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December 01, 2014
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Date:21SundayJanuary 2024Lecture
The Clore Center for Biological Physics
More information Time 13:15 - 14:15Title How informative are structures of dna-bound proteins for revealing binding mechanisms inside cells? the case of the Origin of Replication Complex (ORC)Location Nella and Leon Benoziyo Physics BuildingLecturer Prof. Naama Barkai
Department of Molecular Genetics- Faculty of BiochemistryOrganizer Department of Physics of Complex SystemsContact Abstract Show full text abstract about The Origin Recognition Complex (ORC) seeds the replication-f...» The Origin Recognition Complex (ORC) seeds the replication-fork by binding DNA replication origins, which in budding yeast contain a 17bp DNA motif. High resolution structure of the ORC-DNA complex revealed two base-interacting elements: a disordered basic patch (Orc1-BP4) and an insertion helix (Orc4-IH).
To define ORC elements guiding its DNA binding in-vivo, we mapped genomic locations of 38 designed ORC mutants. We revealed that different ORC elements guide binding at different motifs sites, and these correspond only partially to the structure- described interactions. In particular, we show that disordered basic patches are key for ORC-motif binding in-vivo, including one lacking from the structure. Finally i will discuss how those disordered elements, which insert into the minor-groove can still guide specific ORC-DNA recognition.
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Date:25ThursdayJanuary 2024Lecture
Special Guest Seminar
More information Time 11:00 - 12:00Title "Discovery of a novel class of antivirals: single-dose, 'drive' therapies with a high genetic barrier to resistance"Location Nella and Leon Benoziyo Building for Biological SciencesLecturer Prof. Leor Weinberger
University of California San FranciscoContact -
Date:25ThursdayJanuary 2024Lecture
Vision and AI
More information Time 12:15 - 13:15Title Towards a Realistic Immersive Audio GenerationLocation Jacob Ziskind BuildingLecturer Eliya Nachmani
Google ResearchOrganizer Department of Computer Science and Applied MathematicsContact Abstract Show full text abstract about Recent advancements in audio and language processing have yi...» Recent advancements in audio and language processing have yielded significant progress in audio analysis and synthesis. In the realm of audio analysis, researchers are addressing the crucial challenges of Automatic Speech Recognition (ASR), Sound Localization, Event Detection, Emotion Recognition, Speaker Diarization, and Speaker Identification. Meanwhile, in the synthesis domain efforts are focused on Speech Synthesis, Speech Separation, and Audio Vocoders. Despite the progress made, there remains a significant void in the advancement of neural audio generative models that possess the capability to understand audio landscapes and skillfully create or improve new auditory surroundings. In this talk, I will address two pivotal research directions aimed at closing this gap:
(i) The development of an oracle-powered speechbot involves achieving a profound understanding of the acoustic environment and integrating comprehensive world knowledge. I'll present Spectron, a speechbot that leverages a Large Language Model (LLM) to perform question answering (QA) and speech continuation.
(ii) The second challenge revolves around audio separation for a multitude of sources. While current audio separation literature predominantly focuses on isolating single-source domains like speech or sound events, the real-world scenario demands the separation of diverse sources such as speech, noise, and acoustic events. I will present a solution capable of separating numerous speakers based on a single microphone recording as well as a theoretical upper bound for the single channel speech separation.
Concluding the discussion, I will outline future research directions, focusing on the evolution of multi-agent speechbots, the advancement of generative audio models within the 3D domain, and the fusion of synthetic sounds into real-world environments.
Short Bio:
Eliya Nachmani currently serves as a research scientist at Google Research, specializing in machine learning for audio processing. Prior to his role at Google, he conducted research at Facebook AI Research (FAIR) and pursued his Ph.D. at Tel-Aviv University. Eliya holds a Master of Science in Electrical Engineering from Tel-Aviv University and a Bachelor of Science in Electrical Engineering from the Technion. Website: https://sites.google.com/view/eliya-nachmani/home
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Date:25ThursdayJanuary 2024Lecture
Geometric Functional Analysis and Probability Seminar
More information Time 13:30 - 14:30Title Determinants of Laplacians and heat-kernel boundsLocation Jacob Ziskind BuildingLecturer Renan Gross
TAUOrganizer Department of MathematicsContact Abstract Show full text abstract about In this talk, we will smash together spanning trees, Brownia...» In this talk, we will smash together spanning trees, Brownian motion and negative-curvature manifolds.
