DETAILED AGENDA
Presentation slides are now available. Click on the 'presentation slides' link located below each title.
| 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 • presentation slides 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| 09:45 am | 09:55 am | Withdrawn OP 01 Next Generation Sequencing as a preventive medicine tool.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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides Presenting Author: Marco Cano, Scripps Research |
| 11:45 pm | 11:55 pm | OP 08 Hypergraph Analytics for Computational Virology • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides Presenting Author: Trang Le, University of Pennsylvania |
| 11:45 pm | 11:55 pm | OP 23 Deep learning enables in silico chemical-effect prediction • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides 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 • presentation slides Presenting Author: Dinler Antunes, Rice University |
| 10:10 am | 10:20 am | OP 35 Biotherapeutic Protein Immunogenicity Risk Assessment with TCPro • presentation slides 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 • presentation slides 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 • presentation slides Presenting Author: Ziyou Ren, Northwestern University |
| 11:00 am | 11:10 am | OP 38 How to annotate what we don’t know • presentation slides 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 • presentation slides 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 |