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SUMMARY:Genome Organization: Integrating Mathematics\, Physics and Computa
 tion for Advances in Biology and Medicine
DTSTART;VALUE=DATE:20260317
DTSTAMP:20260416T025128Z
UID:1eb448dceafbe91ae159049c043d355c0d32c11c76eb4aaa51b750ea
CATEGORIES:Conferences - Seminars
DESCRIPTION:You can apply to participate and find all the relevant informa
 tion (speakers\, abstracts\, program\,...) on the event website: https://
 www.cecam.org/workshop-details/genome-organization-integrating-mathematics
 -physics-and-computation-for-advances-in-biology-and-medicine-1466.\n\nReg
 istration is required to attend the full event\, take part in the social a
 ctivities and present a poster at the poster session (if any).  However\,
  the EPFL community is welcome to attend specific lectures without re
 gistration if the topic is of interest to their research. Do not hesitate 
 to contact the CECAM Event Manager if you have any question.\n\nDescript
 ion\n\nAdvances in high-speed computational platforms and innovative algor
 ithms are opening opening opportunities  for modeling in biology as never
  before [1\, 2]. In turn\, these advances are driving biology and medicine
  forward\, as evidenced during the Covid-19 pandemic [3]. \nWhile there a
 re many general mathematical methods that can be applied widely like linea
 r algebra routines and fast summation algorithms\, the most successful app
 roaches are tailored and tightly connected with both the application at ha
 nd and the computing platform. Genome organization is a prominent area whe
 re a variety of models and methods — from atomistic to polymer levels 
 — is critically needed to bridge experimental data and push science fron
 tiers. Genome organization refers to the folding of the genome material\, 
 or the chromatin fiber that makes up chromosomes\, in the cell nucleus of 
 higher organisms. \nThis folding and dynamics of the chromatin fiber regu
 lates life’s essential processes like gene expression\, DNA repair\, and
  cell differentiation\, and thusimpacts human disease. As our appreciation
  for the diversity and flexibility of DNA on the base-pair level has deepe
 ned (e.g.\, [4])\, its large-scale bending and coiling around histone prot
 eins to form the chromosomal material in higher organisms has posed many s
 tructural and mechanistic questions [5–8]. The genomic information in th
 e DNA is packaged in a hierarchy of levels\, from the nucleosome tocondens
 ed chromatin fibers to chromosomes and chromosomal territories. Profound q
 uestions regarding DNA geometry\, topology\, and function span from the si
 ngle nucleosome/base-pair level to condensed chromosomal arrangements on t
 he mega base-pair level in the metaphasecell cycle. We lack an understandi
 ng of both structures and kinetics of the chromatin fiber and chromosomosa
 l arrangements. These transitions are tightly controlled by a host of prot
 eins\, which can directly bind to the chromatin fiber or induce chemical m
 odifications of DNA and histones\, as well as long noncoding RNAs. Cohesin
  and condensin complexes also operate to regulate gene expression as molec
 ular machines in an energy-dependent manner [9–13].\nTheoretical and com
 putational physics have played a pivotal role in advancing our understandi
 ng of these processes\, offering models that describe the dynamic behavior
  of chromatin loops and that predict how physical parameters influence res
 ulting genome organization [14]. Despite major progress\, this field has m
 ajor open questions. At the molecular level\, mechanochemical mechanisms a
 long DNA remain unclear\, as do the influences of DNA longitudinal and tor
 sional tension\, nucleosome positioning\, and transcriptional activity on 
 loop extrusion dynamics [15]. Interdisciplinary research combining theoret
