1.6k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Centre National de la Recherche ScientifiqueFR66 papers
- Sorbonne UniversitéFR61 papers
- Institut de Biologie Paris-SeineFR32 papers
- Université Pierre-et-Marie-CurieFR23 papers
- École Normale Supérieure - PSLFR17 papers
- Laboratoire de Physique de l'Ecole Normale SupérieureFR16 papers
- Politecnico di TorinoIT16 papers
- Université Paris Sciences et LettresFR13 papers
- Italian institute for Genomic MedicineIT12 papers
- Laboratoire Jacques-Louis LionsFR11 papers
- University of MilanIT11 papers
- Sapienza University of RomeIT9 papers
9 papers · 1 filter
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes
Juan Rodriguez-Rivas, Giancarlo Croce, Maureen Muscat +1
The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therap…
adabmDCA: Adaptive Boltzmann machine learning for biological sequences
Anna Paola Muntoni, Andrea Pagnani, Martin Weigt +1
Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are…
Extensible Logging and Empirical Attainment Function for IOHexperimenter
Johann Dreo, Manuel López-Ibáñez
In order to allow for large-scale, landscape-aware, per-instance algorithm selection, a benchmarking platform software is key. IOHexperimenter provides a large set of synthetic pro…
A multiple time renewal equation for neural assemblies with elapsed time model
Nicolás Torres, Benoît Perthame, Delphine Salort
We introduce and study an extension of the classical elapsed time equation in the context of neuron populations that are described by the elapsed time since the last discharge, i.e…
Ancestral Sequence Reconstruction for Co-evolutionary models
Edwin Rodríguez Horta, Alejandro Lage-Castellanos, Roberto Mulet
The ancestral sequence reconstruction problem is the inference, back in time, of the properties of common sequence ancestors from measured properties of contemporary populations. S…
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response
Emma Leschiera, Tommaso Lorenzi, Shensi Shen +2
Intra-tumour heterogeneity (ITH) has a strong impact on the efficacy of the immune response against solid tumours. The number of sub-populations of cancer cells expressing differen…
Modeling sequence-space exploration and emergence of epistatic signals in protein evolution
Matteo Bisardi, Juan Rodriguez-Rivas, Francesco Zamponi +1
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing dat…
An elapsed time model for strongly coupled inhibitory and excitatory neural networks
Maria Caceres, Benoît Perthame, Delphine Salort +1
The elapsed time model has been widely studied in the context of mathematical neuroscience with many open questions left. The model consists of an age-structured equation that desc…
Efficient generative modeling of protein sequences using simple autoregressive models
Jeanne Trinquier, Guido Uguzzoni, Andrea Pagnani +2
Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about…