• 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.

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Coffee & Check-In
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Opening Remarks
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Algorithms for Single Cell RNAseq Analysis
Serafim Batzoglou, Stanford University 
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Spectral Algorithms for Learning HMMs and Tree HMMs for Epigenetics Data
Kevin Chen, Rutgers University 
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Accurate, Fast, and Model-Aware Transcript Expression Quantification with Salmon
Carl Kingsford, Carnegie Mellon University 
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Break
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Reconstructing Dynamic Signaling and Regulatory Networks
Ziv Bar-Joseph, Carnegie Mellon University
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Learning Feature-Based Protein-DNA Recognition Models from SELEX Data
Harmen Bussemaker, Columbia University
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Lunch
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Beyond Enhancer Modularity: Locus-level Control of Gene Expression in Development
Angela DePace, Harvard University
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Co-occupancy Networks for Histone Modifications and Chromatin Associated Proteins
Martin Vingron, Max Planck Institut für molekulare Genetik
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Scoring Transcript Variation in Single Cell RNA-seq Data
Xiuwei Zhang, EMBL
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Reception
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Coffee & Check-In
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Mapping Nucleosome Positions Using DNase
Alexander Hartemink, Duke University
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Computational Genomics of Post-Transcriptional Gene Regulation
Uwe Ohler, Humboldt University/Max-Delbruck Center
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Quantitative Modeling of Transcription Factor Binding Specificities using DNA Shape
Remo Rohs, University of Southern California
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Break
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Deep Learning Frameworks for Regulatory Genomics and Epigenomics
Anshul Kundaje, Stanford University
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Genome in 3D: Modeling Chromosome Organization
Leonid Mirny, MIT
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Lunch
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Incomplete MyoD Transdifferentiation is Mediated by Chromatin Remodeling Deficiencies
Raluca Gordan, Duke University
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The Enhancer Mutation Problem: Figuring out Phenotype Based on Genotype
Nadav Ahituv, UCSF
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Break
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Moderated Discussion
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Coffee & Check-In
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Understanding DNA-binding Preferences of Transcription Factor Homologs
Trevor Siggers, Boston University
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Challenges in Sequence-to-Expression Modeling
Saurabh Sinha, University of Illinois Urbana-Champaign
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Modeling Gene Expression and Chromatin State in Terms of Regulatory Sites
Erik Van Nimwegen, Basel University
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Break
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Selecting Genomics Assays
William Stafford Noble, University of Washington
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Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
Teresa Przytycka, National Institutes of Health
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Lunch
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Personal Transcription Factor Binding Site Mutations Point to Personal Medical Histories
Gill Bejerano (Stanford University)
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Telomere Length, Nature and Nurture
Martin Kupiec, Tel Aviv University
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Break
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Moderated Discussion
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Coffee & Check-In
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Hierarchical Regulatory Domain Inference from Hi-C Data
Bartek Wilczynski, University of Warsaw
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Analysis Methods for Single Cell RNA-seq with Application to T-cell Function
Nir Yosef, UC Berkeley
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Genome-wide Prediction of Enhancers and Their Target Genes using ENCODE data
Zhiping Weng, University of Massachusetts
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Break
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Utilizing de Bruijn Graphs in Universal Sequence Design for Discovery of Regulatory Elements
Ron Shamir, Tel-Aviv University, Yaron Orenstein, MIT
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Modelling Gene Expression Dynamics with Gaussian Processes
Magnus Rattray, University of Manchester
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Lunch
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Discovery of Transcription Factor Binding Motifs from Large Sequence Sets
Esko Ukkonen, Helsinki University
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Chromatin Dynamics and Gene Regulation During Motor Neuron Programming
Mahmoud Ibrahim, Max-Delbrueck-Center, Berlin
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Break
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Moderated Discussion