10th Annual Rocky Mountain Bioinformatics Conference

Full Agenda

Updated Dec 02, 2012
(Schedule and locations are subject to change. Please check back for updates.)

Go directly to: [Friday - December 7] [Saturday - December 8]

THURSDAY – December 6, 2012
Start Time End Time Session Type
12:00 pm 1:30 pm Registration
1:30 pm 2:15 pm Keynote 1
Helping Machines to Help Us: New Advances in Biological Ontologies, Databases and Machine Reasoning

Chris Mungall, PhD
Bioinformatics Scientist
Berkeley Bioinformatics Open-source Projects
Lawrence Berkeley National Laboratory
Berkeley, CA, USA
2:15 pm 2:25 pm Oral Presentation 1
Integrated Database for Analyzing the Impact of Coding SNPs in the Human Genome

Presenting Author: Tal Oron, Buck Institute
2:25 pm 2:35 pm Oral Presentation 2
Biologically Plausible Enhancements to Models of Protein Interaction Network Evolution

Presenting Author: Scott Kirkpatrick, California State University, Chico
2:35 pm 2:45 pm Oral Presentation 3
In-silico Identification of an Epithelial Core Signature in Human Tumors

Presenting Author: Chirayu Goswami, IU School of Medicine, Indiana University Purdue University Indianapolis
2:45 pm 2:55 pm Oral Presentation 4
Analytical Characterization of a Discrete Next Generation Sequencing Panel for Clinical Testing

Presenting Author: Eric Klee, Mayo Clinic
2:55 pm 3:05 pm Oral Presentation 5
Integration of Multiple Genomic Assays in Predicting Breast Cancer Survival

Presenting Author: Howard Yang, National Cancer Institute
3:05 pm 3:15 pm Oral Presentation 6
Determinants of Instability in Cancer Genomes

Presenting Author: Subhajyoti De, University of Colorado
3:15 pm 3:35 pm Break
3:35 pm 3:45 pm Oral Presentation 7
Compression of Structured High-throughput Sequencing Data

Presenting Author: Fabien Campagne, Weill Medical College of Cornell University
3:45 pm 3:55 pm Oral Presentation 8
Scaffold-builder for Combining De Novo and Reference-guided Assembly

Presenting Author: Genivaldo Silva, San Diego State University
3:55 pm 4:05 pm Oral Presentation 9
Expression Genome-wide Association Study (eGWAS) to Identify Therapeutic Targets and Functional Relationships in Huntington's Disease

Presenting Author:
Alexander Alleavitch, The Buck Institute for Research on Aging
4:05 pm 4:15 pm Oral Presentation 10
Compiling Genome Metadata For Comparative Analysis

Presenting Author: Daniel Cuevas, San Diego State University
4:15 pm 4:25 pm Oral Presentation 11
Hypergraph Kernels for Protein Function Prediction using Protein Complexes

Presenting Author: Jose Lugo-Martinez, Indiana University
4:25 pm 4:35 pm Oral Presentation 12
PharmacoMicrobiomics: A Database for Drug-Microbiome Interactions or Pharmacogenomics of the Human Supraorganism

Presenting Author:
Mariam Rizkallah, American University in Cairo
4:35 pm 5:20 pm Keynote 2
Wisdom of Crowds for Constructing Gene Regulatory Networks and Predicting Drug Sensitivities

James Costello, PhD
Howard Hughes Medical Institute
Boston University
Massachusetts - USA
6:30 pm 9:30 pm Banquet, Thursday, December 6, 2012
Location: Il Poggio Restaurant, Snowmass Village

FRIDAY – December 7, 2012
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Start Time End Time Session Type
9:00 am 9:45 am Keynote 3
Deep Sequencing and Assembly of Targeted Amplicons in Microbial Communities

Christopher S. Miller, Ph.D.
Assistant Professor
Department of Integrative Biology
University of Colorado
Denver, USA
9:45 am 9:55 am Oral Presentation 13
Analyzing "Unlikely" Semantic Similarity Across Multiple Ontologies

