2014-15: Bioinformatics: Transition Workshop: May 11-13, 2015
Workshop Information
May 11, 2015 - 8:30am - May 13, 2015 - 12:30pm
Registration for this workshop is currently closed.
Schedule
Participant List
Speaker Titles & Abstracts
Posters
Description
This final, transition workshop for the Beyond Bioinformatics program is 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 will be 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 will be emphasized. This will also be an opportunity to showcase research by post-doctoral associates and graduate students who were active in the program. Finally, the workshop will be designed to enable working group leaders and participants to plan for research collaborations beyond the active time period of the SAMSI research program.
SAMSI Directorate Liaison: Sujit Ghosh, NCSU & SAMSI
If you have any questions please send email to [email protected]
Schedule
Monday, May 11, 2015
at SAMSI
| 8:30-9:15 a.m. | 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 | Alexander Alekseyenko, NYU School of Medicine Update on Microbial Interaction Inference Methodology Working Group |
| 10:35-10:55 | Paul Brooks, Virginia Commonwealth University The Microbiome and Women's Health |
| 10:55-11:15 | Georg Gerber, Harvard University Bayesian Inference of Dynamical Systems Models from Microbiome Time-Series Data |
| 11:15-11:35 | Liyang Diao, Yale University Pitfalls in Microbiome Differential Abundance Analysis using Current RNA-Seq Processing Methods |
| 11:35-11:55 | Katia Smirnova, University of Wyoming Microbiome Normalization Methods: Effect on Ordination Analysis |
| 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 | Karin Dorman, Iowa State University Overview of NGS Errors Working Group |
| 1:40-2:20 | Ashley Cacho, University of California, Riverside A Survey of Base-calling Algorithms for Illumina Sequencing Technology |
| 2:20-3:00 | Xin Yin, Iowa State University PREMIER-bc: Integrated Base-Calling and Error-Correction Approach Using Hidden Markov Model |
| 3:00-3:15 | Break |
| Session 4: Whole Genome Methylation and Chromatin Interaction Chairs: Shili Lin, Ohio State University and Steve Qin, Emory University |
|
| 3:15-3:45 | Shili Lin, Ohio State University and Steve Qin, Emory University Statistical Challenges in Analyzing Methylation and Long-Range Interaction Data |
| 3:45-4:15 | Ben Li, Emory University Comparative Analyses of Whole Genome Bisulphite Sequencing Data Across Multiple Cell Types and Species |
| 4:15-4:45 | Deepak Ayyala, Ohio State University 3D Chromatin Reconstruction using TAD-Penalized Models |
| 5:00 | Dinner on your own |
Tuesday, May 12, 2015
at SAMSI
| 8:30-8:45 a.m. | 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 | Elizabeth McGuffey, UT MD Anderson Cancer Center piBAG: Pathway Based Integrative Analysis of Multiplatform Genomics Data |
| 9:30-9:50 | Yuping Zhang, University of Connecticut Leveraging Multiple Omics Data to Infer Pathway Disturbance in Complex Diseases |
| 9:50-10:10 | Bin Zhu, National Cancer Institute and Ronglai Shen, Memorial Sloan Kettering Cancer Center Integrating Clinical and Molecular Data for Survival Prediction in TCGA |
| 10:10-10:30 | Break |
| Session 6: Data Integration: COPD Chairs: Katerina Kechris, CU Denver, and Hongyu Zhao, Yale University |
|
| 10:30-11:00 | Katerina Kechris (Intro), CU Denver New Directions in Data Integration using Chronic Obstructive Pulmonary Disease (COPD) as a Case Study |
| 11:00-11:30 | Qiongshi Lu, Yale University Post-GWAS Prioritization through Integrated Analysis of Genomic Functional Annotation |
| 11:30-12:00 | Jeihuan Sun, Yale University Discovery of Novel Loci Associated with COPD by Pooling Information from Related Clinical Feature and Functional Annotation |
| 12:00-1:30 | Lunch |
| Session 7: Analysis of High-dimensional Discrete Data Chair: Fei Zou, UNC-Chapel Hill |
|
| 1:30-2:00 | Jyotishka Dutta, SAMSI and Duke University Multiscale Bayesian Cluster Detection and Testing for Whole Genome Sequencing Studies |
| 2:00-2:30 | Yumou Qiu, University of Nebraska-Lincoln Thresholding Tests for Signal Detection on High-dimensional Count Distributions |
| 2:30-3:00 | Fei Zou, UNC-Chapel Hill Allelic-Specific Gene Expression and Quantitative Trait Analysis |
| 3:00-3:15 | Break |
| Session 8: Multiple Hypothesis Testing and Simultaneous Inference Chair: Fred Wright, N.C. State University |
|
| 3:15-3:45 | Fred Wright, N.C. State University Update on the Multiple Hypothesis Testing Working Group |
| 3:45-4:15 | Yihui Zhou, N.C. State University The Moment Corrected Correlation Method for High Dimensional Data |
| 4:15-4:45 | Pratyaydipta Rudra, UNC-Chapel Hill A Procedure to Detect General Association Based on Concentration of Ranks |
| 4:45-5:30 | Break |
| 5:30-7:00 | Poster Session and Reception SAMSI will provide poster presentation boards and tape. The board dimensions are 4 ft. wide by 3 ft. high. They are tri-fold with each side being 1 ft. wide and the center 2 ft. wide. Please make sure your poster fits the board. The boards can accommodate up to 16 pages of paper measuring 8.5 inches by 11 inches. |
Wednesday, May 13, 2015
at SAMSI
| 8:30-8:45 a.m. | 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 | Wei Pan, University of Minnesota Approximate Score-Based Testing with Application to Multivariate Trait Association Analysis |
| 9:30-10:00 | Yize Zhao, SAMSI and UNC-Chapel Hill Bayesian Hierarchical Variable Selection for Genome-wide Association Studies |
| 10:00-10:30 | Tian Ge, MGH, Harvard Medical School Probing the Genetic Underpinnings of Structural Neuroimaging Phenotypes |
| 10:30-10:45 | Break |
| Session 10: Dependence in Evolutionary Models Chair: Seth Sullivant, N.C. State University |
|
| 10:45-11:15 | Scott Schmidler, Duke University Incorporating Dependence into Evolutionary Models for Protein Structure Alignment |
| 11:15-11:45 | Jotun Hein, Oxford University Models of Gene Duplications |
| 11:45-12:15 | Jeff Thorne, N.C. State University Evolutionary Inference with Interlocus Gene Conversion |
| 12:15-12:30 | Concluding Remarks |
| 12:30 | Box lunch and Adjourn |