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Yves Lussier, MD, FACMI

Languages spoken: English, French

Academic Information

Departments Primary - Biomedical Informatics

Academic Office Information

Board Certification

  • Licentiate of the Medical Council of Canada

Yves A. Lussier, MD, FACMI, is the Chair of Biomedical Informatics at University of Utah School of Medicine. As a professional engineer and physician-scientist, he is an international expert in translational bioinformatics and a pioneer in research informatics techniques including systems biology, data representation through ontologies, and high-throughput methods in personalized medicine.

Dr. Lussier comes to the University Utah from the University of Arizona, where he was the Associate Vice President for Information Science and Chief Knowledge Officer of the UArizona Health Sciences (UAHS), Founding Director of the Center for Biomedical Informatics and Biostatistics, and Professor of Medicine. During his time at UArizona, he developed novel programs in biomedical informatics, computational genomics, and precision health, as well as provided critical leadership to advance precision health approaches to health outcomes and healthcare delivery and in the development of big data analytical tools and resource services. Prior to his tenure at UArizona, Dr. Lussier was professor of medicine, bioengineering and biopharmaceutical sciences at University of Illinois at Chicago (UIC), and assistant vice president for health affairs and chief research information officer for the University of Illinois Hospital and Health Sciences System (2011-13). From 2006-2011, he was the associate director of informatics for the University of Chicago Comprehensive Cancer Center as well as co-director of biomedical informatics for the Clinical and Translational Science Award (CTSA)-funded Institute for Translational Medicine. From 2001-2006, Dr. Lussier was an assistant professor in the Departments of Biomedical Informatics and Medicine at Columbia University in New York.

Lussier’s research group conducts pioneering hypothesis-driven computational modeling predictions in precision medicine that are then validated in vitro, in vivo and in clinical trials. As a leader of the fields of translational bioinformatics and of Data Science-augmented precision medicine, he has launched successful companies and international conferences, authored 185 publications, and delivered more than 100 invited presentations in precision medicine, systems medicine, and translational bioinformatics, including 28 opening keynotes at international conferences. He has been awarded $190,000,000 in grants as principal, core leader, or co-investigator, and mentored or co-mentored over 90 graduates, post graduate fellows, and junior faculty members, of which twelve are faculty members, seven obtained K-awards, and five obtained R awards. Dr. Lussier’s honors include three IBM Faculty Awards, inducted Fellow of the American College of Medical Informatics (ACMI), 1st recipient of the Columbia University Faculty Mentoring Award, “Ambassador for Health Sciences” at the University of Sherbrooke (Canada), and 16 outstanding publication awards from the American Medical Informatics Association (AMIA), the International Society for Computational Biology (ISCB), and the Translational Bioinformatics Conference (TBC). In 2016, Dr. Lussier was invited among ten USA academic leaders invited by the White House for its Precision Medicine Summit.

Education History

Postdoctoral Fellowship Columbia University
Postdoctoral Research Fellow
University of Sherbrooke
Internship Université Laval
Clinical Internship
University of Sherbrooke
Undergraduate University of Sherbrooke

