DETAILED AGENDA
| Go directly to: Friday - December 6 | Saturday - December 7 | ||
| WEDNESDAY – December 4, 2019 | ||
| START TIME | END TIME | SESSION TYPE |
| 04:00 pm | 06:00 pm | Registration |
| THURSDAY – December 5, 2019 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 06:00 pm | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:45 am | Keynote 1 KEVIN BRETONNEL COHEN, PhD Director, Biomedical Text Mining Group Computational Bioscience Program University of Colorado School of Medicine, USA Two Existential Threats to Biomedical Text Mining...and How to Address Them with Natural Language Processing |
| 09:45 am | 09:55 am | Withdrawn OP 01 Next Generation Sequencing as a preventive medicine tool. A Mexico-United States collaboration. Presenting Author: Gilberto de la Garza-Galvan, University of Texas Health Science Center at Houston |
| 09:55 am | 10:05 am | OP 02 Enabling the next generation of microbiome science with QIIME 2 Presenting Author: Greg Caporaso, Northern Arizona University |
| 10:05 am | 10:15 am | OP 03 Evolutionary Action is a unifying framework for assessing missense variant structures within and across phyla Presenting Author: Nicholas Abel, Baylor College of Medicine |
| 10:15 am | 10:25 am | OP 04 A toxicogenomics approach to identify liver and kidney injuries Presenting Author: Patric Schyman, Biotechnology HPC Software Applications Institute (BHSAI) |
| 10:25 am | 10:45 am | Break |
| 10:45 am | 11:15 am | Keynote 2 JOSEPH ALLISON, PhD Bioinformatic Scientist SomaLogic, Inc. Colorado, USA A Story of Proteomic Statistical Process Control at SomaLogic |
| 11:15 am | 11:25 am | OP 05 Towards Automating Computational Phenotyping: Exploring the Trade-offs of Different Vocabulary Mapping Strategies Presenting Author: Tiffany Callahan, University of Colorado Denver Anschutz Medical Campus- Computational Bioscience Program |
| 11:25 am | 11:35 pm | OP 06 Open PBTA: Collaborative analysis of the Pediatric Brain Tumor Atlas Presenting Author: Joshua Shapiro, Childhood Cancer Data Lab (Alex's Lemonade Stand Foundation) |
| 11:35 pm | 11:45 pm | OP 07 Data Discovery Engine: A web-based toolset for maximizing data discoverability and promoting reusable data-sharing best practices Presenting Author: Marco Cano, Scripps Research |
| 11:45 pm | 11:55 pm | OP 08 Hypergraph Analytics for Computational Virology Presenting Author: Cliff Joslyn, Pacific Northwest National Laboratory |
| 12:00 pm | 04:00 pm | -->Ski Break |
| 04:00 pm | 04:30 pm | Keynote 3 OLUWATOSIN OLUWADARE, PhD Assistant Professor Department of Computer Science and Bachelor of Innovation College of Engineering and Applied Science University of Colorado USA 3D Chromosome and Genome Structure Modeling |
| 04:30 pm | 04:40 pm | OP 09 Containerized pipeline for the identification of compound heterozygous variants in trios Presenting Author: Dustin Miller, Brigham Young University |
| 04:40 pm | 04:50 pm | OP 10 The design of an interactive lung map for studying premalignant lesions in the lung over time Presenting Author: Carsten Görg, Colorado School of Public Health |
| 04:50 pm | 05:00 pm | OP 11 Apollo: an efficient tool to collaboratively refine and attribute genome-wide genomic annotationsc Annotations Presenting Author: Nathan Dunn, University of California, Berkeley |
| 05:00 pm | 05:10 pm | OP 12 An online end-to-end pipeline for virus phylogeography that leverages Natural Language Processing for finding host locations Presenting Author: Matthew Scotch, Arizona State University |
| 05:10 pm | 05:30 pm | Break |
| 05:30 pm | 05:40 pm | OP 13 Evolutionary Action as a Tool for Quantifying Differentiation Across the Primate Family Tree Presenting Author: Harley Peters, Baylor College of Medicine |
