---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21269'
abstract:
- lang: eng
  text: The spatial organization of chromatin within the nucleus plays a crucial role
    in gene expression and genome function. However, the quantitative relationship
    between this organization and nuclear biochemical processes remains under debate.
    In this study, we present a graph-based generative model, bioSBM, designed to
    capture long-range chromatin interaction patterns from Hi-C data and, importantly,
    simultaneously link these patterns to biochemical features. Applying bioSBM to
    Hi-C maps of the GM12878 lymphoblastoid cell line, we identified a latent structure
    of chromatin interactions, revealing seven distinct communities that strongly
    align with known biological annotations. Additionally, we infer a linear transformation
    that maps biochemical observables, such as histone marks, to the parameters of
    the generative graph model, enabling accurate genome-wide predictions of chromatin
    contact maps on out-of-sample data, both within the same cell line and on the
    completely unseen HCT116 cell line under RAD21 depletion. These findings highlight
    bioSBM's potential as a powerful tool for elucidating the relationship between
    biochemistry and chromatin architecture and predicting long-range genome organization
    from independent biochemical data.
acknowledgement: G.S. acknowledges co-funding from Next Generation EU, in the context
  of the National Recovery and Resilience Plan, Investment PE1 - Project FAIR “Future
  Artificial Intelligence Research”. This resource was co-financed by the Next Generation
  EU [DM 1555 del 11.10.22]. A.R. acknowledges financial support from PNRR Grant CN
  00000013 CN-HPC, M4C2I1.4, spoke 7, funded by Next Generation EU.
article_number: '043006'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Chen Y
  full_name: Zhang, Chen Y
  id: 81b43fb8-c9d5-11ef-bf68-ade532a1f204
  last_name: Zhang
- first_name: Angelo
  full_name: Rosa, Angelo
  last_name: Rosa
- first_name: Guido
  full_name: Sanguinetti, Guido
  last_name: Sanguinetti
citation:
  ama: 'Zhang CY, Rosa A, Sanguinetti G. bioSBM: A random graph model to integrate
    epigenomic data in chromatin structure prediction. <i>PRX Life</i>. 2025;3(4).
    doi:<a href="https://doi.org/10.1103/gy1p-4256">10.1103/gy1p-4256</a>'
  apa: 'Zhang, C. Y., Rosa, A., &#38; Sanguinetti, G. (2025). bioSBM: A random graph
    model to integrate epigenomic data in chromatin structure prediction. <i>PRX Life</i>.
    American Physical Society. <a href="https://doi.org/10.1103/gy1p-4256">https://doi.org/10.1103/gy1p-4256</a>'
  chicago: 'Zhang, Chen Y, Angelo Rosa, and Guido Sanguinetti. “BioSBM: A Random Graph
    Model to Integrate Epigenomic Data in Chromatin Structure Prediction.” <i>PRX
    Life</i>. American Physical Society, 2025. <a href="https://doi.org/10.1103/gy1p-4256">https://doi.org/10.1103/gy1p-4256</a>.'
  ieee: 'C. Y. Zhang, A. Rosa, and G. Sanguinetti, “bioSBM: A random graph model to
    integrate epigenomic data in chromatin structure prediction,” <i>PRX Life</i>,
    vol. 3, no. 4. American Physical Society, 2025.'
  ista: 'Zhang CY, Rosa A, Sanguinetti G. 2025. bioSBM: A random graph model to integrate
    epigenomic data in chromatin structure prediction. PRX Life. 3(4), 043006.'
  mla: 'Zhang, Chen Y., et al. “BioSBM: A Random Graph Model to Integrate Epigenomic
    Data in Chromatin Structure Prediction.” <i>PRX Life</i>, vol. 3, no. 4, 043006,
    American Physical Society, 2025, doi:<a href="https://doi.org/10.1103/gy1p-4256">10.1103/gy1p-4256</a>.'
  short: C.Y. Zhang, A. Rosa, G. Sanguinetti, PRX Life 3 (2025).
