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ROCKY 2018 | Dec 6 – 8, 2018 | Aspen/Snowmass, CO | Detailed Agenda

DETAILED AGENDA


Go directly to: Friday - December 7 | Saturday - December 8
WEDNESDAY – December 5, 2018
START TIME END TIME SESSION TYPE
04:00 pm 06:00 pm REGISTRATION
 
THURSDAY – December 6, 2018
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
ZHIYONG LU, Ph.D.
Deputy Director for Literature Search
National Center for Biotechnology Information (NCBI)
Senior Investigator, NCBI/NLM/NIH

Machine Learning in Biomedicine: from PubMed Search to Autonomous Disease Diagnosis
09:45 am 09:55 am OP01
Proteomics of natural bacterial isolates powered by deep learning-based de novo identification

Presenting Author:
Samuel Payne, Brigham Young University
09:55 am 10:05 am OP02
A platform for community-scale transcriptome-wide association studies

Presenting Author:
YoSon Park, Perelman School of Medicine University of Pennsylvania
10:05 am 10:15 am OP03
Harmonizing and Analyzing Clinical Trials Data in the AHA Precision Medicine Platform

Presenting Author:
Carsten Goerg, University of Colorado
10:15 am 10:25 am OP04
anexVis: visual analytics framework for analysis of RNA expression

Presenting Author:
Diem-Trang Tran, University of Utah
10:25 am 10:45 am Break
10:45 am 11:15 am Keynote 2
AARON VON HOOSER, PhD
Principal Scientist
Computational Biology
PatientsLikeMe, Inc.

Building a Learning System that Helps Individuals to Thrive by Connecting Their Experiences and Goals with Molecular Measures of Health
11:15 am 11:25 am OP05
The characterization of different cell types using the Benford law

Presenting Author:
Sne Morag, Ariel University
11:25 am 11:35 am OP06
Use of metadata and Bag-of-words to map measurements across observational study data

Presenting Author:
Laura Stevens, University of Colorado Anschutz Medical Campus
11:35 am 11:45 am OP07
ExtRamp: A novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness

Presenting Author:
Justin Miller, Brigham Young University
11:45 am 11:55 am OP08
Using machine learning algorithms for classification of medulloblastoma subgroups based on gene expression data

Presenting Author:
Sivan Gershanov, Ariel University
12:00 pm 04:00 pm -->Ski Break
04:00 pm 04:30 pm Keynote 3
JOSLYNN S. LEE, Ph.D.
Science Education Fellow
Howard Hughes Medical Institute


Training and Engaging URM Undergraduate Students in Genomics Research Through a Place-based Microbiome Research Project
04:30 pm 04:40 pm OP09
A human disease network from gene-publication relationships on PubMed

Presenting Author:
Edward Lau, Stanford University
04:40 pm 04:50 pm OP10
Transcriptome analysis of cancer adjacent normal tissues reveal genes co-expressed with LINE elements

Presenting Author:
Mira Han, University of Nevada Las Vegas
04:50 pm 05:00 pm OP11
Highly Accurate Computational Characterization of Protein Kinase Family-specific Phosphorylation Sites

Presenting Author:
Chen Li, ETH Zürich
05:00 pm 05:10 pm OP12
ORCHID: a method for detecting short-range chromatin interactions in high-resolution 5C and Hi-C datasets

Presenting Author:
Fei Ji, Massachusetts General Hospital
05:10 pm 05:30 pm Break
05:30 pm 05:40 pm OP13
Using Adversarial Deep Neural Networks to Remove Nonlinear Batch Effects from Expression Data

Presenting Author:
Jonathan Dayton, Brigham Young University
05:40 pm 05:50 pm OP14
Med2Mech: Neural-Symbolic Representation of Molecular Mechanisms Underlying Pediatric Disease

Presenting Author:
Tiffany Callahan, University of Colorado Anschutz Medical Campus
05:50 pm 06:00 pm OP15
A Machine Learning Classifier for Assigning Individual Patients with Systemic Sclerosis to Intrinsic Molecular Subsets

Presenting Author:
Jennifer Franks, Geisel School of Medicine at Dartmouth
06:30 pm 09:30 pm Dinner - Il Poggio
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FRIDAY – December 7, 2018
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
DEBORAH L. MCGUINNESS, PhD

Tetherless World Senior Constellation Chair
Professor of Computer Science and Cognitive Science
Rensselaer Polytechnic Institute

Semantic Data Resources Enabling Science: Building, Using, and Maintaining Ontology-Enabled Biology Data Resources
09:45 am 09:55 am OP16
A Data Quality Testing Tool for Cross-institutional OMOP Electronic Health Record Data Repositories

Presenting Author:
Timothy Bergquist, University of Washington
09:55 am 10:05 am OP17
Comparative Analysis of Germline Microsatellites in the 1,000 Genomes Project

Presenting Author:
Nicholas Kinney, Virginia College of Osteopathic Medicine
10:05 am 10:15 am OP18
Unbiased Pathway Detection Expands Cancer Pathways

Presenting Author:
Chih-Hsu Lin, Baylor College of Medicine
10:15 am 10:25 am OP19
A systems biology approach to define essential kinases in small cell lung cancer

Presenting Author:
Jihye Kim, University of Colorado Anschutz Medical Campus
10:25 am 10:45 am Break
10:45 am 11:15 am Keynote 5
DAVID ASTLING, PhD
Scientist, Bioinformatics
SomaLogic Inc.

