Lussier Lab
  • RESEARCH
  • TEAM
  • PROJECTS
  • TOOLS
  • PUBLICATIONS
  • HONORS
  • NEWSpregnant-hd.net

BIOLOGY & ENVIRONMENT

Tailoring protocols leveraging ‘omics interactions with the environment to unveil individual responses

NETWORK SCIENCE

Network models integrating practice-anchored evidence with system and network biology underpinning disease mechanisms

PRECISION MEDICINE

Designing precision therapy and repositioning & rescuing drugs

biology

BIOLOGY & ENVIRONMENT

Tailoring protocols leveraging ‘omics interactions with the environment to unveil individual responses

computer science

NETWORK SCIENCE

Network models integrating practice-anchored evidence with system and network biology underpinning disease mechanisms

medicine

PRECISION MEDICINE

Designing precision therapy and repositioning & rescuing drugs

RESEARCH

FOCUS

Computational precision medicine: Data science for healing humanity - one person at a time

VISION

Our group conducts hypothesis-driven translational research in biomedical informatics that focuses on the use of big clinical or genomic data, knowledge technologies, and networks to accurately personalize our understanding of the pathology, progression, and treatment for diseases.

TEAM

Yves A. Lussier, MD

Yves A. Lussier, MD, FACMI

Chair of Biomedical Informatics

Jianrong Li, MSc

Jianrong Li, MSc

Dir. Strategic Informatics

Colleen Kenost, EdD

Colleen Kenost, EdD

Dir. Strategic Operations

Nima Pouladi

Nima Pouladi, PhD

Research Associate Professor

Dillon Aberasturi, PhD Student

Dillon Aberasturi

PhD Student

Samir Rachid Zaim

Liam Wilson

College Student

Lussier Group Alumni

PROJECTS

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TOOLS

  • ICD-9-CM To ICD-10-CM Conversion Tool
  • ICD-10-CM To ICD-9-CM Conversion Tool
  • Vol.3 ICD-9-CM to ICD-10-PCS Conversion Tool
  • ICD-9-CM Classification
  • N-of-1-pathways Tool
  • GO-Module
  • PhenoGo

PUBLICATIONS

  • 2018

    Genome-Wide Association Study in African Americans with Acute Respiratory Distress Syndrome Identifies the Selectin P Ligand Gene as a Risk Factor Christian Bime, Nima Pouladi, Saad Sammani, Ken Batai, Nancy Casanova, Tong Zhou, Carrie L. Kempf, Xiaoguang Sun, Sara M. Camp, Ting Wang, Rick A. Kittles, Yves A. Lussier, Tiffanie K. Jones, John P. Reilly, Nuala J. Meyer, Jason D. Christie, Jason H. Karnes, Manuel Gonzalez-Garay, David C. Christiani, Charles R. Yates, Mark M. Wurfel, Gianfranco U. Meduri, and Joe G. N. Garcia Am J Respir Crit Care Med
  • 2018

    ICD-10 procedure codes produce transition challenges Andrew D. Boyd MD, Jianrong ‘John’ Li MSc, Colleen Kenost, Samir Rachid Zaim, Jacob Krive PhD, Manish Mittal PhD, Richard A. Satava MD, Michael Burton MSc, Jacob Smith, Yves A. Lussier MD AMIA Jt Summits Transl Sci Proc 2018
  • 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? Andrew D. Boyda, Karen Dunn Lopezb, Camillo Lugaresic, Tamara Macieirab, Vanessa Sousab, Sabita Acharyac, Abhinaya Balasubramanianc, Khawllah Roussia, Gail M. Keenand, Yves A. Lussiere,f, Jianrong ‘John’ Lie, Michel Burtona, and Barbara Di Eugenioca Int J Med Inform
  • 2018

    Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews Jung-wei Fan, PhD, Yves A. Lussier, MD AMIA Annu Symp Proc. 2018
  • 2018

    Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes Francesca Vitali, Qike Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, and Yves A. Lussier Briefings in Bioinformatics
  • 2018

    Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li, Yves A. Lussier Pac Symp Biocomput
  • 2018

    Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses Samir Rachid Zaim, Qike Li, A. Grant Schissler, Yves A. Lussier Pac Symp Biocomput ( Second best of the year in Pathway-level versus gene-level analyses )
  • 2018

    Single subject transcriptome analysis to identify functionally signed gene set or pathway activity Joanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A. Lussier Pac Symp Biocomput
  • 2017

