Click here for .pdf

Rocky 2014 Program Book

12th Annual Rocky Mountain Bioinformatics Conference


Updated Feb 09, 2015

ROCKY 2014 slidesPresentations with this icon indicate that the slides are available.  Click on icon to download. 

Go directly to: [Friday - December 12] [Saturday - December 13]

WEDNESDAY – December 10, 2014
04:00 pm 06:00 pm Registration

THURSDAY – December 11, 2014
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LOCATION: Ballroom
08:00 am 09:00 am Breakfast
08:00 am 06:00 pm Registration
09:00 am 09:45 am Keynote 1
The Broad Institute of MIT and Harvard

Integrative Computational Approaches for Genomic Medicine
09:45 am 09:55 am Oral Presentation 1
Automatic Discovery of Regulatory Networks from Morphological Experimental Data

Presenting Author:
Daniel Lobo
Tufts University, USA
09:55 am 10:05 am ROCKY 2014 slidesOral Presentation 2
Polysaccharide A: a widely distributed immunoregulatory microbial product

Presenting Author:
Matthew Rhodes
University of Colorado, Denver
10:05 am 10:15 am Oral Presentation 3
Meta-analysis leads to deeper understanding of cellular senescence

Presenting Author:
Chris Morrissey
Buck Institute
10:15 am 10:25 am Oral Presentation 4
Characterizing the landscape of biomedical ontologies via deductive entailment

Presenting Author:
William Baumgartner Jr
University of Colorado Denver
10:25 am 10:45 am Break
10:45 am 11:15 am ROCKY 2014 slidesKeynote 2
Biodesix, Inc.

Deep Learning, "Deep Data", and Molecular Diagnostics
11:15 am 11:25 am Oral Presentation 5
A Bayesian framework for Signature-driven Protein Quantification

Presenting Author:
Bobbie-Jo Webb-Robertson
Pacific Northwest National Laboratory
11:25 am 11:35 am ROCKY 2014 slidesOral Presentation 6
Integrating Data in a Microbiome Context

Presenting Author:
Michael Shaffer
University of Colorado - Denver
11:35 am 11:45 am Oral Presentation 7
Dietary Influences on the Incidence of Alzheimer Disease: Converging Inferences by Disparate Algorithms

Presenting Author:
George Acquaah-Mensah
MCPHS University
11:45 am 11:55 am Oral Presentation 8
Comparative genomics between frogs Xenopus laevis and Xenopus tropicalis

Presenting Author:
Gonzalo Riadi
Pontificia Universidad Católica de Chile
11:55 am 04:00 pm Ski Break
04:00 pm 04:30 pm Keynote 3
Max Planck Institute for Marine Microbiology
AND University of Colorado Denver

Tackling the rRNA Big-data Problem with ARB and SILVA
04:30 pm 04:40 pm Oral Presentation 9
Comparison of Phylogeographic Node Flux with Local Disease Trends

Presenting Author:
Daniel Magee
Arizona State University
04:40 pm 04:50 pm Oral Presentation 10
Co-expression Network Hubs in Hypoxia and Acclimatization to High Altitude

Presenting Author:
Daniel Dvorkin
University of Colorado
04:50 pm 05:00 pm Oral Presentation 11
Network-based analysis for large environment microbial genomics data

Presenting Author:
Erliang Zeng
University of South Dakota
05:00 pm 05:10 pm Oral Presentation 12
Predicting survival for diverse patient cohorts using large-scale cancer genomics data

Presenting Author:
Nicolle Witte
University of Colorado
- Anschutz Medical Campus
05:10 pm 05:30 pm Break
05:30 pm 06:00 pm Keynote 4
SomaLogic, Inc.

SOMAscan™– Based Prediction of Early Kidney Function Decline
06:00 pm 06:10 pm Oral Presentation 13
Global Survey of Protein Complexes from the Sulfate Reducer Desulfovibrio vulgaris: evidence for lower connectivity within stable bacterial interactomes

Presenting Author:
Maxim Shatsky
Lawrence Berkeley National Lab
06:10 pm 06:20 pm Oral Presentation 14
EMIRGE 2: Improved resolution of microbial community structure

Presenting Author:
Adrienne Narrowe
University of Colorado Denver
06:20 pm 06:30 pm ROCKY 2014 slidesOral Presentation 15
RNABindRPlus Predicts RNA-Protein Interface Residues in Multiple Protein Conformations

Presenting Author:
Carla Mann
Iowa State University
07:00 pm 10:00 pm Banquet, Thursday
December 11, 2014

Location: Il Poggio Restaurant
Snowmass Village
(Transportation provided from Viceroy Hotel Lobby beginning at 6:45pm)
FRIDAY – December 12, 2014
. . . . . . . . . . . . . . . . . . . . . . . . . . .
LOCATION: Ballroom
08:00 am 09:00 am Breakfast
08:00 am 05:30 pm Registration
09:00 am 09:45 am Keynote 5
Tufts University

Human Developmental Bioinformatics: A Case Study in Overcoming Data Limitations
09:45 am 09:55 am Oral Presentation 16
Integrative Genomics Approaches for Predicting Drug Synergies

Presenting Author:
Andrew Goodspeed
University of Colorado-Anschutz
Medical Campus
09:55 am 10:05 am Oral Presentation 17
Prediction and validation of genes regulating breast cancer metastasis

Presenting Author:
Eran Andrechek
Michigan State University
10:05 am 10:15 am Oral Presentation 18
The Inverse Relationship Between Sample Size and Differentially Expressed Genes in the selected Microarray Experiments

Presenting Author:
Akram Samarikhalaj
Ryerson University
10:15 am 10:25 am Oral Presentation 19
Calculating prior and posterior probabilities of concepts in conceptually annotated corpora

Presenting Author:
Negacy Hailu
University of Colorado
10:25 am 10:45 am Break
10:45 am 11:00 am ROCKY 2014 slidesTechnical Talk
Illumina, Inc.