Selected Publications

Journal Article

  1. Chang EH, Pouladi N, Guerra S, Jandova J, Kim A, Li H, Li J, Morgan W, Stern DA, Willis AL, Lussier YA, Martinez FD (2022). Epithelial cell responses to rhinovirus identify an early-life-onset asthma phenotype in adults. J Allergy Clin Immunol.
  2. Li H, Baldwin E, Zhang X, Kenost C, Luo W, Calhoun EA, An L, Bennett CL, Lussier YA (2021). Comparison and impact of COVID-19 for patients with cancer: a survival analysis of fatality rate controlling for age, sex and cancer type. BMJ Health Care Inform, 28(1).
  3. Casanova NG, Zhou T, Gonzalez-Garay ML, Lussier YA, Sweiss N, Ma SF, Noth I, Knox KS, Garcia JGN (2020). MicroRNA and protein-coding gene expression analysis in idiopathic pulmonary fibrosis yields novel biomarker signatures associated to survival. Transl Res, 228, 1-12.
  4. Rachid Zaim S, Kenost C, Zhang HH, Lussier YA (2020). Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products. J Pers Med, 11(1).
  5. Casanova NG, Gonzalez-Garay ML, Sun B, Bime C, Sun X, Knox KS, Crouser ED, Sammani N, Gonzales T, Natt B, Chaudhary S, Lussier Y, Garcia JGN (2020). Differential transcriptomics in sarcoidosis lung and lymph node granulomas with comparisons to pathogen-specific granulomas. Respir Res, 21(1), 321.
  6. Zaim SR, Kenost C, Berghout J, Chiu W, Wilson L, Zhang HH, Lussier YA (2020). Correction to: binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions. BMC Bioinformatics, 21(1), 495.
  7. Rachid Zaim S, Kenost C, Berghout J, Chiu W, Wilson L, Zhang HH, Lussier YA (2020). binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions. BMC Bioinformatics, 21(1), 374.
  8. Li Q, Zaim SR, Aberasturi D, Berghout J, Li H, Vitali F, Kenost C, Zhang HH, Lussier YA (2020). Interpretation of 'Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes. AMIA Annu Symp Proc, 2019, 582-591.
  9. Rajan SS, Amin AD, Li L, Rolland DC, Li H, Kwon D, Kweh MF, Arumov A, Roberts ER, Yan A, Basrur V, Elenitoba-Johnson KSJ, Chen XS, Puvvada SD, Lussier YA, Bilbao D, Lim MS, Schatz JH (2019). The mechanism of cancer drug addiction in ALK-positive T-Cell lymphoma. Oncogene, 39(10), 2103-2117.
  10. Bime C, Casanova N, Oita RC, Ndukum J, Lynn H, Camp SM, Lussier Y, Abraham I, Carter D, Miller EJ, Mekontso-Dessap A, Downs CA, Garcia JGN (2019). Development of a biomarker mortality risk model in acute respiratory distress syndrome. Crit Care, 23(1), 410.
  11. Rachid Zaim S, Kenost C, Berghout J, Vitali F, Zhang HH, Lussier YA (2019). Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine. BMC Med Genomics, 12(Suppl 5), 96.
  12. Vitali F, Li Q, Schissler AG, Berghout J, Kenost C, Lussier YA (2017). Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. Brief Bioinform, 20(3), 789-805.
  13. Schissler AG, Aberasturi D, Kenost C, Lussier YA (2019). A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes. Front Genet, 10, 414.
  14. Vitali F, Berghout J, Fan J, Li J, Li Q, Li H, Lussier YA (2019). Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. Pac Symp Biocomput, 24, 308-319.
  15. Li H, Fan J, Vitali F, Berghout J, Aberasturi D, Li J, Wilson L, Chiu W, Pumarejo M, Han J, Kenost C, Koripella PC, Pouladi N, Billheimer D, Bedrick EJ, Lussier YA (2018). Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities. BMC Med Genomics, 11(Suppl 6), 112.
  16. Schissler AG, Piegorsch WW, Lussier YA (2017). Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation. Stat Methods Med Res, 27(12), 3797-3813.
  17. Bime C, Pouladi N, Sammani S, Batai K, Casanova N, Zhou T, Kempf CL, Sun X, Camp SM, Wang T, Kittles RA, Lussier YA, Jones TK, Reilly JP, Meyer NJ, Christie JD, Karnes JH, Gonzalez-Garay M, Christiani DC, Yates CR, Wurfel MM, Meduri GU, Garcia JGN (2018). Genome-Wide Association Study in African Americans with Acute Respiratory Distress Syndrome Identifies the Selectin P Ligand Gene as a Risk Factor. Am J Respir Crit Care Med, 197(11), 1421-1432.
  18. Boyd AD, Li J, Kenost C, Zaim SR, Krive J, Mittal M, Satava RA, Burton M, Smith J, Lussier YA (2018). ICD-10 procedure codes produce transition challenges. AMIA Jt Summits Transl Sci Proc, 2017, 35-44.