    A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations Vincent Gardeux, Joanne Berghout, Ikbel Achour, A Grant Schissler, Qike Li, Colleen Kenost, Jianrong Li, Yuan Shang, Anthony Bosco, Donald Saner, Marilyn J Halonen, Daniel J Jackson, Haiquan Li, Fernando D Martinez, and Yves A Lussier Journal of the American Medical Informatics Association
  • 2017

    Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context Jung-wei Fan, Jianrong Li, and Yves A. Lussier Journal of Healthcare Engineering
  • 2017

    Exploring Wound-Healing Genomic Machinery with a Network-Based Approach Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A. Lussier, Maria Gabriella Cusella De Angelis, and Ricardo Bellazzi Pharmaceuticals
  • 2017

    N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes Qike Li, A.Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang, and Yves A. Lussier BMC Medical Genomics
  • 2017

    Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation A. Grant Schissler, Walter W. Piegorsch, and Yves A. Lussier Statistical Methods in Medical Research
  • 2017

    kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects Qike Li, A. Grant Schissler, Vincent Gardeux, Joanne Berghout, Ikbel Achour, Colleen Kenost, Haiquan Li, Hao Helen Zhang, Yves A. Lussier Journal of Miomedical Informatics
  • 2016

    Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Pouladi N, Bime C, Garcia JG, Lussier YA. Translational Research: The Journal of Laboratory and Research Medicine
  • 2016

    Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records N. Pouladi, I. Achour, H. Li, J. Berghout, M.L. Gonzalez-Garay, Y.A. Lussier IMIA Yearbook of Medical Informatics
  • 2016

    Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells A. Grant Schissler, Qike Li, James L. Chen, Colleen Kenost, Ikbel Achour, D. Dean Billheimer, Haiquan Li, Walter W. Piegorsch, Yves A. Lussier Bioinformatics
  • 2016

    Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardeux, Jianrong Li, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S Ramos, Ian Foster, Joshua C Denny, Jason H Moore, Yves A Lussier npj Genomic Medicine
  • 2016

    Rethinking the role and impact of health information technology: informatics as an interventional discipline. Payne PR, Lussier Y, Foraker RE, Embi PJ. BMC Medical Informatics and Decision Making
  • 2015

    Simulation of ICD-9 to ICD-10-CM Transition for Family Medicine: Simple or Convoluted? Grief SN, Patel J, Kochendorfer KM, Green LA, Lussier YA, Li J, Burton M, Boyd AD. Journal of the American Board of Family Medicine: JABFM
  • 2015

    A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis. 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. BMC Pulmonary Medicine
  • 2015

    eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs. Li H, Pouladi N, Achour I, Gardeux V, Li J, Li Q, Zhang HH, Martinez FD, 'Skip' Garcia JG, Lussier YA. Journal of Biomedical Informatics
  • 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. Schissler AG, Gardeux V, Li Q, Achour I, Li H, Piegorsch WW, Lussier YA. Bioinformatics
  • 2015

    Evidence Suggesting That Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors. 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. Cancer Research
  • 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. Krive J, Patel M, Gehm L, Mackey M, Kulstad E, Li JJ, Lussier YA, Boyd AD. The American Journal of Emergency Medicine
  • 2015

    Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. Gardeux V, Bosco A, Li J, Halonen MJ, Jackson D, Martinez FD, Lussier YA. Journal of Biomedical Informatics
  • 2015

    Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM. Boyd AD, Li JJ, Kenost C, Joese B, Yang YM, Kalagidis OA, Zenku I, Saner D, Bahroos N, Lussier YA. Journal of the American Medical Informatics Association

HONORS

  • 2018

    Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses Samir Rachid Zaim, etc Award for The Second best paper of the year in Pathway-level versus gene-level analyses among 636 papers
  • 2017

    The University of Arizona's Department of Family and Community Medicine (FCM) Jianrong Li Award for Commitment to Quality Improvement
  • 2017

    Ambassador for Health Sciences, 21st Outreach Gala, University of Sherbrooke Yves A. Lussier University of Sherbrooke Ambassador Award
  • 2016

    Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. Yves A. Lussier TBC 2016 keynote
  • 2013

    'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. Vincent Gardeux TBC 2013 Best Paper Award
  • 2012

    Expression-anchored Gene Ontology Signature Predicts Clinical Outcome in Lung Adenocarcinoma Patients. Kelly Regan AMA 2012 Top Award at AMA Research Symposium
  • 2012

    Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex disease Traits Younghee Lee TBC 2012 Best Paper Award
  • 2011

    Complex Disease Networks of Trait-associated SNPs Unveiled by Information Theory. Haiquan Li AMIA 2011 Distinguished Paper Award
  • 2010

    Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. Xinan Yang, etc AMIA 2010 Outstanding Paper Award
  • 2009

    PGnet: A Novel Method for Predicting Epigenetic Regulatory Networks in Gene Expression Arrays of Acute Lymphoblastic Leukemia. Xinan Yang AMIA 2009 Outstanding Paper Award
  • 2008

    Robust Methods for Accurate Diagnosis Using Microbiological Arrays. Yves Lussier AMIA 2008 Outstanding Paper Award
  • 2008

    PhenoGO: A resource for the multiscale integration of Clinical and Biological Data. Lee Sam AMIA 2008 Outstanding Paper Award
  • 2004

    1st Recipient of the Columbia University Faculty Mentorship Award Yves A. Lussier Columbia University Faculty Mentorship Award
  • 2004

    IBM Faculty Award in recognition of his achievement in the field of biomedical informatics (2003 and 2004) Yves A. Lussier IBM Faculty Award

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UA Center for Biomedical Informatics and Biostatistics

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Department of Biomedical Informatics
421 Wakara Way, Ste 140   |  Salt Lake City, UT 84108-3514
Tel: 801-581-4080  |   Fax: 801-581-4297   |  Email us

Yves A. Lussier, MD, FACMI

Yves A. Lussier, MD, FAMCI, 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.

Jianrong Li, MSc

Jianrong Li has been worked in the Biomedical Informatics field for over 15 years, with several years in the banking industry. He has hands-on skills in I2B2, Bioinformatics, Natural Language Process, Data Mining, Artificial Intelligence, Biotechnology

Clinical Trials, Text Mining, Information Retrieval, and Statistics.

Years of Experience: 30 years

Technology: DB2, MySQL, Microsoft SQL Server, Solaris, Linux, Microsoft Windows (XP, 7, 8), Cytoscape

Programming Languages: PERL, Java, C, R, C#

Certification: CLARITY DATA MODEL - PROFESSIONAL BILLING

Dillon Aberasturi, PhD Student

Dillon Aberasturi is a PhD student in statistics at The University of Arizona with a Masters in Statistics. His previous research involved the connection between self-similar trees and hyperbolic space. His current research focuses on creating new methods for using N-of-1 studies to evaluate differences in disease mechanism in subpopulations and rare diseases.

Liam Wilson

Liam Wilson is an undergraduate at the University of Arizona pursuing degrees in mathematics and computer science, and is a research assistant with the Lussier Group. Liam started working with the Lussier Group as a high school junior as a part of the KEYS Research Internship at the UofA, and has continued with the group both during their time at the UA as well as the University of Utah. Liam’s contributions have been towards a variety of projects, from validating large-scale environmental exposure/disease predictions to extending single-subject methods developed for the transcriptome to other ‘omics. Liam is particularly interested in the efficiency facet of research programming and incorporating more traditional software engineering techniques in research settings to improve productivity and the usability of products of research.

Joanne Berghout, PhD

Joanne Berghout, PhD is a Research Assistant Professor of Biomedical Informatics in the research group of Dr. Yves Lussier. Dr. Berghout received her PhD in Biochemistry from McGill University in Montreal, QC where she researched the genetics of complex traits and susceptibility to infectious disease in humans and mouse models. Following that, she spent three years as the Outreach Coordinator for the Mouse Genome Informatics (MGI) database in Bar Harbor, ME. There, she trained researchers in genetics, genomics, data structures and data mining to answer biological questions, and worked closely with other members of the MGI group to develop and optimize the MGI resource. Dr. Berghout’s research interests include genetics of all kinds, personalized medicine, big data, and scientific communication.

Colleen Kenost, EdD

Colleen Kenost currently has two roles in the Lussier Lab which span the Department of Medicine and the Center for Biomedical Informatics and Biostatistics. Colleen’s main role is to bridge the gap between research and administration and to foster collaborative efforts between multiple units across campus and with external stakeholders. She currently serves as the both CB2 Director of Strategic Operations and the Multidisciplinary Knowledge Management Specialist. In these roles, she oversees all collaborative efforts, both operationally and administratively. She works across traditional boundaries, and is well-versed in translating research prerogatives into action and operationalizing strategic plans.

She received her Bachelors Degree in Business Administration and Masters Degree in Human Resource Development from Northeastern Illinois University. She has currently completed her coursework and is working on her dissertation for her Doctorate of Education in Interdisciplinary Leadership, with a concentration in non-profit social entrepreneurship, at Governors State University. She has been with The University of Arizona since 2013. Prior to this, she worked with Dr. Lussier at the University of Illinois at Chicago from 2011–2013. She also worked in the Departments of Medicine and Otolaryngology at the University of Illinois at Chicago from 2007-11.

