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
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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
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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
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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