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

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

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

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


Pediatric Cytochrome P450 Activity Alterations in Nonalcoholic Steatohepatitis. Hui Li, Mark J. Canet, John D. Clarke, Dean Billheimer, Stavra A. Xanthakos, Joel E. Lavine, Robert P. Erickson, and Nathan J. Cherrington DRUG METAB DISPOS

Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. Jung-wei Fan, Jianrong Li, and Yves A. Lussier JOURNAL OF HEALTHCARE ENGINEERING

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, MJ Halonen, DJ Jackson, Haiquan Li, Fernando. Martinez, and Yves A. Lussier J AM MED INFORM ASSOC

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

Community-level characteristics and environmental factors of child respiratory illnesses in Southern Arizona. Nathan Lothrop, Khaleel Hussaini, Dean Billheimer, and Paloma Beamer BMC Public Health

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

Metabolomic Profiling Distinction of Human Nonalcoholic Fatty Liver Disease Progression from a Common Rat Model. JianHua Hana, Anika L. Dzierlenga, Zhengqiang Lu, Dean D. Billheimer, Elmira Torabzadehkhorasani, April D. Lake, Hui Li, Petr Novak, Petia Shipkova, Nelly Aranibar, Donald Robertson, Michael D. Reily, Lois D. Lehman-McKeeman, and Nathan J. Cherrington OBESITY (SILVER SPRING)

An evaluation of Z-transform algorithms for identifying subject-specific abnormalities in neuroimaging data. Andrew R. Mayer, Andrew B. Dodd, Josef M. Ling, Christopher J. Wertz, Nicholas A. Shaff, Edward J. Bedrick, and Carlo Viamonte BRAIN IMAGING AND BEHAVIOR

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

Childhood hematologic cancer and residential proximity to oil and gas development. Lisa M. McKenzie, William B. Allshouse, Tim E. Byers, Edward J. Bedrick, Berrin Serdar, and John L. Adgate PLOS ONE

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


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

Exploration of Early-Life Candidate Biomarkers for Childhood Asthma Using Antibody Arrays. Haili Xu, Timothy Radabaugh, Zhenqiang Lu1, Michael Galligan1, Dean Billheimer, Donata Vercelli, Anne L. Wright, Terrence J. Monks, Marilyn Halonen, and Serrine S. Lau PEDIATR ALLERGY IMMUNOL

Food Source Prediction of Shiga Toxin-Producing Escherichia coli Outbreaks Using Demographic and Outbreak Characteristics, United States, 1998-2014. Alice White, Alicia Cronquist, Edward J. Bedrick, and Elaine Scallan FOODBORNE PATHOGENS AND DISEASE

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

A Distinct Low Lung Function Trajectory from Childhood to the Fourth Decade of Life. Cristine E. Berry, Dean Billheimer, Isaac C. Jenkins, Zhenqiang J. Lu, Debra A. Stern, Lynn B. Gerald, Tara F. Carr, Stefano Guerra, Wayne J. Morgan, Anne L. Wright, and Fernando D. Martinez AM J RESPIR CRIT CARE MED

Human memory T cells with a naïve phenotype accumulate with aging and respond to persistent viruses. Vesna Pulko, John S. Davies, Carmine Martinez, Marion C. Lanteri, Michael P. Busch, Michael S. Diamond, Kenneth Knox, Erin S. Busch, Peter A. Sims, Shripad Sinari, Dean Billheimer, Elias K. Haddad, Kristy O. Murray, Anne M. Wertheimer, and Janko Nikolich-Žugich NAT IMMUNOL

An approach for quantifying small effects in regression models. Edward J. Bedrick and Lauren Hund SMMR

Association of Children’s Urinary CC16 Levels with Arsenic Concentrations in Multiple Environmental Media. Paloma I. Beamer, Walter T. Klimecki, Miranda Loh, Yoshira Ornelas Van Horne, Anastasia J. Sugeng, Nathan Lothrop, Dean Billheimer, Stefano Guerra, Robert Clark Lantz, Robert A. Canales, and Fernando D. Martinez INT J ENVIRON RES PUBLIC HEALTH

Disialylated apolipoprotein C-III proteoform is associated with improved lipids in prediabetes and type 2 diabetes. Juraj Koska, Hussein Yassine, Olgica Trenchevska, Shripad Sinari, Dawn C. Schwenke, Frances T. Yen, Dean Billheimer, Randall W. Nelson, Dobrin Nedelkov, and Peter D. Reaven JOURNAL OF LIPID RESEARCH

Spatial Clusters of Child Lower Respiratory Illnesses Associated with Community-Level Risk Factors. Paloma I. Beamer, Nathan Lothrop, Zhenqiang Lu, Rebecca Ascher, Kacey Ernst, Debra A. Stern, Dean Billheimer, Anne L. Wright, and Fernando D. Martinez PEDIATR PULMONOL

ntegrative 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

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

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

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


The Association of Human Apolipoprotein C-III Sialylation Proteoforms with Plasma Triglycerides. Hussein N. Yassine, Olgica Trenchevska, Ambika Ramrakhiani, Aarushi Parekh, Juraj Koska, Ryan W. Walker, Dean Billheimer, Peter D. Reaven, Frances T. Yen, Randall W. Nelson, Michael I. Goran, Dobrin Nedelkov PLOS ONE

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

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

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

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

Increased wheezing risk with diesel exposure among children of younger mothers. Paloma I. Beamer, Nathan Lothrop, Debra A. Stern, Dean Billheimer, Anne L. Wright, and Fernando D. Martinez EUR RESPIR J

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

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

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