alerts pertaining to 130 thousand critical events. Lussier’s team also co-designed the first comprehensive panmicrobial microarray for human diagnosis. In spite of its coverage of 1,200 distinct vertebrate viruses, it remains compact because less probes are required per organism as they have been designed in “essential protein domains” that are less likely to mutate (Nucleic Acids Res 36:e3, 2008). Since 2003, the array has been used in Australia, China, and Africa and has established the diagnosis of a patient that eluded traditional methods of investigation (Emerg Infect Dis 13:73-81, 2007). The panmicrobial array also has served to rule out known human pathogens in the discovery of novel ones (N Engl J Med 358:991-998, 2008).

The Lussier Research Group is conducting hypothesis-driven translational research in biomedical informatics that focuses on the use of knowledge technologies to accurately individualize the understanding, prediction and treatments of diseases. More specifically, Dr. Lussier has developed computational methods that bring together molecular bioinformatics, ontologies, natural language processing, and heterogeneous data integration to analyze an increasingly large and complex wealth of textual and semi-structured phenotypic, clinical, genomic, and molecular databases. Using phenomic- and systems biology approaches, his team has recently (i) predicted a novel tumor suppressor gene, and (ii) developed a “network rewiring”-based combination therapy and demonstrated its robust, synergistic anti-tumor effects achieved via effective co-targeting of cancer cells and tumor stroma. Based on these insightful discoveries, a NIH-funded multi-center Phase II clinical trial and correlative mechanistic investigations led by the UCCCC is underway [A phase II study evaluating synergy of temsirolimus when added to cetuximab in patients with recurrent/metastatic head and neck cancer after failure of anti-EGFR therapy].

Selected Publications from 2010 – 2011

  • Yang X, Lee Y, Li J, Lussier YA. GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics [in press], 2011.
  • Chen J, Li J, Stadler W, Lussier YA. Protein-Network Modeling of Prostate Cancer Gene Signatures Reveals Essential Pathways in Disease Recurrence. J Am Med Inform Assoc 18:392-402, 2011.
  • Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Youngfei Wu, Li J, Hasina R, Cheng C , Lingen MW, Gerstein M, Weichselbaum RR, Xing HR, Lussier YA. Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. PLoS Comput Biol 6: e1000730, 2010.
  • Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, Xing HR, Lussier YA. Protein Interaction Network Underpins Concordant Prognosis Among Heterogeneous Breast Cancer Signatures. J Biomed Inform 43:385-396, 2010.
  • Yang X, Huang Y, Crowson M, Li J,  Maitland M, Lussier YA. Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. J Biomed Inform 43:376–384, 2010.
  • Yang X, Lee Y,  Fan H, Sun X, Lussier YA. Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer. Chi Sci Bull 55:3576-3589, 2010.
  • Yang X, Lee Y, Huang Y, Chen J, Xing HR, Lussier YA. Stromal Microenvironment Processes Unveiled by Biological Component Analysis of Gene Expression in Xenograft Tumor Models. BMC Bioinformatics 11:S11, 2010.


  • Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM. An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol 38:215-224, 2011.

Selected Presentations

  • “Quantized phenotypes emerge as multiscale mechanisms underpinning complex traits”
    Keynote Spear at the 1st CALB Workshop on the Collaborative Annotation of a Large Biomedical Corpus Challenge, Joint Wellcome Trust Sanger Institute & European Bioinformatics Institute (EBI)
    Cambridge, UK
    June 2010
  • “Beyond synergies, hypothesis-driven translational informatics as a catalyst in targeted therapy development”
    Invited Speaker at Dartmouth College and Dartmouth-Hitchcock Norris Cotton Cancer Center
    Lebanon, NH
    November 2010
  • “Network and Biological Models For Reversing Resistance to Targeted Therapy Spawn a NIH-funded Phase II Trial”
    Keynote Speaker at the 1st Congress of Personalized Medicine
    Shanghai, China
    November 2010
  • “Hypothesis-driven translational bioinformatics: from in silico models to clinical trials with transit in vitro and in vivo”
    Invited Speaker at University of Vermont Grand Rounds of Informatics
    Burlington, VT
    December 2010
  • “Network modeling of therapeutic resistance initiates Phase II trial in oral cancer”
    Invited Speaker for the Marshfield Clinic Genetics Seminar
    Marshfield, WI
    December 2010
  • “Network models of therapeutic resistance and personal genomics in clinical practice”
    Invited Speaker at University of Illinois Chicago School of Medicine, Center for Evidence-based Practice in the Underserved and the Reducing Health Disparities Through Informatics (RHeaDI)
    Chicago, IL
    April 2011
  • Guest Speaker for the Committee for Advanced Scientific Education (CASE) Seminar, FDA, Center for Drug Evaluation and Research (CDER)
    Washington D.C.
    October 2011
  • Keynote Speaker for the Network Tools and Applications in Biology 2011 Workshop
    Pavia, Italy
    October 2011
  • “Network models of therapeutic resistance translated in vitro, in vivo and in clinical trials”
    Invited Speaker at University of Wisconsin-Milwaukee and Medical College of Wisconsin, Biomedical Informatics Program
    Milwaukee, WI
    December 2011