11th Annual Rocky Mountain Bioinformatics Conference

DETAILED AGENDA

Updated December 09, 2013. Schedule and locations are subject to change. Please check back for updates.

Go directly to: [Friday - December 13] [Saturday - December 14]

WEDNESDAY – December 11, 2013
START TIME END TIME SESSION TYPE
04:00 pm 06:00 pm Registration

THURSDAY – December 12, 2013
LOCATION: Ballroom
START TIME END TIME SESSION TYPE
08:00 am 09:00 am Registration
09:00 am 09:45 am Keynote 1
Gary Bader, PhD
Associate Professor
University of Toronto, Canada

Pathway Analysis of Genomics Data – from Correlation to Causation
09:45 am 09:55 am Oral Presentation 1
AssemblSprint: Examining Genome Assemblies of Ion PGM next generation sequencing data from Mycobacterium species

Presenting Author: Nabeeh Hasan, University of Colorado, Denver

Co-Author(s):

Rebecca Davidson, National Jewish Health
Paul Reynolds, National Jewish Health
Eveline Farias-Hesson, Life Technologies
Michael Strong, National Jewish Health
09:55 am 10:05 am Oral Presentation 2
Host-pathogen interactions and microRNAs

Presenting Author: Christian Forst, Icahn School of Medicine at Mount Sinai
10:05 am 10:15 am Oral Presentation 3
Recalibration of p-values for Multiple Testing Problems in Genomics

Presenting Author: Dean Palejev, Bulgarian Academy of Sciences

Co-Author(s):
John Ferguson, University of Limerick
10:15 am 10:25 am Oral Presentation 4
Predicting disease related and pharmacogenes through curated and text-mined annotations

Presenting Author: Christopher Funk, University of Colorado

Co-Author(s):
Lawrence Hunter, University of Colorado
Kevin Cohen, University of Colorado
10:25 am 10:45 am Break
10:45 am 11:15 am Keynote 2
Benjamin Good, Ph.D.
Senior Staff Scientist
The Scripps Research Institute
La Jolla, CA, USA


The Cure: A Game with the Purpose of Gene Selection for Breast Cancer Survival Prediction
11:15 am 11:25 am Oral Presentation 5
PAIRpred: A large margin method for partner-specific prediction of protein interfaces

Presenting Author: Fayyaz Minhas, Colorado State University
11:25 am 11:35 am Abstract Withdrawn

Oral Presentation 6
MP2GO: Inferring Gene Function from Phenotype

Presenting Author: Judith Blake, The Jackson Laboratory

Co-Author(s):
Joao Ascensao, Rice University
Mary Dolan, The Jackson Laboratory
David Hill, The Jackson Laboratory
11:35 am 11:45 am Oral Presentation 7
Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature

Presenting Author: Negacy Hailu, University of Colorado Computational Bioscience Program

Co-Author(s):
Kevin Cohen, University of Colorado School of Medicine
11:45 am 11:55 am Oral Presentation 8
Analyzing biological networks using degree-of-interest functions

Presenting Author: Corinna Vehlow, Visualization Research Center, University of Stuttgart

Co-Author(s):
Carsten Goerg, University of Colorado Anschutz Medical Campus
David Kao, University of Colorado Anschutz Medical Campus
11:55 am 04:00 pm Ski Break
04:00 pm 04:30 pm Keynote 3
Peter Karp, Ph.D.
Director, Bioinformatics Research Group
Artificial Intelligence Center
SRI International
Menlo Park, CA, USA

A Flux Balance Analysis Model of E. coli K-12 MG1655 Derived From the EcoCyc Database
04:30 pm 04:40 pm Oral Presentation 9
The Critical Assessment of Function Annotation experiment: a community-wide effort towards a better functional annotation of genes and genomes

Presenting Author: Sean Mooney, Buck Institute for Research on Aging

Co-Author(s):
Predrag Radivojac, Indiana University
Iddo Friedberg, Miami University
04:40 pm 04:50 pm Oral Presentation 10
Conceptual comparison through integrative functional genomics in GeneWeaver.org

Presenting Author: Elissa Chesler, The Jackson Laboratory

Co-Author(s):
Erich J. Baker, Baylor University
Chales Phillips, University of Tennessee
Michael Langston, Unviersity of Tennessee
04:50 pm 05:00 pm Oral Presentation 11
Integrative Visualization for Discovery of Phenotype Associations in Clinical and miRNA Data

Presenting Author: Michael Hinterberg, University of Colorado-Denver

Co-Author(s):
Lawrence Hunter, University of Colorado
David Kao, University of Colorado
05:00 pm 05:10 pm Oral Presentation 12
Evolution of palmitoyl acyl transferases (PATs) in apicomplexa

Presenting Author: Swapna Seshadri, Research Institute, Hospital for Sick Children

Co-Author(s):
John Parkinson, Research Institute, Hospital for Sick Children
Tim Gilberger, McMaster University
05:10 pm 05:30 pm Break
05:30 pm 06:00 pm Keynote 4
Chijioke O. Elekwachi, Ph.D.
University of Nottingham, UK

eMBRLitMine and eMBRHelper: Bioinformatics Approaches for Improved Microbial Bioremediation Outcomes
06:00 pm 06:10 pm Oral Presentation 13
From Sample to Answer - Sequencing in the Cloud Era with the Illumina BaseSpace® Bioinformatics Platform

