2014-15: Bioinformatics: Transition Workshop: May 11-13, 2015


This final, transition workshop for the Beyond Bioinformatics program was designed as an opportunity for the active working groups in the 2014-15 research program to present the work of their groups. In contrast to the Opening Workshop where the focus was on overview talks and talks that emphasized open problems in various areas of bioinformatics, this workshop was narrower in focus, only emphasizing the research progress that was made since early Fall 2014 in the program’s working groups. Talks that present research that is in progress or research that was completed as a consequence of the SAMSI program was emphasized. This was an opportunity to showcase research by post-doctoral associates and graduate students who were active in the program. Finally, the workshop was designed to enable working group leaders and participants to plan for research collaborations beyond the active time period of the SAMSI research program.

Questions: email bioinformatics@samsi.info

Schedule and Supporting Media

Participant List
Speaker Titles & Abstracts

Monday, May 11, 2015

Time Description Speaker Slides Videos
8:30-9:15 Registration
9:15 – 9:30 Introduction and Welcome Sujit Ghosh, SAMSI & N.C. State University
9:30-10:00 Session 1: Program Overview and Updates Chair: Snehalata Huzurbazar, University of Wyoming
10:00-10:15 Break
Session 2: Microbial Community Dynamics and Complexity Chair: Snehalata Huzurbazar, University of Wyoming
10:15-10:35 Update on Microbial Interaction Inference Methodology Working Group Alexander Alekseyenko, NYU School of Medicine pdf
10:35-10:55 The Microbiome and Women’s Health Paul Brooks, Virginia Commonwealth University pdf
10:55-11:15 Bayesian Inference of Dynamical Systems Models from Microbiome Time-Series Data Georg Gerber, Harvard University
11:15-11:35 Pitfalls in Microbiome Differential Abundance Analysis using Current RNA-Seq Processing Methods Liyang Diao, Yale University
11:35-11:55 Microbiome Normalization Methods: Effect on Ordination Analysis Katia Smirnova, University of Wyoming
11:55-12:00 Group Photo
12:00-1:30 Lunch
Session 3: Next Generation Sequencing Errors Chair: Xinping Cui, University of California, Riverside
1:30-1:40 Overview of NGS Errors Working Group Karin Dorman, Iowa State University pdf
1:40-2:20 A Survey of Base-calling Algorithms for Illumina Sequencing Technology Ashley Cacho, University of California, Riverside
2:20-3:00 PREMIER-bc: Integrated Base-Calling and Error-Correction Approach Using Hidden Markov Model Xin Yin, Iowa State University
3:00-3:15 Break
Session 4: Whole Genome Methylation and Chromatin Interaction Chairs: Shili Lin, Ohio State University
Steve Qin, Emory University
3:15-3:45 Statistical Challenges in Analyzing Methylation and Long-Range Interaction Data Shili Lin, Ohio State University
Steve Qin, Emory University
3:45-4:15 Comparative Analyses of Whole Genome Bisulphite Sequencing Data Across Multiple Cell Types and Species Ben Li, Emory University pdf
4:15-4:45 3D Chromatin Reconstruction using TAD-Penalized Models Deepak Ayyala, Ohio State University
5:00 Dinner on your own

Tuesday, May 12, 2015

Time Description Speaker Slides Videos
8:30-8:45 Registration
8:45-9:00 Introduction Snehalata Huzurbazar, University of Wyoming
Session 5: Data Integration: TCGA Chairs: Ronglai Shen, Memorial Sloan Kettering Cancer Center
Veera Baladandayuthapani, UT MD Anderson Cancer Center
9:00-9:30 piBAG: Pathway Based Integrative Analysis of Multiplatform Genomics Data Elizabeth McGuffey, UT MD Anderson Cancer Center
9:30-9:50 Leveraging Multiple Omics Data to Infer Pathway Disturbance in Complex Diseases Yuping Zhang, University of Connecticut
9:50-10:10 Kettering Cancer Center
Integrating Clinical and Molecular Data for Survival Prediction in TCGA
Bin Zhu, National Cancer Institute
Ronglai Shen, Memorial Sloan
10:10-10:30 Break
Session 6: Data Integration: COPD Chairs: Katerina Kechris, CU Denver
Hongyu Zhao, Yale University
10:30-11:00 New Directions in Data Integration using Chronic Obstructive Pulmonary Disease (COPD) as a Case Study Katerina Kechris (Intro), CU Denver
11:00-11:30 Post-GWAS Prioritization through Integrated Analysis of Genomic Functional Annotation Qiongshi Lu, Yale University pdf
11:30-12:00 Discovery of Novel Loci Associated with COPD by Pooling Information from Related Clinical Feature and Functional Annotation Jiehuan Sun, Yale University pdf
12:00-1:30 Lunch
Session 7: Analysis of High-dimensional Discrete Data Chair: Fei Zou, UNC-Chapel Hill
1:30-2:00 Multiscale Bayesian Cluster Detection and Testing for Whole Genome Sequencing Studies Jyotishka Datta, SAMSI and Duke University
2:00-2:30 Thresholding Tests for Signal Detection on High-dimensional Count Distributions Yumou Qiu, University of Nebraska-Lincoln pdf
2:30-3:00 Allelic-Specific Gene Expression and Quantitative Trait Analysis Fei Zou, UNC-Chapel Hill pdf
3:00-3:15 Break
Session 8: Multiple Hypothesis Testing and Simultaneous Inference Chair: Fred Wright, N.C. State University
3:15-3:45 Update on the Multiple Hypothesis Testing Working Group Fred Wright, N.C. State University
3:45-4:15 The Moment Corrected Correlation Method for High Dimensional Data Yihui Zhou, N.C. State University
4:15-4:45 A Procedure to Detect General Association Based on Concentration of Ranks Pratyaydipta Rudra, UNC-Chapel Hill pdf
4:45-5:30 Break
5:30-7:00 Poster Session and Reception

Wednesday, May 13, 2015

Time Description Speaker Slides Videos
8:30-8:45 Registration
8:45-9:00 Introduction Snehalata Huzurbazar, University of Wyoming
Session 9: Imaging Genetics Chair: Hongtu Zhu, UNC-Chapel Hill
9:00-9:30 Approximate Score-Based Testing with Application to Multivariate Trait Association Analysis Wei Pan, University of Minnesota
9:30-10:00 Bayesian Hierarchical Variable Selection for Genome-wide Association Studies Yize Zhao, SAMSI and UNC-Chapel Hill
10:00-10:30 Probing the Genetic Underpinnings of Structural Neuroimaging Phenotypes Tian Ge, MGH, Harvard Medical School pdf
10:30-10:45 Break
Session 10: Dependence in Evolutionary Models Chair: Seth Sullivant, N.C. State University
10:45-11:15 Incorporating Dependence into Evolutionary Models for Protein Structure Alignment Scott Schmidler, Duke University
11:15-11:45 Models of Gene Duplications Jotun Hein, Oxford University pdf
11:45-12:15 Evolutionary Inference with Interlocus Gene Conversion Jeff Thorne, N.C. State University pdf
12:15-12:30 Concluding Remarks
12:30 Box lunch and Adjourn