  19. Boyd AD, Dunn Lopez K, Lugaresi C, Macieira T, Sousa V, Acharya S, Balasubramanian A, Roussi K, Keenan GM, Lussier YA, Li J, Burton M, Di Eugenio B (2018). Physician nurse care: A new use of UMLS to measure professional contribution: Are we talking about the same patient a new graph matching algorithm? Int J Med Inform, 113, 63-71.
  20. Fan JW, Lussier YA (2018). Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews. AMIA Annu Symp Proc, 2017, 689-695.
  21. Berghout J, Li Q, Pouladi N, Li J, Lussier YA (2017). Single subject transcriptome analysis to identify functionally signed gene set or pathway activity. Pac Symp Biocomput, 23, 400-411.
  22. Zaim SR, Li Q, Schissler AG, Lussier YA (2017). Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses. Pac Symp Biocomput, 23, 484-495.
  23. Lussier YA, Berghout J, Vitali F, Ramos KS, Kann M, Moore JH (2017). Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA. Pac Symp Biocomput, 23, 507-511.
  24. Han J, Li J, Achour I, Pesce L, Foster I, Li H, Lussier YA (2017). Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. Pac Symp Biocomput, 23, 524-535.
  25. Gardeux V, Berghout J, Achour I, Schissler AG, Li Q, Kenost C, Li J, Shang Y, Bosco A, Saner D, Halonen MJ, Jackson DJ, Li H, Martinez FD, Lussier YA (2016). A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations. J Am Med Inform Assoc, 24(6), 1116-1126.
  26. Huang Y, Ma SF, Espindola MS, Vij R, Oldham JM, Huffnagle GB, Erb-Downward JR, Flaherty KR, Moore BB, White ES, Zhou T, Li J, Lussier YA, Han MK, Kaminski N, Garcia JGN, Hogaboam CM, Martinez FJ, Noth I, COMET-IPF Investigators (2017). Microbes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med, 196(2), 208-219.
  27. Zhou T, Casanova N, Pouladi N, Wang T, Lussier Y, Knox KS, Garcia JGN (2017). Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Sci Rep, 7(1), 4237.
  28. Vitali F, Marini S, Balli M, Grosemans H, Sampaolesi M, Lussier YA, Cusella De Angelis MG, Bellazzi R (2017). Exploring Wound-Healing Genomic Machinery with a Network-Based Approach. Pharmaceuticals (Basel), 10(2).
  29. Desai AA, Lei Z, Bahroos N, Maienschein-Cline M, Saraf SL, Zhang X, Shah BN, Nouraie SM, Abbasi T, Patel AR, Lang RM, Lussier Y, Garcia JGN, Gordeuk VR, Machado RF (2017). Association of circulating transcriptomic profiles with mortality in sickle cell disease. Blood, 129(22), 3009-3016.
  30. Li Q, Schissler AG, Gardeux V, Achour I, Kenost C, Berghout J, Li H, Zhang HH, Lussier YA (2017). N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes. BMC Med Genomics, 10(Suppl 1), 27.
  31. Li Q, Schissler AG, Gardeux V, Berghout J, Achour I, Kenost C, Li H, Zhang HH, Lussier YA (2016). kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects. J Biomed Inform, 66, 32-41.
  32. Fan JW, Li J, Lussier YA (2017). Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. J Healthc Eng, 2017, 3818302.
  33. Pouladi N, Achour I, Li H, Berghout J, Kenost C, Gonzalez-Garay ML, Lussier YA (2016). Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records. Yearb Med Inform, (1), 194-206.
  34. Schissler AG, Li Q, Chen JL, Kenost C, Achour I, Billheimer DD, Li H, Piegorsch WW, Lussier YA (2016). Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. Bioinformatics, 32(12), i80-i89.
  35. Payne PR, Lussier Y, Foraker RE, Embi PJ (2016). Rethinking the role and impact of health information technology: informatics as an interventional discipline. BMC Med Inform Decis Mak, 16, 40.
  36. Pouladi N, Bime C, Garcia JGN, Lussier YA (2015). Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Transl Res, 168, 22-39.
  37. Grief SN, Patel J, Kochendorfer KM, Green LA, Lussier YA, Li J, Burton M, Boyd AD (2016). Simulation of ICD-9 to ICD-10-CM Transition for Family Medicine: Simple or Convoluted? J Am Board Fam Med, 29(1), 29-36.
  38. Li H, Achour I, Bastarache L, Berghout J, Gardeux V, Li J, Lee Y, Pesce L, Yang X, Ramos KS, Foster I, Denny JC, Moore JH, Lussier YA (2016). Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. NPJ Genom Med, 1.
  39. Li H, Pouladi N, Achour I, Gardeux V, Li J, Li Q, Zhang HH, Martinez FD, Skip Garcia JGN, Lussier YA (2015). eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs. J Biomed Inform, 58, 226-234.
