CONFERENCE SPONSORS


CONFERENCE HOST UNIVERSITY AND GOLD SPONSOR:

Purdue University
Vice President, Office of Research
Bioinformatics Core


 SILVER SPONSORS:


Indiana University
University Information Technology Services
Department of Biology
School of Informatics and Computing
----------


University of Michigan, Dept of Computational Medicine and Bioinformatics

BRONZE SPONSORS:


The Research Division
of Ohio University
----------


Department of Computer Science and Engineering
Eck Institute for Global Health
Complex Networks Lab
University of Notre Dame


EXHIBITOR SHOWCASE SPONSOR:

 

Cincinnati Childrens’s Hospital Medical Center
Division of Biomedical Informatics, University of Cincinnati


POSTER AWARDS SPONSOR:


Faculty of 1000


BEST PAPER AWARD SPONSOR:


Springer


INDUSTRY SPONSOR:



University of Michigan Bioinformatics Core
----------

PerkinElmer


GENERAL SPONSOR:


Purdue University

Agricultural Research

Great Lakes Bioinformatics Conference 2015

GLBIO DETAILED AGENDA

As of May 17, 2015. Schedule and locations are subject to change. Please check back for updates. A printed agenda will be available on site in the conference program book.

All rooms are in the Stewart Center on the Purdue campus unless otherwise noted.


Go directly to: [Monday] [Tuesday] [Wednesday]


DAY 1 - MONDAY – May 18, 2015
Start Time End
Time
SESSION TYPE
10:00am 11:30am FASEB Career Talk
Dr. Philip Clifford, Associate Dean for Research and Professor of Kinesiology and Nutrition, University of Illinois at Chicago

Location: Room 202
12:00pm 2:00pm TUTORIAL 1
NGS Sequencing

Rich McEachin

University of Michigan

Location: Room 202
TUTORIAL 2 CourseSource
Publishing Teaching Materials in CourseSource, a New Peer-reviewed, Open-access Journal for Undergraduate Biology Education


Robin Wright
University of Minnesota

Location: Room 214CD
WORKSHOP 1
Core Facilities
Workshop


Location: Room 279
1:00pm 6:00pm Open Career Counseling with Dr. Clifford
2:00pm 2:30pm Coffee Break: Room 206
2:30pm 4:30pm TUTORIAL 3
Medical Imaging

Li Shen
Indiana University

Location:
Room 202

TUTORIAL 4
Personalized
Medicine


Yana Bromberg
Rutgers University

Location: Room 214CD
WORKSHOP 2
Bioinformatics
Education Workshop

Location:
Room 279
4:30pm 6:15pm Free Time / Dinner on Own
5:00pm 6:00pm Student Bowling activity
Location: Purdue Memorial Union, Bowling Center
6:15pm 7:15pm KEYNOTE 1
DR. NANCY J. COX
Large-scale Data Integration: Genomes, Transcriptomes, and Electronic Medical Records
Location: Fowler Auditorium

Start
Time
End
Time
RESEARCH SESSION 1
Location: Room 202
RESEARCH SESSION 2
Location: Room 214CD
7:30pm 8:00pm INVITED SPEAKER:
Tijana Milenkovic

Redefining Homology by Transferring Function Between Conserved Network Regions
INVITED SPEAKER:
Russell Schwartz

What sequencing can (and can't) tell us about tumor evolution
8:00pm 8:20pm Adam Gregory Roth and Madhavi Ganapathiraju

Literature Based Similarity Core of Protein-Protein Interactions
Hachem Saddiki and Patrick Flaherty

Subtype Prediction Intervals for Samples with Intratumor Heterogeneity
8:20pm 8:30pm Manoj Kandpal, Yingtao Bi, and Ramana Davuluri

Comparative Differential Network Analysis for Identifying Cancer Markers in Gene and Isoform Based Networks
Theodore Roman, Lu Xie, and Russell Schwartz

Mixed Membership Geometric Unmixing of Tumor Data
8:30pm 8:40pm Ping Ye

Dissecting Germ Cell Metabolism through Network Modeling
Xiaolin Liu, Carly Schaeffer, Nathanial Figueroa, and John Karro