 ical modeling\, single-molecule biophysics\, and high-resolution imaging c
 ontinues to advance our understanding of these active processes and their 
 implications for cellular function and disease [16]. In addition to a brid
 ging between modeling and experimentation on nucleosome and fiber levels w
 ith genome studies on the kilo-base level  [5\, 17]\, tailored multiscale
  computational approaches are needed to help interpret experimental struct
 ural and kinetic data.\nOur program targeted for early 2026 continues a ve
 ry successful dialogue among the mathematics\, physics\, biology\, chemist
 ry\, and scientific computing communities started in Les Houches in 2017 a
 nd continued at ESI in March 2024. Our proposed program for 2026 aims to c
 ontinue to bring these scientists together to discuss the current state-of
 -the-art in chromatin modeling\, identify future challenges\, inspire new 
 collaborations and multiscale integrative approaches\, and help educate a
  new generation of multidisciplinary scientists. The increasing amount of 
 genomic chromosome capture data at varying levels of resolution for both 
 single cells and multiple cell populations\, as well as the increasing pot
 ential of AI approaches will be important areas of discuss and explore.\n
 \nWe will assemble  a leading group of collaborative and broad mathematic
 al biologists and physicists\, computational biophysicists\, and experimen
 talists to address these multiscale challenges and establish/ continue col
 laborations and scientific idea exchange. We would like to continue to ins
 pire more scientists to work in this fascinating area of biophysics/ molec
 ular biology and encourage more of these cross-discipline and multiscale e
 xperimental/ theory/ modeling collaborations in our workshop.\n\nReference
 s\n\n[1] J. Dekker\, L. Mirny\, Cell\, 187\, 6424-6450 (2024)\n[2] G. Oze
 r\, A. Luque\, T. Schlick\, Current Opinion in Structural Biology\, 31\, 
 124-139 (2015)\n[3] K. Samejima\, J. Gibcus\, S. Abraham\, F. Cisneros-Sob
 eranis\, I. Samejima\, A. Beckett\, N. Puǎčeková\, M. Abad\, C. Spanos\
 , B. Medina-Pritchard\, J. Paulson\, L. Xie\, A. Jeyaprakash\, I. Prior\, 
 L. Mirny\, J. Dekker\, A. Goloborodko\, W. Earnshaw\, Science\, 388\, (20
 25)\n[4] C. Dekker\, C. Haering\, J. Peters\, B. Rowland\, Science\, 382\
 , 646-648 (2023)\n[5] E. Banigan\, A. van den Berg\, H. Brandão\, J. Mark
 o\, L. Mirny\, eLife\, 9\, (2020)\n[6] M. Karpinska\, A. Oudelaar\, Curre
 nt Opinion in Genetics & Development\, 79\, 102022 (2023)\n[7] E. Kim\, R
 . Barth\, C. Dekker\, Annu. Rev. Biochem.\, 92\, 15-41 (2023)\n[8] J. Gib
 cus\, K. Samejima\, A. Goloborodko\, I. Samejima\, N. Naumova\, J. Nuebler
 \, M. Kanemaki\, L. Xie\, J. Paulson\, W. Earnshaw\, L. Mirny\, J. Dekker\
 , Science\, 359\, (2018)\n[9] J. Horsfield\, The FEBS Journal\, 290\, 16
 70-1687 (2022)\n[10] T. Schlick\, S. Portillo-Ledesma\, C. Myers\, L. Belj
 ak\, J. Chen\, S. Dakhel\, D. Darling\, S. Ghosh\, J. Hall\, M. Jan\, E. L
 iang\, S. Saju\, M. Vohr\, C. Wu\, Y. Xu\, E. Xue\, Annu. Rev. Biophys.\,
  50\, 267-301 (2021)\n[11] S. Meyer\, D. Jost\, N. Theodorakopoulos\, M. 
 Peyrard\, R. Lavery\, R. Everaers\, Biophysical Journal\, 105\, 1904-1914
  (2013)\n[12] G. Felsenfeld\, M. Groudine\, Nature\, 421\, 448-453 (2003)
 \n[13] G. Felsenfeld\, Cell\, 86\, 13-19 (1996)\n[14] S. Portillo‐Ledes
 ma\, T. Schlick\, WIREs. Comput. Mol. Sci.\, 10\, (2019)\n[15] M. Levitt\
 , Proc. Natl. Acad. Sci. U.S.A.\, 75\, 640-644 (1978)\n[16] J. Boyett\, D
 . Duniphin\, F. Miller\, M. Moon\, B. Varalli-Claypool\, J. Physician. Ass
 ist. Educ.\, 32\, 266-267 (2021)\n[17] T. Schlick\, S. Portillo-Ledesma\,
  Nat. Comput. Sci.\, 1\, 321-331 (2021)
LOCATION:BCH 2103 https://plan.epfl.ch/?room==BCH%202103
STATUS:CONFIRMED
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