9:00 am - 12:00 pm

Ohio Union
Room 1050

Evolutionary Genomics & Infectious Diseases

Session Chair: Daniel Janies - The Ohio State University

Keynote Speaker: Ward Wheeler - American Museum of Natural History
Title: Complexity-based viral phylogenetics

Coffee Break: 10:00 am

Presenters: Shahid Bokhari, Laura Pomeroy and Daniel Janies -
The Ohio State University
Title: Massively Multithreaded Analysis of Influenza Evolution using Reassortment Networks

Presenters: Sinu Paul and Helen Piontkivska - Kent State University
Title: Frequently Associated CTL and T-Helper Epitopes as Multi-epitope HIV- 1 Vaccine Candidates

Presenters: Samuel K. Handelman, Surender Kumar, Daniel Janies, and Jesse J. Kwiek -The Ohio State University & Victor Mwapasa - University of Malawi
Title: Mutations In The Hiv Env Protein May Promote In-uterine Mother-to-Child Transmission

Presenters: Annie Lindgren, Sabrina Pankey and Todd Oakley - University of California Santa Barbara
Title: The Cephalopod Cornea: Testing for Convergence using a Super-matrix Approach and Next-generation Sequencing

Presenters: Clifford Beall, Eugene Leys and Ann Griffen - The Ohio State University
Title: Examination of the Oral Microbiome by Illumina Deep Sequencing

Presenters: Luis M. Rodriguez-R, Alejandro Grajales, Mario Luis Arrieta, Camilo Salazar, Boris Szurek, Valerie Verdier,
Ralf Koebnik, Silvia Restrepo and Adriana Bernal - University of the Andes, Colombia; AMNH; Montpellier, France
Title: Bacterial Phylogenomics Revisited: A Case Study for the Xanthomonas Genus  

12:00 pm -
1:30 pm

Ohio Union
Room 1050

Lunch (Box Lunch) and
Choose Ohio First Workshop
Session Chair: Sarah Wyatt, Ohio University

1:30 pm -
4:00 pm

Ohio Union
Room 1050

Personalized Medicine

Session Chair: Daniel Janies - The Ohio State University

Keynote Speaker: Wolfgang Sadee, The Ohio State University
Title: Genomics in Personalized Medicine: Views of Fitness, Wellness and Disease – a Path Towards Biomarkers
in Therapy and Prevention

Presenters:John D. Blischak, Edward O. List, Darlene E. Berryman, Kaiyu Shen, Jacob Wright-Piekarski and John J. Kopchick - Ohio University
Title: The Use of Agilent 4 x 44K Whole-Mouse Genome MicroArrays for Analysis of Nonalcoholic Fatty Liver Disease

Presenters:Michael A. Freitas, John P. Shapiro and Brad H. Rovin, The Ohio State University
Title: Improved Informatics for Proteomic Based Disease Stratification/Classifications: Application of Mass
Spectrometry Based Proteomics in Personalized Medicine

Presenters: Yu Liu and Mark Chance - Case Western Reserve University
Title: Novel Method to Identify Dysregulated Pathways in Complex Diseases

Presenters: Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance and Mehmet Koyuturk - Case Western Reserve University
Title: Subnetwork State Functions Define Dysregulated Subnetworks in Cancer

Presenters: Daniel A. Janies, Igor O. Voronkin, Jonathon Studer, Jori Hardman, Boyan B. Alexandrov, Travis W. Treseder, and Chandni Valson - The Ohio State University
Title: Evolution of Drug Resistance in Influenza – Implications for Personalized Medicine and Disease Surveillance

Presenters: Xiaowei Guan, Salim Akhter Chowdhury, Mark Chance, Mehmet Koyutürk and Jill Barnholtz-Sloan - Case Western Reserve University
Title: Dominant Genes that Distinguish Between Glioma Subtypes Using Subnetwork Analysis

4:00 pm -
5:30 pm

Ohio Union
Room 1101

Plant Gene Regulatory Genomics

Session Chairs: Lonnie Welch, Ohio University &
Erich Grotewold, The Ohio State University