Fast Genome-Wide De Novo Identification of Elementary Repeats
8:40pm 8:50pm Nawar Malhis, Eric Wong, Roy Nassar, and Joerg Gsponer

Computational Identification of Disordered Protein Binding Regions
Gabriel Al-Ghalith, Emmanuel Montassier, and Dan Knights

NINJA: A Fast Free Open-Source Pipeline for Reference Gene Mapping
8:50pm 9:00pm Badri Adhari, Debswapna Bhattacharya, Renzhi Cao, and Jianlin Cheng

CONFOLD: Residue-Residue Contact-guided Ab Initio Protein Folding
Rick Westerman

Denovo Sequencing of Prairie Falcon using Moleculo Reads as Scaffolds (pdf)
9:00pm 9:10pm Alvin Farrel and Jun-Tao Guo

Structure-Based Prediction of Homeodomain Binding Specificity using an Integrative Energy Function
Jiajie Huang, Kejie Li, and Michael Gribskov

Identification of Conserved RNA Structural Motifs using Subgraph Sampling
9:10pm 9:20pm Hyung-Rae Kim and Daisuke Kihara

Residue Environment Score for Selecting Protein Structure Models and Protein-Protein Docking Models
Tony Hazbun

Synthetic Dosage Lethality Screening in Yeast to Predict Pathway Dependencies in Cancer
9:20pm 9:30pm   Rohit Gupta and Fabian Filipp

Cancer Systems Biology of Melanoma to Identify Cancer Drivers
Go directly to: [Monday] [Tuesday] [Wednesday]
DAY 2 - TUESDAY – May 19, 2015
Start Time End
Time
SESSION TYPE
9:00am 10:00am KEYNOTE 2
DR. MONA SINGH
Data Driven Approaches For Uncovering Variation in Protein Interaction Networks
Location: Fowler Auditorium
Chair:Predrag Radivojac
10:00am 10:30am Coffee Break
Start Time End
Time
RESEARCH SESSION 3
Location: Room 202
RESEARCH SESSION 4
Location: Room 214CD
10:30am 11:00am INVITED SPEAKER:
Yana Bromberg

Functional basis of microorganism classification
INVITED SPEAKER:
Jeffrey Kidd

Paralog-Specific Copy-Number Variation Detection Using Exact K-mer Matching
11:00am 11:20am Seyedsasan Hashemikhabir, Ran Xia, Yang Xiang, and Sarath Chandra Janga

A Framework for Identifying Genotypic Information from Clinical Records: Exploiting Integrated Ontology Structures to Transfer Annotations Between ICD Codes and Gene Ontologies
Rodrigo F Ramalho, Sujun Li, Predrag Radivojac, and Matthew Hahn

Proteomic Evidence for In-frame and Out-of-frame Alternatively Spliced Isoforms in Mammals
11:20am 11:30am Yuriy Hulovatyy, Boyoung Yoo, Huili Chen, Fazle Faisal, and Tijana Milenkovic

Revealing Missing Parts of the Interactome via Link Prediction: Implications for Aging
Xiangjia Min, Brian Powell, Jonathan Braessler...Gaurav Sablok

Comparative Genome-Wide Analyses of Alternative Splicing Genes in Cereal Plants
11:30am 11:40am Baharak Saberidokht, Ariful Azad Bartek Rajwa, Paul Wallace, and Alex Pothen

Classifying Flow Cytometry Samples into AML Subclasses by Identifying Immunophenotypes
Matthew Dapas, Manoj Kandpal,
Yingtao Bi, and Ramana Davuluri


Comparative Study of Gene Isoform Expression Estimates Using RNA-seq Exon-array and RT-qPCR Platforms in Glioblastoma Multiforme
11:40am 11:50am Reeba Paul, Madara Hetti Arachchilage, and Helen Piontkivska

Elucidating Effects of HAART on Molecular Evolutionary Patterns of HIV-1 in Countries with Different Socio-economic Status
Huiguang Wu, Xuanmin Guang, Mohamed B. Al-Fageeh...Jun Wang

Camelid Genomes Reveal Evolution and Adaptation to Desert Environments
11:50am 12:00pm Deborah Chasman, Kevin Walters, Amie J. Eisfeld...Sushmita Roy

