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CC = Colorado Convention Center   H = Hyatt Regency Denver at Colorado Convention Center
* = applied session       ! = JSM meeting theme

Activity Details


21 * !
Sun, 7/28/2019, 2:00 PM - 3:50 PM CC-109
Aligning Data Normalization with Analysis Goals for Reproducible Research — Topic Contributed Papers
Biometrics Section, ENAR, Section on Statistics in Genomics and Genetics
Organizer(s): Li-Xuan Qin, Memorial Sloan Kettering Cancer Center
Chair(s): Yize Zhao, Weill Cornell Medical College
2:05 PM On the ‘Off-Label’ Use of Data Normalization for Sample Classification and Prognostication
Li-Xuan Qin, Memorial Sloan Kettering Cancer Center; Ai Ni, The Ohio State University; Mengling Liu, New York University
2:25 PM Batch Effects Correction with Unknown Subtypes with Application to Paired MicroRNA Data Sets
Yingying Wei, The Chinese University of Hong Kong; Li-Xuan Qin, Memorial Sloan Kettering Cancer Center
2:45 PM Multiple Testing Under Dependence and Non-Sparsity with Applications in Genomics and Toxicology
Hongyuan Cao, Florida State University; Shyamal Peddada, University of Pittsburgh; Li-Xuan Qin, Memorial Sloan Kettering Cancer Center
3:05 PM Discussant: Lisa McShane, National Cancer Institute
3:25 PM Discussant: George Tseng, University of Pittsburgh
3:45 PM Floor Discussion
 
 

40 *
Sun, 7/28/2019, 2:00 PM - 3:50 PM CC-101
Statistical Methods for Microbiome and Tumor Data — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Zhigang Li, University of Florida
2:05 PM Discriminative Factor Model for Microbiome Analysis
Presentation
Yiwen Liu, Duke University; Peter Merrill, Duke Clinical Research Institute; Noelle Younge, Duke University School of Medicine; C. Michael Cotten, Duke University School of Medicine; Ricardo Henao, Duke University
2:20 PM A Novel Normalization and Differential Abundance Test Framework for Microbiome Data
Presentation
Yuanjing Ma; Yuan Luo, Northwestern University ; Hongmei Jiang, Northwestern University
2:35 PM A Bayesian Framework for Uncovering Association Between Microbial Composition and Host Phenotypes
Subhajit Sengupta, NorthShore University HealthSystem; Riten Mitra, University of Louisville; Robert Butler III, NorthShore University HealthSystem; Abhishek Bhattacharjee, University of Northern Colorado; Pablo Gejman, NorthShore University HealthSystem
2:50 PM A Hidden Markov Modeling Approach for Identifying Tumor Subclones in Next-Generation Sequencing Studies
Presentation
BIN ZHU, NIH/NCI; HYOYOUNG CHOO-WOSOBA, NCI; Paul Albert , National Cancer Insititute
3:05 PM Predicting Cancer Immunotherapy Treatment Response with Neoantigen Burden
Laura Zhou, University of North Carolina at Chapel Hill ; Fei Zou, University of North Carolina at Chapel Hill; Wei Sun, Fred Hutchinson Cancer Research Center
3:20 PM Predictive Models for Detecting Association Between MiRNAs and Lympho Vascular Invasion
Moumita Karmakar, Texas A&M University; Pei-chun Lai, Texas A&M University; Samiran Sinha, Texas A&M University; Sanjukta Chakraborty, Texas A&M University
3:35 PM A Mixed-Model Approach for Powerful Testing of Genetic Associations with Cancer Risk Incorporating Tumor Characteristics
Haoyu Zhang, Johns Hopkins University; Ni Zhao, Johns Hopkins University; Thomas U. Ahearn, National Cancer Institute; William Wheeler, Information Management Services, Inc.; Montserrat Garcia-Closas, National Cancer Institute; Nilanjan Chatterjee, Johns Hopkins University
 
 

58 * !
Sun, 7/28/2019, 4:00 PM - 5:50 PM CC-102
Artificial Intelligence (AI) in Healthcare and Medical Research in the Big Data Era — Invited Panel
Section on Statistics in Genomics and Genetics, WNAR, International Chinese Statistical Association
Organizer(s): Haiyan Huang, University of California, Berkeley
Chair(s): Ruixiao Lu, Genomic Health, Inc.
4:05 PM Artificial Intelligence (AI) in Healthcare and Medical Research in the Big Data Era
Presentation 1 Presentation 2 Presentation 3 Presentation 4
Panelists: Bin Chen, Michigan State University
Haoda Fu, Eli Lilly and Company
Jean Yee Hwa Yang, University of Sydney, Australia
Jing Huang, Veracyte Inc.
Ying Lu, Stanford University
5:45 PM Floor Discussion
 
 

102 * !
Mon, 7/29/2019, 8:30 AM - 10:20 AM CC-110
Challenges and Developments in Microbiome Data Science — Invited Papers
ENAR, Section on Statistics in Genomics and Genetics, WNAR
Organizer(s): Zhengzheng Tang, University of Wisconsin-Madison
Chair(s): Long Wang, Johns Hopkins University
8:35 AM It’s Just a Matter of Perspective - Robust Regression for Microbiome Data via Perspective M-Estimation
Christian Lorenz Mueller, Flatiron Institute, Simons Foundation
9:00 AM Modeling Evolutionary Dynamics of Bacteria in the Human Microbiome
Katherine S. Pollard, ASA
9:25 AM Beta-Diversity Discriminatory Power: Comparison of PERMANOVA, Mirkat, and Using Standard Microbiome Reference Groups
Presentation
Mitchell Henry Gail, National Cancer Institute, Division of Cancer Epidemiology and Genetics; Yunhu Wan, National Cancer Institute, Division of Cancer Epidemiology and Genetics
9:50 AM Robust and Powerful Differential Composition Tests on Clustered Microbiome Data
Zhengzheng Tang, University of Wisconsin-Madison; Guanhua Chen, University of Wisconsin-Madison
10:15 AM Floor Discussion
 
 

126
Mon, 7/29/2019, 8:30 AM - 10:20 AM CC-105
SPEED: New Methods in Statistical Genomics and Genetics Part 1 — Contributed Speed
Section on Statistics in Genomics and Genetics
Chair(s): Tianzhong Yang, The University of Minnesota Twin Cities
Poster Presentations for this session.
8:35 AM Comparing Performance of Gene Set Test Methods Using Biologically Relevant Simulated Data
Presentation
Richard Lambert, Utah State University; John Stevens, Utah State University
8:40 AM A Bottom-Up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with False Discovery Rate Control
Yunxiao Li, Emory University; Yijuan Hu, Emory University; Glen Alan Satten, Centers for Disease Control and Prevention
8:45 AM A Generalized Multi-Response Permutation Procedure to Evaluate Associations of Multivariate Data with Quantitative and Censored-Event Time Variables
Presentation
Stanley Pounds, St. Jude Children's Research Hospital; Natasha Sahr, St. Jude's Children's Hospital; Xueyuan Cao, University of Tennessee Health Science Center
8:50 AM The Robust Kernel Association Test
Kara Martinez, North Carolina State University
8:55 AM Regularized Regression by Graph Propagation for Genomic Data Analysis
Presentation
Han Yu, Roswell Park Comprehensive Cancer Center; Rachael Hageman Blair, the State University of New York at Buffalo
9:00 AM Assessing Exposure Effects on Gene Expression Using Inverse Probability Weighting and the Parametric G-Formula
Sarah Reifeis, University of North Carolina at Chapel Hill; Michael Hudgens, University of North Carolina at Chapel Hill; Michael Love, UNC-Chapel Hill; Karen Mohlke, University of North Carolina at Chapel Hill; Melissa Troester, University of North Carolina at Chapel Hill
9:05 AM Methods for Handling Correlated Covariates in Integrative Genomics Analysis
Presentation
Lauren Spirko-Burns; Karthik Devarajan, Fox Chase Cancer Center; Camille Ragin, Fox Chase Cancer Center
9:10 AM OncoCast: An Improved Interface for Survival Analysis Using Genomic Data
Presentation 1 Presentation 2
Axel Martin, Memorial Sloan Kettering Cancer Center
9:15 AM Identifying Appropriate Probabilistic Models for Sparse Discrete Omics Data
Presentation
Hani Aldirawi, UIC
9:20 AM Bayesian Inference for Reconstructing Intra-Tumor Phylogeny
Presentation
Tingting of Zhai, University of Kentucky; Jinpeng of Liu, University of Kentucky; Chi of Wang, University of Kentucky
9:35 AM Efficient Estimation of Ancestry Proportions Using Genotype Frequencies
Presentation
Jordan Hall, University of Colorado Denver; Megan Sorenson, University of Colorado Denver; Ryan Scherenberg; Alexandria Ronco, University of Colorado Denver; Yinfei Wu, University of Colorado Denver; James Vance, University of Colorado Denver; Jinyan Lyu, University of Colorado Denver; Christopher Gignoux, University of Colorado Denver; Audrey E Hendricks, University of Colorado Denver
9:40 AM Likelihood Based Mixture Modeling of Genetic Regulatory Networks
Presentation
David S. Burton, University of Rochester Biostatistics; Matthew N McCall, University of Rochester Medical Center
9:45 AM Control Confounding by Familial Relatedness in Genome-Wide Association Studies
Annie J Lee, Columbia University; Donglin Zeng, UNC Chapel Hill; Badri N Varadarajan, Columbia University; Karen Marder, Columbia University ; Yuanjia Wang, Columbia University
9:50 AM A Powerful and Versatile Colocalization Test
Yangqing Deng, University of Minnesota
9:55 AM The Rabl Configuration Limits Topological Entanglement of Chromosomes in Budding Yeast
Presentation
Maxime Pouokam, UC Davis Statistics Club
10:00 AM OASW Clustering
Fatima Batool
10:05 AM Comparing Methods for Familial Relationship Inference in Populations with Complex Demographic History
Presentation
Daniel Yorgov, Purdue University Fort Wayne
10:10 AM On Simulating Ultra High-Dimensional Multivariate Data
Presentation
Alfred Schissler, University of Nevada, Reno
 