Progress Report: From Sample to Answer - Sequencing in the Cloud Era with the Illumina BaseSpace®Bioinformatics Platform
11:00 am 11:10 am Oral Presentation 20
RNABindRPlus Parallelization: Faster Prediction of RNA-Binding Residues in Proteins

Presenting Author:
John Hsieh
Iowa State University
11:10 am 11:20 am Oral Presentation 21
A phylogenomic approach to assess global genetic diversity and intrapatient evolution of clinical Mycobacterium abscessus strains

Presenting Author:
Rebecca Davidson
National Jewish Health
11:20 am 11:30 am Oral Presentation 22
Discovering Disease Associated Molecular Interactions Using Discordant Correlation

Presenting Author:
Charlotte Siska
University of Colorado
Anschutz Medical Campus
11:30 am 11:40 am Oral Presentation 23
A pipeline for virus phylogeography that accounts for geospatial observation error

Presenting Author:
Matthew Scotch
Arizona State University
11:40 am 11:50 am Oral Presentation 24
Prediction of bacteriocin associated operons

Presenting Author:
James Morton
University of Colorado Boulder
11:50 am 04:00 pm -->Ski Break

Group Hike
(see Suzi at Registration Desk)
04:00 pm 05:00 pm Keynote 6
IBM T.J. Watson Research

Experience in Improving de novo Transcriptome Assembly to Address Large Data Sets


BM Technical & Platform Computing Worldwide

Tackling Big Data Challenges of Genomics by PowerGene
05:00 pm 05:10 pm Oral Presentation 25
A Novel Visualization Technique for the Discovery of Inter-strain Recombination in Apicomplexans

Presenting Author:
Javi Zhang
University of Toronto
05:10 pm 05:20 pm Oral Presentation 26
Computational Methods to Study Differential Transcription

Presenting Author:
Debra Goldberg, University of Colorado Boulder
05:20 pm 05:30 pm Oral Presentation 27
Modeling Binding Affinity of the Multiple Zinc-Finger Protein Prdm9

Presenting Author:
Greg Carter
The Jackson Laboratory
05:30 pm 05:40 pm Oral Presentation 28
Taking an omics approach to phenotype responses to cigarette smoke in humans in vivo and in vitro: comparison with healthy smokers and those with COPD

Presenting Author:
Mark Pau-Clark
Imperial College London
05:40 pm 05:50 pm ROCKY 2014 slidesOral Presentation 29
SASE-hunter – a method for detecting signatures of accelerated somatic evolution in cancer genomes

Presenting Author:
Kyle Smith
University of Colorado
05:50 pm 06:00 pm Oral Presentation 30
Phylogeny-wide Discovery of Bacterial Transcription Factor Binding Motifs by Protein Family-based Approach

Presenting Author:
Maxim Shatsky
Lawrence Berkeley National Lab
06:00 pm 08:00 pm Poster Session:
-->Information for presenters
-->Detailed Poster Abstracts
-->Brief Poster List
SATURDAY – December 13, 2014
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LOCATION: Ballroom
08:00 am 09:00 am Breakfast
08:00 am 11:30 am Registration
09:00 am 09:30 am Keynote 7
University of Colorado

Complex Querying Across Multiple Data Sources Using a Common Biological Model
09:30 am 09:40 am ROCKY 2014 slidesOral Presentation 31
A Model of the Colonic Crypt Microenvironment

Presenting Author:
Violeta Kovacheva
University of Warwick
09:40 am 09:50 am Oral Presentation 32
Dev Ops and Automation, key tools in the bioinformaticians tool box

Presenting Author:
Simon Twigger
09:50 am 10:00 am Oral Presentation 33
Characterizing bladder cancer cell lines as models of solid tumor biology

Presenting Author:
Somsak Phattarasukol
University of Colorado
Anschutz Medical Campus
10:00 am 10:10 am Oral Presentation 34
A computational and experimental method for combinatorial drug discovery

Presenting Author:
Muhammad Kashif
Uppsala University
10:10 am 10:20 am ROCKY 2014 slidesOral Presentation 35
Biomed Summarization Of Topics

Presenting Author:
Prabha Yadav
University of Colorado
School of Medicine, Denver
10:20 am 10:40 am Break
10:40 am 10:50 am Oral Presentation 36
Beyond the coding mutations in Pan-cancer genomes

Presenting Author
Subhajyoti De
University of Colorado
10:50 am 11:00 am ROCKY 2014 slidesOral Presentation 37
MEseq, a software package for bisulfite sequencing data analysis by regression hidden Markov model

Presenting Author:
Kui Shen
National Institute of Allergy and Infectious Diseases
11:00 am 11:10 am Oral Presentation 38
Coreference Annotations in the CRAFT Corpus – Statistics and Performance Analysis

Presenting Author:
Natalya Panteleyeva
University of Colorado
11:10 am 11:20 am Withdrawn

Oral Presentation 39
Virulence-Associated Role for the Universal Stress Protein in Helicobacter pylori Infections

Presenting Author:
Shaneka Simmons
Jackson State University
11:20 am 12:00 pm Keynote 8

The Jackson Laboratory

Glycolysis Pathways in the Gene Ontology: All Roads Lead to Pyruvate
12:00 pm   Closing