Presenting Author: Darcy Davis, Buck Institute for Research on Aging
9:55 am 10:05 am Oral Presentation 14
lcmix: An R Package for Integration of Genome-scale Data

Presenting Author:
Daniel Dvorkin, University of Colorado
10:05 am 10:15 am Oral Presentation 15
Detection of Differential Polyadenylation as an Alternative Cancer

Presenting Author: Marker Jimin Shin, Soongsil University
10:15 am 10:25 am Oral Presentation 16
Mining Social Network Postings for Mentions of Potential Adverse Drug Reactions

Presenting Author: Graciela Gonzalez, Arizona State University
10:25 am 10:35 am Oral Presentation 17
Understanding Heart Remodelling in Congestive Heart Failure through Analysis of High-Dimensional miRNA, mRNA, and Clinical Data

Presenting Author: Michael Hinterberg, University of Colorado School of Medicine
10:35 am 10:50 am Break
10:50 am 11:00 am Oral Presentation 18
Gene Content Based Functional Trait Analysis through Comparative Microbial Whole Genome Sequences

Presenting Author: Erliang Zeng, University of Notre Dame
11:00 am 11:10 am Oral Presentation 19
Genetic Programming Based Feature Generation for Automated Functional Analysis and Annotation of DNA Sequences

Presenting Author: Amarda Shehu, George Mason University
11:10 am 11:20 am Oral Presentation 20
Of Random Forests and Networks: Insights into the Alzheimer Etiology

Presenting Author:
George Acquaah-Mensah, Massachusetts College of Pharmacy and Health Sciences
11:20 am 11:30 am Oral Presentation 21
Discovering Transcription Factor Regulatory Targets Using Gene Expression and Binding Data

Presenting Author:
Mark Maienschein-Cline, University of Chicago
11:30 am 11:40 am Oral Presentation 22
Dynamics of sRNA Expression in the Human Intestinal Microbiota

Presenting Author: Jin Park, California State University, Fresno
11:40 am 11:50 am Oral Presentation 23
Negation of Gene Ontology Concepts

Presenting Author: Richard Osborne, University of Colorado School of Medicine
11:50 am 12:00 pm Oral Presentation 24
A Correlation-based Gene Selection Method On Microarray Data Using Support Vector Machines

Presenting Author: Juana Canul-Reich, Universidad Juarez Autonoma de Tabasco
12:00 pm 4:00 pm Ski Break
4:00 pm 4:45 pm Keynote 4
From Tissue-specific Functional Networks to Understanding Human Disease

Olga Troyanskaya, PhD
Department of Computer Science and
Lewis-Sigler Institute for Integrative Genomics
Princeton University
New Jersey, USA
4:45 pm 4:55 pm Oral Presentation 25
KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research

Presenting Author: Kevin Keegan, Argonne National Laboratory
4:55 pm 5:05 pm Oral Presentation 26
Pharmacogenetic Annotation on Human Non-synonymous Variants By Machine Learning

Presenting Author: Chet Seligman, Buck Institute for Research in Aging
5:05 pm 5:15 pm Oral Presentation 27
A Dynamic Model of Protein Fold Evolution

Presenting Author: Guy Tal, University of Illinois at Urbana-Champaign
5:15 pm 5:25 pm Oral Presentation 28
Identifying Driver Mutations in Cancer with Protein Structures

Presenting Author: Andrew Bordner, Mayo Clinic
5:25 pm 5:35 pm Oral Presentation 29
Multi-Scale Visualizations of Biological Data

Presenting Author: Carsten Görg, University of Colorado
5:35 pm 8:30 pm Reception and Poster Session
Viceroy Room - Ballroom
SATURDAY – December 8, 2012
[return to top]

Start Time End Time Session Type
9:00 am 9:45 am Keynote 5
The Human Gene Connectome: A Map of Short Cuts for Morbid Allele Discovery

Yuval Itan, PhD
The Rockefeller University
New York - USA
9:45 am 9:55 am Oral Presentation 30
Automated Concept Annotation: How Are We Doing?

