Leading Professional Society for Computational Biology and Bioinformatics
Connecting, Training, Empowering, Worldwide

banner

GLBIO 2019 | May 19-22, 2019 | Univ. of Wisconsin at Madison | Detailed Agenda

DETAILED AGENDA



Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Wednesday, May 22, 2019: The Marquee | Varsity Hall I

General Track: Macromolecular Structure & Function | Gene Regulation I | Gene Regulation II | Comparative Genomics & Phylogenetics | Networks I | Networks II | Algorithms & Machine Learning | Genome Informatics | Clinical and Health Informatics I |
Clinical and Health Informatics II
Special Sessions: Precision Medicine I | Precision Medicine II | Precision Medicine III | Education I | Education II | Education III | Microbiome I | Microbiome II | Microbiome III | RNA Sequence to Structure I | RNA Sequence to Structure II | RNA Sequence to Structure III


Talk Abstracts are available on the App and Here

The Marquee on Monday, May 20, 2019

Links for Monday, May 20, 2019: Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
9:30 AM Keynote #1 - Data-enabled integrative analysis for fine mapping and interpretation of associated genetic variants Sunduz Keles
Introduction by Sushmita Roy
General Track - Macromolecular Structure & Function
Chair: Catherine Welsh
11:00 AM Improved protein structure refinement using machine learning based restrained relaxation Debswapna Bhattacharya
11:15 AM Improving the prediction of loops and drug binding in GPCR structure models. Bhumika Arora, Venkatesh Kareenhalli, Denise Wootten and Patrick Sexton.
11:30 AM Modeling the Functional Activity of Protein Sequence Variants Using Graph Convolutional Neural Networks Sam Gelman, Zhiyuan Duan, Philip Romero and Anthony Gitter
11:45 AM Chemoinformatic signature analysis of aspen seedling root exudates under biotic and abiotic stress conditions Peter Larsen
General Track - Gene Regulation I
Chair: Matthew Weirauch
1:30 PM Integrative analysis of epigenetics data identifies gene-specific regulatory elements Florian Schmidt, Alexander Marx, Marie Hebel, Martin Wegner, Nina Baumgarten, Manuel Kaulich, Jonathan Goeke, Jilles Vreeken and Marcel Schulz.
1:45 PM WACS: Improving Peak Calling by Optimally Weighting Controls Aseel Awdeh, Marcel Turcotte and Theodore Perkins.
2:00 PM refine.bio: A resource of harmonized public gene expression data sets. Jaclyn N. Taroni, Kurt G. Wheeler, Richard W. W. Jones, Deepashree Venkatesh Prasad, Ariel Rodriguez Romero, Candace L. Savonen and Casey S. Greene.
2:15 PM Leveraging public epigenomic datasets to examine the role of regulatory variation in the three-dimensional organization of the genome Brittany Baur, Jacob Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun Song, William Stafford Noble and Sushmita Roy.
General Track - Comparative Genomics & Phylogenetics
Chair: Dannie Durand
3:00 PM TreeCluster: Clustering Biological Sequences using Phylogenetic Trees Metin Balaban, Niema Moshiri, Uyen Mai and Siavash Mirarab
3:30 PM JalviewJS: Reintroducing Jalview as JavaScript on the Web Robert Hanson, Geoffrey Barton, James Procter, Mungo Carstairs and Benedict Soares.
3:45 PM Cross-species transcription factor binding prediction via domain adapted neural networks Kelly Cochran, Divyanshi Srivastava, Akshay Balsubramani, Anshul Kundaje and Shaun Mahony.
4:00 PM Evolution of the Metazoan Protein Domain Toolkit Maureen Stolzer, Yuting Xiao and Dannie Durand.
4:15 PM Mechanism of biocide resistance of bacterial isolates from hydraulic fracturing-impacted streams from Pennsylvania Lindsey Schenten, Jeremy Chen See, Maria Fernanda Campa, Terry Hazen, Regina Lamendella and Stephen Techtmann.
4:30 PM snacc: Sequence Non-Alignment Compression and Comparison for Inferring Microbial Phylogenies Alex Sweeten, Rafal Mostowy and Leonid Chindelevitch.
5:00 PM Keynote #2 - Less is More: Extracting features from shallow sequencing data  Dan Knights
Introduction by Chad Myers