  40. Huang Y, Ma SF, Vij R, Oldham JM, Herazo-Maya J, Broderick SM, Strek ME, White SR, Hogarth DK, Sandbo NK, Lussier YA, Gibson KF, Kaminski N, Garcia JG, Noth I (2015). A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis. BMC Pulm Med, 15, 147.
  41. Bikkavilli RK, Avasarala S, Van Scoyk M, Arcaroli J, Brzezinski C, Zhang W, Edwards MG, Rathinam MK, Zhou T, Tauler J, Borowicz S, Lussier YA, Parr BA, Cool CD, Winn RA (2015). Wnt7a is a novel inducer of β-catenin-independent tumor-suppressive cellular senescence in lung cancer. Oncogene, 34(42), 5317-28.
  42. Amin AD, Rajan SS, Liang WS, Pongtornpipat P, Groysman MJ, Tapia EO, Peters TL, Cuyugan L, Adkins J, Rimsza LM, Lussier YA, Puvvada SD, Schatz JH (2015). Evidence Suggesting That Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors. Cancer Res, 75(14), 2916-27.
  43. Schissler AG, Gardeux V, Li Q, Achour I, Li H, Piegorsch WW, Lussier YA (2015). Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. Bioinformatics, 31(12), i293-302.
  44. Gardeux V, Bosco A, Li J, Halonen MJ, Jackson D, Martinez FD, Lussier YA (2015). Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. J Biomed Inform, 55, 94-103.
  45. Boyd AD, Li JJ, Kenost C, Joese B, Yang YM, Kalagidis OA, Zenku I, Saner D, Bahroos N, Lussier YA (2015). Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM. J Am Med Inform Assoc, 22(3), 730-7.
  46. Krive J, Patel M, Gehm L, Mackey M, Kulstad E, Li JJ, Lussier YA, Boyd AD (2015). The complexity and challenges of the International Classification of Diseases, Ninth Revision, Clinical Modification to International Classification of Diseases, 10th Revision, Clinical Modification transition in EDs. Am J Emerg Med, 33(5), 713-8.
  47. Boyd AD, Yang YM, Li J, Kenost C, Burton MD, Becker B, Lussier YA (2014). Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM. J Am Med Inform Assoc, 22(1), 19-28.
  48. Kim H, Lussier YA, Noh OK, Li H, Oh YT, Heo J (2014). Prognostic implication of pulmonary function at the beginning of postoperative radiotherapy in non-small cell lung cancer. Radiother Oncol, 113(3), 374-8.
  49. Lee YJ, Boyd AD, Li JJ, Gardeux V, Kenost C, Saner D, Li H, Abraham I, Krishnan JA, Lussier YA (2014). COPD Hospitalization Risk Increased with Distinct Patterns of Multiple Systems Comorbidities Unveiled by Network Modeling. AMIA Annu Symp Proc, 2014, 855-64.
  50. Gardeux V, Achour I, Li J, Maienschein-Cline M, Li H, Pesce L, Parinandi G, Bahroos N, Winn R, Foster I, Garcia JG, Lussier YA (2014). 'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. J Am Med Inform Assoc, 21(6), 1015-25.
  51. Wang AL, Rao VR, Chen JJ, Lussier YA, Rehman J, Huang Y, Jager RD, Grassi MA (2014). Role of FAM18B in diabetic retinopathy. Mol Vis, 20, 1146-59.
  52. Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB, Martinez FJ, COMET Investigators (2014). Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med, 2(7), 548-56.
  53. Caskey R, Zaman J, Nam H, Chae SR, Williams L, Mathew G, Burton M, Li JJ, Lussier YA, Boyd AD (2014). The transition to ICD-10-CM: challenges for pediatric practice. Pediatrics, 134(1), 31-6.
  54. Maienschein-Cline M, Lei Z, Gardeux V, Abbasi T, Machado RF, Gordeuk V, Desai AA, Saraf S, Bahroos N, Lussier Y (2014). ARTS: automated randomization of multiple traits for study design. Bioinformatics, 30(11), 1637-9.
  55. Huang LS, Mathew B, Li H, Zhao Y, Ma SF, Noth I, Reddy SP, Harijith A, Usatyuk PV, Berdyshev EV, Kaminski N, Zhou T, Zhang W, Zhang Y, Rehman J, Kotha SR, Gurney TO, Parinandi NL, Lussier YA, Garcia JG, Natarajan V (2014). The mitochondrial cardiolipin remodeling enzyme lysocardiolipin acyltransferase is a novel target in pulmonary fibrosis. Am J Respir Crit Care Med, 189(11), 1402-15.
  56. Venepalli NK, Qamruzzaman Y, Li JJ, Lussier YA, Boyd AD (2014). Identifying clinically disruptive International Classification of Diseases 10th Revision Clinical Modification conversions to mitigate financial costs using an online tool. J Oncol Pract, 10(2), 97-103.
  57. Gardeux V, Arslan AD, Achour I, Ho TT, Beck WT, Lussier YA (2014). Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. BMC Med Genomics, 7 Suppl 1, S1.
  58. Yang X, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, Rebman E, Li H, Lussier YA (2014). In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. BMC Med Genomics, 7 Suppl 1, S2.
