Workshops

Spring 2016

Regulatory Genomics and Epigenomics

Mar 7, 2016 to Mar 10, 2016

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Click on the titles of individual talks for abstract, slides and archived video.

Please note that this schedule is subject to change. All events take place in the Calvin Lab Auditorium.

Monday, March 7th, 2016
8:30 am–8:50 am		Coffee & Check-In
8:50 am–9:00 am		Opening Remarks
9:00 am–9:30 am		Algorithms for Single Cell RNAseq Analysis Serafim Batzoglou, Stanford University
9:30 am–10:00 am		Spectral Algorithms for Learning HMMs and Tree HMMs for Epigenetics Data Kevin Chen, Rutgers University
10:00 am–10:30 am		Accurate, Fast, and Model-Aware Transcript Expression Quantification with Salmon Carl Kingsford, Carnegie Mellon University
10:30 am–11:00 am		Break
11:00 am–11:30 am		Reconstructing Dynamic Signaling and Regulatory Networks Ziv Bar-Joseph, Carnegie Mellon University
11:30 am–12:00 pm		Learning Feature-Based Protein-DNA Recognition Models from SELEX Data Harmen Bussemaker, Columbia University
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Beyond Enhancer Modularity: Locus-level Control of Gene Expression in Development Angela DePace, Harvard University
2:30 pm–3:00 pm		Co-occupancy Networks for Histone Modifications and Chromatin Associated Proteins Martin Vingron, Max Planck Institut für molekulare Genetik
3:00 pm–3:30 pm		Scoring Transcript Variation in Single Cell RNA-seq Data Xiuwei Zhang, EMBL
3:30 pm–5:00 pm		Reception

Tuesday, March 8th, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Mapping Nucleosome Positions Using DNase Alexander Hartemink, Duke University
9:30 am–10:00 am		Computational Genomics of Post-Transcriptional Gene Regulation Uwe Ohler, Humboldt University/Max-Delbruck Center
10:00 am–10:30 am		Quantitative Modeling of Transcription Factor Binding Specificities using DNA Shape Remo Rohs, University of Southern California
10:30 am–11:00 am		Break
11:00 am–11:30 am		Deep Learning Frameworks for Regulatory Genomics and Epigenomics Anshul Kundaje, Stanford University
11:30 am–12:00 pm		Genome in 3D: Modeling Chromosome Organization Leonid Mirny, MIT
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Incomplete MyoD Transdifferentiation is Mediated by Chromatin Remodeling Deficiencies Raluca Gordan, Duke University
2:30 pm–3:00 pm		The Enhancer Mutation Problem: Figuring out Phenotype Based on Genotype Nadav Ahituv, UCSF
3:00 pm–3:30 pm		Break
3:30 pm–4:30 pm		Moderated Discussion

Wednesday, March 9th, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Understanding DNA-binding Preferences of Transcription Factor Homologs Trevor Siggers, Boston University
9:30 am–10:00 am		Challenges in Sequence-to-Expression Modeling Saurabh Sinha, University of Illinois Urbana-Champaign
10:00 am–10:30 am		Modeling Gene Expression and Chromatin State in Terms of Regulatory Sites Erik Van Nimwegen, Basel University
10:30 am–11:00 am		Break
11:00 am–11:30 am		Selecting Genomics Assays William Stafford Noble, University of Washington
11:30 am–12:00 pm		Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments Teresa Przytycka, National Institutes of Health
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Personal Transcription Factor Binding Site Mutations Point to Personal Medical Histories Gill Bejerano (Stanford University)
2:30 pm–3:00 pm		Telomere Length, Nature and Nurture Martin Kupiec, Tel Aviv University
3:00 pm–3:30 pm		Break
3:30 pm–4:30 pm		Moderated Discussion

Thursday, March 10th, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Hierarchical Regulatory Domain Inference from Hi-C Data Bartek Wilczynski, University of Warsaw
9:30 am–10:00 am		Analysis Methods for Single Cell RNA-seq with Application to T-cell Function Nir Yosef, UC Berkeley
10:00 am–10:30 am		Genome-wide Prediction of Enhancers and Their Target Genes using ENCODE data Zhiping Weng, University of Massachusetts
10:30 am–11:00 am		Break
11:00 am–11:30 am		Utilizing de Bruijn Graphs in Universal Sequence Design for Discovery of Regulatory Elements Ron Shamir, Tel-Aviv University and Yaron Orenstein, MIT
11:30 am–12:00 pm		Modelling Gene Expression Dynamics with Gaussian Processes Magnus Rattray, University of Manchester
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Discovery of Transcription Factor Binding Motifs from Large Sequence Sets Esko Ukkonen, Helsinki University
2:30 pm–3:00 pm		Chromatin Dynamics and Gene Regulation During Motor Neuron Programming Mahmoud Ibrahim, Max-Delbrueck-Center, Berlin
3:00 pm–3:30 pm		Break
3:30 pm–4:30 pm		Moderated Discussion