ROCKY 2016 PROGRAM BOOK
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Rocky 2016 Program Book

14th Annual Rocky Mountain Bioinformatics Conference

DETAILED AGENDA

(All sessions will be held at the Snowmass Convention Center CC)


ROCKY slidesPresentations with this icon indicate that slides are available.


Go directly to: [Friday - December 9] [Saturday - December 10]
WEDNESDAY – December 7, 2016
START TIME END TIME SESSION TYPE
04:00 pm 06:00 pm REGISTRATION in the lobby of the Westin
 
THURSDAY – December 8, 2016
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
Joshua M. Stuart, PhD
Professor
UC Santa Cruz

The Blue-prints of Tumors Uncovered Through Network Integration
> Click here for details <
09:45 am 09:55 am OP 01
IndeCut: A Cut-norm Based Method for Evaluating Independent and Uniform Sampling in Network Motif Discovery Algorithms
Mitra Ansariola

Oregon State University, Corvallis
ROCKY slidesClick here for slides (pdf).
09:55 am 10:05 am OP 02
Reproducible Computational Workflows with Continuous Analysis
Brett Beaulieu-Jones
University of Pennsylvania
10:05 am 10:15 am OP 03
Application Ontologies Supporting Phenotyping from Clinical Text
Wendy Chapman
University of Utah
10:15 am 10:25 am OP 04
SPARQLer: Making Knowledge Functional
Daniel McShan
University of Colorado School of Medicine
10:25 am 10:45 am Break
10:45 am 11:15 am Keynote 2
Renee Deehan Kenney, PhD
Head of Biology and Bioinformatics
PatientsLikeMe

Measuring Disease Through Real World Evidence and Biological State: Impact For Patients (and Animal Models, too)
> Click here for details <
11:15 am 11:25 am OP 05
Improved Network Ontology Analysis by Segmentation
Ananda Mondal
Claflin University
11:25 am 11:35 am OP 06
An Image Phenotyping Environment Based on Open-Source Tools
Brian Chapman
University of Utah
11:35 am 11:45 am OP 07
InterViewer, a new Cytoscape-based viewer that displays interactions between selected sets of proteins
Marek Tutaj
Medical College of Wisconsin
11:45 am 11:55 am OP 08
CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies
Max Alekseyev
George Washington University
12:00 pm 04:00 pm -->Ski Break
04:00 pm 04:30 pm Keynote 3
Marco Masseroli, PhD
Associate Professor
Politecnico di Milano


Next Generation Genomic Computing
> Click here for details <
04:30 pm 04:40 pm OP 09
Analysis of Tobacco Users Admitted to Intensive Care Units
Andrey Soares
University of Colorado School of Medicine
04:40 pm 04:50 pm OP 10
A new molecular signature approach for prediction of driver cancer pathways from transcriptional data
Boris Reva
Icahn School of Medicine at Mount Sinai
ROCKY slidesClick here for slides (pdf).
04:50 pm 05:00 pm OP 11
Computational analysis of breakome reveals replication fork movement and elucidates mechanisms of DNA double-stranded break formation
Maga Rowicka

University of Texas Medical Branch at Galveston
05:00 pm 05:10 pm OP 12
HRC3 – A new class of motifs involved in chromatin organization and development
Andrzej Kudlicki
University of Texas Medical Branch
05:10 pm 05:30 pm Break
05:30 pm 05:40 pm OP 13
Network Inference and the Knowledge Base of Biomedicine
Tiffany Callahan
University of Colorado Denver Anschutz Medical Campus
ROCKY slidesClick here for slides (pdf).
05:40 pm 05:50 pm OP 14
ShinyLearner: Enabling biologists to perform robust machine-learning classification
Stephen Piccolo
Brigham Young University
05:50 pm 06:00 pm OP 15
Stratification of prostate cancer patients based on molecular interaction profiles
Roland Mathis

IBM Research
ROCKY slidesClick here for slides (pdf).
06:30 pm 09:30 pm Dinner - Il Poggio
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FRIDAY – – December 9, 2016
START TIME END TIME SESSION TYPE
08:00 am 06:00 pm Registration
08:30 am 09:00 am Breakfast
09:00 am 09:45 am Keynote 4
Laura K. Wiley, PhD
Assistant Professor
University of Colorado Anschutz Medical Campus


Precision Medicine and the Learning Healthcare System: Leveraging Informatics to Improve Care
> Click here for details <
09:45 am 09:55 am OP 16
Medication Data Mining of Electronic Medical Records Reveal Race-Specific Prescription Patterns
Benjamin Glicksberg
Icahn School of Medicine at Mount Sinai
09:55 am 10:05 am OP 17
Comparative analysis of the expression patterns and regulation of histone variant genes reveals a novel epigenetic pathway related to cancer
Michael Tolstorukov
Massachusetts General Hospital and Harvard Medical School
10:05 am 10:15 am OP 18
The Cognoma Collaborative creates a webapp to predict cancer mutations from gene expression
Daniel Himmelstein
University of Pennsylvania
ROCKY slidesSlides are available here:
- Slides
- Video
10:15 am 10:25 am OP 19
Functionally prioritizing candidate genes from genome-wide association studies
Kelsey Anderson
University of Colorado School of Medicine
10:25 am 10:45 am Break
10:45 am 11:15 am Keynote 5
Alan Williams, PhD
Chief Informatics Officer
SomaLogic