  59. Herazo-Maya JD, Noth I, Duncan SR, Kim S, Ma SF, Tseng GC, Feingold E, Juan-Guardela BM, Richards TJ, Lussier Y, Huang Y, Vij R, Lindell KO, Xue J, Gibson KF, Shapiro SD, Garcia JG, Kaminski N (2013). Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Sci Transl Med, 5(205), 205ra136.
  60. Lee Y, Li H, Li J, Rebman E, Achour I, Regan KE, Gamazon ER, Chen JL, Yang XH, Cox NJ, Lussier YA (2013). Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. J Am Med Inform Assoc, 20(4), 619-29.
  61. Boyd AD, Li JJ, Burton MD, Jonen M, Gardeux V, Achour I, Luo RQ, Zenku I, Bahroos N, Brown SB, Vanden Hoek T, Lussier YA (2013). The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study, and mitigating tools. J Am Med Inform Assoc, 20(4), 708-17.
  62. Embi PJ, Tachinardi U, Lussier Y, Starren J, Silverstein J (2013). Integrating Governance of Research Informatics and Health Care IT Across an Enterprise: Experiences from the Trenches. AMIA Jt Summits Transl Sci Proc, 2013, 60-2.
  63. Payne PR, Pressler TR, Sarkar IN, Lussier Y (2013). People, organizational, and leadership factors impacting informatics support for clinical and translational research. BMC Med Inform Decis Mak, 13, 20.
  64. Perez-Rathke A, Li H, Lussier YA (2013). Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data. Pac Symp Biocomput, 159-70.
  65. Chen JL, Hsu A, Yang X, Li J, Lee Y, Parinandi G, Li H, Lussier YA (2013). Curation-free biomodules mechanisms in prostate cancer predict recurrent disease. BMC Med Genomics, 6 Suppl 2, S4.
  66. Lussier YA, Li H (2012). Breakthroughs in genomics data integration for predicting clinical outcome. J Biomed Inform, 45(6), 1199-201.
  67. Lussier YA, Li H (2012). The rise of translational bioinformatics. Genome Biol, 13(8), 319.
  68. Chen JL, Li J, Kiriluk KJ, Rosen AM, Paner GP, Antic T, Lussier YA, Vander Griend DJ (2012). Deregulation of a Hox protein regulatory network spanning prostate cancer initiation and progression. Clin Cancer Res, 18(16), 4291-302.
  69. Grassi MA, Tikhomirov A, Ramalingam S, Lee KE, Hosseini SM, Klein BE, Klein R, Lussier YA, Cox NJ, Nicolae DL (2012). Replication analysis for severe diabetic retinopathy. Invest Ophthalmol Vis Sci, 53(4), 2377-81.
  70. Wang T, Lang GD, Moreno-Vinasco L, Huang Y, Goonewardena SN, Peng YJ, Svensson EC, Natarajan V, Lang RM, Linares JD, Breysse PN, Geyh AS, Samet JM, Lussier YA, Dudley S, Prabhakar NR, Garcia JG (2011). Particulate matter induces cardiac arrhythmias via dysregulation of carotid body sensitivity and cardiac sodium channels. Am J Respir Cell Mol Biol, 46(4), 524-31.
  71. Li Z, Huang H, Li Y, Jiang X, Chen P, Arnovitz S, Radmacher MD, Maharry K, Elkahloun A, Yang X, He C, He M, Zhang Z, Dohner K, Neilly MB, Price C, Lussier YA, Zhang Y, Larson RA, Le Beau MM, Caligiuri MA, Bullinger L, Valk PJ, Delwel R, Lowenberg B, Liu PP, Marcucci G, Bloomfield CD, Rowley JD, Chen J (2012). Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically abnormal AML. Blood, 119(10), 2314-24.
  72. Lussier YA, Stadler WM, Chen JL (2011). Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. J Am Med Inform Assoc, 19(2), 156-60.
  73. Li H, Lee Y, Chen JL, Rebman E, Li J, Lussier YA (2012). Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. J Am Med Inform Assoc, 19(2), 295-305.
  74. Regan K, Wang K, Doughty E, Li H, Li J, Lee Y, Kann MG, Lussier YA (2012). Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants. J Am Med Inform Assoc, 19(2), 306-16.
  75. Ferreira CM, Chen JL, Li J, Shimomura K, Yang X, Lussier YA, Pinto LH, Solway J (2012). Genetic interactions between chromosomes 11 and 18 contribute to airway hyperresponsiveness in mice. PLoS One, 7(1), e29579.
  76. Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA (2012). Single sample expression-anchored mechanisms predict survival in head and neck cancer. PLoS Comput Biol, 8(1), e1002350.
  77. Lee Y, Gamazon ER, Rebman E, Lee Y, Lee S, Dolan ME, Cox NJ, Lussier YA (2012). Variants affecting exon skipping contribute to complex traits. PLoS Genet, 8(10), e1002998.