Presenter: Quinn Li, Miami University
Title: Messenger RNA Alternative Polyadenylation and Gene Expression Regulation in Plants

Presenter: Eric Stockinger, Ohio Agricultural Research and Development Center
Title: Structural and Regulatory Features of Barley CBF Genes at the Frost Resistance-2 Locus in Relation to Freezing Tolerance and VRN-1 Allelic States

Presenters: Praveen K. Raj Kumar and Chun Liang, Miami University
Title: In-silico Exploration of Alternatively Spliced Introns in Chlamydomonas Reinhardtii

Presenter: Matt Geisler, Southern Illinois University
Title: Identification and Annotation of the Biological Roles for the 8-Base Word Lexicon in the Rice Genome Using Meta-Analysis of Rice Transcriptomes

Presenter: David Bisaro, The Ohio State University
Title: Viral Genome Methylation as an Epigenetic Defense Against DNA Viruses in Plants

4:00 pm -
5:30 pm

Ohio Union
Room 1105

Workshop 1: Bioinformatics infrastructure

Introduction: Jim Giuliani, Ohio Supercomputer Center
Title: Bioinformatics Infrastructure, HPC Systems, Desktop Software, Web Portal and Installed Software

Presenter: Terry Camerlengo, The Ohio State University
Title: QUEST: A Software Platform for General Data Management and Biological Analysis

Presenter: Hyundeok Song, University of Cincinnati
Title: Temperature Dependence of Gramicidin Channel Conductance

Presenter: Feng Jie, University of Akron
Title: Molecular Mechanisms of Selective Peptide-Metal Interactions and Effects on Particle Growth

Presenters: Scott Cain, Dave Clements and Lincoln Stein, Ontario Institute for Cancer Research, National Evolutionary Synthesis Center
Title: GBrowse and Next-generation Sequencing Data

Presenter: Eric Stahlberg, Wittenberg University
Title: Use of Parallel Computing Algorithms to Accelerate MD Applications

Presenters: David E. Vincent and Iddo Friedberg, Miami University
Title: Resources for Annotating Metagenomic Data

5:30 pm -
7:00 pm

Ohio Union
Room 3145

Poster Session & Cash Bar / Dinner on your own

9:00 am - 12:00 pm

Ohio Union
Room 1050

Biological Networks

Session Chair: Jeff Parvin, The Ohio State University

Keynote speaker: Fritz Roth, Harvard Medical School
Title: Systematic Analysis of Genetic Interactions

Coffee Break: 9:50 am- 10:10 am

Presenter: Victor Jin, Ohio State University
Title: Combinatorial Analysis Predicts Dynamic Hierarchical Gene Regulatory Networks During Osteoclast Differentiation

Presenter: Daniel Youhon, The University of Akron
Title: Modeling the Gene Regulatory Network of Persister Cells

Presenter: Dan Siegal-Gaskins, The Ohio State University
Title: Identification of Novel Genetic Switch Topologies in a Large Class of Biochemical Networks

Presenter: Gurkan Bebek, Case Western Reserve University
Title: PETALS: Proteomic Evaluation and Topological Analysis of a Mutated Locus Signaling

Presenter: Rob Ewing, Case Western Reserve University
Title: Pathway-Centric Proteomics: An Integrated Computational Approach to Understanding the Wnt Signaling Network

Presenter: Mark Chance, Case Western Reserve University
Title: Integrative Proteomics Approaches to Identify Functional Sub-networks in Human Colorectal Cancer

1:30 pm -
4:00 pm

Ohio Union
Room 1050

Structural Bioinformatics

Session Chair: Thomas Magliery, The Ohio State University

Presenter: John Hawes, Miami University
Title: Protein Structural Modeling as a Tool for Functional Studies of Enzymes

Presenter: Aleksey Porollo, University of Cincinnati, and Cincinnati Children’s Hospital Medical Center
Title: Prediction of Interaction Sites in Membrane Proteins

Presenter: Helen Piontkivska, Kent State University
Title: Contrasting the Extent of Sequence Conservation of Conformational and Linear Epitopes In HIV-1 Genome