 

137 *
Mon, 7/29/2019, 8:30 AM - 10:20 AM CC-113
Statistical Methods for Analyzing Genetic Variants and QTLs — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Zheng Xu, University of Nebraska-Lincoln
8:35 AM Cross-Tissue EQTL Calling via Surrogate Expression Analysis
Presentation
Zachary R McCaw, Harvard T.H. Chan School of Public Health; Sheila Gaynor, Harvard T.H. Chan School of Public Health; Ryan Sun, Harvard T.H. Chan School of Public Health; Xihong Lin, Harvard
8:50 AM Phylogenetic Derivative: a Tool for Assessing Local Tree Reconstruction
Presentation
Katherine Thompson, University of Kentucky; Jacque Kane, Hobart and William Smith Colleges; Haixin Liu, Hobart and William Smith Colleges; Joseph Rusinko, Hobart and William Smith Colleges
9:20 AM Omnibus Weighting Incorporating Multiple Functional Annotations for Whole Genome Sequencing Rare Variant Association Studies
Xihao Li, Harvard T.H. Chan School of Public Health; Zilin Li, Harvard TH Chan School of Public Health; Hufeng Zhou, Harvard University; Sheila Gaynor, Harvard T.H. Chan School of Public Health; Yaowu Liu, Harvard TH Chan School of Public Health; Han Chen, the University of Texas Health Science Center at Houston; Alanna C. Morrison, University of Texas School of Public Health; Eric Boerwinkle, University of Texas School of Public Health; Xihong Lin, Harvard
9:35 AM Flexible Approach for Gene-Level Genetic Analysis via Combinations of Summary Statistics
Dmitri Zaykin, National Institute of Environmental Health Sciences; Olga Vsevolozhskaya, University of Kentucky
9:50 AM Statistical Inference for Gene-Level Analysis Based on Functional Linear Models
Presentation
Olga Vsevolozhskaya, University of Kentucky; Adam Dugan, University of Kentucky; David Fardo, University of Kentucky; Dmitri Zaykin, National Institute of Environmental Health Sciences
10:05 AM Pathway Association Analysis Under High Dimensions
Yang Liu, Wright State University; Qianchuan He, Fred Hutchinson Cancer Research Center
 
 

140 * !
Mon, 7/29/2019, 10:30 AM - 12:20 PM CC-203
Frontiers of Statistical Genetics: Genomics, Transcriptomics, and PheWAS — Invited Papers
WNAR, Section on Statistics in Genomics and Genetics, Biometrics Section
Organizer(s): Wei Sun, Fred Hutchinson Cancer Research Center
Chair(s): Wei Sun, Fred Hutchinson Cancer Research Center
10:35 AM Weighted Hypothesis Testing Accounting for Correlated Predictors
Li Hsu, Fred Hutchinson Cancer Research Center, USA
11:00 AM Scalable and Accurate Association Analysis for Big Biobank Data
Presentation 1 Presentation 2
Seunggeun Lee, University of Michigan
11:25 AM Mediation Analyzes for Dissecting the Role of DNA Methylation in Epidemiologic Studies
Presentation
James Dai, Fred Hutchinson Cancer Research Center
11:50 AM Predictive Modeling of Transcriptomics in Ancestrally Diverse Populations
Presentation
Timothy Thornton, University of Washington; Anya Mikhaylova, Universtiy of Washington
12:15 PM Floor Discussion
 
 

156 * !
Mon, 7/29/2019, 10:30 AM - 12:20 PM CC-709
Statistical Interactions – Making an Impact in Health Science — Topic Contributed Papers
Section on Risk Analysis, International Indian Statistical Association, Section on Statistics in Epidemiology, Section on Statistics in Genomics and Genetics
Organizer(s): Jaya M Satagopan, Memorial Sloan Kettering Cancer Center
Chair(s): Jaya M Satagopan, Memorial Sloan Kettering Cancer Center
10:35 AM Identification of Gene-Gene and Gene-Environment Interactions in Genetic Association Studies
Presentation
Charles Kooperberg, Fred Hutchinson Cancer Research Center
10:55 AM Detection of Set-Based Gene-Environment Interactions for Substance Use Disorders
Presentation
Saonli Basu, University of Minnesota, Biostatistics SPH; Brandon Coombes, Mayo Clinic; Matt McGue, University of Minnesota
11:15 AM Test for Gene (G)-Environment (E) Interaction Based on the Trend Effect of Genotype Under an Additive Risk Model Using an Empirical Bayes-Type Shrinkage Estimator
Summer Han, Stanford University; Matthieu de Rochemonteix, Stanford University; Nilanjan Chatterjee, Johns Hopkins University
11:35 AM Statistical Interaction and Mendelian Randomization: What They Have in Common?
Presentation
Mariza de Andrade, Mayo Clinic
11:55 AM Estimating Additive Interaction Effect in Stratified Two-Phase Case-Control Design
Ai Ni, The Ohio State University; Jaya M Satagopan, Memorial Sloan Kettering Cancer Center
12:15 PM Floor Discussion
 
 

180 *
Mon, 7/29/2019, 10:30 AM - 12:20 PM CC-210/212
Statistical Methods for Functional Genomic and Epigenomic Data — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Weiqiang Zhou, Johns Hopkins Bloomberg School of Public Health
10:35 AM Detection and Classification of Changes in Protein-DNA Binding Activity with Applications in Diffuse ChIP-Seq Data
Pedro L. Baldoni, University of North Carolina At Chapel Hill; Naim U. Rashid, University of North Carolina at Chapel Hill; Joseph G Ibrahim, UNC
10:50 AM Cross-Platform Prediction of Regulatory Activities
Presentation
Runzhe Li, Johns Hopkins Bloomberg School of Public Health; Weiqiang Zhou, Johns Hopkins Bloomberg School of Public Health; Hongkai Ji, Johns Hopkins Bloomberg School of Public Health
11:05 AM A Change-Point Approach to Identify Hierarchical Organization of Topologically Associated Domains in Hi-C Data
Yingru Wu, SUNY Stony Brook; Haipeng Xing, SUNY Stony Brook; Yong Chen, UT Dallas; Michael Q. Zhang, UT Dallas
11:20 AM SpectralTAD: Defining Hierarchy of Topologically Associated Domains Using Graph Theoretical Clustering
Presentation
Mikhail Dozmorov, Virginia Commonwealth University; Kellen Cresswell, Virginia Commonwealth University; John Stansfield, Virginia Commonwealth University
11:35 AM Exploring Functional Data Analysis to Identify Differentially Methylated Regions in Plants
Presentation
Mohamed Milad, Arkansas State University , Jonesboro; Gayla Olbricht, Missouri Science and Technology University
11:50 AM Identifying Patterns of Multi-Genetic/Epigenetic Factors via Non-Parametric Clustering
Meredith Ray, University of Memphis; Lauren Sobral, University of Memphis; S. Hasan Arshad, University of Southampton; John Holloway, University of Southampton; Wilfried JJ Karmaus, University of Memphis; Hongmei Zhang, University of Memphis
12:05 PM Multiple-Gene Targeting and Mismatch Tolerance Can Confound Analysis of Genome-Wide Pooled CRISPR Screens
Jean-Philippe Fortin, Genentech; Jenille Tan, Genentech; Karen Gascoigne, Genentech; Peter Haverty, Genentech; William Forrest, Genentech, Inc; Michael Costa, Genentech; Scott Martin, Genentech
 