The "tree entropy" of a converging sequence of graphs roughly counts how many spanning trees per vertex each graph has, and can be calculated using the Laplacian of the graph. A similar quantity can be defined for compact hyperbolic surfaces, but is much trickier to compute. In this talk we will discuss spectral and geometric conditions which lead to its convergence for locally-converging surfaces. The proof involves analyzing the return density of Brownian motion to the origin, averaged over the entire surface.
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Date:25ThursdayJanuary 2024Lecture
p53: not just a cell-autonomous tumor suppressor
More information Time 14:00 - 15:00Location Max and Lillian Candiotty BuildingLecturer Prof. Moshe Oren
Professor emeritus Director, the Moross Integrated Cancer Center Dept. of Molecular Cell Biology Weizmann Institute of ScienceOrganizer Dwek Institute for Cancer Therapy ResearchContact -
Date:25ThursdayJanuary 2024Lecture
The interplay of bulky DNA damages, transcription and epigenetics
More information Time 15:00 - 16:00Location Nella and Leon Benoziyo Building for Biological SciencesLecturer Dr. Sheera Adar
Dept. of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University of JerusalemOrganizer Department of Biomolecular SciencesContact Abstract Show full text abstract about DNA damages compromise the ability of the genome to function...» DNA damages compromise the ability of the genome to function. Cells from all organisms have mechanisms to recognize DNA damage, initiate a signaling response, and recruit repair enzymes. Complete failure of these mechanisms leads to cell death. Incorrect or inefficient repair leads to mutations and cancer. Our work focuses on damages that distort the DNA helix, specifically the carcinogenic dimers induced by ultraviolet (UV) radiation, and the bulky DNA adducts induced by cigarette smoke and by the chemotherapy drug cisplatin. These types of damages are especially deleterious as they block RNA and DNA polymerases. We apply genomic methods to map DNA damages and their repair at high resolution in human genomes. In parallel, we study the effects of damage on gene expression and chromatin accessibility. Both chromatin structure and transcription influence the sensitivity to damage and the efficiency of repair. At the same time, damages elicit changes in chromatin accessibility and a dramatic gene expression shutdown. In my talk, I will give an overview of ongoing research projects in our lab that study the cellular responses to UV-, smoking- and cisplatin-induced damages, and are central to understanding both the carcinogenic process and the mechanisms of chemotherapy resistance. -
Date:28SundayJanuary 2024Lecture
The Clore Center for Biological Physics
More information Time 13:15 - 14:15Title Some organizing principles behind microbial community dynamicsLocation Nella and Leon Benoziyo Physics BuildingLecturer Dr. Amir Erez -Racah
Institute of Physics of the Hebrew University of JerusalemOrganizer Clore Center for Biological PhysicsContact Abstract Show full text abstract about Microbial ecosystems, pivotal in global ecological stability...» Microbial ecosystems, pivotal in global ecological stability, display a diverse array of species, influenced by complex interactions. When considering environments with changing nutrient levels, we have recently suggested an 'early bird' effect. This phenomenon, which results from changing nutrient levels, initial and fast uptake of resources confers an advantage, significantly altering microbial growth dynamics. In serial dilution cultures with varying nutrient levels, this effect leads to shifts in diversity, demonstrating that microbial communities do not adhere to a universal nutrient-diversity relationship. Using a consumer-resource, serial dilution modeling framework, we simulate scenarios of changing nutrient balance, such as variations in phosphorous availability in rainforest soils, to predict a possible lag in ecosystems response near a loss of diversity transition point. Lastly, we explore the notion of 'microbial debt', a form of the early bird advantage, where microbes initially grow rapidly at the cost of later growth or increased mortality. This dynamic, exemplified in both classical chemostat and serial dilution cultures, reveals that such debt can convey an advantage, with varying outcomes on community structure depending on the nature of the trade-off involved. Together, these studies illuminate some organizing principles behind microbial dynamics, balancing growth and survival in changing environments. -
Date:29MondayJanuary 2024Lecture
Foundations of Computer Science Seminar
More information Time 11:15 - 12:15Title Memory Checking Requires Logarithmic OverheadLocation Jacob Ziskind BuildingLecturer Ilan Komargodski
Hebrew U.Organizer Department of Computer Science and Applied MathematicsContact Abstract Show full text abstract about In this talk, I will explain the challenges that arise from ...» In this talk, I will explain the challenges that arise from the task of maintaining a large database in a remote and untrusted storage. The technical part of the talk will describe a new and tight logarithmic lower bound for memory checkers, an algorithmic tool used to enforce the integrity of the remote server.