- top -


Fifth Quarter on Monday, May 20, 2019

Links for Monday, May 20, 2019: The Marquee | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
Precision Medicine I
Chair: Aritro Nath
11:00 AM Imputed gene expression associations identify replicable trans-acting genes enriched in immune traits Heather Wheeler
11:20 AM Testing and controlling for horizontal pleiotropy with the probabilistic Mendelian randomization in transcriptome-wide association studies Xiang Zhou
11:40 AM Integrative analysis of transcriptomic annotation data and biobank-scale GWAS summary statistics identifies risk factors for Alzheimer’s disease Qiongshi Lu
Precision Medicine II
Chair: Heather Wheeler
1:30 PM Long non-coding RNAs are crucial pharmacogenomic biomarkers of anticancer agents beyond protein-coding genes Aritro Nath, R. Stephanie Huang
1:50 PM Using cancer eQTL profiles and GWAS to prioritize drug targets in cancer Paul Geeleher
2:10 PM Peering into germline and somatic breast cancer genomes in women of African descent Yonglan Zheng
Precision Medicine III
Chair: Qiongshi Lu
3:00 PM Patient derived xenografts for precision cancer medicine Arvind Singh Mer, Wail Ba-Alawi, Petr Smirnov, Yi Wang, Ben Brew, Anna Goldenberg, Benjamin Haibe-Kains
3:15 PM Genetically regulated gene expression underlies lipid traits in Hispanic cohorts Angela Andaleon, Lauren S. Mogi, Heather E. Wheeler
3:30 PM NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers Gaurav Pandey, Mehmet Eren Ahsen, Supinda Bunyavanich, Alexandar Grishen, Galina Grishina, Yoojin Chun
3:45 PM Systematic characterization of a set of variants from heterogeneous information Xiaoman Xie, Casey Hanson, Saurabh Sinha
4:00 PM Characterization of clonal evolution in microsatellite unstable metastatic cancers through multi-regional tumor sequencing Russell Bonneville, Lianbo Yu, Julie Reeser, Thuy Dao, Michele Wing, Hui-Zi Chen, Melanie Krook, Jharna Miya, Eric Samorodnitsky, Amy Smith, Nicholas Nowacki, Sameek Roychowdhury
4:15 PM iFunMed: Integrative Functional Mediation Analysis of GWAS and eQTL Studies Constanza Rojo, Qi Zhang, Sunduz Keles
4:30 PM A Pathway Perspective on Drug Response for Targeted Therapies in Acute Myeloid Leukemia Aurora Blucher, Steve Kurtz, Cristina Tognon, Brian Druker, Guanming Wu, Shannon McWeeney
4:45 PM GraPhyC: Using Consensus to Infer Tumor Evolutionary Histories Layla Oesper, Kiya Govek, Camden Sikes


- top -


Varsity Hall I on Monday, May 20, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
Education I
Chair: Anna Ritz
11:00 AM Interdisciplinary biology education: a holistic approach to an intractable problem Kristin Jenkins
11:20 AM Expanding Undergraduate Participation in Computational Biology: Resources and Lessons Learned from a Hands-on Workshop Layla Oesper
11:40 AM Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Recent Activities William Morgan
Education II
Chair: Catie Welsh
1:30 PM Increasing data analysis skills in the pediatric cancer community with the Childhood Cancer Data Lab training workshops Candace Savonen, Deepashree Prasad, Casey Greene and Jaclyn Taroni
1:50 PM Bioinformatics in the Library: Bridging the Skills Gap for Biomedical Researchers Pamela Shaw, Matthew Carson, Sara Gonzales, Kristi Holmes, Robin Champieux and Ted Laderas
2:10 PM The ml4bio Workshop: Machine Learning Literacy for Biologists Chris Magnano, Fangzhou Mu, Debora Treu and Anthony Gitter
Education III
Chair: Pamela Shaw
3:00 PM Conference-based Undergraduate Experiences: Lowering the Barrier for Learning about Computational Biology Anna Ritz
3:20 PM Teaching introductory bioinformatics with Jupyter notebook-based active learning Colin Dewey
3:40 PM NIBLSE Incubators: A community-based model for the development of bioinformatics learning resources Michael Sierk, Sam Donovan, William Morgan, Hayley Orndorf, Mark Pauley, Sabrina Robertson, Elizabeth Ryder and William Tapprich
4:00 PM Next steps for the bioinformatics education community Kristin Jenkins, William Morgan, Layla Oesper, Anna Ritz, Michael Sierk, Russell Schwartz


