Program

PDI2020 Program

Tuesday, October 18
Time	Session/Lecture info
08:30-09:15	Registration & Coffee
08:30-09:15
09:15-09:30	Welcome and opening remarks
09:15-09:30
09:30-11:00	Protein-DNA binding: A protein perspective
09:30-10:00	Peter Wolynes, Rice University, USA The NfKB-IkB Network and other stories at the nexus of Systems Biology and Physical Chemistry
10:00-10:30	Barry Stoddard, Fred Hutchinson Cancer Research Center, USA Self or non-self: structural and mechanistic studies of multifunctional phage restriction endonuclease
10:30-11:00	Yael Mandel-Guterfreund, Technion - Israel Institute of Technology, IL A novel role for a lncRNA-Transcription Factor Interaction in human
11:00-11:30	Coffee Break
11:00-11:30
11:30-13:00	Protein-DNA: Affinity
11:30-12:00	Junji Iwahara, University of Texas at Galveston, USA Electrostatics of proteins and DNA by NMR spectroscopy
12:00-12:30	Aseem Ansari, St. Jude Children's Research Hospital, USA Unveiling masked recognition modes of natural and synthetic DNA binders
12:30-13:00	Raluca Gordan, Duke University, USA The mutagenic consequences of transcription factor binding to DNA
13:00-14:00	Lunch
13:00-14:00
14:00-15:30	Protein-DNA binding: A DNA perspective
14:00-14:30	Polly Fordyce, Stanford University, USA Short tandem repeats bind transcription factors to tune eukaryotic gene expression
14:30-15:00	David Lukatsky, Ben Gurion University, IL Repetitive DNA Sequence Elements Regulate Gene Expression in Embryonic Stem Cells
15:00-15:15	Sudipta Kumar Sinha, Indian Institute of Technology Ropar, IN The Functional Responses of Protein-DNA Interactions
15:15-15:30	Flash Talks: I
15:30-16:00	Coffee Break
15:30-16:00
16:00-17:15	Protein-DNA binding: A DNA perspective
16:00-16:30	Hagen Hofmann, Weizmann Institute of Science, IL Allostery in DNA drives phenotype switching
16:30-17:00	Remo Rohs, University of Southern California, USA Deep learning reveals mechanisms of protein-DNA binding
17:00-17:15	Flash Talks: II
17:15-19:00	Poster Session
17:15-19:00

Wednesday, October 19
Time	Session/Lecture info
08:30-09:00	Morning Coffee
08:30-09:00
09:00-10:30	Protein-DNA: Specificity
09:00-09:30	Naama Barkai, Weizmann Institute of Science, IL How transcription factor find their binding sites in large genomes: a role for intrinsically disordered regions
09:30-10:00	Yacine Graba, Aix-Marseille University, FR Hox protein mode of action: insights from genetic and molecular approaches
10:00-10:30	Harmen Bussemaker, Columbia University, USA Probing the DNA binding specificity of transcription factor complexes with deep sequencing and biophysically interpretable machine learning
10:30-11:00	Coffee Break
10:30-11:00
11:00-12:30	DNA Search mechanism
11:00-11:30	Victor Muñoz, University of California, Merced, USA Experimental Analysis of the Molecular Mechanisms used by Eukaryotic Master Transcription Factors for Efficient Scanning of Highly Rugged DNA Landscapes
11:30-12:00	Achillefs Kapanidis, Oxford University, UK Unlocking transcription mechanisms via imaging real-time reactions
12:00-12:15	Yaron Orenstein, Bar-Ilan University, IL DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class convolutional neural networks
12:15-12:30	Martin Pacesa, EPFL, CH Target-induced conformational activation and mismatch tolerance of CRISPR-Cas9
12:30-14:00	Lunch
12:30-14:00
14:00-15:15	DNA Search mechanism
14:00-14:30	Ralf Metzler, University of Potsdam, DE Diffusion and reaction control in molecular signalling
14:30-15:00	Robert Holyst, Institute of Physical Chemistry, Warsaw, PL Diffusion and flow in complex liquids - 100 years after Albert Einstein
15:00-15:15	Khalil Joron, The Hebrew University of Jerusalem, IL The structural basis of apo sigma-70's typical inability to bind DNA on its own
15:15-15:45	Coffee Break
15:15-15:45
15:45-17:00	DNA Search mechanism
15:45-16:15	Richard Fishel, Ohio State University, USA The Sliding Clamps of Mismatch Repair
16:15-16:45	Norbert Reich, University of California, Santa Barbara, USA DNA methyltransferses: novel translocation and recognition mechanisms
16:45-17:00	Tanaya Bose, Weizmann Institute of Science, IL Glimpse into origin of life: From RNA to proteins

Thursday, October 20
Time	Session/Lecture info
08:30-09:00	Morning Coffee
08:30-09:00
09:00-10:30	Protein-DNA: from nucleosome to Chromatin
09:00-09:30	José Onuchic, Rice University, USA The Three-dimensional Architecture Of The Human Genome: Understanding The Physical Mechanisms Controlling Gene Expression
09:30-10:00	Andrew Spakowitz, Stanford University, USA Physical Modeling of Chromosomal Dynamics during Meiosis
10:00-10:30	Anatoly Kolomeisky, Rice University, USA How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA
10:30-11:00	Coffee Break
10:30-11:00
11:00-12:30	Protein-DNA: from nucleosome to Chromatin
11:00-11:30	Gijs Wuite, Vrije Universiteit Amsterdam, NL Nonlinear mechanics of human mitotic chromosomes
11:30-12:00	Ariel Kaplan, Technion - Israel Institute of Technology, IL Nucleosomes, linker histones and DNA: Extended and dynamic interactions control compaction
12:00-12:15	Cameron Glasscock, University of Washington, USA De novo design of sequence-specific DNA binding proteins
12:15-12:30	Sujeet Kumar Mishra, Jawaharlal Nehru University, IN How Multiple Transcription Factors binds to Nucleosomal DNA
12:30-14:00	Lunch
12:30-14:00
14:00-15:15	Protein-DNA: from nucleosome to Chromatin
14:00-14:30	Yuval Garini, Technion - Israel Institute of Technology, IL Order and Chaos in the nucleus mediated by DNA-Protein interaction
14:30-15:00	Vladimir Teif, University of Essex, UK Transcription factors and nucleosomes: playmates, competitors and more
15:00-15:15	Haim Rozenberg, Weizmann Institute of Science, IL How a small drug molecule stabilizes the tumor-suppressor protein p53 and its binding to DNA
15:15-15:45	Coffee Break
15:15-15:45
15:45-17:15	Biophysics of gene-expression machinery
15:45-16:15	Eric Greene, Columbia University, USA single molecule studies of homologous DNA recombination
16:15-16:45	Aleksei Aksimentiev, University of Illinois, USA Single molecule biophysics in silico: from replication proteins to viruses
16:45-17:15	Tali Haran, Technion - Israel Institute of Technology, IL The mechanistic origin of p53 selectivity and functionality

Organizers

Yaakov (Koby) Levy
Department of Chemical and Structural Biology
Ariel Afek
Department of Chemical and Structural Biology

Coordinator

Lior Drori
Lior.drori@weizmann.ac.il
+972 (8)9343957

Program

PDI2020 Program

Tuesday, October 18

Organizers

Sponsors

Coordinator