 

182
Mon, 7/29/2019, 10:30 AM - 11:15 AM CC-Hall C
SPEED: New Methods in Statistical Genomics and Genetics Part 2 — Contributed Poster Presentations
Section on Statistics in Genomics and Genetics
Chair(s): Wendy Meiring, University of California At Santa Barbara
Oral Presentations for this session.
21: Comparing Performance of Gene Set Test Methods Using Biologically Relevant Simulated Data
Richard Lambert, Utah State University; John Stevens, Utah State University
22: A Bottom-Up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with False Discovery Rate Control
Yunxiao Li, Emory University; Yijuan Hu, Emory University; Glen Alan Satten, Centers for Disease Control and Prevention
23: A Generalized Multi-Response Permutation Procedure to Evaluate Associations of Multivariate Data with Quantitative and Censored-Event Time Variables
Stanley Pounds, St. Jude Children's Research Hospital; Natasha Sahr, St. Jude's Children's Hospital; Xueyuan Cao, University of Tennessee Health Science Center
24: The Robust Kernel Association Test
Kara Martinez, North Carolina State University
25: Regularized Regression by Graph Propagation for Genomic Data Analysis
Han Yu, Roswell Park Comprehensive Cancer Center; Rachael Hageman Blair, the State University of New York at Buffalo
26: Assessing Exposure Effects on Gene Expression Using Inverse Probability Weighting and the Parametric G-Formula
Sarah Reifeis, University of North Carolina at Chapel Hill; Michael Hudgens, University of North Carolina at Chapel Hill; Michael Love, UNC-Chapel Hill; Karen Mohlke, University of North Carolina at Chapel Hill; Melissa Troester, University of North Carolina at Chapel Hill
27: Methods for Handling Correlated Covariates in Integrative Genomics Analysis
Lauren Spirko-Burns; Karthik Devarajan, Fox Chase Cancer Center; Camille Ragin, Fox Chase Cancer Center
28: OncoCast: An Improved Interface for Survival Analysis Using Genomic Data
Axel Martin, Memorial Sloan Kettering Cancer Center
29: Identifying Appropriate Probabilistic Models for Sparse Discrete Omics Data
Hani Aldirawi, UIC
30: Bayesian Inference for Reconstructing Intra-Tumor Phylogeny
Tingting of Zhai, University of Kentucky; Jinpeng of Liu, University of Kentucky; Chi of Wang, University of Kentucky
31: WITHDRAWN: PasLINCS: Pathway Activity Signatures from LINCS L1000 Consensus Gene Signatures
Yan Ren, University of Cincinnati; Siva Sivaganesan, University of Cincinnati; Nicholas Clark, University of Cincinnati; David Plas, University of Cincinnati; Mario Medvedovic, University of Cincinnati
32: Efficient Estimation of Ancestry Proportions Using Genotype Frequencies
Jordan Hall, University of Colorado Denver; Megan Sorenson, University of Colorado Denver; Ryan Scherenberg; Alexandria Ronco, University of Colorado Denver; Yinfei Wu, University of Colorado Denver; James Vance, University of Colorado Denver; Jinyan Lyu, University of Colorado Denver; Christopher Gignoux, University of Colorado Denver; Audrey E Hendricks, University of Colorado Denver
33: Likelihood Based Mixture Modeling of Genetic Regulatory Networks
David S. Burton, University of Rochester Biostatistics; Matthew N McCall, University of Rochester Medical Center
35: A Powerful and Versatile Colocalization Test
Yangqing Deng, University of Minnesota
36: The Rabl Configuration Limits Topological Entanglement of Chromosomes in Budding Yeast
Maxime Pouokam, UC Davis Statistics Club
37: OASW Clustering
Fatima Batool
38: Comparing Methods for Familial Relationship Inference in Populations with Complex Demographic History
Daniel Yorgov, Purdue University Fort Wayne
39: On Simulating Ultra High-Dimensional Multivariate Data
Alfred Schissler, University of Nevada, Reno
40: Control Confounding by Familial Relatedness in Genome-Wide Association Studies
Annie J Lee, Columbia University; Donglin Zeng, UNC Chapel Hill; Badri N Varadarajan, Columbia University; Karen Marder, Columbia University ; Yuanjia Wang, Columbia University
Oral Presentations for this session.
 
 

Register 205
Mon, 7/29/2019, 12:30 PM - 1:50 PM H-Centennial Ballroom G-H
Section on Statistics in Genomics and Genetics P.M. Roundtable Discussion (Added Fee) — Roundtables PM Roundtable Discussion
Section on Statistics in Genomics and Genetics
Organizer(s): Qiongshi Lu, University of Wisconsin-Madison
ML16: Omics Data Integration: Why and How?
Ali Shojaie, University of Washington
 
 

225 * !
Mon, 7/29/2019, 2:00 PM - 3:50 PM CC-710
The Human Microbiome: From Discovery Studies to Statistical Predictive Personalized Medicine — Topic Contributed Papers
Section on Statistics in Genomics and Genetics, Biometrics Section, Section on Statistics in Epidemiology
Organizer(s): Yi-Hui Zhou, North Carolina State University
Chair(s): Wenxuan Zhong, University of Georgia
2:05 PM The Machine Learning Methods Review for Microbiome Host Trait Prediction
Yi-Hui Zhou, North Carolina State University
2:25 PM A Zero?Inflated Beta?Binomial Model for Microbiome Data Analysis
Tao Hu, Clindata Insight Inc.
2:45 PM Predictive Modeling of Microbial Community Data Using Phylogeny-Regularized Regression Models
Jun Chen, Mayo Clinic
3:05 PM Meta-Analysis of Large Metagenomic Data Sets at Strain-Level Resolution
Presentation
Edoardo Pasolli, University of Naples Federico II
3:25 PM Discussant: Fred A Wright, North Carolina State University
3:45 PM Floor Discussion
 
 

233 !
Mon, 7/29/2019, 2:00 PM - 3:50 PM CC-712
Innovative Approaches for High-Dimensional Omics and Neuroimaging Data — Topic Contributed Papers
International Indian Statistical Association, Biometrics Section, Section on Statistics in Genomics and Genetics
Organizer(s): Subharup Guha, University of Florida
Chair(s): Subharup Guha, University of Florida
2:05 PM Are We There Yet: Differential Analysis of Single-Cell RNA Sequencing Data?
Susmita Datta, ASA Committee on Women in Statisitcs
2:25 PM Expression-Level-Dependent Correlation Structure Estimation for Repeated-Measures RNA-Seq Data
Presentation
Dan Nettleton, Iowa State University; Meiling Liu, Iowa State University
2:45 PM Efficient Approaches for Dynamic Modeling of Multivariate Time Series
Raquel Prado, UC Santa Cruz-Baskin School of Engineering
3:05 PM Mediation Analysis for Zero-Inflated Mediators
Presentation
Zhigang Li, University of Florida; Janaka Peragaswaththe Liyanage, University of Florida; A. James O'Malley, Dartmouth College; Susmita Datta, ASA Committee on Women in Statisitcs
3:25 PM Nonparametric Bayes Multiresolution Testing for Detecting Rare Variants
Jyotishka Datta, University of Arkansas; David Dunson, Duke University
3:45 PM Floor Discussion
 
 

