Session 1a:
Invited Session
"Plant Biology I"

Session Chair
Allan M. Showalter Ohio University

Allan M. Showalter, Jason Yerardi, Tom Conley, Brian Keppler, and Lonnie R. Welch (Ohio University)

A Bioinformatics-Based Approach to the Identification, Classification, and Expression of Genes Encoding Plant Cell Wall Hydroxyproline-Rich Glycoproteins (HRGPs)

M. Lia Molas, Ashley L. Kuntz, Melanie J. Correll and John Z. Kiss (Miami University)

Gene Profiling Studies of Red Light-Induced Signal Transduction in Roots

Rebecca Lamb (Ohio State University)

Regulatory Networks during Arabidopsis Thaliana Development

Annkatrin Rose, Iris Meier (Ohio State University) and Eric A. Stahlberg (Ohio Supercomputer Center)

Genome-Wide Identification and Comparative Analysis of Coiled-Coil Proteins

Session 1b:
Invited Session
"Proteomics I"

Session Chair
John J. Kopchick Edison Biotech Ohio University

Edward List, D. Berryman, A. Palmer (Edison Biotechnology Institute) and John J. Kopchick (Edison Biotechnology Institute, Ohio University)

Proteomics Analysis of Skin From Mice With Type 2 Diabetes

Shigeru Okada, John J. Kopchick (Ohio University, Edison Biotechnology Institute) and Sudha Sankaran (Edison Biotechnology Institute)

Analysis of the Serum Proteome of Diet Induced Type 2 Diabetic Mice

Shigeru Okada, John J. Kopchick (Ohio University, Edison Biotechnology Institute), Sudha Sankaran, , Stephanie Keeton (Edison Biotechnology Institute), Pamela U Freda (Columbia University ), Jens. O L Jørgensen (Aarhus University Hospital ), Peter J Trainer (Christie Hospital)

Proteomic Analysis of Serum from Patients with Acromegaly

James Conway, Heather Hargett, Suma Kaveti, Belinda Willard and Dongmei Zhang (Cleveland Clinic)

Proteomic Analysis of Atherosclerosis: What are the challenges for analyzing the data and where are the opportunities for bioinformatics to help us understand our results?

Session 1c:
Regular Session
"Classification I"

Session Chair Michael Wagner Cincinnati Children's Hospital Research Foundation

Erik M. Boczko ( Vanderbilt University Medical Center), Andrew DiLullo and Todd R. Young (Ohio University)

Binary Classification Based on Potential Functions

Douglas W. Raiford (Wright State University)

An Investigation of Codon Usage Bias Including Visualization and Quantification in Organisms Exhibiting Multiple Biases

Hongyuan Li (Ohio State University)

Analyzing Multi-Dimensional Fuzzy Scientific Data Through Flexible Discretization, Association, and Density-Based Clustering

Pando Georgiev, Anca Ralescu and Dan Ralescu (University of Cincinnati)

Fuzzy Subspace Skeletons and Applications to Blind Signal Separation

Session 1d:
Regular Session
"Phylogeny I"

Session Chair Frank Drews Ohio University

Bhakti Dwivedi and Sudhindra R. Gadagkar (University of Dayton)

How many alignment gaps are too many for accurate phylogenetic inference? A simulation study

Daniel Janies (Ohio State University), Pablo Goloboff and Diego Pol (Consejo Nacional de Investigaciones Científicas y Técnicas)

Applications of Large-Scale Phylogenetic Analysis for Research in Emerging Infectious Disease

Dean L. Zeller (Kent State University)

Education of Computational Biology

Farhat Habib, Andrew Johnson, Ralf Bundschuh, and Daniel Janies (Ohio State University)

Genotype-Phenotype Correlations Using Phylogenetic Trees for Large Datasets

Session 2a:
Invited Session
"Plant Biology II"

Session Chair
Allan M. Showalter Ohio University

Q. Quinn Li, Yingjia Shen (Miami University), Jianti Li, Han Rong and Guoli Ji (Xiamen University)

Modeling of mRNA poly(A) Sites in Arabidopsis

Chun Liang, Gang Wang and Lin Liu (Miami University )

ConiferEST: an integrated bioinformatics system of data processing, integration and mining for Expressed Sequence Tags (ESTs) in conifers

Ramana Davuluri (Ohio State University)

Bioinformatics Approaches to Model cis-Regulatory Modules and Putative Transcription Factor Partners

Guo-liang Wang (Ohio State University)

Deep Transcriptome Analysis of the Rice and Rice Genome Using LongSAGE and MPSS Technologies

Session 2b:
Invited Session
"Proteomics II"

Session Chair
John J. Kopchick Edison Biotech Ohio University

Peter de B. Harrington (Ohio University)

Chemometric Opportunities in Proteomic Biomarker Discovery via Mass Spectrometry.