- top -


The Marquee on Tuesday, May 21, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
9:00 AM Keynote #3 - Reading the fossil record of a cancer Quaid Morris
Introduction by Shaun Mahony
General Track - Gene Regulation II
Chair: Dennis Kostka
10:30 AM Direct prediction of regulatory elements from partial data without imputation Yu Zhang and Shaun Mahony
11:00 AM Discovering structural units of chromosomal organization with matrix factorization and graph regularization Da-Inn Lee and Sushmita Roy.
11:15 AM FreeHi-C enables systematic benchmarking of analysis methods for Hi-C Data and improves FDR control for differential Hi-C analysis Ye Zheng and Sunduz Keles.
11:30 AM Using Markov Random Field to Model Gene Expression in the 3D Genome Naihui Zhou, Iddo Friedberg and Mark Kaiser.
11:45 AM Analysis of ChIP-exo read profiles reveals spatial organizations of protein complexes Naomi Yamada, Nina Farrell, B. Franklin Pugh and Shaun Mahony
General Track - Networks I
Chair: Anna Ritz

1:30 PM Incorporating noisy priors for estimating transcription factor activities for genome-scale regulatory network inference Alireza Fotuhi Siahpirani, Rupa Sridharan and Sushmita Roy.
1:45 PM Building Robust Gene Co-expression Networks from RNA-seq Data Kayla Johnson and Arjun Krishnan.
2:00 PM Network analysis of synonymous codon usage Khalique Newaz, Gabriel Wright, Jun Li, Patricia Clark, Scott Emrich and Tijana Milenkovic.
2:15 PM Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data Atul Deshpande, Li-Fang Chu, Ron Stewart and Anthony Gitter.
General Track - Algorithms & Machine Learning
Chair: Lana Garmire

3:00 PM A new resolution function to evaluate tree shape statistics Maryam Hayati, Bita Shadgar and Leonid Chindelevitch
3:30 PM Topic modeling enables identification of regulatory complexes in a comprehensive epigenome Guray Kuzu, Matthew Rossi, Naomi Yamada, Prashant Kuntala, Chitvan Mittal, Nitika Badjatia, Gretta Kellog, Frank Pugh and Shaun Mahony.
3:45 PM The k is a lie Gregory Way and Casey Greene.
4:00 PM Machine learning is fast and accurate for network-based gene classification Arjun Krishnan, Renming Liu, Christopher Mancuso and Anna Yannakopoulos.
4:15 PM Nearest-neighbor Projected-Distance Regression (NPDR) detects network interactions and controls for confounding and multiple testing Brett Mckinney, Trang Le and Bryan Dawkins.
4:30 PM Gene Expression Prediction: A Machine Learning Approach Paul Okoro, Ryan Schubert, Amy Luke, Lara Dugas and Heather Wheeler.
5:00 PM Keynote #4 - Leveraging Large Scale Genome and Transcriptome to Decode the Biology of Complex Traits Hae Kyung Im
Introduction by Tony Gitter


