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 |
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| 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 |
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| 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 |
TUTORIAL 4 Personalized Medicine Yana Bromberg Rutgers University Location: Room 214CD |
WORKSHOP 2 Bioinformatics Education Workshop Location: Room 279 |
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| 4:30pm | 6:15pm | Free Time / Dinner on Own | |||
| 5:00pm | 6:00pm | Student Bowling activity Location: Purdue Memorial Union, Bowling Center |
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| 6:15pm | 7:15pm | KEYNOTE 1 DR. NANCY J. COX Large-scale Data Integration: Genomes, Transcriptomes, and Electronic Medical Records Location: Fowler Auditorium |
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| Start Time |
End Time |
RESEARCH SESSION 1 Location: Room 202 |
RESEARCH SESSION 2 Location: Room 214CD |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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) |
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| 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 |
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| 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 |
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| 9:20pm | 9:30pm | Rohit Gupta and Fabian Filipp Cancer Systems Biology of Melanoma to Identify Cancer Drivers |
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| 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 |
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| 10:00am | 10:30am | Coffee Break | |||
| Start Time | End Time |
RESEARCH SESSION 3 Location: Room 202 |
RESEARCH SESSION 4 Location: Room 214CD |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Start Time | End Time |
RESEARCH SESSION 5 Location: Room 202 |
RESEARCH SESSION 6 Location: Room 214CD |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 10:00am | 11:30am | Poster Reception - Join us for posters and morning refreshments! Rooms 206/218 |
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| Start Time | End Time |
RESEARCH SESSION 7 Location: Room 202 |
RESEARCH SESSION 8 Location: Room 214CD |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 4:30pm | 4:45pm | GLBIO AWARDS PRESENTATION Location: Fowler Auditorium |
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| Go directly to: [Monday] [Tuesday] [Wednesday] | |||||