Session 2c:
Regular Session
"Classification II"

Session Chair Gwenn Volkert Kent State University

Ruoming Jin, Helen Piontkivska and Dong Wang (Kent State University)

Mining Protein Space: Discovering Frequent Topological Structures

Reshmi Sobhanakumari and Helen Piontkivska (Kent State University)

Comparative Evolutionary Analysis of Virulence-Associated and Housekeeping Genes Among Species of Genus Clostridium

Amit Sinha and Raj Bhatnagar (University of Cincinnati)

Design for Efficient Motif Finding Algorithm

Jesse Stombaugh (Bowling Green State University)

Automated Geometric Search for Structural Motifs in RNA 3D Structures

Session 2d:
Regular Session
"Protein Disorder"

Session Chair Anthony Johnson University of Toledo

Deborah A. Stoffer (Kent State University)

Predicting Protein Disorder using a Neural Network and Amino Acid Hydropathy Values

Karthikeyan Swaminathan (Children's Hospital Research Foundation) and Jarosław Meller (Children's Hospital Research Foundation, Nicolaus Copernicus University)

Prediction of Disordered regions in Proteins Using Amino-Acid Properties, Secondary Structure and Relative Solvent Accessibility

L. Gwenn Volkert (Kent State University)

Prediction Protein Disorder for Use in Peptide Analysis

Mukta Phatak (University of Cincinnati)

Predicting Residue Contact Numbers in Proteins Using Support Vector Regression.

Session 2e:
Invited Session
"Protein Structure and Analysis I"

Session Chair
Gerald M. Alter Wright Sate University

G.M. Alter, M. Raymer (Wright State University)

High Confidence Structure Prediction Using M-ran

Aleksey Porollo (Children's Hospital Research Foundation, Cincinnati)

Prediction-based Fingerprints of Protein Interactions

Session 3a:
Invited Session
"Algorithmics for Bioinformatics"

Session Chairs
David Juedes and Liming Cai

Ralf Bundschuh (Ohio State University)

Computational Approaches to the Prediction of Insertional RNA Editing Sites

Jing Li (Case Western Reserve University )

An Efficient Algorithm for the Zero-Recombinant Haplotype Configuration Problem

Yinglei Song, Chunmei Liu, Russel Malmberg, Fangfang Pan and Liming Cai (University of Georgia)

Tree Decomposition-Based Fast Search of RNA Structures Including Pseudoknots in Genomes.

Erik Boczko, Di Wu , Minhui Xie (Vanderbilt University Medical Center) and Todd R. Young (Ohio University)

Comparison of Signed Distance Function Methods with Support Vector Machines on Binary Classifcation

H. Bian and R. Bhatnagar (University of Cincinnati)

An Efficient and Flexible Bi-clustering Algorithm

Session 3b:
Invited Session
"Protein Structure and Analysis I"

Session Chair
Gerald M. Alter

Jarek Meller (Children's Research Foundation, Cincinnati)

Prediction of Solvent Accessibility in Soluble and Membrane Proteins

Michael Raymer (Wright State University)

Computation and Experimental Methods for High Confidence Protein Structure Prediction

Thomas J. Magliery (The Ohio State University)

Combinatorial Biophysics: Library and Statistical Protein Design

Patrick Wintrode (Case Western Reserve University)

The Dynamical Properties of a Metastable Protein Studies by Molecular Dynamics Simulations and Normal Mode Analysis

Sam Holton, Tyler Miller, and Xiu-Feng Wan (Miami University)

Intrinsic Terminators across Prokaryotes Genomes

Session 3c:
Regular Session
"Modeling I"

Session Chair Jungdon Liu Ohio University

Vaishali Vallurupalli and Carla Purdy (University of Cincinnati)

Agent Based Modeling of Biomolecular Reactions

Xuan Zhang, Kaushik Sinha, Gagan Agrawal (Ohio State University) and Ruoming Jin (Kent State University)

Automating Biological Data Integration With a Three-Step Approach

J. Fonseca, R. F. Rakowski, and S. Kaya (Ohio University)

Models, Electrostatics and Molecular Dynamics of the Na+/K+-ATPase

Ranga Chandra Gudivada (University of Cincinnati, Cincinnati Children's Hospital Medial Center)

Semantic Data Integration and Knowledge Representation Using Biomedical Ontologies

Debbi Ryle (Accelerated Data Concepts)

Applying Field Programmable Gate Arrays to Biological Problems

Session 3d:
Regular Session
"Proteomics"

Session Chair Henry Wan Miami University

J. Ding, S. Sankaran, S. Okada and J. J. Kopchick (Edison Biotechnology Institute, Ohio University)

Small Molecular Weight Serum Protein Profiles in Growth Hormone Transgenic Mice And Growth Hormone Receptor/Binding Protein Knock-Out Mice

Rachana Jain (University of Cincinnati) and Michael Wagner (Cincinnati Children's Hospital Research Foundation)

Peptide Mass Fingerprinting using Machine Learning

Rephael Wenger (Ohio State University)

Conime: Automated Analysis and Generation of RLGS Electrophoresis gels

S. Foisy, J. DeGreef (GenoLogics)

An Open, Application Driven LIMS For Proteomic Facilities

Wayne Li (University of Toledo) and John M. Frazier (Air Force Research Laboratory)

Eventual Reaction Time in General Bio-Molecular Networks