Weizmann Magazine, Spring 2021
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Tsvi Tlusty – C.V
TSVI TLUSTY – C.V. 06/2021 Center for Soft and Living Matter, Institute for Basic Science, Bldg. (#103), Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulju-gun, Ulsan 44919, Korea email: [email protected] homepage: life.ibs.re.kr EDUCATION AND EMPLOYMENT 2015– Distinguished Professor, Department of Physics, UNIST, Ulsan 2015– Group Leader, Center for Soft and Living Matter, Institute for Basic Science 2011–2015 Long-term Member, Institute of Advanced Study, Princeton. 2005–2013 Senior researcher, Physics of Complex Systems, Weizmann Institute. 2000–2004 Fellow, Center for Physics and Biology, Rockefeller University, New York. Host: Prof. Albert Libchaber 1995–2000 Ph.D. in Physics, Weizmann Institute, “Universality in Microemulsions”, Supervisor: Prof. Samuel A. Safran. 1991–1995 M.Sc. in Physics, Weizmann Institute. 1988–1990 B.Sc. in Physics and Mathematics (Talpyot), Hebrew University, Jerusalem. Teaching: Landmark Experiments in Biology (2006); Statistical Physics (2007, 2017-20); Information in Biology (2012); Errors and Codes (IAS, 2012); Theory of Living Matter (2016); Students and post-doctoral fellows (03/2020) Pineros William (postdoc, 2019- ) John Mcbride (postdoc, 2018- ) Somya Mani (postdoc, 2018- ) Tamoghna Das (postdoc, 2018- ) Ashwani Tripathi (postdoc, 2018- ) Sandipan Dutta (postdoc, 2016-2021), Prof. at BIRS Pileni, India Vladimir Reinharz (postdoc, 2018-2020), Prof. at U. Montreal. YongSeok Jho (research fellow, 2016-2017), Prof. at GyeongSang U. Yoni Savir (Ph.D., 2005-2011) Prof. at Technion. Adam Lampert (Ph.D., 2008-2012) Prof. at U. Arizona. Arbel Tadmor (M.Sc., 2006-2008) researcher at TRON. Maria Rodriguez Martinez (Postdoc, 2007-2009), PI at IBM Zurich Tamar Friedlander (Postdoc, 2009 -2012) Prof. -
Mechanistic Mathematical Modeling of Spatiotemporal Microtubule Dynamics and Regulation in Vivo
Research Collection Doctoral Thesis Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo Author(s): Widmer, Lukas A. Publication Date: 2018 Permanent Link: https://doi.org/10.3929/ethz-b-000328562 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library diss. eth no. 25588 MECHANISTICMATHEMATICAL MODELINGOFSPATIOTEMPORAL MICROTUBULEDYNAMICSAND REGULATION INVIVO A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (dr. sc. eth zurich) presented by LUKASANDREASWIDMER msc. eth cbb born on 11. 03. 1987 citizen of luzern and ruswil lu, switzerland accepted on the recommendation of Prof. Dr. Jörg Stelling, examiner Prof. Dr. Yves Barral, co-examiner Prof. Dr. François Nédélec, co-examiner Prof. Dr. Linda Petzold, co-examiner 2018 Lukas Andreas Widmer Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo © 2018 ACKNOWLEDGEMENTS We are all much more than the sum of our work, and there is a great many whom I would like to thank for their support and encouragement, without which this thesis would not exist. I would like to thank my supervisor, Prof. Jörg Stelling, for giving me the opportunity to conduct my PhD research in his group. Jörg, you have been a great scientific mentor, and the scientific freedom you give your students is something I enjoyed a lot – you made it possible for me to develop my own theories, and put them to the test. I thank you for the trust you put into me, giving me a challenge to rise up to, and for always having an open door, whether in times of excitement or despair. -
Weizmann Magazine, Spring 2021
COVID-19 Research Highlights 15 Updates from the Moross Integrated Cancer Center 24 Q&A with International Board Chair Cathy Beck 34 למדע ויצמן מכון ויצמן למדע 13 46 NEW SCIENTISTS UPDATE ON THE FLAGSHIPS MAGAZINE MAGAZINE WEIZMANN MAGAZINE A publication of the Department of Resource WEIZMANN WEIZMANN Development Healing what ails the Earth The new nerve center for neuroscience EDITORIAL STAFF Prof. Roee Ozeri, Vice President for Resource Development Tamar Levine, Director, Department of Resource 6 15 Development SCIENCE BRIEFS COVER STORY Tamar Morad, Head, Donor Communications Maria Yakhnin, Visual and Digital Production TABLE OF CONTENTS TABLE Yarden Jaron, Visual and Digital Production EDITOR Tamar Morad The vaccines are here, and research abounds COPYEDITOR Sharon Reinheimer 20 SCIENCE FEATURES From the President WRITING STAFF Sandy Cash Jennifer Racz Dear Friends, Dinah Elashvili Anne Sperling The one-year mark of the COVID-19 pandemic has passed Tali Galsky Edward Truitt and here in Israel, where the rate of vaccination is the highest in the world, we are starting to see the light at the end of the With thanks to the Department tunnel. Our thoughts are with our many friends around the of Communications world; this is a network which keeps the Institute strong and The anthropocene is upon us Rx for the ocean thriving. DONOR RECOGNITION Coronavirus-related research on campus is bounding Daphna Freeman ahead, and we expect a range of insights from this virus to play Irit Oz a starring role in fending off future pandemics and broaden- 28 34 Ayelet Rais SPOTLIGHT ON Q&A SCIENCE BRIEFS ing our understanding of the immune system. -