  78. Lussier YA, Khodarev NN, Regan K, Corbin K, Li H, Ganai S, Khan SA, Gnerlich JL, Darga TE, Fan H, Karpenko O, Paty PB, Posner MC, Chmura SJ, Hellman S, Ferguson MK, Weichselbaum RR (2012). Oligo- and polymetastatic progression in lung metastasis(es) patients is associated with specific microRNAs. PLoS One, 7(12), e50141.
  79. Yang X, Li H, Regan K, Li J, Huang Y, Lussier YA (2012). Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. AMIA Annu Symp Proc, 2012, 1040-9.
  80. Sammani S, Park KS, Zaidi SR, Mathew B, Wang T, Huang Y, Zhou T, Lussier YA, Husain AN, Moreno-Vinasco L, Vigneswaran WT, Garcia JG (2011). A sphingosine 1-phosphate 1 receptor agonist modulates brain death-induced neurogenic pulmonary injury. Am J Respir Cell Mol Biol, 45(5), 1022-7.
  81. Patwa LG, Fan TJ, Tchaptchet S, Liu Y, Lussier YA, Sartor RB, Hansen JJ (2011). Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli. Gastroenterology, 141(5), 1842-51.e1-10.
  82. Mathew B, Jacobson JR, Berdyshev E, Huang Y, Sun X, Zhao Y, Gerhold LM, Siegler J, Evenoski C, Wang T, Zhou T, Zaidi R, Moreno-Vinasco L, Bittman R, Chen CT, LaRiviere PJ, Sammani S, Lussier YA, Dudek SM, Natarajan V, Weichselbaum RR, Garcia JG (2011). Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs. FASEB J, 25(10), 3388-400.
  83. Lussier YA, Chen JL (2011). The emergence of genome-based drug repositioning. Sci Transl Med, 3(96), 96ps35.
  84. Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L (2011). Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc, 18(4), 354-7.
  85. Chen JL, Li J, Stadler WM, Lussier YA (2011). Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. J Am Med Inform Assoc, 18(4), 392-402.
  86. Yang X, Li J, Lee Y, Lussier YA (2011). GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics, 27(10), 1444-6.
  87. 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 (2011). An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol, 38(2), 215-24.
  88. Mathew B, Huang Y, Jacobson JR, Berdyshev E, Gerhold LM, Wang T, Moreno-Vinasco L, Lang G, Zhao Y, Chen CT, LaRiviere PJ, Mauceri H, Sammani S, Husain AN, Dudek SM, Natarajan V, Lussier YA, Weichselbaum RR, Garcia JG (2010). Simvastatin attenuates radiation-induced murine lung injury and dysregulated lung gene expression. Am J Respir Cell Mol Biol, 44(3), 415-22.
  89. Mirzapoiazova T, Moitra J, Moreno-Vinasco L, Sammani S, Turner JR, Chiang ET, Evenoski C, Wang T, Singleton PA, Huang Y, Lussier YA, Watterson DM, Dudek SM, Garcia JG (2010). Non-muscle myosin light chain kinase isoform is a viable molecular target in acute inflammatory lung injury. Am J Respir Cell Mol Biol, 44(1), 40-52.
  90. Lussier YA, Xing HR, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR (2011). MicroRNA expression characterizes oligometastasis(es). PLoS One, 6(12), e28650.
  91. Chard K, Russell M, Lussier YA, Mendona EA, Silverstein JC (2011). A cloud-based approach to medical NLP. AMIA Annu Symp Proc, 2011, 207-16.
  92. Yang X, Lee Y, Fan H, Sun X, Lussier YA (2011). Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers. Chin Sci Bull, 55(31), 3576-3589.
  93. Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA (2010). Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. BMC Bioinformatics, 11 Suppl 9, S11.
  94. Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W (2010). Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One, 5(10), e13534.
  95. Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, Xing HR, Lussier YA (2010). Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. J Biomed Inform, 43(3), 385-96.
  96. Yang X, Huang Y, Crowson M, Li J, Maitland ML, Lussier YA (2010). Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. J Biomed Inform, 43(3), 376-84.
  97. Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein MB, Weichselbaum RR, Xing HR, Lussier YA (2010). Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol, 6(4), e1000730.
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  101. Yang X, Huang Y, Chen JL, Xie J, Sun X, Lussier YA (2009). Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics, 10 Suppl 9, S6.
  102. Pantazatos SP, Li J, Pavlidis P, Lussier YA (2010). Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Inform, 8, 75-94.
  103. Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenoski CL, Husain AN, Mitra S, Moreno-Vinasco L, Jacobson JR, Lussier YA, Garcia JG (2009). GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling. FASEB J, 23(5), 1325-37.