- top -


Fifth Quarter on Tuesday, May 21, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
Microbiome I
Chair: Sailendharan Sudakaran
10:35 AM Viral discovery in Freshwater Environments Catherine Putonti, Jonathon Brenner, Thomas Hatzopoulos and Andrea Garretto
11:00 AM Microbial communities within Lake Michigan nearshore waters in Chicago area Carine Mores, Michael Zilliox and Catherine Putonti
11:15 AM The microbial communities of bilge water, boat surfaces and external port water: a global comparison Laura Schaerer, Ryan Ghannam, Tim Butler and Stephen Techtmann
11:30 AM Environmental Monitoring of Crude Oil using Natural Microbial Communities and Machine Learning Stephen Techtmann, Timothy Butler and Paige Webb
Microbiome II
Chair: Sailendharan Sudakaran
1:30 PM Zero-Inflated Generalized Dirichlet Multinomial (ZIGDM) Regression Model for Microbiome Compositional Data Zheng Zhen Tang
2:00 PM Virus-Driven Metabolism of Sulfur Compounds: From Genes to Ecosystems Karthik Anantharaman
Microbiome III
Chair: Catherine Putonti
3:00 PM An Improved Species-level Taxonomic Classification Method for Marker Gene Sequences Qunfeng Dong, Xiang Gao, Huaiying Lin and Kashi Revanna
3:25 PM Controlling contaminant sequences in low microbial biomass microbiome studies Lisa Karstens
3:50 PM The microbiome in severe ocular surface diseases Michael Zilliox, William Gange, John Thompson, Gina Kuffel, Carine Mores, Cara Joyce and Charles Bouchard
4:15 PM The influence of environmental, dietary, and pharmaceutical agents on the human gut microbiome Michael Burns
4:40 PM Dynamic interaction network inference from longitudinal microbiome data Jose Lugo-Martinez, Daniel Ruiz Perez, Giri Narasimhan and Ziv Bar-Joseph


- top -


Varsity Hall I on Tuesday, May 21, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter
Links for Wednesday, May 22, 2019: The Marquee | Varsity Hall I
Start Time Title Author(s)
RNA I
Chair:  Sarath Chandra Janga
10:40 AM Synthetic biology approaches to study and exploit RNA regulation Bryan Dickinson
11:20 AM Deep learning framework for accurate transcriptome-wide identification of Gm RNA modification events at single molecule resolution from direct RNA sequencing data Sasank Vemuri, Swapna Vidhur, Raja Shekar Varma Kadumuri, Sarath Janga
11:40 AM RNA editing in neural transcriptomes and antiviral immunity Helen Piontkivska, Noel-Marie Plonski, Heather Milliken Mercer, Caroline Nitirahardjo
RNA II
Chair:  Heidi Dvinge
1:30 PM Algorithmic decision-making in single-cell genomic data analyses Jun Li
2:10 PM Evaluation of Computational Methods to Deconvolute Cell Types in Single-Cell Transcriptomics data Qianhui Huang, Yu Liu, Lana Garmire
RNA III
Chair:  Heidi Dvinge
3:00 PM RNA Structure Prediction David Mathews
3:40 PM RNA structure elucidation at single molecule resolution using an integrated framework of long read sequencing and machine learning Swapna Vidhur Daulatabad, Molly Evans, Quoseena Mir, Julius Lucks, Sarath Chandra Janga
4:00 PM Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction Yunan Luo, Yufeng Su, Xiaoming Zhao, Yang Liu, Jian Peng
4:20 PM Integrative analysis of RNA-seq and eCLIP-seq with SURF for elucidating alternative splicing roles of RNA binding proteins Fan Chen, Sunduz Keles
4:40 PM A deep learning-based method for the normalization of data from genome-wide CRISPR-Cas9 screens Henry Ward, Ahm Mahfuzur Rahman, Chad Myers


- top -


The Marquee on Wednesday, May 22, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: Varsity Hall I
Start Time Title Author(s)
9:00 AM Keynote #5 - Bridging Pre-Clinical Drug Screening with Patient Molecular Profiles for Biomarker Discovery and Drug Repurposing R. Stephanie Huang
Introduction by Russell Schwartz
General Track - Networks II
Chairs: Arjun Krishnan