Presenting Author: Raymond Tecotzky, Illumina
06:10 pm 06:20 pm Oral Presentation 14
MSProcess – Summarization, Normalization, and Diagnostics for Processing of Mass Spectrometry Based Metabolomic Data

Presenting Author: Katerina Kechris, University of Colorado Denver

Co-Author(s):
Grant Hughes, University of Colorado Denver
06:20 pm 06:30 pm Oral Presentation 15
Metabolic Reconstruction Identifies Strain-Specific Regulation of Virulence in Toxoplasma gondii

Presenting Author: Nirvana Nursimulu, University of Toronto
07:00 pm 10:00 pm Banquet, Thursday, December 12, 2013
Location: Il Poggio Restaurant
Snowmass Village
(Transportation provided from Viceroy Hotel Lobby beginning at 6:45pm)

FRIDAY – December 13, 2013
LOCATION: Ballroom
START TIME END TIME SESSION TYPE
08:00 am 05:30 pm Registration
09:00 am 09:45 am Keynote 5
Melissa Haendel, PhD
Assistant Professor
Oregon Health & Science University
Oregon, USA

Tales from the Crypt: Do You Know Where Your Data Has Been?
09:45 am 09:55 am Oral Presentation 16
Introducing Computations in Biology/Bioinformatics – An Undergraduate Perspective

Presenting Author: Maheen Kibriya,
Chapman University

Co-Author(s):
Shehzein Khan, Chapman University
Louis Ehwerhemuepha, Chapman University
09:55 am 10:05 am Oral Presentation 17
A Corpus-Based Study of Temporal Relations in Clinical Text

Presenting Author: Natalya Panteleyeva, University of Colorado

Co-Author(s):
Lawrence Hunter, University of Colorado
Kevin Cohen, University of Colorado
10:05 am 10:15 am Oral Presentation 18
Building an optimally informative machine-learning model of gene regulatory control

Presenting Author: Molly Megraw, Oregon State University
10:15 am 10:25 am Oral Presentation 19
Characterizing Unknown Viral Genes Through Metabolomics

Presenting Author: Tiffany Liang, San Diego State University
10:25 am 10:45 am Break
10:45 am 10:55 am Oral Presentation 20
GeneSeer Aids Drug Discovery by Exploring Evolutionary Relationships Between Genes Across Genomes

Presenting Author: Douglas Fenger, Dart NeuroScience

Co-Author(s):
Matthew Shaw, Dart NeuroScience
Philip Cheung, Dart NeuroScience
Tim Tully, Dart NeuroScience
10:55 am 11:05 am Oral Presentation 21
The Human Gene Connectome Server: an Online Tool for Prioritizing Genes by Biological Distance

Presenting Author: Yuval Itan, The Rockefeller University

Co-Author(s):
Mark Mazel,
The Rockefeller University
Benjamin Mazel,
The Rockefeller University
Avinash Abhyankar,
New York Genome Center
Bertrand Boisson,
The Rockefeller University
Patrick Nitschke, INSERM
Lluis Quintana-Murci,
Pasteur Institute
Laurent Abel, INSERM
Shen-Ying Zhang,
The Rockefeller University
Jean-Laurent Casanova,
The Rockefeller University
11:05 am 11:15 am Abstract Withdrawn

Oral Presentation 22
Type I Error Rate Analysis of Methods for Correlated Binary Outcomes

Presenting Author: Aarti Munjal, University of Colorado Denver

Co-Author(s):
Jacqueline Johnson, University of North Carolina at Chapel Hill
Sarah Kreidler, University of Colorado Denver
Deborah Glueck, University of Colorado Denver
Keith Muller, University of Florida
11:15 am 11:25 am Oral Presentation 23
An Optimal Metabolic Route Search Tool: RouteSearch

Presenting Author: Mario Latendresse, SRI International
11:25 am 11:35 am Oral Presentation 24
Computational and Mathematical Modeling of the segmentation genes of Honeybee (Apis Mellifera)

Presenting Author: Maryam Bagher Oskouei, University of Otago

Co-Author(s):
Brendan McCane, University of Otago
Peter Dearden, University of Otago
11:35 am 12:05 pm Keynote 6
Greg Carter, Ph.D.
The Jackson Laboratory
Bar Harbor, ME USA

Modeling Genetic Complexity with Integrated Interaction Analysis across Multiple Phenotypes
12:05 pm 04:00 pm Ski Break
04:00 pm 04:30 pm Keynote 7
Catherine Lozupone, Ph.D.
Anschutz Medical Campus
Aurora, CO USA

Application of Network Analysis to the Human Gut Microbiota and Use of Comparative Genomics to Understand the Driving Factors of Microbial Associations

04:30 pm 04:40 pm Oral Presentation 25
Improved RNAi interference target sequencing (RIT-seq) enables dissection of cellular function in Trypanosome brucei