Causal Queries from Observational Data in Biological Systems Via Bayesian Networks: an Empirical Study in Small Networks
Causal Queries from Observational Data in Biological Systems via Bayesian Networks: An Empirical Study in Small Networks Alex White and Matthieu Vignes Abstract Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and post- genomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the con- sideration of causal representations of the interactions in living systems. We present the causal formalism and bring it out in the context of biological networks, when the data is observational. We also discuss its ability to decipher the causal infor- mation flow as observed in gene expression. We also illustrate our exploration by experiments on small simulated networks as well as on a real biological data set. Key words: Causal biological networks, Gene regulatory network reconstruction, Direct Acyclic Graph inference, Bayesian networks 1 Introduction Throughout their lifetime, organisms express their genetic program, i.e. the instruc- tion manual for molecular actions in every cell. The products of the expression of this program are messenger RNA (mRNA); the blueprints to produce proteins, the cornerstones of the living world. The diversity of shapes and the fate of cells is a re- sult of different readings of the genetic material, probably because of environmental factors, but also because of epigenetic organisational capacities. The genetic mate- rial appears regulated to produce what the organism needs in a specific situation. We now have access to rich genomics data sets. We see them as instantaneous images of cell activity from varied angles, through different filters. -
Multiscale Modeling in Systems Biology
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051 Multiscale Modeling in Systems Biology Methods and Perspectives ADRIEN COULIER ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1225-5 UPPSALA URN urn:nbn:se:uu:diva-442412 2021 Dissertation presented at Uppsala University to be publicly examined in 2446 ITC, Lägerhyddsvägen 2, Uppsala, Friday, 10 September 2021 at 10:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Mark Chaplain (University of St Andrews). Abstract Coulier, A. 2021. Multiscale Modeling in Systems Biology. Methods and Perspectives. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051. 60 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1225-5. In the last decades, mathematical and computational models have become ubiquitous to the field of systems biology. Specifically, the multiscale nature of biological processes makes the design and simulation of such models challenging. In this thesis we offer a perspective on available methods to study and simulate such models and how they can be combined to handle biological processes evolving at different scales. The contribution of this thesis is threefold. First, we introduce Orchestral, a multiscale modular framework to simulate multicellular models. By decoupling intracellular chemical kinetics, cell-cell signaling, and cellular mechanics by means of operator-splitting, it is able to combine existing software into one massively parallel simulation. Its modular structure makes it easy to replace its components, e.g. to adjust the level of modeling details. We demonstrate the scalability of our framework on both high performance clusters and in a cloud environment. -
Advancing a Systems Cell-Free Metabolic Engineering Approach to Natural Product Synthesis and Discovery
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery Benjamin Mohr University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Mohr, Benjamin, "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6837 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Mohr entitled "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Energy Science and Engineering. Mitchel Doktycz, Major Professor We have read this dissertation and recommend its acceptance: Jennifer Morrell-Falvey, Dale Pelletier, Michael Simpson, Robert Hettich Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Pintz Mohr December 2019 c by Benjamin Pintz Mohr, 2019 All Rights Reserved. -
Weizmann Magazine, Spring 2021