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  106. Liu Y, Sam L, Li J, Lussier YA (2009). Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. BMC Bioinformatics, 10 Suppl 2, S11.
  107. Sam LT, Mendona EA, Li J, Blake J, Friedman C, Lussier YA (2009). PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics, 10 Suppl 2, S8.
  108. Wang T, Moreno-Vinasco L, Huang Y, Lang GD, Linares JD, Goonewardena SN, Grabavoy A, Samet JM, Geyh AS, Breysse PN, Lussier YA, Natarajan V, Garcia JG (2008). Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness. Environ Health Perspect, 116(11), 1500-8.
  109. Hong SB, Huang Y, Moreno-Vinasco L, Sammani S, Moitra J, Barnard JW, Ma SF, Mirzapoiazova T, Evenoski C, Reeves RR, Chiang ET, Lang GD, Husain AN, Dudek SM, Jacobson JR, Ye SQ, Lussier YA, Garcia JG (2008). Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury. Am J Respir Crit Care Med, 178(6), 605-17.
  110. Moreno-Vinasco L, Gomberg-Maitland M, Maitland ML, Desai AA, Singleton PA, Sammani S, Sam L, Liu Y, Husain AN, Lang RM, Ratain MJ, Lussier YA, Garcia JG (2008). Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension. Physiol Genomics, 33(2), 278-91.
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  112. Bales ME, Lussier YA, Johnson SB (2007). Topological analysis of large-scale biomedical terminology structures. J Am Med Inform Assoc, 14(6), 788-97.
  113. Chen ES, Stetson PD, Lussier YA, Markatou M, Hripcsak G, Friedman C (2007). Detection of practice pattern trends through Natural Language Processing of clinical narratives and biomedical literature. AMIA Annu Symp Proc, 120-4.
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  117. Nonas SA, Moreno-Vinasco L, Ma SF, Jacobson JR, Desai AA, Dudek SM, Flores C, Hassoun PM, Sam L, Ye SQ, Moitra J, Barnard J, Grigoryev DN, Lussier YA, Garcia JG (2007). Use of consomic rats for genomic insights into ventilator-associated lung injury. Am J Physiol Lung Cell Mol Physiol, 293(2), L292-302.
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  128. Choi J, Bakken S, Lussier YA, Mendona EA (2006). Improving the human readability of Arden Syntax medical logic modules using a concept-oriented terminology and object-oriented programming expressions. Comput Inform Nurs, 24(4), 220-5.
  129. Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C (2006). PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing. Pac Symp Biocomput, 64-75.
  130. Stevens R, Bodenreider O, Lussier YA (2006). Semantic webs for life sciences. Pac Symp Biocomput, 112-5.
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  133. Williams R, Jalan S, Stern E, Lussier YA (2011). Cascading Policies Provide Fault Tolerance for Pervasive Clinical Communications. Proc IEEE Int Conf Pervasive Comput Commun, 2005, 209-212.
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  137. Tao Y, Liu Y, Friedman C, Lussier YA (2010). Information Visualization Techniques in Bioinformatics during the Postgenomic Era. Drug Discov Today Biosilico, 2(6), 237-245.
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  140. Tao Y, Mendona EA, Lussier YA (2004). A tool for abstracting relevant classes of concepts: the Common Ancestry Summarizer. Stud Health Technol Inform, 107(Pt 1), 449-53.
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  142. Cantor MN, Lussier YA (2004). Mining OMIM for insight into complex diseases. Stud Health Technol Inform, 107(Pt 2), 753-7.
  143. Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA (2003). Linking biomedical language information and knowledge resources: GO and UMLS. Pac Symp Biocomput, 439-50.
  144. Cantor MN, Sarkar IN, Gelman R, Hartel F, Bodenreider O, Lussier YA (2003). An evaluation of hybrid methods for matching biomedical terminologies: mapping the gene ontology to the UMLS. Stud Health Technol Inform, 95, 62-7.
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  1. Atun R, Lussier Y, Poon C, Wong ST, Yang GZ (2015). Editorial: big data for health. IEEE J Biomed Health Inform, 19(4), 1191-2.
  2. Lussier YA, Butte AJ, Hunter L (2010). Current methodologies for translational bioinformatics. J Biomed Inform, 43(3), 355-7.