| 05:40 pm | 05:50 pm | OP 14 Haplocravat: LD-based calculation built on top of a platform to annotate variants Presenting Author: Ben Busby, Mountain Genomics/Johns Hopkins University |
| 05:50 pm | 06:00 pm | OP 15 Characterizing the Regulatory Framework in an Aggressive Breast Cancer Phenotype: A Bayesian Regression-Based Enhancement Presenting Author: George Acquaah-Mensah, Massachusetts College of Pharmacy & Health Sciences |
| 06:30 pm | 09:30 pm | Dinner - Il Poggio |
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| FRIDAY – December 6, 2019 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 06:00 pm | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:45 am | Keynote 4 JOYCE C. HO, PhD Assistant Professor Computer Science Department Emory University Georgia, USA Developing an Evidence Matching Framework Using Web-based Medical Literature |
| 09:45 am | 09:55 am | OP 16 Discovering Subclones in Tumors Sequenced at Standard Depths Presenting Author: Li Liu, Arizona State University |
| 09:55 am | 10:05 am | OP 17 Pathogenic Synonymous Variants Are More Likely to Affect Codon Usage Biases than Benign Synonymous Variants Presenting Author: Justin Miller, Brigham Young University |
| 10:05 am | 10:15 am | OP 18 Map and model — moving from observation to prediction in toxicogenomics Presenting Author: Wibke Busch, Helmholtz Centre for Environmental Research - UFZ |
| 10:15 am | 10:25 am | OP 19 Combining the Evolutionary Trace Algorithm and Covariation Metrics Yields Improved Structural Predictions Presenting Author: Daniel Konecki, Baylor College of Medicine |
| 10:25 am | 10:45 am | Break |
| 10:45 am | 11:15 am | Keynote 5 Joint Presentation: NIMISHA SCHNEIDER, PhD QuartzBio, part of Precision for Medicine Maryland, USA TED FOSS, PhD Director, Systems and Data Integration Precision For Medicine QuartzBio, part of Precision for Medicine Maryland, USA Coupling Data-Driven and Mechanistic Modeling Approaches Through the Application of a Scalable, Knowledge-Driven Framework and High-Throughput Public Omics Data Sources |
| 11:15 am | 11:25 am | OP 20 Toxicological Mechanistic Inference: Generating mechanistic explanations of adverse outcomes Presenting Author: Ignacio Tripodi, University of Colorado, Boulder |
| 11:25 am | 11:35 pm | OP 21 Giving credit where credit is due: How to make more meaningful connections between people and their roles, work, and impact Presenting Author: Nicole Vasilevsky, Oregon Health & Science University |
| 11:35 pm | 11:45 pm | OP 22 Nearest-neighbor Projected-Distance Regression to detect network interactions and control for confounders and multiple testing Presenting Author: Trang Le, University of Pennsylvania |
| 11:45 pm | 11:55 pm | OP 23 Deep learning enables in silico chemical-effect prediction Presenting Author: Jana Schor, Helmholtz Centre for Environmental Research - UFZ |
| 12:00 pm | 04:00 pm | -->Ski Break |
| 04:00 pm | 04:30 pm | Keynote 6 JUSTIN GUINNEY, PhD VP, Computational Oncology Sage Bionetworks Affiliate Associate Professor University of Washington Director, DREAM Challenges Washington, USA The Model-to-Data Paradigm: Overcoming Data Access Barriers in Biomedical Competitions |
| 04:30 pm | 04:40 pm | OP 24 Correlations and curses of dimensionality: optimizing k in nearest-neighbor feature selection Presenting Author: Bryan Dawkins, University of Tulsa |
| 04:40 pm | 04:50 pm | OP 25 Deep Learning based Multi-view model for deciphering gene regulatory keywords Presenting Author: Pramod Bharadwaj Chandrashekar, Arizona State University |