234
Mon, 7/29/2019, 2:00 PM - 3:50 PM CC-707
Novel Statistical Methods for High-Dimensional Microbiome and Metagenomics Data Analysis — Topic Contributed Papers
Section on Statistics in Epidemiology, Section on Statistics in Genomics and Genetics, Biometrics Section
Organizer(s): Chan Wang, Division of Biostatistics, NYU School of Medicine
Chair(s): Jiyuan Hu, New York Unversity School of Medicine
2:05 PM Analyzing Matched Sets of Microbiome Data Using LDM
Presentation
Yijuan Hu, Emory University; Zhengyi Zhu, Emory University; Caroline Mitchell, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Harvard Medical S; Glen Alan Satten, Centers for Disease Control and Prevention
2:25 PM Association Testing and Feature Selection for Microbiome and Host Genomics
Anna Plantinga, Williams College; Michael C. Wu, Fred Hutchinson Cancer Research Center
2:45 PM Multivariable Association in Population-Scale Meta'omic Surveys
Himel Mallick, Merck & Co., Inc.; Timothy Tickle, Broad Institute; Lauren McIver, Harvard University; Gholamali Rahnavard, Broad Institute; Long Nguyen, Massachusetts General Hospital; George Weingart, Harvard University; Siyuan Ma, Harvard University; Boyu Ren, Harvard University; Emma Schwager, Harvard University; Ayshwarya Subramanian, Broad Institute; Joseph Paulson, Genentech; Eric A. Franzosa, Harvard University; Hector Corrada Bravo, University of Maryland; Curtis Huttenhower, Harvard University
3:05 PM Robust Regression for Microbiome Data Analysis
Presentation 1 Presentation 2
Aditya Mishra, Flatiron Institute; Christian Lorenz Mueller, Flatiron Institute, Simons Foundation
3:25 PM Estimating and Testing the Microbial Causal Mediation Effect with High-Dimensional and Compositional Microbiome Data
Presentation
Chan Wang, Division of Biostatistics, NYU School of Medicine; Jiyuan Hu, New York Unversity School of Medicine; Martin Blaser, New York University School of Medicine and Rutgers University; Huilin Li, NYU School of Medicine
3:45 PM Floor Discussion
 
 

237
Mon, 7/29/2019, 2:00 PM - 3:50 PM CC-501
SPEED:Statistical Methods for GWAs, Genetics, Genomics, and Other Omics Studies, Part 1 — Contributed Speed
Section on Statistics in Genomics and Genetics, International Chinese Statistical Association, Section on Bayesian Statistical Science, Biometrics Section
Chair(s): Stanley Pounds, St. Jude Children's Research Hospital
Poster Presentations for this session.
2:05 PM Multivariate Association Analysis with Correlated Traits in Families
Presentation
Souvik Seal, Division of Biostatistics, University of Minnesota
2:10 PM Trans-Ethnic Meta-Analysis of Metabolic Syndrome in a Multi-Ethnic Study
Presentation
Emileigh L. Willems, University of Colorado Denver; Jia Y. Wan, University of California Irvine; Trina M. Norden-Krichmar, University of California Irvine; Karen L. Edwards, University of California Irvine; Stephanie A. Santorico, University of Colorado Denver
2:15 PM Rare Variant Association Tests for Multiple Ancestries Using Common Controls
Presentation
Megan Sorenson, University of Colorado Denver; Audrey E Hendricks, University of Colorado Denver
2:20 PM GWEB: An Empirical-Bayes-Based Approach for Heritability Estimation, Statistical Fine-Mapping and Genetic Risk Prediction Using GWAS Summary Statistics
Wei Jiang, Yale University; Hongyu Zhao, Yale
2:25 PM Sparse Estimation of Genetic Relatedness to Control for Population Structure and Sample Relatedness in Genome-Wide Association Studies
Rounak Dey, Harvard TH Chan School of Public Health; Yaowu Liu, Harvard TH Chan School of Public Health; Zilin Li, Harvard TH Chan School of Public Health; Junwei Lu, Harvard TH Chan School of Public Health; Zheng Tracy Ke, Harvard University; Xihong Lin, Harvard
2:25 PM Sparse Mediation Analysis Using Mixture Models
Yanyi Song, University of Michigan; Xiang Zhou, University of Michigan; Min Zhang, University of Michigan; Wei Zhao, University of Michigan; Yongmei Liu, Wake Forest School of Medicine; Sharon Kardia, University of Michigan; Ana Diez Roux, Drexel University; Belinda Needham, University of Michigan; Jennifer Smith, University of Michigan; Bhramar Mukherjee, University of Michigan
2:30 PM Fine Mapping Causal Variants with Functional Annotations
Sheila Gaynor, Harvard T.H. Chan School of Public Health; Xihong Lin, Harvard
2:35 PM Leveraging EQTLs to Identify Tissue-Specific Genetic Subtype of Complex Trait
Arunabha Majumdar, University of California, Los Angeles; Claudia Giambartolomei, University of California, Los Angeles; Na Cai, European Bioinformatics Institute (EMBL-EBI); Malika Kumar Freund, University of California, Los Angeles; Bogdan Pasaniuc, University of California, Los Angeles
2:40 PM Trait Evolution on Two Gene Trees
Presentation
James Degnan, University of New Mexico; Huan Jiang, Dialysis INC
2:45 PM Intergrated Quantile Rank Test (IQRAT) for Heterogeneous Joint Effect of Rare and Common Variants in Sequencing Studies
Tianying Wang, Columbia University, Biostatistics Department; Iuliana Ionita-Laza , Columbia University, Biostatistics Department; Ying Wei, Columbia University, Biostatistics Department
2:50 PM An Integrative Analysis of DNA Copy Number and SNP Markers to Localize Causal Gene Region
Qi You Yu, National Taiwan University; Chuhsing Kate Hsiao, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taiwan; Tzu-Pin Lu, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taiwan; Jung-Ying Tzeng, North Carolina State University; Tzu-Hung Hsiao, Taichung Veterans General Hospital, Taiwan; Ching-Heng Lin, Taichung Veterans General Hospital, Taiwan
3:00 PM Bayesian Generalized Fused Hierarchical Structured Variable Selection Prior for Pathway-Based GWAS Using Summary Statistics
Presentation
Yi Yang, University of Minnesota; Saonli Basu, University of Minnesota, Biostatistics SPH; Lin Zhang, Division of Biostatistics, University of Minnesota
3:05 PM A Flexible Bayesian Framework to Study Viral Trait Evolution
Paul Bastide, Rega Institute, KU Leuven; Guy Baele, Rega Institute / KU Leuven; Marc Suchard, UCLA; Philippe Lemey, Rega Institute, KU Leuven
3:10 PM Fully Bayesian Imputation Model for MNAR Data in QPCR
Presentation
Valeriia Sherina; Matthew N McCall, University of Rochester Medical Center; Tanzy M.T. Love, University of Rochester Medical Center
3:15 PM Predicting Patient Sensitivity Using Gene-Treatment Interactions with Bayesian Shrinkage Models
Presentation
Arinjita Bhattacharyya, University of Louisville; Subhadip Pal, University of Louisville; Riten Mitra, University of Louisville; Shesh N Rai, University of Louisville
3:20 PM Prediction with Microbiome Sequencing Data via Multi-Kernel Learning
Presentation
Bing Li, Brown University; Huilin Li, NYU School of Medicine; Shuang Wang, Columbia University
3:25 PM A Hierarchical Pitman-Yor Model for the Evolution of Phenotype Distribution on a Phylogenetic Tree
Presentation
Hanxi Sun, Purdue Statistics; Heejung Shim, University of Melbourne, Australia; Vinayak Rao, Purdue University
3:30 PM A New Sparse Network Model for High-Throughput Count Data
Presentation
Caesar (Zexuan) Li, University of California, Los Angeles; Gang Li, UCLA; Eric Kawaguchi, UCLA Department of Biostatistics
3:35 PM A Bayesian Zero-Inflated Negative Binomial Regression Model for the Integrative Analysis of Microbiome Data
Presentation
Shuang Jiang, Southern Methodist University
3:45 PM A Feature Allocation Model for Cytometry by Time-Of-Flight Data
Arthur Lui, University of California - Santa Cruz; Juhee Lee, University of California, Santa Cruz; Peter Thall, U.T. M.D. Anderson Cancer Center; Katy Rezvani, M.D. Anderson Cancer Center
 
 

Register 267
Tue, 7/30/2019, 7:00 AM - 8:15 AM H-Centennial Ballroom G-H
Section on Statistics in Genomics and Genetics A.M. Roundtable Discussion (Added Fee) — Roundtables AM Roundtable Discussion
Section on Statistics in Genomics and Genetics
Organizer(s): Qiongshi Lu, University of Wisconsin-Madison
TL06: WITHDRAWN: Estimation and Inference of Heteroskedasticity Models with Latent Semiparametric Factors for Multivariate Time Series
Lyuou Zhang
 