Integrative Reconstruction of the Regulatory Network Controlling Host Response to Influenza Infections
Javi Zhang, Michael E. Grigg, Asis Khan...John Parkinson

Discovery of Inter-strain Recombination in Apicomplexans
12:00pm 12:10pm Md Shihab Hasan, Martha Zakrzewski, Don McManus, and Lutz Krause

Finding a Needle in a Haystack: Bioinformatic Approach for Identifying Vaccine Targets by Comparative Studies of Schistosoma Genomes & Proteomes
Ingrid Montes-Rodriguez, Alexander Ropelewski, Ricardo Gonzalez...Juan Lopez-Garriga

Molecular Evolution and Tissue Expression of a Sulfur-transporting Hemoglobin in the Clam Lucina Pectinata
12:10pm 12:20pm Gladys Andino, Michael Gribskov, Denis Anderson, Jay Evans, and Greg Hu

Differential Gene Expression in Varroa Jacobsoni Mites Following a Host Shift to European Honey Bees (Apis mellifera)
Andrzej Kudlicki

G-Quadruplexes Involving Both Strands of dsDNA in the Human Genome
Go directly to: [Monday] [Tuesday] [Wednesday]
CONTINUED - DAY 2 - TUESDAY – May 19, 2015
Start Time End
Time
SESSION TYPE
12:20pm 1:30pm Lunch on own
1:30pm 3:30pm Hike (meet at registration)
or free time
Student Session: Birds of a Feather

Join us for an interactive session - Hands-on RNASeqworkshop/analysis.

Click here to sign up.

Location: Stewart Center
Room 214CD
Start Time End
Time
RESEARCH SESSION 5
Location: Room 202
RESEARCH SESSION 6
Location: Room 214CD
3:30pm 4:00pm INVITED SPEAKER:
Yunlong Liu

Roles of Regulatory Variants in Complex Disease
INVITED SPEAKER:
Yuzhen Ye

Targeted Analysis of Metagenomes: What’s Working and What’s Not
4:00pm 4:20pm Rami Al-Ouran, Robert Schmidt, Ashwini Naik...Lonnie Welch

Discovering Gene Regulatory Elements Using Coverage-based Heuristics
Yu-Wei Wu, Blake Simmons, and Steven Singer

Improving the Assembly Qualities of Draft Genomes Extracted from Metagenomes
4:20pm 4:40pm James Pease and Benjamin Rosenzweig

The Multisample Variant Format (MVF) for Phylogenomics and Population Genomics
Peter Larsen and Yang Dai

Metabolome of Human Gut Metabolome is Predictive of Host Health
4:40pm 4:50pm Yaseswini Neelamraju, Abel Gonzalez, Perez Nuria...Sarath Chandra Janga

Mutational Landscape of RNA-binding Proteins in Human Cancers
Ceth Parker

Fermentative Iron-Reducing Bacteria Implicated in Iron Ore Cave Formation
4:50pm 5:00pm Christopher Gates, Jessica Bene, Ashwini Bhasi

Jacquard: A Practical Approach to Integrating Complex Somatic Variant Data Sets
Shuzhao Li and Andrei Todor

Deep Sequencing the Human Metabolome and Interpretation with Mummichog
5:00pm 5:10pm Senthilkumar Damodaran, Jharna Miya, Esko Kautto...Sameek Roychowdhury

Cancer Driver Log (CanDL): Catalogue of Potentially Actionable Cancer Mutations
Samantha Halliday and John Parkinson

An Ensemble Approach to the Taxonomic Classification of Meta-transcriptomic Sequence Data
5:10pm 5:30pm Break
5:30pm 7:00pm Poster Session and Celebratory Reception, Rooms 206/218
7:15pm 9:30pm Student Speed Networking Event
Location: Purdue Memorial Union Building, Anniversary Drawing Room
Go directly to: [Monday] [Tuesday] [Wednesday]
DAY 3 - WEDNESDAY – May 20, 2015
Start Time End
Time
SESSION TYPE
9:00am 10:00am KEYNOTE 3
DR. JIAN-KANG ZHU
Regulation of DNA methylation in plants
Location:
Fowler Auditorium
Chair: Daisuke Kihara
10:00am 11:30am Poster Reception - Join us for posters and morning refreshments!
Rooms 206/218

