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


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


Go directly to: Friday - December 6 | Saturday - December 7
WEDNESDAY – December 4, 2019
04:00 pm 06:00 pm Registration
THURSDAY – December 5, 2019
08:00 am 06:00 pm Registration
08:00 am 09:00 am Breakfast
09:00 am 09:45 am Keynote 1
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 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
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
Assistant Professor
Department of Computer Science and Bachelor of Innovation
College of Engineering and Applied Science
University of Colorado

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
- top -
FRIDAY – December 6, 2019
08:00 am 06:00 pm Registration
08:00 am 09:00 am Breakfast
09:00 am 09:45 am Keynote 4
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
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
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
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
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
- top -
SATURDAY – December 7, 2019
08:00 am 11:00 am Registration
08:00 am 09:00 am Breakfast
09:00 am 09:30 am Keynote 7
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
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,
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
IBM Distinguished Engineer
Data Centric Solutions
IBM T.J. Watson Research
Chief Science Officer
IBM Research UK

Intelligent Simulations - Incorporating AI into Computational Simulations
12:00 pm 12:15 pm Closing Raffle and Awards


- top -