Presenting Author: Jonathan Wilkes, University of Glasgow

Co-Author(s):
Graham Hamilton, University of Glasgow
Richard McCulloch, University of Glasgow
04:40 pm 04:50 pm Oral Presentation 26
What you did not know your transcription factor was doing


Presenting Author: Mary Allen, University of Colorado

Co-Author(s):
Justin Freeman, University of Colorado
Hestia Mellert, University of Colorado
Joaquin Espinosa, University of Colorado
Robin Dowell, University of Colorado
04:50 pm 05:00 pm Oral Presentation 27
Linking genotype and enterotype in inflammatory bowel disease

Presenting Author: Dan Knights, University of Minnesota

Co-Author(s):
Mark Silverberg, University of Toronto
Rinse Weersma,
University Medical Center Groningen
Dirk Gevers,
Broad Institute of Harvard and MIT
Gerard Dijkstra,
University Medical Center Groningen
Hailiang Huang, Massachusetts General Hospital
Andrea Tyler, Mount Sinai Hospital
Suzanne von Sommeren,
University Medical Center Groningen
Floris Imhann,
University Medical Center Groningen
Joanne Stempak, Mount Sinai Hospital
Caitlin Russell, Massachusetts General Hospital
Jenny Sauk, Massachusetts General Hospital
Jo Knight, University of Toronto
Mark Daly, Massachusetts General Hospital
Curtis Huttenhower,
Harvard School of Public Health
Ramnik Xavier, Massachusetts General Hospital
05:00 pm 05:10 pm Oral Presentation 28
Probing chromatin with digestion assays: from static nucleosome positioning to dynamic response

Presenting Author: Michael Tolstorukov, Massachusetts General Hospital
05:10 pm 05:20 pm Oral Presentation 29
GIST – an ensemble approach to the taxonomic classification of metatranscriptomic reads

Presenting Author: John Parkinson, Hospital for Sick Children

Co-Author(s):
Geoffrey Halliday, University of Toronto
05:20 pm 05:30 pm Oral Presentation 30
Comparative metagenomics by cross-assembly

Presenting Author: Bas Dutilh, Radboud University Medical Centre

Co-Author(s):
Rob Edwards, San Diego State University
05:30 pm 07:30 pm Poster Session

SATURDAY – December 14, 2013
LOCATION: Ballroom
START TIME END TIME SESSION TYPE
08:00 am 11:30 am Registration
09:00 am 09:30 am Keynote 8
Kirk E. Jordan, PhD
IBM Distinguished Engineer
Emerging Solutions Executive & Assoc. Program Director
Computational Science Center
IBM T.J. Watson Research
Cambridge, MA, USA

Solving Life Sciences Problems Requires Systems that Optimize the Workflow
09:30 am 09:40 am Oral Presentation 31
An Update on KaBOB: towards an integrated knowledge base of biomedicine

Presenting Author: Kevin Livingston, University of Colorado


Co-Author(s):
Michael Bada, University of Colorado
William Baumgartner, University of Colorado
Lawrence Hunter, University of Colorado
09:40 am 09:50 am Oral Presentation 32
Hypernetworks: the Future of Network Modeling

Presenting Author: Debra Goldberg, University of Colorado Boulder
09:50 am 10:00 am Oral Presentation 33
The changing view of protein interaction networks based on data availability

Presenting Author: Barrett Hostetter-Lewis, California State University, Chico

Co-Author(s):
Todd A Gibson, California State University, Chico
10:00 am 10:10 am Oral Presentation 34
Experimental Determination of Useful and Informative Visualizations of Microbial Ecology Data for Public and Scientific Audiences

Presenting Author: Megan Pirrung, University of Colorado
10:10 am 10:20 am Oral Presentation 35
Modeling Transcriptional Regulation through simulation of the dynamic changes in DNA binding factor configuration


Presenting Author: David Knox, University of Colorado Anschutz Medical Campus

Co-Author(s):

Robin Dowell, University of Colorado Boulder
10:20 am 10:30 am Oral Presentation 36
Deletion of COX-2 is associated with reduced expression of rgl1: relevance to chemopreventative effect of COX-2 inhibitors


Presenting Author: Nicholas Kirkby, Imperial College London

Co-Author(s):

Jane Mitchell, Imperial College London
10:30 am 10:50 am Break
10:50 am 11:00 am Oral Presentation 37
Prioritizing hypotheses for epigenetic mechanisms in Huntington’s Disease using an e-Science approach

Presenting Author: Eleni Mina, Leiden University Medical Center
11:00 am 11:10 am Oral Presentation 38
Variance component score test in a mixed-effects model framework to map tissue-specific eQTL

Presenting Author: Chaitanya Acharya, Duke University

Co-Author(s):
Andrew Allen, Duke University
11:10 am 11:20 am Oral Presentation 39
High Throughput Phenotype Profiling for Bacterial Flux-Balance Model Optimization

Presenting Author: Daniel Cuevas, San Diego State University

Co-Author(s):
Rob Edwards, San Diego State University
Daniel Garza, Evandro Chagas Institute
Savannah Sanchez, San Diego State University
11:30 am   Closing

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