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Date:30TuesdayJanuary 2024Lecture
The impact of gene amplification on cellular physiology and cell-cell interactions
More information Time 10:00 - 11:00Location Nella and Leon Benoziyo Building for Biological SciencesLecturer Shir Marom
Dept. of Biomolecular SciencesOrganizer Department of Biomolecular SciencesContact -
Date:30TuesdayJanuary 2024Lecture
One molecular- and one circuit-level insight into cognition from studying Drosophila
More information Time 12:30 - 13:30Location Gerhard M.J. Schmidt Lecture HallLecturer Prof. Gaby Maimon
HHMI, The Rockfeller University, NYOrganizer Department of Brain SciencesContact Abstract Show full text abstract about A major goal of cognitive neuroscience is to clarify the fun...» A major goal of cognitive neuroscience is to clarify the functions of central brain regions. Over the past decade, the high-level functional architecture of a region in the middle of the insect brain––the central complex––has come into focus. I will start by briefly summarizing our understanding of the central complex as a microcomputer that calculates the values of angles and two-dimensional vectors important for guiding navigational behavior. I will then describe some recent findings on this brain region, revealing (1) how neuronal calcium spikes, mediated by T-type calcium channels, augment spatial-vector calculations and (2) how an angular goal signal is converted into a locomotor steering signal. These results provide inspiration for better understanding the roles of calcium spikes and goal signals in mammalian brains.
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Date:30TuesdayJanuary 2024Lecture
Modeling protein complexes in the age of deep learning
More information Time 14:30 - 15:30Location Gerhard M.J. Schmidt Lecture HallLecturer Prof. Dina Schneidman
School of Computer Science and Engineering The Hebrew UniversityOrganizer Department of Chemical and Structural BiologyContact -
Date:01ThursdayFebruary 2024Lecture
Keeping up with the times: From Stem Cells to Organoids, Metabolism and more
More information Time 09:00 - 10:00Location Max and Lillian Candiotty BuildingLecturer Dr. Elena Ainbinder
Stem Cell, Organoids and Advanced Cell Technologies UnitOrganizer Department of Life Sciences Core FacilitiesContact -
Date:01ThursdayFebruary 2024Lecture
Vision and AI
More information Time 12:15 - 13:15Title Building Better Benchmarks to Drive Progress in Language ModelingLocation Jacob Ziskind BuildingLecturer Ofir Press
PrincetonOrganizer Department of Computer Science and Applied MathematicsContact Abstract Show full text abstract about Language models (LMs) have vastly improved over the past few...» Language models (LMs) have vastly improved over the past few years, but they still have not made their way into most people’s daily lives. In this talk, I argue that almost all of the existing language modeling benchmarks are saturated. I explain why I believe that the most important task in NLP right now is to build new, natural and challenging benchmarks that resemble how we want people to use LMs in the real world. I explain why I believe testing language model’s ability to program is the best current method to benchmark them, and discuss a few recent papers in this direction, both mine (SWE-bench) and from other groups.
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Date:01ThursdayFebruary 2024Lecture
Geometric Functional Analysis and Probability Seminar
More information Time 13:30 - 14:30Title Scaling limits for growth driven by reflecting Brownian motionLocation Jacob Ziskind BuildingLecturer Amir Dembo
Stanford UniversityOrganizer Department of MathematicsContact Abstract Show full text abstract about In joint works with Kevin Yang, we consider a stochastic Lap...» In joint works with Kevin Yang, we consider a stochastic Laplacian growth model, that can be viewed as a continuum version of origin-excited random walks. Here, we grow the (d 1)-dimensional manifold M(t) according to a reflecting Brownian motion (RBM) on M(t), stopped at level sets of its boundary local time. An averaging principle for the RBM characterizes the scaling limit for the leading order behavior of the interface (namely, the boundary of M(t)). This limit is given by a locally well-posed, geometric flow-type PDE, whose blow-up times correspond to changes in the diffeomorphism class of the growing set.
Smoothing the interface as we inflate M(t), yields an SPDE for the large-scale fluctuations of an associated height function.
This SPDE is a regularized KPZ-type equation, modulated by a Dirichlet-to-Neumann operator. For d=1 we can further remove the regularization, so the fluctuations of M(t) now have a double-scaling limit given by a singular KPZ-type equation.