 

279 * !
Tue, 7/30/2019, 8:30 AM - 10:20 AM CC-207
Bioinformatics: Accomplishments and Challenges — Invited Papers
Caucus for Women in Statistics, Section on Statistics in Genomics and Genetics, Section on Statistical Learning and Data Science
Organizer(s): Nusrat Jahan, James Madison University
Chair(s): Nusrat Jahan, James Madison University
8:35 AM Optimal Permutation Recovery and Estimation of Bacterial Growth Dynamics
Presentation
Hongzhe Li, University of Pennsylvania
9:00 AM Estimating Somatic Variant Richness in the Cancer Genome
Ronglai Shen, Memorial Sloan-Kettering Cancer Center; Saptarshi Chakraborty, Memorial Sloan-Kettering Cancer Center; Colin Begg, Memorial Sloan Kettering Cancer Center
9:25 AM Integrative Network Modeling Approaches to Precision Cancer Medicine
Kim-Anh Do, University of Texas M.D. Anderson Cancer Center
9:50 AM Statistical Inference of Chromatin 3D Structures from DNA Methylation Data
Shili Lin, The Ohio State University
10:15 AM Floor Discussion
 
 

287 * !
Tue, 7/30/2019, 8:30 AM - 10:20 AM CC-113
Advanced Stochastic Models and Inference Methods for Large-Scale Phylogenetics — Topic Contributed Papers
Section on Statistics in Genomics and Genetics, Section on Statistical Computing, Section on Statistics in Epidemiology
Organizer(s): Guy Baele, Rega Institute / KU Leuven
Chair(s): Mandev Gill, Rega Institute, KU Leuven
8:35 AM Fast and Robust Evolutionary Rate and Selection Pressure Inference Using Variational Bayes Techniques
Presentation
Sergei Pond, Temple University
8:55 AM Modeling Site-To-Site Variability of Synonymous Substitution Rates: Impacts on Statistical Inference
Spencer Muse, North Carolina State University; Sadie Wisotsky, Temple University; Sergei Kosakovsky Pond, Temple University
9:15 AM Fitness-Dependent Birth-Death Models for Phylodynamic Inference of Adaptive Evolution
Presentation
David Rasmussen, North Carolina State University; Tanja Stadler, ETH Zurich
9:35 AM Towards Real­time Bayesian Inference for Pathogen Phylodynamics
Presentation
Guy Baele, Rega Institute / KU Leuven; Mandev Gill, Rega Institute, KU Leuven; Philippe Lemey, Rega Institute, KU Leuven; Marc Suchard, UCLA; Andrew Rambaut, University of Edinburgh
9:55 AM Floor Discussion
 
 

310
Tue, 7/30/2019, 9:25 AM - 10:10 AM CC-Hall C
SPEED:Statistical Methods for GWAs, Genetics, Genomics, and Other Omics Studies, Part 2 — Contributed Poster Presentations
Section on Statistics in Genomics and Genetics, International Chinese Statistical Association, Section on Bayesian Statistical Science, Biometrics Section
Chair(s): Stanley Pounds, St. Jude Children's Research Hospital
Oral Presentations for this session.
1: Multivariate Association Analysis with Correlated Traits in Families
Souvik Seal, Division of Biostatistics, University of Minnesota
2: Trans-Ethnic Meta-Analysis of Metabolic Syndrome in a Multi-Ethnic Study
Emileigh L. Willems, University of Colorado Denver; Jia Y. Wan, University of California Irvine; Trina M. Norden-Krichmar, University of California Irvine; Karen L. Edwards, University of California Irvine; Stephanie A. Santorico, University of Colorado Denver
3: Rare Variant Association Tests for Multiple Ancestries Using Common Controls
Megan Sorenson, University of Colorado Denver; Audrey E Hendricks, University of Colorado Denver
4: GWEB: An Empirical-Bayes-Based Approach for Heritability Estimation, Statistical Fine-Mapping and Genetic Risk Prediction Using GWAS Summary Statistics
Wei Jiang, Yale University; Hongyu Zhao, Yale
5: Sparse Estimation of Genetic Relatedness to Control for Population Structure and Sample Relatedness in Genome-Wide Association Studies
Rounak Dey, Harvard TH Chan School of Public Health; Yaowu Liu, Harvard TH Chan School of Public Health; Zilin Li, Harvard TH Chan School of Public Health; Junwei Lu, Harvard TH Chan School of Public Health; Zheng Tracy Ke, Harvard University; Xihong Lin, Harvard
6: Fine Mapping Causal Variants with Functional Annotations
Sheila Gaynor, Harvard T.H. Chan School of Public Health; Xihong Lin, Harvard
7: Leveraging EQTLs to Identify Tissue-Specific Genetic Subtype of Complex Trait
Arunabha Majumdar, University of California, Los Angeles; Claudia Giambartolomei, University of California, Los Angeles; Na Cai, European Bioinformatics Institute (EMBL-EBI); Malika Kumar Freund, University of California, Los Angeles; Bogdan Pasaniuc, University of California, Los Angeles
8: Trait Evolution on Two Gene Trees
James Degnan, University of New Mexico; Huan Jiang, Dialysis INC
9: Intergrated Quantile Rank Test (IQRAT) for Heterogeneous Joint Effect of Rare and Common Variants in Sequencing Studies
Tianying Wang, Columbia University, Biostatistics Department; Iuliana Ionita-Laza , Columbia University, Biostatistics Department; Ying Wei, Columbia University, Biostatistics Department
10: An Integrative Analysis of DNA Copy Number and SNP Markers to Localize Causal Gene Region
Qi You Yu, National Taiwan University; Chuhsing Kate Hsiao, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taiwan; Tzu-Pin Lu, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taiwan; Jung-Ying Tzeng, North Carolina State University; Tzu-Hung Hsiao, Taichung Veterans General Hospital, Taiwan; Ching-Heng Lin, Taichung Veterans General Hospital, Taiwan
11: Bayesian Generalized Fused Hierarchical Structured Variable Selection Prior for Pathway-Based GWAS Using Summary Statistics
Yi Yang, University of Minnesota; Saonli Basu, University of Minnesota, Biostatistics SPH; Lin Zhang, Division of Biostatistics, University of Minnesota
12: A Flexible Bayesian Framework to Study Viral Trait Evolution
Paul Bastide, Rega Institute, KU Leuven; Guy Baele, Rega Institute / KU Leuven; Marc Suchard, UCLA; Philippe Lemey, Rega Institute, KU Leuven
13: Fully Bayesian Imputation Model for MNAR Data in QPCR
Valeriia Sherina; Matthew N McCall, University of Rochester Medical Center; Tanzy M.T. Love, University of Rochester Medical Center
14: Predicting Patient Sensitivity Using Gene-Treatment Interactions with Bayesian Shrinkage Models
Arinjita Bhattacharyya, University of Louisville; Subhadip Pal, University of Louisville; Riten Mitra, University of Louisville; Shesh N Rai, University of Louisville
15: Prediction with Microbiome Sequencing Data via Multi-Kernel Learning
Bing Li, Brown University; Huilin Li, NYU School of Medicine; Shuang Wang, Columbia University
16: A Hierarchical Pitman-Yor Model for the Evolution of Phenotype Distribution on a Phylogenetic Tree
Hanxi Sun, Purdue Statistics; Heejung Shim, University of Melbourne, Australia; Vinayak Rao, Purdue University
17: A New Sparse Network Model for High-Throughput Count Data
Caesar (Zexuan) Li, University of California, Los Angeles; Gang Li, UCLA; Eric Kawaguchi, UCLA Department of Biostatistics
18: A Bayesian Zero-Inflated Negative Binomial Regression Model for the Integrative Analysis of Microbiome Data
Shuang Jiang, Southern Methodist University
19: Sparse Mediation Analysis Using Mixture Models
Yanyi Song, University of Michigan; Xiang Zhou, University of Michigan; Min Zhang, University of Michigan; Wei Zhao, University of Michigan; Yongmei Liu, Wake Forest School of Medicine; Sharon Kardia, University of Michigan; Ana Diez Roux, Drexel University; Belinda Needham, University of Michigan; Jennifer Smith, University of Michigan; Bhramar Mukherjee, University of Michigan
20: A Feature Allocation Model for Cytometry by Time-Of-Flight Data
Arthur Lui, University of California - Santa Cruz; Juhee Lee, University of California, Santa Cruz; Peter Thall, U.T. M.D. Anderson Cancer Center; Katy Rezvani, M.D. Anderson Cancer Center
Oral Presentations for this session.
 