Presenting Author: Christopher Funk, University of Colorado
9:55 am 10:05 am Oral Presentation 31
How Aneuploidy and Polyploid Impact Adaptation

Presenting Author: Robin Dowell, University of Colorado
10:05 am 10:15 am Oral Presentation 32
PePr: A Peak-calling and Prioritization Pipeline to Test Group Differences in ChIP-Seq Data

Presenting Author: Yanxiao Zhang, University of Michigan
10:15 am 10:25 am Oral Presentation 33
Provenance of Unaligned Reads in ChIP-Seq Studies

Presenting Author: Zachary Ouma, Ohio State University
10:25 am 10:35 am Oral Presentation 34
Constructing Informative Prior from Multiple Knowledge Sources to Improve Network Inference

Presenting Author: Paurush Praveen, University of Bonn
10:35 am 10:50 am Break 15
10:50 am 11:20 am Keynote 6
How to Interpret One Thousand Proteins From (lmost) One Thousand Samples, and What This Can Tell Us About Heart Disease Biology And Individual Risk.

Alex Stewart
Boulder, CO, USA
11:20 am 11:10 am Oral Presentation 35
Molecular Prediction by Regression (MPR) a New Platform for Predicting Molecular Targets and Multiple Drug Classes for Tumor Subtypes

Presenting Author: David Astling, University of Colorado School of Medicine
11:30 am 11:40 am Oral Presentation 36
Systems Biology Study of Automated Gene Functional Annotations Reveals Highly Predictable Concepts in Various Biomedical Ontologies

Presenting Author: Tobias Wittkop, Buck Institute for Research on Aging
11:40 am 11:50 am Oral Presentation 37
Characterizing the SOS Response of the Human Microbiome

Presenting Author: Ivan Erill, University of Maryland Baltimore County
11:50 am 12:00 pm Oral Presentation 38
Using Index-based Alignments to Determine Clade Specificity in Metagenomic Samples

Presenting Author: Ashok Sivakumar, Johns Hopkins University
12:00 pm 12:10 pm Oral Presentation 39
Phylogeography of Avian and Human Influenza in the Southwest United States

Presenting Author: Matthew Scotch, Arizona State University
12:10 pm 12:20 pm Oral Presentation 40
Analysis of Genome Wide DNA Methylation Changes in Human Skeletal Muscle Associated with Aging

Presenting Author: Artem Zykovich, Buck Institute for Research on Aging
12:20 pm 4:00 pm Break
4:00 pm 4:10 pm Oral Presentation 41
Identifying Molecular Mechanisms Underlying Variable Penetrance

Presenting Author: Kymberleigh Pagel, Indiana University Bloomington
4:10 pm 4:20 pm Oral Presentation 42
Comparative Genomics and Species-Specific Gene Testing in Emerging Nontuberculous Mycobacterial Pathogens

Presenting Author: Rebecca Davidson, National Jewish Health
4:20 pm 4:30 pm Oral Presentation 43
Rediscovery of the p53 Transcriptome

Presenting Author: Mary Allen, University of Colorado
4:30 pm 4:40 pm Oral Presentation 44
A Comparison of Co-temporal Signals from Real Biological and Simulated Data

Presenting Author: Edward Allen, Wake Forest University
4:40 pm 4:50 pm Oral Presentation 45
What is in Control of Replication Timing

Presenting Author: Sven Bilke, National Cancer Institute
4:50 pm 5:00 pm Oral Presentation 46
Discourse Classification Using the CRAFT Corpus

Presenting Author: Elizabeth White, University of Colorado
5:00 pm 5:45 pm Keynote 7
The Ins and Outs of Developing Biological Applications on a Massively Parallel Multi-Core System

Kirk E. Jordan, PhD
Emerging Solutions Executive & Associate Program Director
Computational Science Center
IBM T.J. Watson Research
Member, IBM Academy of Technology
Massachusetts - USA
5:45 pm   ADJOURN

Go directly to: [Thursday - December 6 ] [Friday - December 7 ]