The Lussier Group

The Lussier Group
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 & 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
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, FACMI
Chair of Biomedical Informatics
Colleen Kenost, EdD
Dir. Strategic Operations
Nima Pouladi, PhD
Research Associate
Madi Shabanian
Data Scientist
Liam Wilson
Software Developer
Lussier Group Alumni
PROJECTS
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
2022
Immunogenetics associated with
severe coccidioidomycosis
Amy P.
Hsu, Agnieszka Korzeniowska, Cynthia C. Aguilar, Jingwen Gu, Eric
Karlins, Andrew J. Oler, Gang Chen, Glennys V. Reynoso, Joie Davis,
Alexandria Chaput, Tao Peng, Ling Sun, Justin B. Lack, Derek J. Bays,
Ethan R. Stewart, Sarah E. Waldman, Daniel A. Powell, Fariba M. Donovan,
Jigar V. Desai, Nima Pouladi, Debra A. Long, Priel, Daisuke Yamanaka,
Sergio D. Rosenzweig, Julie E. Niemela, Jennifer Stoddard, Alexandra F.
Freeman, Christa S. Zerbe, Douglas B. Kuhns, Yves A. Lussier, Kenneth N.
Olivier, Richard C. Boucher, Heather D. Hickman, Jeffrey Frelinger,
Joshua Fierer, Lisa F. Shubitz, Thomas L. Leto, George R. Thompson III,
John N. Galgiani, Michail S. Lionakis, and Steven M. Holland
JCI Insight
2022
Epithelial cell responses to
rhinovirus identify an early-life–onset asthma phenotype in
adults
Eugene H. Chang, MD, Nima
Pouladi, PhD, Stefano Guerra, MD, PhD, Jana Jandova, PhD, Alexander Kim,
BS, Haiquan Li, PhD, Jianrong Li, MSc, Wayne Morgan, MD, Debra A. Stern,
MS, Amanda L. Willis, MS, Yves A. Lussier, MD, and Fernando D. Martinez,
MD
The Journal of Allergy and
Clinical Immunology
2021
‘Single-subject
studies’-derived analyses unveil altered biomechanisms between very
small cohorts: implications for rare diseases
Dillon Aberasturi, Nima Pouladi, Samir Rachid
Zaim, Colleen Kenost, Joanne Berghout, Walter W. Piegorsch, and Yves A.
Lussier
Bioinformatics
2021
Comparison and impact of
COVID-19 for patients with cancer: a survival analysis of fatality rate
controlling for age, sex and cancer type
Haiquan Li, Edwin Baldwin, Xiang Zhang, Colleen
Kenost, Wenting Luo, Elizabeth A Calhoun, Lingling An, Charles L
Bennett, Yves A Lussier
BMJ Health
& Care Informatics
2021
MicroRNA and Protein-Coding
Gene Expression Analysis in Idiopathic Pulmonary Fibrosis Yields Novel
Biomarker Signatures Associated to Survival
Nancy G. Casanova, Tong Zhou, Manuel
Gonzalez-Garay, Yves A. Lussier, Nadera Sweiss, Shwu-Fan Ma, Imre Noth,
Kenneth S. Knox, Joe G.N. Garcia
Translational Research
2020
Rhinovirus Infections in
Individuals with Asthma Increase ACE2 Expression and Cytokine Pathways
Implicated in COVID-19
Eugene H.
