Summary: CSIG workshop features a lineup of invited talks and breakout sessions over a one and a half day period. The location of the workshop in the Lewis-Sigler Institute of Integrative Genomics is located on the campus of Princeton University. The location can be easily reached by NJ Transit from NYC Penn Station or the Newark Airport. The site is under an hour by car from Philadelphia & Philadelphia International Airport.
Posters are to be set up on the bulletin board near the West entrance to the building. Marybeth will have push pins available.
Salim Chowdhury (Simons) - Tissue-aware data integration approach for the inference of pathway interactions
Georgia Doing (Dartmouth) - Elucidating functional signatures in Pseudomonas aeruginosa transcriptional data
Siyuan Ma (Harvard) - Meta-Analysis of Population Heterogeneity in the IBD Gut Microbiome
Weiguang Mao (Pitt) - Pathway-Level Information ExtractoR (PLIER) II: RNA-seq decomposition with overlapping group lasso penalty
Rachel Sealfon (Simons) - Disease-specific and patient-specific networks
Greg Way (Penn) - Stratification of gene expression states in Pan Cancer
Aaron Wong (Flatiron) - HumanBase: data-driven predictions of gene expression, function, regulation and interactions in human
Ran Zhang (Princeton) - Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder
Zidong Zhang (Princeton) - Logistic regression on functional network construction
Qian Zhu (Dana Farber) - Superenhancer landscape of acute myeloid leukemia
Thursday, June 8, 2017
Lewis-Sigler Institute for Integrative Genomics
8:15-8:45 a.m. Registration (west entrance) and Breakfast (Oval lounge)
8:45-9:30 a.m. Casey Greene (Penn) - CSIG Introduction & Welcome Exercise
9:30-9:45 a.m. Faculty Introductions: Maria Chikina (Pitt), Matt Hibbs (Trinity), Curtis Huttenhower (Harvard/Broad), Olga Troyanskaya (Princeton/Simons), Levi Waldron (CUNY)
9:45-10:00 a.m. Lightning Talks (2 mins each ⚡)
Lucas Schiffer (CUNY) - BugSigDB: Curated Metagenomic Signatures
Alicja Tadych (Princeton) - Web apps in Troyanskaya Lab
René Zelaya (Penn) - Working with Tribe: The collaborative platform for reproducible web-based analyses
Raghavendran Partha (Pitt) - Predicting specific biological functions of gene regulatory regions using convergent evolution
Amanda Kowalczy (Pitt) - Identifying Genes Associated with Longevity in Mammals
10:00-10:30 a.m. Vicky Yao (Princeton) - Furthering understanding of Parkinson's disease through integrative analysis in C. elegans
10:30-11:00 a.m. Coffee Break! Coffee not included but available for purchase at the cafe.
11:00-11:15 a.m. Lightning Talks (2 mins each ⚡)
Gholamali Rahnavard (Harvard/Broad) - High-sensitivity pattern discovery in large multi'omic datasets
Matt Huyck (Penn) - The ADAGE webserver
Max Homilius (Princeton) - A network-based approach to detect drug mode-of-action at therapeutic doses.
Matt Hibbs (Trinity) - Visualizing the Gene Ontology with TreeMaps
Brett Beaulieu-Jones (Penn) - Visualizing and Clustering EHR Disease Trajectories
11:15-11:45 p.m. Kathleen Chen (Penn) - PathCORE: visualizing globally co-occurring pathways in large transcriptomic compendia
11:45-12:15 p.m. Himel Mallick (Harvard/Broad) - Metabolite Prediction in the Human Microbiome
12:15-1:45 p.m. Lunch Groups to Princeton - Returning by 1:30:
* Group 1: Kiley Graim, Kurt Wheeler, Georgia Doing, Evan Cofer, Jason Lloyd-Price, Jian Zhu, Raghavendran Partha
* Group 2: Dongbo Hu, Xi Chen, Alicja Tadych, Gholamali Rahnavard, Ruth Dannenfelser, Amanda Kowalczyk
* Group 3: Daniel Himmelstein, Michael Zietz, Himel Mallick, Rachel Sealfon, Vicy Yao, Salim Chowdhury, Weiguang Mao
* Group 4: Aaron Wong, Kathleen Chen, Ran Zhang, Rene Zelaya, Lucas Schiffer, Brett Beaulieu-Jones
* Group 5: Gregory Way, Jaclyn Taroni, Max Homilius, Matt Huyck, Zidong Zhang, Qian Zhu, Siyuan Ma
* Group 6: Matt Hibbs, Casey Greene, Maria Chikina, Curtis Huttenhower, Levi Waldron, Olga Troyanskaya
1:45-2:00 p.m. Lightning Talks (2 mins each ⚡)
Jian Zhou (Princeton) - Predicting the variation potentials of human gene expression from sequence
Dongbo Hu (Penn) - What's New in Angular 2/4
Xi Chen (Simons) - Cell type specific functional enhancer network inference
Kurt Wheeler (Penn) - The Data Refinery
2:00-2:30 p.m. Ruth Dannenfelser (Princeton) - Improving tissue discrimination and cancer recognition for T cell therapies
2:30-3:00 p.m. Daniel Himmelstein (Penn) - Hetnets, Neo4j & Data Integration
3:00-3:15 p.m. Lightning Talks (2 mins each ⚡)
Kiley Graim (Simons) - Persephone Rises: Profiling Postmortem Expression
Michael Zietz (Penn) - Hetnets and Discovery
David Nicholson (Penn) - The future will be distantly supervised
Evan Cofer, Jason Lloyd-Price, and Jaclyn Taroni - Brief self introductions.
3:15-4:30 p.m. Poster Session. Covfefe and snacks provided.
4:30-5:00 p.m. Evan Cofer (Trinity/Princeton) - Determining the Age-Associated Somatic Mutation Rate in Diverse Mouse Tissues
5:00-5:30 p.m. Jason Lloyd-Price (Harvard/Broad) - Characterizing the temporal dynamics of the microbiome with Gaussian Processes
5:30-5:35 p.m. Wrap up & Instructions
6:30-10:00 p.m. Dinner at Chennai Chimney (Address: 19 Chambers St. Princeton NJ)
Friday, June 9, 2017
9:00-9:10 a.m. Casey Greene, Ph.D., University of Pennsylvania
9:10-9:40 a.m. Jaclyn Taroni (Penn) - Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data
9:40-10:10 a.m. Maria Chikina (Pitt) - Deducing generative models of gene expression via constrained matrix decomposition
10:10-11:30 a.m. Skills & Interest Discussion Groups; Coffee not included but available for purchase at the cafe.
11:30-12:00 p.m. Levi Waldron (CUNY) - Multi-omics infrastructure and data for R/Bioconductor
12:00-1:00 p.m. Skills & Interests Shared Lessons + Lunch (Oval Lounge)
1:00-1:10 p.m. Olga Troyanskaya, Ph.D., Princeton University
1:15 p.m. Planned Departure
Organizing Committee: The organizing committee for CSIG consists of Casey Greene (Penn), Curtis Huttenhower (Harvard & Broad), and Olga Troyanskaya (Simons Fdn. & Princeton).
Administrative Support: Administrative support was provided by the Lewis-Sigler Institute of Integrative Genomics.
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