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ROCKY 2019 | Dec 5 – 7, 2019 | Aspen/Snowmass, CO | Detailed Agenda

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09:45 am 09:55 am Withdrawn OP 01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

 


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