Chang, Amanda L. Willis, Casey E. Romanoski, Darren A. Cusanovich, Nima
Pouladi, Jianrong Li, Yves A. Lussier, Fernando D. Martinez
American Journal of Respiratory and Critical
Care Medicine
2020
Correction to: binomialRF:
interpretable combinatoric efficiency of random forests to identify
biomarker interactions
Samir Rachid
Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, Liam Wilson, Hao
Helen Zhang, and Yves A. Lussier
BMC Medical Genomics
2020
Personalized beyond Precision:
Designing Unbiased Gold Standards to Improve Single-Subject Studies of
Personal Genome Dynamics from Gene Products
Samir Rachid Zaim, Colleen Kenost, Hao Helen
Zhang, and Yves A. Lussier
Journal
of Personalized Medicine
2020
The Mechanism of Cancer Drug
Addiction in ALK-Positive T-Cell Lymphoma
Soumya S. Rajan, Amit Dipak Amin, Lingxiao Li,
Delphine C. Rolland, Haiquan Li, Deukwoo Kwon, Mercedes F. Kweh,
Artavazd Arumov, Evan R. Roberts, Aimin Yan, Venkatesha Basrur, Kojo S.J
Elenitoba-Johnson, Xi Steven Chen, Soham D. Puvvada, Yves A. Lussier,
Daniel Bilbao, Megan S. Lim, Jonathan H. Schatz
Oncogene
2020
Interpretation of ‘Omics
dynamics in a single subject using local estimates of dispersion between
two transcriptomes
Qike Li, Samir
Rachid Zaim, Dillon Aberasturi, Joanne Berghout, Haiquan Li, Francesca
Vitali, Colleen Kenost, Helen Hao Zhang, Yves A. Lussier
2019
Evaluating single-subject study
methods for personal transcriptomic interpretations to advance precision
medicine
Samir Rachid Zaim, Colleen
Kenost, Joanne Berghout, Francesca Vitali, Helen Hao Zhang, and Yves A.
Lussier
BMC Medical Genomics
2019
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
2019
A Single-Subject Method to
Detect Pathways Enriched With Alternatively Spliced Genes
Alfred Grant Schissler, Dillon Aberasturi,
Colleen Kenost and Yves A. Lussier
Frontiers in Genetics
2019
Precision drug repurposing via
convergent eQTL-based molecules and pathway targeting independent
disease-associated polymorphisms
Francesca Vitali, Joanne Berghout, Jungwei Fan,
Jianrong Li, Qike Li, Haiquan Li, and Yves A. Lussier
Pacific Symposium on Biocomputing
2019
Workshop during the Pacific
Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes:
interpreting non-coding DNA in high-throughput
Joanne Berghout, Yves A. Lussier, Francesca
Vitali, Martha L. Bulyk, Maricel G. Kann, Jason H. Moore
Pacific Symposium on Biocomputing
2018
Novel disease syndromes
unveiled by integrative multiscale network analysis of diseases sharing
molecular effectors and comorbidities
Haiquan Li, Jungwei Fan, Francesca Vitali,
Joanne Berghout, Dillon Aberasturi, Jianrong Li, Liam Wilson, Wesley
Chiu, Minsu Pumarejo, Jiali Han, Colleen Kenost, Pradeep C. Koripella,
Nima Pouladi, Dean Billheimer, Edward J. Bedrick, and Yves A.
Lussier
BMC Medical Genomics
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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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 worked in the field of Biomedical Informatics for over 22 years, with several years of
experience in the banking industry. With a wealth of expertise in Machine Learning, I2B2,
Bioinformatics, Natural Language Processing, Data Mining, Artificial Intelligence, Biotechnology, Text
Mining, Information Retrieval, and Statistics, he has been at the forefront of the field's evolution. He
has hands-on skills in technologies such as DB2, MySQL, Microsoft SQL Server, Solaris, Linux, FileMaker,
and Cytoscape. He is proficient in programming languages such as PERL, Python, Java, C, R, and C#, which
have enabled him to solve complex problems in the field. His commitment to the field is reflected in his
certification as a CLARITY DATA MODEL - PROFESSIONAL BILLING expert. He is an expert in DAG-anchored
terminology mapping methods for new terms to any target, and his exceptional ability to provide instant
high-quality clinical NLP and coding without training sets using expert-system based NLP over clinical
data is highly regarded.
Liam Wilson
Liam Wilson is a software developer with degrees in computer science and mathematics from the University
of Arizona. His career experience includes working with various data science research groups,
contributing to distributed software orchestration tools, and developing optimization engines in the
manufacturing industry. While with the Lussier group, he has contributed to a variety of projects, from
validating large-scale environmental exposure/disease predictions to extending single-subject methods
developed for the transcriptome to other ‘omics. He currently develops software and tools for analyzing
clinical and ‘omics data, contributes to the writing of grant proposals and scientific papers, and
creates effective development plans and quality assurance procedures to the ultimate end of furthering
translational bioinformatics research.
