The 2nd workshop held by the Center for Evolutionary Genomics and Medicine (EGM) is proud to host Dr. Anshul Kundaje, a genomics expert from Stanford University.
The workshop will be preceded by an open lecture given by Dr. Kundaje in the framework of the Department of Life Sciences seminar series (December 12).
IMPORTANT: This hands-on workshop requires registration and is limited to 20 attendants, preferably students. The list of attendents will close on a 'first come-first serve' basis. To register: please email dmishmar@bgu.ac.il
The Center for Evolutionary Genomics and Medicine (EGM)
Genomics Workshop
December 12, 2016
Dr. Anshul Kundaje will give an open lecture the framework of the Department of Life Sciences seminar series to be held at 14.10 in the Department:
Learning the combinatorial regulatory code of chromatin dynamics during hematopoietic differentiation
Day One - December 13th, 2016: OPEN DAY
Morning Session 08.30-12.00
Auditorium, Ilse Katz Institute for Nanoscale Science and Technology (#51)
lectures given by four speakers (35 minutes each).
Light refreshments
Anshul Kundaje (Stanford University)
Decoding the human genome using large-scale functional genomics and machine learning.
Einat Hazkani-Covo (Open University)
Ancient mitochondrial pseudogenes and the evolution of genome structure
Coffee Break
Tomer Hertz (Ben-Gurion University of the Negev)
TBA
Oren Ram (Hebrew University)
Charting the mammalian chromatin landscape: From mixed populations to single cells
Coffee and Cookies
Lunch: Dr. Kundaje with selected students
Afternoon Session
Room 401, Ruth and Heinz-Horst Deichmann Classroom and Computer Lab Building (#35)
* Introduction to genomic data analysis and basics of machine learning methods for integrative analysis
* IIntroduction to NGS functional genomics data
* Best practices for QC and data processing of common functional genomic data types
* Introduction to state-of-the-art NGS data processing pipelines (ChIP-seq, DNAse-seq, RNA-seq) from the ENCODE projectIntroduction to state-of-the-art NGS data processing pipelines (ChIP-seq, DNAse-seq, RNA-seq) from the ENCODE project
Intended audience: This an introductory session, but participants are expected to have some background on functional genomics.
Dinner – Dr. Kundaje with selected EGM members
Day Two - December 14th, 2016
Room 401, Ruth and Heinz-Horst Deichmann Classroom and Computer Lab Building (#35)
Morning and afternoon sessions: The entire day will be dedicated to introducing novel deep learning techniques for analysis of regulatory genomic data including a hands-on, interactive tutorial to faculty and students. Topics include
* Machine learning basics for integrative genomic data analysisMachine learning basics for integrative genomic data analysis
* Supervised machine learning
* InIntroduction to deep neural networks
* Hands-on interactive session for training deep neural networks on regulatory DNA sequence data
Intended audience: This is an introductory session. Participants are not expected to have any experience with deep machine learning. Only basic knowledge of programming is required (e.g. participants show know what variables and functions are). Participants will not be writing code, but simply running and occasionally editing parameters through interactive sessions in a web browser.
Requirements: Laptops with modern web browsers and an internet connection.
Lunch with selected workshop attendants
Dinner with selected EGM members
Day Three - December 15th, 2016
Room 401, Ruth and Heinz-Horst Deichmann Classroom and Computer Lab Building (#35)
Morning session: Sessions on integrative analysis of histone modification data to learn and visualize chromatin states. Topics covered
* Basics of Hidden Markov Models
* Introduction to the ChromHMM package for learning chromatin statesIntroduction to the ChromHMM package for learning chromatin states
* Interactive session on interacting with the ENCODE and Roadmap Epigenomics portals.
Intended audience: Participants are expected to have some experience in analyzing Next-Gen data.
Lunch