Data Analytics and the SOMAscan™ Proteomic Platform
> Click here for details <
11:15 am 11:25 am OP 20
Deriving Population-Scale Therapeutic Trajectories to Enable Precision Pharmacology
Kipp Johnson
Icahn School of Medicine at Mount Sinai
11:25 am 11:35 am OP 21
Comparison of Relief-F Nucleotide Differences For GWAS Data With Application to Bipolar Disorder
Marziyeh Arabnejad Khanouki
University of Tulsa
11:35 am 11:45 am OP 22
ModEvo: A Web-Based Tool for Modeling Evolutionary Dynamics
Filip Jagodzinski
Western Washington University
11:45 am 11:55 am OP 23
Predicting Neural Fluctuations in the Primary Visual Cortex
William Kindel

University of Colorado School of Medicine
12:00 pm 04:00 pm -->Ski Break
04:00 pm 04:30 pm Keynote 6
Temple F. Smith, PhD
Professor Emeritus
Boston University

Current Insights into the Evolution of the Genetic Translation System and the Genetic Code Itself
> Click here for details <
04:30 pm 04:40 pm OP 24
De novo protein structure prediction by big data and deep learning
Sheng Wang
Toyota Technological Institute at Chicago
04:40 pm 04:50 pm OP 25
Identifying the mechanism for the metastatic spread of breast cancer through integration of gene expression, whole genome sequencing and functional screens
Eran Andrechek
Michigan State University
04:50 pm 05:00 pm OP 26
Allelic Maps of Cancer
Anelia Horvath
George Washington University
05:00 pm 05:10 pm OP 27
Identifying non-specific effects of small molecule treatment through GSEA meta-analysis
Rani Powers

University of Colorado Anschutz Medical Campus
05:10 pm 05:30 pm Break
05:30 pm 05:40 pm OP 28
Insights into Bathyarcheota Ecology and Co-occurrence Patterns as Revealed by Public Metagenome Sequencing Data
David Banks-Richardson
University of Colorado -Denver
05:40 pm 05:50 pm OP 29
The SNPPhenA Corpus: An annotated research abstract corpus for extracting ranked association of single-nucleotide polymorphisms and phenotypes
Hamidreza Chitsaz
Colorado State University
05:50 pm 06:00 pm OP 30
Toward a Metric Learning Model for Protein Fold Recognition Using a Novel Feature Extraction Technique Based on the Mixture of Evolutionary and Secondary Structural Information
Pooya Zakeri
1)KU Leuven. 2)iMinds
06:30 pm 08:30 pm Poster Session
- Poster abstracts
- Poster list
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SATURDAY – – December 10, 2016
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
Krista Meyer, PhD
Director of Proteomic Analysis
Biodesix: Making Medicine Personal®

Leveraging Biology to Guide Feature Enrichment for Designing Multivariate Classifiers for Clinical Tests
> Click here for details <
09:30 am 09:40 am OP 31
Development of a diagnostic to profile eukaryotic microbes of the human microbiome
Ana Popovic
Hospital for Sick Children, University of Toronto
09:40 am 09:50 am OP 32
G4 quadruplexes in and near regulatory elements of maize genes predict tissue type and altered transcriptional and translational response to submergence and heat stress
Mingze He
Iowa State University
09:50 am 10:00 am OP 33
Modeling heterogeneous cell populations using Boolean networks
Brian Ross
University of Colorado
10:00 am 10:10 am OP 34
Enhancer Reprogramming in Mammalian Genomes
Mario Flores
NIH
10:10 am 10:20 am OP 35
The Finite State Projection based Fisher Information Matrix for the Design of Single-Cell Experiments
Zachary Fox
Colorado State University
10:20 am 10:40 am Break
10:40 am 10:50 am OP 36
2-Scale KNN Classifications
Destiny Anyaiwe
Oakland University
ROCKY slidesClick here for slides (pdf).
10:50 am 11:00 am OP 37
Best practices for reproducible and robust data analysis in a bioinformatics core facility
James Denvir
Marshall University
11:00 am 11:10 am OP 38
The Affinity Data Bank for biophysical analysis of regulatory sequences
Todd Riley
University of Massachusetts, Boston
11:10 am 11:20 am OP 39
Pattern-based estimation of the extent of explicit contradiction in the scientific literature
Elizabeth White
University of Colorado Denver, Anschutz
ROCKY slidesClick here for slides (pdf).
11:20 am 11:30 am OP 40
Towards Highly Accurate Mapping of Protein Glycosylation Sites in the Human Proteome
Chen Li
Monash University
ROCKY slidesClick here for slides (pdf).
11:30 am 11:50 am Keynote 8
Kirk E. Jordan, PhD
Chief Science Officer
IBM Research UK

Data Centric Cognitive Computing: IBM’s Direction, Workflow Challenges and Opportunities

> Click here for details <
11:50 am 12:00 pm Closing Raffle and Awards

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