Madi Shabanian
Driven by an unwavering dedication to enhancing patient health, she serves as an AI Data Scientist at the Biomedical Informatics Department at the University of Utah. She is an alum of the University of Tennessee Health Science Center, where she specialized in Biomedical Engineering. With over 5 years of experience in pediatric medical imaging, she has collaborated with renowned institutions including St. Jude Children's Hospital, Le Bonheur Children's Hospital, and Cincinnati Children's Hospital – the latter being recognized as the #1 pediatric hospital in the nation in 2023. As she delves into her PhD, her focus sharpens on devising pioneering deep neural network models. These models are tailor-made to meticulously analyze intricate gene expression datasets, aiming to diagnose complex diseases in their nascent stages, notably cancer. Outside the realm of academia, she channels her artistic flair into canvas paintings and holds an equal passion for traveling and woodworking.
Colleen Kenost, EdD
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 Director of Strategic Operations for the Department of Biomedical Informatics as well as
manages the Lussier Research Group. She works across traditional boundaries, and is well-versed in
translating research prerogatives into action and operationalizing strategic plans. She received her
Bachelor's Degree in Business Administration (2007) and Master's Degree in Human Resource Development
(2013) from Northeastern Illinois University. She received her Doctorate of Education in
Interdisciplinary Leadership, with a concentration in non-profit social entrepreneurship, at Governors
State University in 2016. She recently completed a Master of Public Health degree with a concentration
in Health Services Administration from The University of Arizona (2019). Prior to this, she worked with
Dr. Lussier at the University of Arizona from 2013 to 2020 and the University of Illinois at Chicago
from 2011–2013.
Nima Pouladi, PhD
Nima’s primary research interest is to better understand the underlying molecular mechanisms of complex
diseases and ultimately translate the results into clinical practice. I therefore utilize various
analytical and computational methods developed in evolutionary biology, epigenetics, genetics, and
bioinformatics for analyzing the data derived from distinctive high-throughput assays. However, most of
the currently available analytical methods lack the power to uncover the mechanisms that their
alterations lead to development of diseases for them the large cohort of patients are not available or
hard to obtain such as rare diseases. To address this issue, he is currently working in the Lussier
Research Group on developing, expanding, and implementing single-subject analytical methods which infuse
and anchor the knowledge from various sources of omics’ data with novel statistics to further our
insights into the biology that underpins the development and progression of rare diseases.
Lussier Group Alumni
Name
Name
Employer
Employer
Current Position
Current Position
Dillon Aberasturi, PhD
Corteva
Data Scientist
Ikbel Achour, PhD
MedImmune
Lead Scientist, Translational Medicine
Joanne Berghout, PhD
Pfizer
Senior Computational Geneticist
Michael Cantor
New York University School of Medicine
Director of Clinical Research Informatics and
Associate Professor
James L. Chen
The Ohio State University
Assistant Professor, Internal Medicine & Biomedical
Informatics
Matthew Crowson
Duke University
OHNS Resident
Jungwei Fan, PhD
Mayo Clinic
Researcher
Vincent Gardeux
EPFL Laboratory of Systems Biology & Genetics
Research Collaborator
Young Ji Lee
University of Pittsburgh
Assistant Professor
Younghee Lee
University of Utah
Assistant Professor, Biomedical Informatics Research
Haiquan Li, PhD
The University of Arizona
Assistant Professor, Biosystems Informatics
Qike Li, PhD
Quantiply
Data Scientist
Peter LoPresti
University of Illinois at Chicago
MD Student
David J. Mann
NorthShore University HealthSystem
Dermatologist
Spiro Pantazatos
Dept of Psychiatry at Columbia University
Assistant Professor of Clinical Neurobiology
Gurunadh Parinandi
AIM Specialty Health
Business Information Analyst 2
Alan Perez-Rathke
University of Illinois at Chicago
MD/PhD Graduate Student
Kelly Regan
The Ohio State University
NIH National Library of Medicine Biomedical
Informatics Research Training Program Fellow
Lee Sam
University of Michigan
PhD Candidate
Indra Neil Sarkar
University of Vermont
Director of Biomedical Informatics and Assistant
Professor of Microbiology and Molecular Genetics
A. Grant Schissler, PhD
University of Nevada, Reno
Assistant Professor
Ying Tao
Beijing Laboratory
IBM Researcher
Francesca Vitali, PhD
The University of Arizona
Research Assistant Professor
Kanix Wang
University of Chicago
PhD Candidate
Xinan Yang
The University of Chicago
Assistant Professor
Samir Rachid Zaim, PhD
Code for Venezuela
Biostatistician and Data Scientist
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.
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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