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  • DLBCL
  • DLBCL subtyping papers
  • NF-kB
  • NF-kB in DLBCL
  • Modelling NF-kB
  • Apoptosis
  • Modelling Apoptosis
  • B-cell modelling
  • Cell Cycle
  • Cell cycle modelling
  • Terminal Differentiation

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  1. Lab Policies

Essential reading list

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Last updated 1 year ago

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Some key papers that go behind all our work

DLBCL

DLBCL subtyping papers

NF-kB

NF-kB in DLBCL

Modelling NF-kB

Apoptosis

Modelling Apoptosis

B-cell modelling

DLBCL modelling papers

Cell Cycle

Cell cycle modelling

Terminal Differentiation

Any other cool groups to keep an eye on and perhaps the best journals to stay on top of?

LogoMolecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomesNature
Key subtyping paper
https://onlinelibrary.wiley.com/doi/full/10.1111/bjh.17811onlinelibrary.wiley.com
Dan Hodson's review of DLBCL subtypes
LogoSignaling via the NFκB systemWiley Interdisciplinary Reviews
Simon's review of NFkB
LogoAberrant Activation of NF-κB Signalling in Aggressive Lymphoid MalignanciesMDPI
Kennedy...Klein overview of NF-kB in DLBCL
Logoalternative RelB NF-κB subunit is a novel critical player in diffuse large B-cell lymphomaAmerican Society of Hematology
Veronique Baud's findings on RelB in DLBCL
LogoNF-κB fingerprinting reveals heterogeneous NF-κB composition in diffuse large B-cell lymphoma | Mitchell LabMitchell Lab
Eleanor and Arran's paper characterising variability in DLBCL cell lines using flow cytometry. This also incldues models that match these measures.
LogoStudying NF-κB Signaling with Mathematical ModelsSpringerLink
Simon's textbook chapter, this provide a practical how to for modelling. It is in MATLAB and not Julia like we use now but the principles are the same.
LogoThe IκB-NF-κB Signaling Module: Temporal Control and Selective Gene ActivationScience
The 2002 Hoffmann model that started it all
LogoA Pathway Switch Directs BAFF Signaling to Distinct NFκB Transcription Factors in Maturing and Proliferating B Cells
A much more comprehensive and recent NF-kB model that contains lots of detail
LogoThe NF-κB multidimer system model: A knowledge base to explore diverse biological contexts | Mitchell LabMitchell Lab
The most comprehensive NF-kB model we have. This paper explains how it can be used to model multiple cell types and includes simulations of DLBCL mutations
LogoSpecific interactions of BCL-2 family proteins mediate sensitivity to BH3-mimetics in diffuse large B-cell lymphoma
Smith...Dyer experimental data on the complexities of apoptotic signalling in DLBCL
LogoModeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Deathplosbiology
Peter Sorger's Apoptosis modelling
LogoComputational modeling of DLBCL predicts response to BH3-mimetics | Mitchell LabMitchell Lab
Ielyaas's paper on Apoptosis modeling. We can predict how DLBCL cells will respond to drugs using a new model of apoptosis.
LogoWhat Will B Will B: Identifying Molecular Determinants of Diverse B-Cell Fate Decisions Through Systems BiologyFrontiers
Simon's accessible review of B-cell modelling and fates.
LogoA multi‐scale approach reveals that NF‐κB cRel enforces a B‐cell decision to divideEMBO Press
Shokhirev et al MSB - first multiscale model of B cell fates
LogoPNASPNAS
Mitchell, Roy PNAS - Built on Shokhirev et al above
LogoA Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation
Roy, Mitchell Immunity - built on the PNAS paper above.
LogoPatient-Specific Modeling of Diffuse Large B-Cell LymphomaMDPI
Personalised DLBCL modelling from Jana Wolf. (uses logical modelling not ODEs).
https://febs.onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2009.07473.xfebs.onlinelibrary.wiley.com
Our cell cycle modelling is built on this.
LogoAn incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signalingEMBO Press
Modelling of the IRF4/Blimp1 axis from Harrinder Singh's group.