COVID-19 Research Highlights 14 Updates from the Moross Integrated Cancer Center 24 Q&A with International Board Chair Cathy Beck 34 למדע ויצמן מכון ויצמן למדע 13 46 NEW SCIENTISTS UPDATE ON THE FLAGSHIPS MAGAZINE MAGAZINE WEIZMANN MAGAZINE A publication of the Department of Resource WEIZMANN WEIZMANN Development Healing what ails the Earth The new nerve center for neuroscience EDITORIAL STAFF Prof. Roee Ozeri, Vice President for Resource Development Tamar Levine, Director, Department of Resource 6 14 Development SCIENCE BRIEFS COVER STORY Tamar Morad, Head, Donor Communications Maria Yakhnin, Visual and Digital Production TABLE OF CONTENTS TABLE Yarden Jaron, Visual and Digital Production EDITOR Tamar Morad The vaccines are here, and research abounds From the President COPYEDITOR Dear Friends, Sharon Reinheimer 20 The one-year mark of the COVID-19 pandemic has SCIENCE FEATURES passed and here in Israel, where the rate of vaccination WRITING STAFF is the highest in the world, we are starting to see the Sandy Cash Jennifer Racz light at the end of the tunnel. Our thoughts are with our Dinah Elashvili Anne Sperling many friends around the world; this is a network which Tali Galsky Edward Truitt keeps the Institute strong and thriving. Coronavirus-related research on campus is With thanks to the Department bounding ahead, and we expect a range of insights from of Communications this virus to play a starring role in fending off future The anthropocene is upon us Rx for the ocean pandemics and broadening our understanding of the DONOR RECOGNITION immune system. Daphna Freeman While we were required to pull back on the number Irit Oz of scientists and staff on campus in the last year, it 28 34 Ayelet Rais SPOTLIGHT ON Q&A SCIENCE BRIEFS is remarkable that unlike many other institutions, 2 Discoveries and other news Weizmann has continued to advance its research across all fields. -
Israel Prize
Year Winner Discipline 1953 Gedaliah Alon Jewish studies 1953 Haim Hazaz literature 1953 Ya'akov Cohen literature 1953 Dina Feitelson-Schur education 1953 Mark Dvorzhetski social science 1953 Lipman Heilprin medical science 1953 Zeev Ben-Zvi sculpture 1953 Shimshon Amitsur exact sciences 1953 Jacob Levitzki exact sciences 1954 Moshe Zvi Segal Jewish studies 1954 Schmuel Hugo Bergmann humanities 1954 David Shimoni literature 1954 Shmuel Yosef Agnon literature 1954 Arthur Biram education 1954 Gad Tedeschi jurisprudence 1954 Franz Ollendorff exact sciences 1954 Michael Zohary life sciences 1954 Shimon Fritz Bodenheimer agriculture 1955 Ödön Pártos music 1955 Ephraim Urbach Jewish studies 1955 Isaac Heinemann Jewish studies 1955 Zalman Shneur literature 1955 Yitzhak Lamdan literature 1955 Michael Fekete exact sciences 1955 Israel Reichart life sciences 1955 Yaakov Ben-Tor life sciences 1955 Akiva Vroman life sciences 1955 Benjamin Shapira medical science 1955 Sara Hestrin-Lerner medical science 1955 Netanel Hochberg agriculture 1956 Zahara Schatz painting and sculpture 1956 Naftali Herz Tur-Sinai Jewish studies 1956 Yigael Yadin Jewish studies 1956 Yehezkel Abramsky Rabbinical literature 1956 Gershon Shufman literature 1956 Miriam Yalan-Shteklis children's literature 1956 Nechama Leibowitz education 1956 Yaakov Talmon social sciences 1956 Avraham HaLevi Frankel exact sciences 1956 Manfred Aschner life sciences 1956 Haim Ernst Wertheimer medicine 1957 Hanna Rovina theatre 1957 Haim Shirman Jewish studies 1957 Yohanan Levi humanities 1957 Yaakov -
Scientific Activities 2002
Scientific Activities 2002 Rehovot, Israel Edited, Designed and Typeset by Aviva Ovadia Cover Design by Shoshana Zioni, Graphics Department We wish to thank all the secretarial staff who worked on this project, without whose help this publication would not be possible. Printed in Israel By Publishing Department Weizmann Institute of Science ISSN 0083-7849 Contents Board of Governors vii Scientific and Academic Advisory Committee xv Officers of the Weizmann Institute xvii Weizmann Institute of Science xix Faculty of Biochemistry Faculty of Biochemistry - Overview 3 Biological Chemistry 5 Molecular Genetics 13 Plant Sciences 21 Biological Services 27 Avron-Wilstätter Minerva Center for Research in Photosynthesis 29 Y. Leon Benoziyo Institute for Molecular Medicine 31 Dr. Josef Cohn Minerva Center for Biomembrane Research 33 Crown Human Genome Center 35 Mel Dobrin Center for Nutrition 37 Leo and Julia Forchheimer Center for Molecular Genetics 39 Kekst Family Center for Medical Genetics 41 Charles W. and Tillie K. Lubin Center for Plant Biotechnology 43 M.D. Moross Institute for Cancer Research 45 David and Fela Shapell Family Center for Genetic Disorders Research 47 Harry and Jeannette Weinberg Center for Plant Molecular Genetics Research 49 Faculty of Biology Faculty of Biology - Overview 53 Biological Regulation 55 Immunology 61 Molecular Cell Biology 69 Neurobiology 83 Veterinary Resources 89 Helen and Norman Asher Center for Human Brain Imaging 91 Nella and Leon Benoziyo Center for Neurosciences 93 Carl and Micaela Einhorn-Dominic Institute for Brain Research 95 Murray H. and Meyer Grodetsky Center for Research of Higher Brain Functions 97 Robert Koch-Minerva Center for Research in Autoimmune Diseases 99 Belle S. -
Bioengineering Professor Trey Ideker Wins 2009 Overton Prize