| 04:50 pm | 05:00 pm | OP 26 Identifying optimal mouse models for human asthma using a novel modeling approach Presenting Author: Yihsuan Tsai, University of North Carolina at Chapel Hill |
| 05:00 pm | 05:10 pm | OP 27 Bridging the Bioinformatics Knowledge Gap in the Pediatric Cancer Research Community with the Childhood Cancer Data Lab workshops Presenting Author: Chante Bethell, Childhood Cancer Data Lab (Alex's Lemonade Stand Foundation) |
| 05:10 pm | 05:30 pm | Break |
| 05:30 pm | 05:40 pm | OP 28 Hetnet connectivity search provides rapid insights into how two biomedical entities are related Presenting Author: Daniel Himmelstein, University of Pennsylvania |
| 05:40 pm | 05:50 pm | OP 29 Landmark and Cancer-Relevant Gene Selection of RNA Sequencing Data for Survival Analysis Presenting Author: Carly Clayman, Penn State University - Great Valley |
| 05:50 pm | 06:00 pm | OP 30 The impact of undesired technical variability on large-scale data compendia Presenting Author: Alexandra Lee, Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, |
| 06:00 pm | 06:30 pm | Open Ballroom divider wall, move chairs and boards to accommodate Poster Session |
| 06:30 pm | 08:30 pm | Poster Session |
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| SATURDAY – December 7, 2019 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 11:00 am | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:30 am | Keynote 7 HEINRICH RÖDER, PhD Biodesix, Inc. Colorado, USA Development of Clinically Relevant Tests from Human Serum Samples: A Look at the Circulating Proteome |
| 09:30 am | 09:40 am | OP 31 A pedigree-level examination of Schistosoma japonicum following schistosomiasis reemergence in rural China Presenting Author: Laura Timm, University of Colorado - Anschutz Medical Campus |
| 09:40 am | 09:50 am | OP 32 High Resolution Proteomics and Genomics of CNDP1 Repeat Variants Linked to Diabetic Nephropathy Presenting Author: Nicholas Kinney, Edward Via College of Osteopathic Medicine |
| 09:50 am | 10:00 am | OP 33 Computational Analysis of Kinesin Mutations Implicated in Hereditary Spastic Paraplegias Presenting Author: Shaolei Teng, Howard University |
| 10:00 am | 10:10 am | OP 34 Enabling structure-based data-driven selection of targets for cancer immunotherapy Presenting Author: Dinler Antunes, Rice University |
| 10:10 am | 10:20 am | OP 35 Biotherapeutic Protein Immunogenicity Risk Assessment with TCPro Presenting Author: Osman Yogurtcu, FDA |
| 10:20 am | 10:40 am | Break |
| 10:40 am | 10:50 am | OP 36 Large-scale phylogenetic analysis reveals different sequence divergence patterns in orthologous and paralogous proteins Presenting Author: Joseph Ahrens, University of Colorado Denver Anschutz Medical Campus |
| 10:50 am | 11:00 am | OP 37 A new framework for clustering single cell RNA-seq data Presenting Author: Ziyou Ren, Northwestern University |
| 11:00 am | 11:10 am | OP 38 How to annotate what we don’t know Presenting Author: Mayla Boguslav, University of Colorado Anschutz Medical Campus |
| 11:10 am | 11:20 am | OP 39 Filtering, classification, and selection of new knowledge for model assembly and extension Presenting Author: Natasa Miskov-Zivanov, University of Pittsburgh |
| 11:20 am | 11:30 am | OP 40 Pathway-based Single-Cell RNA-Seq Classification, Clustering, and Construction of Gene-Gene Interactions Networks Using Random Forests Presenting Author: Herbert Pang, University of Hong Kong |
| 11:30 am | 12:00 pm | Keynote 8 KIRK E. JORDAN, Ph.D. IBM Distinguished Engineer Data Centric Solutions IBM T.J. Watson Research and Chief Science Officer IBM Research UK Intelligent Simulations - Incorporating AI into Computational Simulations |
| 12:00 pm | 12:15 pm | Closing Raffle and Awards |