 

351 * !
Tue, 7/30/2019, 10:30 AM - 12:20 PM CC-101
Statistical Methods for Single-Cell Genomics — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Lingling An, University of Arizona
10:35 AM Feature Selection and Dimension Reduction for Single Cell RNA-Seq Based on a Multinomial Model
Presentation
Frederick William Townes, Harvard Biostatistics; Martin Aryee, Massachusetts General Hospital; Stephanie Hicks, Johns Hopkins Bloomberg School of Public Health; Rafael Irizarry, Harvard University
10:50 AM SCINA: Semi-Supervised Analysis of Single Cells in Silico
Presentation 1 Presentation 2
Ze Zhang, University of Texas Southwestern Medical Center at Dallas; Tao Wang, University of Texas Southwestern Medical Center; Payal Kapur, University of Texas Southwestern Medical Center; Xinlei Wang, Southern Methodist University; Gary Hon, University of Texas Southwestern Medical Center; James Brugarolas, University of Texas Southwestern Medical Center
11:05 AM Flexible Experimental Designs for Valid Single-Cell RNA-Sequencing Experiments Allowing Batch Effects Correction
Fangda Song, The Chinese University of Hong Kong; Yingying Wei, The Chinese University of Hong Kong
11:20 AM Correcting Batch Effects in Single Cell RNA Sequencing Data Using Sparse Supervised Canonical Correlation (SCCA) Analysis
Wenlan Zang, Yale’s Section of Pulmonary, Critical Care, and Sleep Medicine (Yale-PCCSM); Michael Kane, Yale; Jen-hwa Chu, Yale University School of Medicine
11:35 AM Single-Cell Transcriptome and Regulome Data Integration
Weiqiang Zhou, Johns Hopkins Bloomberg School of Public Health; Zhicheng Ji, Johns Hopkins Bloomberg School of Public Health; Weixiang Fang, Johns Hopkins Bloomberg School of Public Health; Hongkai Ji, Johns Hopkins Bloomberg School of Public Health
11:50 AM Exponential-Family Embedding with Application to Cell Developmental Trajectories for Single-Cell RNA-Seq Data
Kevin Lin, Carnegie Mellon University, Department of Statistics and Data Science; Jing Lei, Carnegie Mellon University; Kathryn Roeder, Carnegie Mellon University
12:05 PM TWO-SIGMA-Geneset: TWO-Component SInGle Cell Model-Based Association Method for Gene Set Testing
Eric Van Buren, University of North Carolina at Chapel Hill; Di Wu, University of North Carolina at Chapel Hill; Ming Hu, Cleveland Clinic; Yun Li, University of North Carolina at Chapel Hill
 
 

374 * !
Tue, 7/30/2019, 2:00 PM - 3:50 PM CC-605
Statistics in Biosciences (SIB) Special Invited Session – Impacts of Statistics in Genomics and Imaging — Invited Papers
International Chinese Statistical Association, Section on Statistics in Genomics and Genetics, Biometrics Section
Organizer(s): Hongzhe Li, University of Pennsylvania
Chair(s): Hongzhe Li, University of Pennsylvania
2:05 PM Alignment and Integrative Analysis of Single-Cell RNA-Seq and Single-Cell ATAC-Seq Data
Weiqiang Zhou, Johns Hopkins Bloomberg School of Public Health; Zhicheng Ji, Johns Hopkins Bloomberg School of Public Health; Hongkai Ji, Johns Hopkins Bloomberg School of Public Health
2:35 PM Functional Graphical Modeling and Applications in Brain Connectivity Analysis
Presentation
Lexin Li, University of California at Berkeley
3:05 PM Gene-Set Integrative Analysis of Multi-Omics Data Using Tensor-Based Association Tests
Meng Yang, North Carolina State University; Wenbin Lu, North Carolina State University; Fan Zhang, University at Buffalo; Jeff Miecznikowski, University at Buffalo; Jung-Ying Tzeng, North Carolina State University
3:35 PM Floor Discussion
 
 

394 *
Tue, 7/30/2019, 2:00 PM - 3:50 PM CC-502
Brushing up Your Skills in Genomic Data Analysis — Topic Contributed Papers
Korean International Statistical Society, Section on Statistics in Genomics and Genetics, Section on Statistical Consulting
Organizer(s): Kwang-Youn Kim, Northwestern University
Chair(s): Jungwha Julia Lee, Northwestern University
2:05 PM Combining Multiple Genomic Data Sets
Sihai Zhao, University of Illinois at Urbana-Champaign
2:25 PM Approaches for Network-Based Pathway Analysis of Genomic Data
Presentation
Rosemary Braun, Northwestern University; Sahil D. Shah, Northwestern University
2:45 PM Application of Machine Learning to Find Needle in a Genomic Haystack
Kwang-Youn Kim, Northwestern University
3:05 PM Statistical Considerations for Metabolomic Data
Sharon Lutz, Harvard Medical School; Rachel S. Kelly, Channing Division of Network Medicine, Brigham & Women’s Hospital, Harvard Medical School; Joanne E. Sordillo, Harvard Medical School and Harvard Pilgrim Health Care ; Ann Wu, Harvard Medical School and Harvard Pilgrim Health Care
3:25 PM Statistical Approaches for Jointly Analyzing Microbiome and Other -Omics Data Types
Michael C. Wu, Fred Hutchinson Cancer Research Center
 
 

415 *
Tue, 7/30/2019, 2:00 PM - 3:50 PM CC-112
Statistical Methods for Gene Expression and RNA-Seq Analysis — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Peng Liu, Iowa State University
2:05 PM Nonparametric Method for Differential Analysis of RNA-Seq with Quantification Uncertainty
Anqi Zhu, University of North Carolina Chapel Hill; Joseph G Ibrahim, UNC; Michael Love, UNC-Chapel Hill
2:20 PM Can You Trust Differential Expression Methods for RNA-Seq Data Analysis ?
Boris P Hejblum, University of Bordeaux; Marine Gauthier, Université de Bordeaux, Inria/Inserm, VRI; Rodolphe Thiébaut, Université de Bordeaux, Inria/Inserm, VRI; Denis Agniel, RAND Corporation
2:35 PM Flexible Bivariate Correlated Count Data Regression with Application in Gene Coexpression Analysis Based on RNA-Sequencing Data
Presentation
Zichen Ma, University of South Carolina
2:50 PM Latent Dirichlet Model to Compare Expressed Isoform Proportions to a Reference Panel
Sean McCabe, University of North Carolina at Chapel Hill; Andrew B Nobel, University of North Carolina at Chapel Hill; Michael Love, UNC-Chapel Hill
3:05 PM Genome-Wide Detection of Allele-Specific Gene Expression by a Bayesian Logistic Regression Model
Tieming Ji, University of Missouri At Columbia; Jing Xie, University of Missouri at Columbia; Marco Ferreira, Virginia Tech
3:20 PM Multiple Hypothesis Testing in RNA Sequencing Gene Isoform Expression Analysis
Bo Li, The Citadel
3:35 PM Floor Discussion
 
 

218956
Tue, 7/30/2019, 5:30 PM - 7:00 PM CC-304
Section on Statistics in Genomics and Genetics Business Meeting — Other Cmte/Business
Section on Statistics in Genomics and Genetics
Chair(s): Dan Nettleton, Iowa State University
 
 

453 * !
Wed, 7/31/2019, 8:30 AM - 10:20 AM CC-102
Advances on the Analysis of Single-Cell Sequencing Data — Topic Contributed Papers
Section on Statistics in Genomics and Genetics, WNAR, ENAR
Organizer(s): Lingling An, University of Arizona
Chair(s): Xiaoxiao Sun, University of Arizona
8:35 AM Accurate Correction on Dropout Events in Single-Cell RNAseq Data
Presentation
Lingling An, University of Arizona; Di Ran, University of Arizona; Shanshan Zhang, University of Arizona; Nick Lytal, University of Arizona
8:55 AM Advantages of Modeling Zero-Inflation in ScRNA-Seq Data
Presentation
Davide Risso, University of Padova
9:15 AM From Bulk to Single-Cell RNA-Seq Data: Differential Gene Expression Analysis
Jingyi Jessica Li, University of California, Los Angeles; Yiling Chen, University of California, Los Angeles
9:35 AM Exploring Topologically Associating Domains (TADs) for Single-Cell Hi-C Data
Qunhua Li, Penn State University; Di Wu, University of North Carolina at Chapel Hill
9:55 AM Novel Methods for Analyzing Population-Based Single Cell Transcriptomic Data
Presentation
Wei Chen, University of Pittsburgh
10:15 AM Floor Discussion
 
