Essential reading list

Some key papers that go behind all our work

DLBCL

DLBCL subtyping papers

Molecular 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

NF-kB

Signaling via the NFκB systemWiley Interdisciplinary Reviews

Simon's review of NFkB

NF-kB in DLBCL

Aberrant Activation of NF-κB Signalling in Aggressive Lymphoid MalignanciesMDPI

Kennedy...Klein overview of NF-kB in DLBCL

alternative 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

NF-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.

Modelling NF-kB

Studying 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.

The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene ActivationScience

The 2002 Hoffmann model that started it all

A 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

The 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

Apoptosis

Specific 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

Modelling Apoptosis

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Deathplosbiology

Peter Sorger's Apoptosis modelling

Computational 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.

B-cell modelling

What 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.

A 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

PNASPNAS

Mitchell, Roy PNAS - Built on Shokhirev et al above

A 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.

DLBCL modelling papers

Patient-Specific Modeling of Diffuse Large B-Cell LymphomaMDPI

Personalised DLBCL modelling from Jana Wolf. (uses logical modelling not ODEs).

Cell Cycle

Cell cycle modelling

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.

Terminal Differentiation

An 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.

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