  1. Chang EH, Willis AL, Romanoski CE, Cusanovich DA, Pouladi N, Li J, Lussier YA, Martinez FD (2020). Rhinovirus Infections in Individuals with Asthma Increase ACE2 Expression and Cytokine Pathways Implicated in COVID-19. [Letter to the editor]. Am J Respir Crit Care Med, 202(5), 753-755.


  1. Aberasturi D, Pouladi N, Zaim SR, Kenost C, Berghout J, Piegorsch WW, Lussier YA (2021). 'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. Bioinformatics (37(Suppl_1), pp. i67-i75). England.
  2. Berghout J, Lussier YA, Vitali F, Bulyk ML, Kann MG, Moore JH (2019). Workshop during the Pacific Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes: interpreting non-coding DNA in high-throughput. Pac Symp Biocomput (24, pp. 444-448).
  3. Lussier YA, Li H, Pouladi N, Li Q (2014). Accelerating precision biology and medicine with computational biology and bioinformatics. Genome Biol (15(9), p. 450). England.
  4. Lussier YA, Li H, Maienschein-Cline M (2013). Conquering computational challenges of omics data and post-ENCODE paradigms. Genome Biol (14(8), p. 310). England.


  1. Friedman C, Lussier YA, Ena L (2009). Methods and systems for Extracting Phenotypic Information from the Literature via natural Language processing. U.S. Patent No. US20100010804A1 12/498,898. Washington, D.C.:U.S. Patent and Trademark Office.
  2. Lussier YA, Cantor M, Sarkar IN (2003). System and method for generating an amalgamated database. U.S. Patent No. 20060074991 WO 2004/044818. Washington, D.C.:U.S. Patent and Trademark Office.