 

480 * !
Wed, 7/31/2019, 10:30 AM - 12:20 PM CC-203
Novel Statistical Methods for Bioinformatics and Computational Biology — Invited Papers
Section on Statistics in Genomics and Genetics, Section on Statistical Computing, WNAR
Organizer(s): Ping Ma, University of Georgia
Chair(s): Ping Ma, University of Georgia
10:35 AM Statistical Methods for Single Cell Regulomics
Sunduz Keles, UW Madison; Daniel Conn, University of Wisconsin
11:00 AM Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Presentation
Scott V Edwards, Harvard University; Jun S. Liu, Harvard University; Zhirui Hu, Harvard University; Timothy B Sackton, Harvard University
11:25 AM Reference-Free Learning with Multiple Metagenomic Samples
Presentation
Wenxuan Zhong, University of Georgia
11:50 AM B-Scaling: A Novel Nonparametric Data Fusion Method
Yiwen Liu, University of Arizona; Xiaoxiao Sun, University of Arizona; Wenxuan Zhong, University of Georgia; Bing Li, The Pennsylvania State University
12:15 PM Floor Discussion
 
 

498 * !
Wed, 7/31/2019, 10:30 AM - 12:20 PM CC-505
Designs and Statistical Methods Used in Genetics and Mental Health for Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) — Topic Contributed Papers
Mental Health Statistics Section, Section on Statistics in Genomics and Genetics, Section on Statistics in Epidemiology
Organizer(s): Tzu-Cheg Kao, Uniformed Services University of the Health Sciences
Chair(s): Tzu-Cheg Kao, Uniformed Services University of the Health Sciences
10:35 AM Genome-Wide Association Studies of PTSD in 2 Cohorts of US Army Soldiers
Presentation
Steven Heeringa, University of Michigan Institute for Social Research
10:55 AM Genome Wide Association Studies of Suicide Attempts in US Soldiers
Erin Ware; Murray B. Stein, UCSD; Colter M Mitchell, University of Michigan; Chia-Yen Chen, Broad Institute of MIT and Harvard; Jordan W Smoller, Harvard Medical School
11:15 AM A Genome-Wide Gene-By-Trauma Interaction Study of Alcohol Misuse in Two Independent Cohorts Identifies PRKG1 as a Risk Locus
Presentation
Renato Polimanti; Joan Kaufman, Johns Hopkins School of Medicine; Hongyu Zhao, Yale; Henry R. Kranzler, University of Pennsylvania School of Medicine; Robert J Ursano, Uniformed Services University of the Health Sciences; Ron Kessler, Harvard Medical School; Joel Gelernter, Yale University; Murray B. Stein, UCSD
11:35 AM Discussant: Tamar Sofer, Brigham and Women’s Hospital, Harvard Medical School
11:55 AM Discussant: Wei-Ting Hwang, University of Pennsylvania
12:15 PM Floor Discussion
 
 

527
Wed, 7/31/2019, 10:30 AM - 12:20 PM CC-Hall C
Contributed Poster Presentations: Section on Statistics in Genomics and Genetics — Contributed Poster Presentations
Section on Statistics in Genomics and Genetics
Chair(s): Wendy Meiring, University of California At Santa Barbara
55: HierCM: a Hierarchical Mixture Model Approach for Detecting Chromatin Interactions in Hi-C Data
Frank Shen, Penn State University; Qunhua Li, Penn State University; Naomi S Altman, Pennsylvania State University
56: Sparse Probabilistic NMF for Single Cell RNA Sequencing
Xiaotian Wu, Brown University; Zhijin Wu, Brown University
57: Detection of Inversely Enriched Pathways in PBMC Cells in Alzheimer’s Disease and Cancer
Lisa Neums, University of Kansas Medical Center; Jeffrey A. Thompson, University of Kansas Medical Center
58: A Novel Statistical Framework for Trio-Based Transcriptome-Wide Association Study
Kunling Huang, University of Wisconsin-Madison, Statistics Department
59: Evaluation of Modern Approaches for the Complex Trait Prediction Using Genetic Data
Miao Zhang, Ancestry.com; Julie Granka, Ancestry.com
60: Probabilities of Unranked and Ranked Anomaly Zones Under Birth-Death Models
Anastasiia Kim, University of New Mexico; James Degnan, University of New Mexico; Noah Rosenberg, Stanford University
61: Separating Subtype Specific Signals from Mixed Tumor Genomic Data
Liuqing Yang, AbbVie; Hongtu Zhu, DiDi Chuxing and UNC-Chapel Hill; Steve Marron , University of North Carolina at Chapel Hill
62: Establishing Single Cell RNA-Seq Data Analysis Pipeline in the Industry Setting
Oleg Mayba, Genentech, Inc; Milena Duerrbaum, Genentech, Inc; Robert Piskol, Genentech, Inc; Leonard Goldstein, Genentech, Inc; Kevin Huang, Genentech, Inc; Josh Kaminker, Genentech, Inc; Aaron Lun, Genentech, Inc; Kiran Mukhyala, Genentech, Inc; Luz Orozco-Guerra, Genentech, Inc; Thomas Wu, Genentech, Inc; Matthew Chang, Genentech, Inc; Brad Friedman, Genentech, Inc; Jason Hackney, Genentech, Inc
64: Inferring Complex Phylogenetic Networks Efficiently
Cora Allen-Coleman, University of Wisconsin - Madison; Cécile Ané, University of Wisconsin - Madison
65: Assessment of Differential Expression Methods for 10x Genomics Data Sets
Jacob Gagnon, Biogen; Wenting Wang, Biogen; Eugenia Lyashenko, Biogen; Dann Huh, Biogen; Dipen Sangurdekar, Biogen; Liping Hou, BioStat Solutions, Inc
66: Integrating GWAS and Omics QTL Summary Statistics in Elucidating Molecular Mechanisms of Trait-Associated SNPs and Detecting Pleiotropy in Human Complex Traits
Kevin J Gleason, University of Chicago; Fan Yang, University of Colorado Denver; Lin Chen, University of Chicago
68: Proposed Methylation Processing Pipeline for Meta Analyzes Using Illumina’s 450K and EPIC Platforms
Lauren A Vanderlinden, Colorado School of Public Health; Randi K Johnson, Colorado School of Public Health; Patrick M Carry, Colorado School of Public Health; Fran Dong, Colorado School of Public Health; Ivana V Yang, Colorado School of Public Health; Jill M Norris, Colorado School of Public Health; Katerina Kechris, Colorado School of Public Health
69: A GWAS Analysis to Identify Genotypes Corresponding to Delayed Senescence in Maize
Brandon Lumsden, Clemson University; Yuan Yang, Clemson University; Christopher McMahan, Clemson University; William C. Bridges Jr., Clemson University
71: Testing Complex Survey Data for Hardy-Weinberg Equilibrium on the X Chromosome: Utilizing Male and Female Data
John R. Pleis, NCHS
72: Integration of Metabolomics and Transcriptomics to Improve Pediatric Drug Dosing
Christopher Wilson; Brooke Fridley, Moffitt Cancer Center
73: Integrating Gene Regulatory Pathways into Differential Network Analysis of Gene Expression Data
Tyler Grimes; Somnath Datta, University of Florida
74: The Additive Model in Genetic Association Studies
Zhengyang Zhou, University of North Texas Health Science Center; HUNG-CHIH KU, DePaul University; Chao Xing, UT Southwestern Medical Center
 
 