Start Time End
Time
RESEARCH SESSION 7
Location: Room 202
RESEARCH SESSION 8
Location: Room 214CD
11:30am 12:00pm INVITED SPEAKER:
Chad Myers

Mining Chemical-genetic Interaction Networks for Genome-wide Discovery of New Molecular Probes
INVITED SPEAKER:
Hyonho Chun

Heterogeneous Data Integration: Heritability Estimation from Multiple Phenotypes
12:00pm 12:20pm Eric Samorodnitsky, Benjamin Jewell, Raffi Hagopian...Sameek Roychowdhury

Evaluation of Hybridization Capture Versus Amplicon-based Methods for Whole Exome Sequencing
Pranjal Patra, Tatsuo Izawa, and Lourdes Pena-Castillo

REPA: Applying Pathway Analysis to Genome-wide Transcription Factor Binding Data
12:20pm 12:30pm Jagadeesh Patchala and Anil Jegga

Topic Modeling on Gene Annotations to Discover Drug Repositioning Candidates
Sophia Banton, Ruiyan Luo, and Shuzhao Li

Pathway Group LASSO for Integrating Metabolomics and Transcriptomics
12:30pm 12:40pm Donglai Chen, Zach McBride, Uma Aryal...Jun Xie

Method Development for the Discovery of Membrane-associated Protein Complexes in Arabidopsis
Aditi Gupta

DiffPath: Finding Differentially Expressed Biological Pathways
12:40pm 12:50pm Haiyang Fang, Rongcai Yue, Yang Ga, Yi Zhang, Lei Shan and Jing Zhao

Analysis of Cynandione A's Anti-ischemic Stroke Effects from Pathways and Protein-protein Interactome
Daifeng Wang, Koon-Kiu Yan, Cristina Sisu...Mark Gerstein

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
12:50pm 1:00pm David Ream, Asma Bamkapur, Jake Gregg, and Iddo Friedberg

An Event-Driven Approach for Studying Gene Block Evolution in Bacteria
Yu-Wei Wu, Blake Simmons, and Steven Singe

MaxBin 2.0: Integrating Multiple Metagenomes to Recover More High Quality Individual Genomes from the Environmental Data
1:00pm 2:00pm Lunch - Rooms 278 and 279. Join your fellow attendees for a salad and pizza lunch and time to mix and mingle! Grab a slice and sit in a classroom, or head outside for some fresh air!
Start Time End Time RESEARCH SESSION 9
Location: Room 202
RESEARCH SESSION 10
Location: Room 214CD
2:00pm 2:30pm INVITED SPEAKER:
Anna Goldenberg

Omic Data Integration - Striving Towards Personalized Medicine
INVITED SPEAKER:
Matthew Hahn

Phylogenomics and the Procrustean Bed of the Species Tree
2:30pm 2:50pm Satwica Yerneni, Ishita Khan, Qing Wei, and Daisuke Kihara

IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks
Nikolaos Alachiotis and Pavlos Pavlidis

Scalable Linkage Disequilibrium-based Selective Sweep Detection: A Performance Guide
2:50pm 3:00pm Jose Lugo-Martinez, Sean Mooney, and Predrag Radivojac

In Silico Analysis from Protein Structures Reveals Loss and Gain of Functional Sites as Active Mechanism of Disease
Eric Ho and Han Xu

Stop Codon Avoidance Analysis in Vertebrate Genes
3:00pm 3:10pm Jeremy Prokop

Understanding Disease Variants at a Clinical Pace: a Computational Analysis to Characterize Clinical Variants and Predict Protein Function
Igor Berezovsky and Alexander Goncearenco

Protein Function from its Emergence to Diversity in Contemporary Proteins
3:10pm 3:30pm Coffee Break
3:30pm 4:30pm KEYNOTE 4
DR. TANDY WARNOW
Grand Challenges in Phylogenomics
Location:
Fowler Auditorium
Chair: Lonnie Welch
4:30pm 4:45pm GLBIO AWARDS PRESENTATION


Location: Fowler Auditorium
Go directly to: [Monday] [Tuesday] [Wednesday]