Bioengineering Professor Trey Ideker Wins 2009 Overton Prize March 13, 2009 Daniel Kane University of California, San Diego bioengineering professor Trey Ideker-a network and systems biology pioneer-has won the International Society for Computational Biology's Overton Prize. The Overton prize is awarded each year to an early-to-mid-career scientist who has already made a significant contribution to the field of computational biology. Trey Ideker is an Associate Professor of Bioengineering at UC San Diego's Jacobs School of Engineering, Adjunct Professor of Computer Science, and member of the Moores UCSD Cancer Center. He is a pioneer in using genome-scale measurements to construct network models of cellular processes and disease. His recent research activities include development of software and algorithms for protein network analysis, network-level comparison of pathogens, and genome-scale models of the response to DNA-damaging agents. "Receiving this award is a wonderful honor and helps to confirm that the work we have been doing for the past several years has been useful to people," said Ideker. "This award also provides great recognition to UC San Diego which has fantastic bioinformatics programs both at the undergraduate and graduate level. I could never have done it without the help of some really first-rate bioinformatics and bioengineering graduate students," said Ideker. Ideker is on the faculty of the Jacobs School of Engineering's Department of Bioengineering, which ranks 2nd in the nationfor biomedical engineering, according to the latest US News rankings. The bioengineering department has ranked among the top five programs in the nation every year for the past decade. -
The Myth of Junk DNA
The Myth of Junk DNA JoATN h A N W ells s eattle Discovery Institute Press 2011 Description According to a number of leading proponents of Darwin’s theory, “junk DNA”—the non-protein coding portion of DNA—provides decisive evidence for Darwinian evolution and against intelligent design, since an intelligent designer would presumably not have filled our genome with so much garbage. But in this provocative book, biologist Jonathan Wells exposes the claim that most of the genome is little more than junk as an anti-scientific myth that ignores the evidence, impedes research, and is based more on theological speculation than good science. Copyright Notice Copyright © 2011 by Jonathan Wells. All Rights Reserved. Publisher’s Note This book is part of a series published by the Center for Science & Culture at Discovery Institute in Seattle. Previous books include The Deniable Darwin by David Berlinski, In the Beginning and Other Essays on Intelligent Design by Granville Sewell, God and Evolution: Protestants, Catholics, and Jews Explore Darwin’s Challenge to Faith, edited by Jay Richards, and Darwin’s Conservatives: The Misguided Questby John G. West. Library Cataloging Data The Myth of Junk DNA by Jonathan Wells (1942– ) Illustrations by Ray Braun 174 pages, 6 x 9 x 0.4 inches & 0.6 lb, 229 x 152 x 10 mm. & 0.26 kg Library of Congress Control Number: 2011925471 BISAC: SCI029000 SCIENCE / Life Sciences / Genetics & Genomics BISAC: SCI027000 SCIENCE / Life Sciences / Evolution ISBN-13: 978-1-9365990-0-4 (paperback) Publisher Information Discovery Institute Press, 208 Columbia Street, Seattle, WA 98104 Internet: http://www.discoveryinstitutepress.com/ Published in the United States of America on acid-free paper. -
Snapshot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
SnapShot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel 326 Cell 143, October 15, 2010 ©2010 Elsevier Inc. DOI 10.1016/j.cell.2010.09.050 See online version for legend and references. SnapShot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel Transcription regulation and signaling networks are composed of recurring patterns called network motifs. Network motifs are much more prevalent in biological networks than would be expected by comparison to random networks and comprise almost the entire network structure. The same small set of network motifs has been found in diverse organ- isms ranging from bacteria to plants to humans. Experiments show that each network motif can carry out specific dynamic functions in the computation done by the cell. Here we review the main classes of network motifs and their biological functions. Autoregulation Negative autoregulation (NAR) occurs when a transcription factor represses the transcription of its own gene. (We use transcription to help make examples concrete; all circuits described here could operate also in other regulatory modes, e.g., a protein inhibiting its own activity by autophosphorylation.) This occurs in about half of the repressors in E. coli and can speed up the response time of gene circuits and reduce cell–cell variation in protein levels that are due to fluctuations in production rate. Positive autoregulation occurs when a transcription factor enhances its own rate of production. Response times are slowed and variation is usually enhanced. This motif, given sufficient cooperativity, can lead to bimodal (all-or-none) distributions, where the concentration of X is low in some cells but high in others.