575 * !
Wed, 7/31/2019, 2:00 PM - 3:50 PM CC-113
Statistical Methods for Batch Effect Correction and Cell Type Deconvolution — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Di Wu, University of North Carolina at Chapel Hill
2:05 PM Assessing Reproducibility of High-Throughput Experiments in Case of Missing Data
Presentation
Roopali Singh; Qunhua Li, Penn State University
2:20 PM ComBat-Seq: Batch Correction Algorithm for RNA-Seq Count Data
Presentation
Yuqing Zhang, Boston University; Giovanni Parmigiani, Dana-Farber Cancer Institute; W. Evan Johnson, Boston University
2:35 PM Learning from Unobserved Covariates for Improved Classification Accuracy
Yujia Pan, University of Michigan; Johann A Gagnon-Bartsch, University of Michigan
2:50 PM Surrogate Variable Analysis Based Deconvolution of Transcriptomics Data
Li Dong, University of North Carolina at Chapel Hill; Xiaojing Zheng, University of North Carolina at Chapel Hill; Fei Zou, University of North Carolina at Chapel Hill
3:05 PM Analysis of Longitudinal Metabolite Data with Substantial Missingness and Batch Effects
Presentation
Evan Sticca, University of Colorado Anschutz Medical Campus; Audrey E Hendricks, University of Colorado Denver; Stephanie P Gilley, University of Colorado Anschutz Medical Campus; K Michael Hambidge, University of Colorado Anschutz Medical Campus; Nancy F Krebs, University of Colorado Anschutz Medical Campus; Sarah J Borengasser, University of Colorado Anschutz Medical Campus
3:20 PM An Empirical Bayes Method for Deconvolving Multi-Measure Bulk Gene Expression
Jiebiao Wang, Carnegie Mellon University; Bernie Devlin, University of Pittsburgh; Kathryn Roeder, Carnegie Mellon University
3:35 PM Determining Brain Cell-Types in the Presence of Complex Biology
Presentation
Gregory Hunt, William & Mary; Johann A Gagnon-Bartsch, University of Michigan
 
 

593 * !
Thu, 8/1/2019, 8:30 AM - 10:20 AM CC-712
Statistical Challenges and New Developments in Genomics — Invited Papers
Section on Statistics in Genomics and Genetics, Biometrics Section, ENAR
Organizer(s): Nancy Zhang, University of Pennsylvania
Chair(s): Nancy Zhang, University of Pennsylvania
8:35 AM Evaluation of Cell Clustering in Single Cell Data
Zhijin Wu, Brown University
9:00 AM Removing Unwanted Variation Reveals the Impact of Genetic Variation on 3D Genome Structure
Presentation
Kasper Daniel Hansen, Johns Hopkins University
9:25 AM Transfer Learning in Single Cell Transcriptomics
Presentation
Nancy Zhang, University of Pennsylvania; Divyansh Agarwal, University of Pennsylvania; Zilu Zhou, University of Pennsylvania; Mo Huang, University of Pennsylvania; Gang Hu, Nankai University; Chengzhong Ye, Tsinghua University; Jingshu Wang, The University of Chicago
9:50 AM GeneFishing: a Computational Method to Reconstruct Comprehensive Context-Specific Portraits of Biological Processes and Its Application to Cholesterol Metabolism
Presentation
Haiyan Huang, University of California, Berkeley
10:15 AM Floor Discussion
 
 

596 * !
Thu, 8/1/2019, 8:30 AM - 10:20 AM CC-605
Statistical and Mathematical Methods in Cancer Etiology and Cancer Early Detection — Invited Papers
ENAR, Section on Statistics in Genomics and Genetics, Section on Medical Devices and Diagnostics
Organizer(s): Cristian Tomasetti, Johsn Hopkins University
Chair(s): Cristian Tomasetti, Johsn Hopkins University
8:35 AM Statistical Methods Behind the CancerSEEK Blood Test and the DYNAMICS Study
Kamel Lahouel, Johns Hopkins University
9:05 AM Statistical and Mathematical Approaches to Cancer Etiology
Cristian Tomasetti, Johsn Hopkins University; Lu Li, Johns Hopkins University
9:35 AM Mutational Signatures and Cancer Etiology
Presentation
Bahman Afsari, Johns Hopkins University
10:05 AM Floor Discussion
 
 

622 *
Thu, 8/1/2019, 8:30 AM - 10:20 AM CC-709
Statistical Methods for Genome- and Epigenome-Wide Association Studies and Gene Environment Interactions — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Chao Xing, UT Southwestern Medical Center
8:35 AM A Novel Method for Phenome-Wide GxE Analysis and Its Application to UK Biobank
Presentation
Wenjian Bi, University of Michigan; Lars Fritsche, University of Michigan; Zhangchen Zhao, University of Michigan; Seunggeun Lee, University of Michigan
8:50 AM Statistical Methods for Leveraging Public Controls in a Two-Stage Epigenome-Wide Association Study
Ziqiao Wang, The University of Texas MD Anderson Cancer Center; Yue Lu, The University of Texas MD Anderson Cancer Center; Donghui Li, The University of Texas MD Anderson Cancer Center; Peng Wei, The University of Texas MD Anderson Cancer Center
9:05 AM Semiparametric Bayesian Variable Selection for Gene-Environment Interactions
Jie Ren, Kansas State University; Fei Zhou, Kansas State University; Cen Wu, Kansas State University
9:20 AM A Parallel Algorithm for Penalized Variable Selection in Gene-Environment Interactions
Presentation
Yinhao Du; Jie Ren, Kansas State University; Fei Zhou, Kansas State University; Cen Wu, Kansas State University
9:35 AM Structured Variable Selection for High-Dimensional Data, with Applications in Gene-Environment Interactions in Longitudinal Studies
Fei Zhou, Kansas State University; Jie Ren, Kansas State University; Cen Wu, Kansas State University
9:50 AM Floor Discussion
 
 

648 * !
Thu, 8/1/2019, 10:30 AM - 12:20 PM CC-702
Are Statistical Methods Developed for Bulk RNAseq Data Appropriate for Single Cell Data Sets? — Topic Contributed Papers
Biometrics Section, Section on Statistics in Genomics and Genetics, ENAR
Organizer(s): Roula Tsonaka, Leiden University MC
Chair(s): Roula Tsonaka, Leiden University MC
10:35 AM Assumptions and Methods for Normalizing Single-Cell RNA-Seq Data
Rhonda Bacher, University of Florida
10:55 AM Robust Normalisation and Differential Variability Testing for Noisy ScRNAseq Data
Presentation
Catalina Vallejos, MRC Human Genetics Unit, University of Edinburgh
11:15 AM Statistical Methods for Flexible Differential Analysis of Cross-Sample Single-Cell RNA-Seq Data Sets
Presentation
Mark Robinson, University of Zurich
11:35 AM Unlocking Bulk RNA-Seq Tools for Single Cell Applications
Presentation
Lieven Clement, Ghent University
11:55 AM Characterization of Differential Correlation Across Single Cell Differentiation Trajectories with ScDCARS
Presentation
Shila Ghazanfar, Cancer Research UK Cambridge Institute
12:15 PM Floor Discussion
 
 

663 *
Thu, 8/1/2019, 10:30 AM - 12:20 PM CC-709
Regression, Clustering and Gene Set Methods in Genomics — Contributed Papers
Section on Statistics in Genomics and Genetics
Chair(s): Xuefeng Wang, MOFFITT Cancer Center
10:35 AM Robust Inference Based on High-Dimensional Multiple Regressions with Application to Biomarker Screening
Youngseok Song, Colorado State University; Wen Zhou, Colorado State University; Wenxin Zhou, University of California, San Diego; Kim Hoke, Colorado State University
10:50 AM Moment-Based Estimation of Mixtures of Regression Models and Their Application in Genetic Studies
Presentation
Claus Ekstrom, Biostatistics, University of Copenhagen
11:05 AM Advances in the Hard Clustering of Categorical Data
Karin Dorman, Iowa State University
11:20 AM FSCseq: Simultaneous Feature Selection and Clustering of RNA-Seq Data
David Lim, UNC Chapel Hill; Naim U. Rashid, University of North Carolina at Chapel Hill; Joseph G Ibrahim, UNC
11:35 AM Covariance Thresholding to Detect Differentially Co-Expressed Gene Sets
Presentation
Hokeun Sun, Pusan National University; Mingyu Oh, Pusan National University; Kipoong Kim, Pusan National University
11:50 AM Incorporating Prior Information into Signal-Detection Analyzes Across Biologically Informed Gene-Sets
Presentation
Mengqi Zhang, Duke University; Sahar Gelfman, Institute of Genomic Medicine,Columbia University; Janice McCarthy, Duke University; David B Goldstein, Institute of Genomic Medicine, Columbia University; Andrew S Allen, Duke University
12:05 PM Integrating Pathway Information with Boosting to Construct a Sufficient Gene Set for Phenotype Classification
Nusrat Jahan, James Madison University; Huining Kang, University of New Mexico; Li Luo, University of New Mexico