Essential reading list

Some key papers that go behind all our work

DLBCL

DLBCL subtyping papers

https://www.nature.com/articles/s41591-018-0016-8www.nature.com

Key subtyping paper

Molecular profiling in diffuse large B‐cell lymphoma: why so many types of subtypes?Wiley Online Library

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

The 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

https://link.springer.com/protocol/10.1007/978-1-4939-2422-6_38link.springer.com

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

https://www.sciencedirect.com/science/article/pii/S2211124714009905www.sciencedirect.com

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 lymphomahaematologica.org

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

Frontiers | 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.

https://www.embopress.org/doi/full/10.15252/msb.20145554www.embopress.org

Shokhirev et al MSB - first multiscale model of B cell fates

Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation | PNASPNAS

Mitchell, Roy PNAS - Built on Shokhirev et al above

https://www.sciencedirect.com/science/article/pii/S1074761319300494?via%3Dihubwww.sciencedirect.com

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

https://www.embopress.org/doi/full/10.1038/msb.2011.25www.embopress.org

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?