Nima Pouladi, PhD

Nima Pouladi is in his second year as a postdoctoral research fellow. His primary research goal is to combine the results from different ‘omics data in order uncover the hidden links among diseases and ultimately translate the findings to clinical practice, such as through the repurposing the available treatment options for various diseases

Lussier Group Alumni

Name
Name
Employer
Employer
Current Position
Current Position
Joanne Berghout, PhD Pfizer Senior Computational Geneticist
Francesca Vitali, PhD The University of Arizona Research Assistant Professor
Samir Rachid Zaim, PhD Code for Venezuela biostatistician and Data Scientist
Jungwei Fan, PhD Mayo Clinic Researcher
Dillon Aberasturi The University of Arizona PhD Student
Qike Li, PhD Quantiply Data Scientist
A. Grant Schissler, PhD University of Nevada, Reno Assistant Professor
Ikbel Achour, PhD MedImmune Lead Scientist, Translational Medicine
Haiquan Li, PhD The University of Arizona Assistant Professor, Biosystems Informatics
Nima Pouladi, MD, PhD The University of Arizona, Center for Biomedical Informatics and Biostatistics Computational Researcher in Genomics
Michael Cantor New York School of Medicine Director of Clinical Research Informatics and Associate Professor
Younghee Lee University of Utah Assistant Professor, Biomedical Informatics Research
David J. Mann NorthShore University HealthSystem Dermatologist
Xinan Yang The University of Chicago Research Associate Professor
James L. Chen Ohio State University Assistant Professor, Internal Medicine & Biomedical Informatics
Vincent Gardeux EPFL Laboratory of Systems Biology & Genetics Research Collaborator
Young Ji Lee University of Pittsburgh Assistant Professor
Peter LoPresti University of Illinois at Chicago MD Student
Alan Perez-Rathke University of Illinois at Chicago MD/PhD Graduate Student
Gurunadh Parinandi AIM Specialty Health Business Information Analyst 2
Kelly Regan Ohio State University NIH National Laboratory of Medicine Biomedical Informatics Research Training Program Fellow
Kanix Wang University of Chicago PhD Candidate
Ying Tao Beijing Laboratory IBM Researcher
Indra Neil Sarkar University of Vermont Director of Biomedical Informatics and Assistant Professor of Micorbiology and Molecular Genetics
Matthew Crowson Duke University OHNS Resident
Lee Sam University of Michigan PhD Candidate
Spiro Pantazatos Columbia University, Dept. of Psychiatry Assistant Professor of Clinical Neurobiology

PRECISION HEALTH INITIATIVE

FACT SHEET: Obama Administration Announces Key Actions to Accelerate Precision Medicine Initiative

White House Announcement: UA Health Sciences Commits Biomedical Informatics and Genome Medicine Teams to National Precision Medicine Initiative

In response to the national Precision Medicine Initiative (PMI), UAHS has committed significant resources to expand the clinical utility of its open-source, patient-centric analytic methods, such as the N-of-1-pathways software, which aids physicians in interpreting the dynamic changes of disease-associated gene expression arising from patients’ own DNA blueprints. As part of the initiative, UAHS will translate large-scale clinical and genomic data into actionable individual outcomes through two of its centers: the UA Center for Biomedical Informatics and Biostatistics (CB2) and the UA Center for Applied Genetics and Genomic Medicine (TCAG2M). Both centers bring together physicians, scientists, patients and other key stakeholders to develop strategies that advance understanding of the factors contributing to individual health and disease and personalized approaches to disease prevention, early detection and treatment.

Yves Lussier, MD, FACMI, will lead the UAHS patient-centric analytical methods and was invited to attend the Precision Medicine Initiative Summit held Feb 25th in Washington, D.C. UAHS’ involvement in the PMI was initiated and facilitated by Ikbel Achour, PhD, who serves as CB2’s director for precision health. Dr. Lussier collaborates closely with Kenneth S. Ramos, MD, PhD, PharmB, associate vice president for precision health sciences, director of the UA TCAG2M and an elected member of the National Academy of Medicine.

ICD-9/ICD-10

ICD-9-CM To ICD-10-CM Conversion Tool

Vol.3 ICD-9-CM to ICD-10-PCS Conversion Tool

About: Automatically identify errors from ICD-9-CM to CD-10-CM code transition that potentially can disrupt billing and clinical practice.