Beyond Genomics: Deriving Actionable Health Insights from the Human Proteome
11:15 am 11:25 am OP20
Clustering of Protein Conformations using Parallelized Dimensionality Reduction

Presenting Author:
Arpita Joshi, University of Massachusetts, Boston
11:25 am 11:35 am OP21
PredHPI: an integrated web-server platform for the prediction and visualization of host-pathogen interactions

Presenting Author:
Rakesh Kaundal, Utah State University
11:35 am 11:45 am OP22
Searching for translatable alternative splice isoforms in the human proteome

Presenting Author:
Maggie Pui Yu Lam, University of Colorado Anschutz Medical Campus
11:45 am 11:55 am OP23
Text Mining Novel Disease- and Drug-Specific Pathways

Presenting Author:
Minh Pham, Baylor College of Medicine
12:00 pm 04:00 pm -->Ski Break
04:00 pm 04:30 pm Keynote 6
NICOLE A. VASILEVSKY, Ph.D.
Research Assistant Professor
Department of Medical Informatics and Clinical Epidemiology (DMICE)
Oregon Health & Science University

LOINC2HPO: Improving Translational Informatics by Standardizing EHR Phenotypic Data Using the Human Phenotype Ontology
04:30 pm 04:40 pm OP24
Optimizing nontuberculous mycobacteria (NTM) de novo genome assemblies for application in clinical case studies

Presenting Author:
Sara Kammlade, National Jewish Health
04:40 pm 04:50 pm OP25
REAL-neo, a comprehensive neoantigen prediction and prioritization pipeline using tumor sequencing data

Presenting Author:
Yesesri Cherukuri, Mayo Clinic
04:50 pm 05:00 pm OP26
Measuring chromosome conformation

Presenting Author:
Brian Ross, University of Colorado Anschutz Medical Campus
05:00 pm 05:10 pm OP27
Modeling the Structure of BioGRID PPI Networks

Presenting Author:
Sridevi Maharaj, University of California-Irvine
05:10 pm 05:30 pm Break
05:30 pm 05:40 pm OP28
Addressing the compositional data problem in sequencing with a novel, robust normalization method

Presenting Author:
James St. Pierre, University of Toronto
05:40 pm 05:50 pm OP29
A Case Study on the Effects of Noisy, Long-read Correction Approaches on Assembly Contiguity

Presenting Author:
Brandon Pickett, Brigham Young University
05:50 pm 06:00 pm OP30
Integrative analysis of transcriptomics and proteomics to detect novel protein isoforms from alternatively spliced transcripts induced by SF3B1 spliceosomal mutations

Presenting Author:
Kelsey Nassar, University of Colorado Anschutz Medical Campus
06:30 pm 08:30 pm Poster Session
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SATURDAY – December 8, 2018
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
BENJAMIN M. GOOD, PhD
Consultant
Lawerence Berkeley National Labs


Integrating Pathway Databases with Gene Ontology Causal Activity Models
09:30 am 09:40 am OP31
Exploring the Fabric of Breast Cancer Using Gene Sets

Presenting Author:
Judith Blake, The Jackson Laboratory
09:40 am 09:50 am OP32
Measuring and Protecting the Sensitive Linking Information Leakage Across Epigenetic and Transcriptomics Datasets Through Genotype and Assay Prediction

Presenting Author:
Arif Harmanci, University of Texas Health Science Center
09:50 am 10:00 am OP33
Education, Networking and Building Next Generation Prototypes -- Hackathons and Analyzeathons for Bioinformaticians, Biomedical Informaticians and Computational Biologists!

Presenting Author:
Ben Busby, NCBI
10:00 am 10:10 am OP34
Alternative Splicing of Single Cells in Squamous Cell Lung Cancer Premalignancy

Presenting Author:
Hyunmin Kim, University of Colorado Anschutz Medical Campus
10:10 am 10:20 am OP35
Inferring trade-offs in protein folding networks

Presenting Author:
Sebastian Pechmann, Université de Montréal
10:20 am 10:40 am Break
10:40 am 10:50 am OP36
Fully Bayesian model for non-random missing data in qPCR

Presenting Author:
Valeriia Sherina, University of Rochester Medical Center
10:50 am 11:00 am OP37
Homologous Inter-Domain Segments in Protein Families

Presenting Author:
Dylan Barth, University of Nevada Las Vegas
11:00 am 11:10 am OP38
Integrating extracted relations into existing knowledge bases

Presenting Author:
Harrison Pielke-Lombardo, University of Colorado
11:10 am 11:20 am OP39
The Use of Scientific Ignorance to Drive Literature-Based Discovery in Prenatal Nutrition Across Disciplinary Boundaries

Presenting Author:
Mayla Boguslav, University of Colorado Anschutz Medical Campus
11:20 am 11:30 am OP40
Governance Innovations for Promoting Cross-institutional Electronic Health Data Sharing

Presenting Author:
Kari A. Stephens, University of Washington
11:30 am 12:00 pm Keynote 8
KIRK E. JORDAN, PhD
IBM Distinguished Engineer
Data Centric Solutions
IBM T.J. Watson Research & Chief Science Officer

Algorithm Exploitation & Evolving AI/Cognitive Examples on IBM’s Data Centric Systems
12:00 pm 12:15 pm Closing Raffle and Awards

 


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