15 papers
Amplifying gene expression sensitivity by surface condensation on DNA
Tarek Tohme, Henry Alston, Jacqueline Janssen +2
Condensation of proteins on DNA is a central aspect of genome organisation, and has been proposed as a mechanism of gene regulation in eukaryotes, notably by mediating the action o…
Neutralization titers reveal the structure of polyclonal antibody responses
Henry Alston, Thierry Mora, Aleksandra M. Walczak
The composition of a polyclonal antibody response is hard to measure experimentally but contains vital information about the robustness of immunity. Here, we argue that the statist…
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
Leonardo Di Bari, Thierry Mora, Andrea Pagnani +3
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics…
Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics
Gabriel Athènes, Adam Woolfe, Thierry Mora +1
The specific region of an antibody responsible for binding to an antigen, known as the paratope, is essential for immune recognition. Accurate identification of this small yet crit…
Dynamics of memory B cells and plasmablasts in healthy individuals
Andrea Mazzolini, Aleksandra M. Walczak, Thierry Mora
Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us aga…
Theoretical limits for sensing through phase separation
Henry Alston, Mason Rouches, Arvind Murugan +2
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing s…
Fast decisions with biophysically constrained gene promoter architectures
Tarek Tohme, Massimo Vergassola, Thierry Mora +1
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory ci…
Integrating computational detection and experimental validation for rapid GFRAL-specific antibody discovery
Maria Francesca Abbate, Pierre Toxe, Nicolas Maestrali +5
The identification and validation of therapeutic antibodies is critical for developing effective treatments for many diseases. We present a computational approach for identifying a…
Learning via mechanosensitivity and activity in cytoskeletal networks
Deb S. Banerjee, Martin J. Falk, Margaret L Gardel +3
In this work we show how a network inspired by a coarse-grained description of actomyosin cytoskeleton can learn - in a contrastive learning framework - from environmental perturba…
Inferring resource competition in microbial communities from time series
Xiaowen Chen, Kyle Crocker, Seppe Kuehn +2
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized int…
Energy-based generative models for monoclonal antibodies
Paul Pereira, Hervé Minoux, Aleksandra M. Walczak +1
Since the approval of the first antibody drug in 1986, a total of 162 antibodies have been approved for a wide range of therapeutic areas, including cancer, autoimmune, infectious,…
Single cells can resolve graded stimuli
Mirna Kramar, Lauritz Hahn, Aleksandra M Walczak +2
Cells use signalling pathways as windows into the environment to gather information, transduce it into their interior, and use it to drive behaviours. MAPK (ERK) is a highly conser…
How host mobility patterns shape antigenic escape during viral-immune co-evolution
Natalie Blot, Caelan Brooks, Daniel W. Swartz +6
Viruses like influenza have long coevolved with host immune systems, gradually shaping the evolutionary trajectory of these pathogens. Host immune systems develop immunity against…
Computational detection of antigen specific B cell receptors following immunization
Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne +3
B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immuniza…
Physical observables to determine the nature of membrane-less cellular sub-compartments
Mathias L. Heltberg, Judith Miné-Hattab, Angela Taddei +2
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations…