Description
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 [email protected]
Schedule and Supporting Media
Participant List
Speaker Titles & Abstracts
Posters
Monday, May 11, 2015
at SAMSI
Time | Description | Speaker | Slides | Videos |
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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 | ||
10:35-10:55 | The Microbiome and Women’s Health | Paul Brooks, Virginia Commonwealth University | ||
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 | ||
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 |
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3:15-3:45 | Statistical Challenges in Analyzing Methylation and Long-Range Interaction Data | Shili Lin, Ohio State University Steve Qin, Emory University |
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3:45-4:15 | Comparative Analyses of Whole Genome Bisulphite Sequencing Data Across Multiple Cell Types and Species | Ben Li, Emory University | ||
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
at SAMSI
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 |
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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 |
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10:10-10:30 | Break | |||
Session 6: Data Integration: COPD | Chairs: Katerina Kechris, CU Denver Hongyu Zhao, Yale University |
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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 | ||
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 | ||
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 | ||
2:30-3:00 | Allelic-Specific Gene Expression and Quantitative Trait Analysis | Fei Zou, UNC-Chapel Hill | ||
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 | ||
4:45-5:30 | Break | |||
5:30-7:00 | Poster Session and Reception |
Wednesday, May 13, 2015
at SAMSI
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 | ||
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 | ||
11:45-12:15 | Evolutionary Inference with Interlocus Gene Conversion | Jeff Thorne, N.C. State University | ||
12:15-12:30 | Concluding Remarks | |||
12:30 | Box lunch and Adjourn |