10:30 AM Connectivity measures for signaling pathway topologies Nicholas Franzese, Adam Groce, T. M. Murali and Anna Ritz
11:00 AM A computational framework for benchmarking human CRISPR screens Ahm Mahfuzur Rahman, Maximilian Billmann, Michael Costanzo, Matej Usaj, Brenda Andrews, Charles Boone, Jason Moffat and Chad Myers.
11:15 AM Parameter Selection in Biological Pathway Prediction with Graphlet Based Similarity Score Chris Magnano and Anthony Gitter
11:30 AM Rice Genes Prioritization for Cold Tolerance Using Random Walk with Restart on Multiplex Heterogeneous Network Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schlappi and Serdar Bozdag.
11:45 AM Network-driven discovery of influenza virus replication host factors Jason Shoemaker
General Track - Genome Informatics
Chair: Jaclyn Taroni

1:30 PM A tool for automatically identifying and correcting plant breeding location data Getiria Onsongo, Samantha Fritsche, Thy Nguyen, Jeffery Thompson and Kevin A.T. Silverstein.
1:45 PM scds: Computational Annotation of Doublets in Single Cell RNA Sequencing Data Abha Bais and Dennis Kostka.
2:00 PM Gene Prediction and Genome Functional Annotation of the Almond ‘Nonpareil’ genome Wilberforce Zachary Ouma, Tea Meulia, Thomas Gradziel and Jonathan Fresnedo Ramirez.
2:15 PM Tracking the popularity and outcomes of all bioRxiv preprints Richard Abdill and Ran Blekhman
3:00 PM Keynote #6 - Inferring Host-Virus Interactions from Diverse Data Sources Mark Craven
Introduction by Tijana Milkovic


- top -


Varsity Hall I on Wednesday, May 22, 2019

Links for Monday, May 20, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Tuesday, May 21, 2019: The Marquee | Fifth Quarter | Varsity Hall I
Links for Wednesday, May 22, 2019: The Marquee
Start Time Title Author(s)
General Track - Clinical and Health Informatics I
Chair: Serdar Bozdag

10:30 AM Autoimmune risk allele-dependent human gene regulation by Epstein-Barr Virus EBNA2 Matthew Weirauch, Xiaoting Chen, Ted Hong, Mario Pujato, Daniel Miller, Sreeja Parameswaran, Omer Donmez, Mariana Saint Just Ribeiro, Carmy Forney, Yongbo Huang, Kenneth Kaufman, Bo Zhao, Iouri Chepelev, John Harley and Leah Kottyan.
10:45 AM The Clinical Implications of Subclonal Copy Number Alterations in Chronic Lymphocytic Leukemia Mark Zucker and Kevin Coombes.
11:00 AM Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images Bino Varghese, Frank Chen, Darryl Hwang, Suzanne Palmer, Andre Luis De Castro Abreu, Osamu Ukimura, Monish Aron, Manju Aron, Inderbir Gill, Vinay Duddalwar and Gaurav Pandey.
11:15 AM Systematic analysis of genetic interactions in Parkinson’s disease reveals interactions with known risk genes Wen Wang, Benjamin Vandersluis and Chad Myers.
General Track - Clinical and Health Informatics II
Chair: Debbie Chasman

1:30 PM An integrative computational modeling approach to identify repurposable metabolic drug targets in CD4+ T cells Bhanwar Lal Puniya, Bailee Lichter, Robert Moore, Sydney Townsend, Alex Ciurej, Ab Rauf Shah, Matteo Barberis and Tomas Helikar.
1:45 PM Linear Drug-Target Interaction Model Predicts Effective Drugs and Also Identifies Disease-Related Proteins and Pathways from Phenotypic Screens Feng Guo
2:00 PM Using histopathology whole-slide images quantitative features to predict liver cancer survival Noshad Hosseini, Fadhl M. Alakwaa, Olivier B. Poiron and Lana X. Garmire.
2:15 PM Machine Learning Classifier for Endometriosis Using Transcriptomics and Methylomics Data Sadia Akter, Dong Xu, Susan Nagel, John Bromfield, Katherine Pelch, Gilbert Wilshire and Trupti Joshi.

- top -