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Date:01ThursdayFebruary 2024Lecture
Amino acid substitutants, cancer development, and anti-tumor immunity
More information Time 14:00 - 15:00Location Max and Lillian Candiotty BuildingLecturer Prof. Reuven Agami
Head, Division of Oncogenomics, The Netherlands Cancer Institute Professor, Molecular Genetics, Erasmus Medical Center Rotterdam, And a member of the Oncode institute The NetherlandsOrganizer Dwek Institute for Cancer Therapy ResearchContact -
Date:04SundayFebruary 2024Lecture
Using artificial intelligence to help cows go green
More information Time 13:00 - 14:00Title SAERI -Sustainability and Energy Research Initiative Seminar SeriesLocation Nella and Leon Benoziyo Building for Biological SciencesLecturer Dr. Yaniv Altshuler
MIT Media LabOrganizer Sustainability and Energy Research Initiative (SAERI)Contact -
Date:04SundayFebruary 2024Lecture
The Clore Center for Biological Physics
More information Time 13:15 - 14:30Title Multiscale Lattice Modeling and Simulations of Heterogeneous MembranesLocation Nella and Leon Benoziyo Physics LibraryLecturer Prof. Oded Farago
Biomedical Engineering Department, BGUOrganizer Clore Center for Biological PhysicsContact Abstract Show full text abstract about Mixtures of lipids and cholesterol (Chol) have been served a...» Mixtures of lipids and cholesterol (Chol) have been served as simple model systems for studying the biophysical principles governing the formation of liquid ordered raft domains in complex biological systems. These mixtures exhibit a rich phase diagram as a function of temperature and composition. Much of the focus in these studies has been given to the coexistence regime between liquid ordered and liquid disordered phases which resembles rafts floating in the sea of disordered lipids. In the talk, I will present a new lattice model of binary [1] and ternary [2, 3] mixtures containing saturated and unsaturated lipids, and Chol. Simulations of mixtures of thousands of lipids and cholesterol molecules on time scales of hundreds of microseconds show a very good agreement with experimental and atomistic simulation observations across multiple scale, ranging from the local distributions of lipids to the macroscopic phase diagram of such mixtures. Importantly, we find that the liquid ordered domains are highly heterogeneous and consist of Chol-poor hexagonally packed gel-like clusters surrounded by Chol-rich regions at the domain boundaries. The presence of such nano-domains within the liquid ordered regions appears as a characteristic feature of the liquid-ordered state, and makes the interpretation of scattering data ambiguous in mixtures not exhibiting macroscopic phase separation. -
Date:05MondayFebruary 2024Lecture
Midrasha on Groups Seminar
More information Time 11:15 - 13:00Title The Laplacian on hyperbolic surfaces and minimaxLocation Elaine and Bram Goldsmith Building for Mathematics and Computer SciencesLecturer Guy Kapon
WeizmannOrganizer Department of MathematicsContact Abstract Show full text abstract about The talk is based on Nicolas Bergeron’s book, Sections 5.1–5...» The talk is based on Nicolas Bergeron’s book, Sections 5.1–5.2.
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Date:05MondayFebruary 2024Lecture
Midrasha on Groups Seminar
More information Time 11:15 - 13:00Title The Laplacian on hyperbolic surfaces and minimaxLocation Elaine and Bram Goldsmith Building for Mathematics and Computer SciencesLecturer Guy Kapon
WeizmannOrganizer Department of MathematicsContact Abstract Show full text abstract about The talk is based on Nicolas Bergeron’s book, Sections 5.1–5...» The talk is based on Nicolas Bergeron’s book, Sections 5.1–5.2.
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Date:05MondayFebruary 2024Lecture
Foundations of Computer Science Seminar
More information Time 11:15 - 12:15Title Conflict Checkable and Decodable Codes and Their ApplicationsLocation Jacob Ziskind BuildingLecturer Eliran Kachlon
Tel Aviv UniversityOrganizer Department of Computer Science and Applied MathematicsContact Abstract Show full text abstract about Let C be an error-correcting code over a large alphabet q of...» Let C be an error-correcting code over a large alphabet q of block length n, and assume that a possibly corrupted codeword c is distributively stored among n servers where the ith entry is being held by the ith server. Suppose that every pair of servers publicly announce whether the corresponding coordinates are ``consistent'' with some legal codeword or ``conflicted''. What type of information about c can be inferred from this consistency graph? Can we check whether errors occurred and if so, can we find the error locations and effectively decode? We initiate the study of conflict-checkable and conflict-decodable codes and prove the following main results:
(1) (Almost-MDS conflict-checkable codes:) For every distance d = n-d 0.99. Interestingly, the code is non-linear, and we give some evidence that suggests that this is inherent. Combinatorially, this yields an n-partite graph over [q]^n that contains q^k cliques of size n whose pairwise intersection is at most n-d