corr_author: '1'
date_created: 2026-02-17T07:53:01Z
date_published: 2025-10-21T00:00:00Z
date_updated: 2026-02-18T08:01:00Z
day: '21'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1103/gy1p-4256
external_id:
  arxiv:
  - '2409.14425'
file:
- access_level: open_access
  checksum: 76ddfee3efdb4c9d085059b5a142ed78
  content_type: application/pdf
  creator: dernst
  date_created: 2026-02-18T07:57:39Z
  date_updated: 2026-02-18T07:57:39Z
  file_id: '21314'
  file_name: 2025_PRXLife_Zhang.pdf
  file_size: 1888053
  relation: main_file
  success: 1
file_date_updated: 2026-02-18T07:57:39Z
has_accepted_license: '1'
intvolume: '         3'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PRX Life
publication_identifier:
  issn:
  - 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'bioSBM: A random graph model to integrate epigenomic data in chromatin structure
  prediction'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2025'
...
---
_id: '14277'
abstract:
- lang: eng
  text: Living tissues are characterized by an intrinsically mechanochemical interplay
    of active physical forces and complex biochemical signaling pathways. Either feature
    alone can give rise to complex emergent phenomena, for example, mechanically driven
    glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion
    instabilities. An important question is how to quantitatively assess the contribution
    of these different cues to the large-scale dynamics of biological materials. We
    address this in Madin-Darby canine kidney (MDCK) monolayers, considering both
    mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling
    activity and cellular density as well as a mechanically active tissue rheology
    via a self-propelled vertex model. We show that the relative strength of active
    migration forces to mechanochemical couplings controls a transition from a uniform
    active glass to periodic spatiotemporal waves. We parametrize the model from published
    experimental data sets on MDCK monolayers and use it to make new predictions on
    the correlation functions of cellular dynamics and the dynamics of topological
    defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers
    are best described by an intermediary parameter region in which both mechanochemical
    couplings and noisy active propulsion have a strong influence on the dynamics.
    Finally, we study how tissue rheology and ERK waves produce feedback on one another
    and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical
    waves at both the local and global levels.
acknowledgement: We thank all members of the Hannezo group for discussions and suggestions,
  as well as Sound Wai Phow for technical assistance. This work received funding from
  the European Research Council under the EU Horizon 2020 research and innovation
  program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and
  the Ministry of Education under the Research Centres of Excellence program through
  the MBI at NUS.
article_number: '013001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel R
  full_name: Boocock, Daniel R
  id: 453AF628-F248-11E8-B48F-1D18A9856A87
  last_name: Boocock
  orcid: 0000-0002-1585-2631
- first_name: Tsuyoshi
  full_name: Hirashima, Tsuyoshi
  last_name: Hirashima
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
citation:
  ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning
    and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a
    href="https://doi.org/10.1103/prxlife.1.013001">10.1103/prxlife.1.013001</a>
  apa: Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between
    mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX
    Life</i>. American Physical Society. <a href="https://doi.org/10.1103/prxlife.1.013001">https://doi.org/10.1103/prxlife.1.013001</a>
  chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay
    between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.”
    <i>PRX Life</i>. American Physical Society, 2023. <a href="https://doi.org/10.1103/prxlife.1.013001">https://doi.org/10.1103/prxlife.1.013001</a>.
  ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical
    patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol.
    1, no. 1. American Physical Society, 2023.
  ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical
    patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.
  mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and
    Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001,
    American Physical Society, 2023, doi:<a href="https://doi.org/10.1103/prxlife.1.013001">10.1103/prxlife.1.013001</a>.
  short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).
corr_author: '1'
date_created: 2023-09-06T08:30:59Z
date_published: 2023-07-20T00:00:00Z
date_updated: 2025-04-14T07:52:27Z
day: '20'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1103/prxlife.1.013001
ec_funded: 1
file:
- access_level: open_access
  checksum: f881d98c89eb9f1aa136d7b781511553
  content_type: application/pdf
  creator: dernst
  date_created: 2023-09-15T06:30:50Z
  date_updated: 2023-09-15T06:30:50Z
  file_id: '14335'
  file_name: 2023_PRXLife_Boocock.pdf
  file_size: 2559520
  relation: main_file
  success: 1
file_date_updated: 2023-09-15T06:30:50Z
has_accepted_license: '1'
intvolume: '         1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '851288'
  name: Design Principles of Branching Morphogenesis
publication: PRX Life
publication_identifier:
  issn:
  - 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Interplay between mechanochemical patterning and glassy dynamics in cellular
  monolayers
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2023'
...