Goal: Clarify and quantify the administrative and financial impact from ICD-10-CM implementation in clinical datasets to reduce inaccuracies and reporting errors.

Impact. ICD-9 to ICD-10 transition based on:

  • All reimbursed payments for primary care patients of University of Illinois
  • 38,644 patients
  • 1,446,581 patient encounters
  • $382 million in payments
  • 299 institutions included

Publications

  • The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study, and mitigating tools. - JAMIA 2013 Editor Pick

  • COPD Hospitalization Risk Increased with Distinct Patterns of Multiple Systems Comorbidities Unveiled by Network Modeling - AMIA Annu Symp Proc. 2014

  • Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM. - JAMIA, 2015

  • Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM. - JAMIA 2015

N-OF-1-PATHWAYS

N-of-1-Pathways Tool

In this era of precision medicine, accurate personal transcriptome interpretation and N-of-1 (single-subject) efficacy trials remain unmet challenges. We therefore developed a method, “N-of-1-pathways,” that translates gene expression data profiles into disease mechanism significance for a pair of samples - one patient at the time.

The emergence of precision medicine ushered in the opportunity to incorporate individual molecular data into patient care. In contrast to personal DNA sequencing profiling increasingly pursued in clinical practice, genome-wide transcriptome profiling has often provided biological information at the gene and pathway levels that are common and applicable only to a larger cohort. The N-of-1-pathways method, a global framework, relies on three principles: i) the statistical universe is a single patient/sample; ii) significance is derived from genesets/biomodules; and iii) similarity metric of inter-mechanisms’ relationships. N-of-1-pathways provides a unique and novel framework for N-of-1-studies (e.g. patients, cell-lines, tissues, etc.) aimed at predicting individual response to therapy and biomarker discovery. N-of-1-pathways offers opportunities to include patient-centered “omics” reports into electronic medical records for individualized clinical interpretation and precise treatment.

Publications

  • 'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. 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. - J Am Med Inform Assoc. 2014

    JAMIA Editor Pick 2014 - AWARD Best TBC Research Paper 2013; Presentation at Translational Bioinformatics Conference (TBC) - TBI AMIA 2013 Joint Summits on Translational Science

  • Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. Gardeux V*, Arslan AD*, Achour I*, Ho TT*, Beck WT, Lussier YA. - BMC Med Genomics. 2014.

    Presentation at Translational Bioinformatics Conference (TBC)

  • Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. Schissler AG*, Gardeux V*, Li Q*, Achour I*, Li H, Piegorsch WW, Lussier YA. - Bioinformatics. 2015

    Presentation at Intelligent Systems for Molecular Biology, ISMB 2015

  • Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. Gardeux V, Bosco A, Li J, Halonen MJ, Jackson D, Martinez FD, Lussier YA. - J Biomed Inform. 2015

* These authors contributed equally to the work

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

Haiquan Li*, Ikbel Achour*, Lisa Bastarache*, Joanne Berghout, Vincent Gardeux, Jianrong Li,Younghee Lee, Lorenzo Pesce7, Xinan Yang, Kenneth S Ramos, Ian Foster, Joshua C Denny, Jason H Moore and Yves A Lussier.

* These authors contributed equally to this work

Functionally altered biological mechanisms arising from disease-associated polymorphisms, remain difficult to characterise when those variants are intergenic, or, fall between genes. We sought to identify shared downstream mechanisms by which inter- and intragenic single-nucleotide polymorphisms (SNPs) contribute to a specific physiopathology. Using computational modelling of 2 million pairs of disease-associated SNPs drawn from genome-wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology functional annotations, we predicted 3,870 inter–intra and inter–intra SNP pairs with convergent biological mechanisms (FDR 0.05). These prioritised SNP pairs with overlapping messenger RNA targets or similar functional annotations were more likely to be associated with the same disease than unrelated pathologies (OR412). We additionally confirmed synergistic and antagonistic genetic interactions for a subset of prioritised SNP pairs in independent studies of Alzheimer’s disease (entropy P = 0.046), bladder cancer (entropy P = 0.039), and rheumatoid arthritis (PheWAS case–control Po10− 4). Using ENCODE data sets, we further statistically validated that the biological mechanisms shared within prioritised SNP pairs are frequently governed by matching transcription factor binding sites and long-range chromatin interactions. These results provide a ‘roadmap’ of disease mechanisms emerging from GWAS and further identify candidate therapeutic targets among downstream effectors of intergenic SNPs.

npj Genomic Medicine (2016) 1, 16006; doi:10.1038/npjgenmed.2016.6; published online 27 April 2016

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