Break: 2:30 pm -2:40 pm

Presenter: Thomas J. Magliery, The Ohio State University,
Title: Statistical Protein Design

Keynote speaker: Mark Gerstein, Yale University
Title: Analysis of Molecular Networks

4:00 pm -
5:30 pm

Ohio Union
Room 1050

Data Mining and Machine Learning

Session Chair: Razvan Bunescu, Ohio University
& Mike Raymer, Wright State University

Presenter: Shaojun Wang, Wright State University
Title: Semi-supervised Conditional Random Fields

Presenter: Daniel Evans, Ohio University
Title: A Genome-Wide Association Study Analysis Pipeline Using Biologically-guided SNP Selection and Machine Learning Techniques

Presenter: John Karro - Miami University
Title: PEACE: Parallel Environment for Assembly and Clustering of Gene Expression

4:00 pm -
5:30 pm

Ohio Union
Room 1101

CTSA Informatics

Session Chairs: Mark Chance, Case Western Reserve University & Philip Payne, The Ohio State University

Presenter: Mark Chance, Case Western Reserve University
Title: Systems Biology Informatics Pipelines for CTSA Translational Research

Presenter: Philip R.O. Payne, Ph.D., The Ohio State University
Title: Generating Translational Biomedical Knowledge: The OSU Center for Clinical and Translational Science

Presenters: Justin Permar, Philip Payne and Tara Borlawsky, The Ohio State University
Title: The TRIAD Project: Adopting and Adapting caGrid to Support Multidisciplinary Clinical and Translational Research

Presenter: GQ Zhang, Case Western Reserve University
Title: Physio-MIMI: Multi-Modality, Multi-Resource Environment for Physiological and Clinical Research

4:00 pm -
5:30 pm

Ohio Union
Room 1105

Workshop 2: Integrating Bioinformatics Skills into the Educational Curriculum

Session Chair: Steve Gordon, Ohio Supercomputer Center
This session will present examples of classroom exercises and projects that have been successfully used to promote student research skills in bioinformatics topics.

Presenters: Sarah Wyatt, Kaiyu Shen and Vijayanand Nadella, Ohio University
Title: Micro OUGF: A Microarray Data Analysis Pipeline for Teaching (and Research)

Presenters: Jennifer Duann and Ross Nehm - The Ohio State University
Title: Assessing the Educational Efficacy of Genomics Modules, Labs, and Curricula: Finding Out What Works

Presenters: Jean Zorko and Amy Jo Sanders, Stark State College
Title: Connecting the Dots in Computational Biology

Presenter:Helen Piontkivska, Kent State University
Title: Bioinformatics SNP module: Looking for Needles in Haystacks, or Exploring SNPs and Personalized Medicine

5:30 pm -
7:00 pm

Ohio Union
Room 3145

7:00 pm -
9:00 pm

OSU Faculty Club
181 South Oval Drive

9:00 am -
12:00 pm

Ohio Union
Room 1050

Sequencing

Session Chair: Jeff Parvin, The Ohio State University

Keynote Speaker: Tim Huang, The Ohio State University
Title: Applications of Massively Parallel Sequencing to Epigenomic Analysis in Cancer

Coffee Break: 9:50 am -10:10 am

Presenter: Gulcin Ozer, The Ohio State University
Title: Comparing Multiple Protein Binding Profiles in ChIP-seq Experiments

Presenter: Umit Catalyurek, The Ohio State University
Title: Benchmarking Short Sequence Alignment Tools

Presenter: Andrew McSweeny, University of Toledo
Title: Binary-abstraction Markov models and their application to sequence classification

Presenter: Alper Yilmaz, The Ohio State University
Title: Maize transcriptome analysis by RNA-Seq

Presenter: Xiaohui Wu, Miami University
Title: Alternative and Antisense Polyadenylation in Arabidopsis Revealed by Deep Sequencing

Presenter: Brian Kennedy, The Ohio State University
Title: Genome-wide Analysis of SMAD4 Binding Patterns from Tgf-signaling in Ovarian Cancer Cells