Aleksandra M Walczak (A M Walczak)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 59

Top Topics

Single Molecule

Immune Response

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Vadim K Karnaukhov, Anne-Laure Le Gac, Linda Bilonda Mutala, Aurelie Darbois-Delahousse, Laetitia Perrin, Francois Legoux, Aleksandra M Walczak, Thierry Mora, Olivier Lantz
Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proceedings of the National Academy of Sciences of the United States of America 121 (14) (2024)
Vadim K Karnaukhov, Anne-Laure Le Gac, Linda Bilonda Mutala, Aurelie Darbois-Delahousse, Laetitia Perrin, Francois Legoux, Aleksandra M Walczak, Thierry Mora, Olivier Lantz
Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proceedings of the National Academy of Sciences of the United States of America 121 (14) (2024)
Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody A Shahsavarian, Aleksandra M Walczak, Thierry Mora
Computational detection of antigen-specific B cell receptors following immunization. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Barthelemy Meynard-Piganeau, Christoph Feinauer, Martin Weigt, Aleksandra M Walczak, Thierry Mora
TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes. Proceedings of the National Academy of Sciences of the United States of America 121 (24) (2024)
Vadim K Karnaukhov, Anne-Laure Le Gac, Linda Bilonda Mutala, Aurelie Darbois-Delahousse, Laetitia Perrin, Francois Legoux, Aleksandra M Walczak, Thierry Mora, Olivier Lantz
Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proceedings of the National Academy of Sciences of the United States of America 121 (14) (2024)
Benoît Manfroi, Bui Thi Cuc, Aurélien Sokal, Alexis Vandenberghe, Sarah Temmam, Mikaël Attia, Mohamed El Behi, Francesco Camaglia, Ngan Thu Nguyen, Jelka Pohar, Layale Salem-Wehbe, Valentine Pottez-Jouatte, Sibyline Borzakian, Narcisse Elenga, Caroline Galeotti, Guillaume Morelle, Camille de Truchis de Lays, Michaela Semeraro, Anne-Sophie Romain, Mélodie Aubart, Naim Ouldali, Florence Mahuteau-Betzer, Claire Beauvineau, Elsa Amouyal, Romain Berthaud, Célia Crétolle, Marc Duval Arnould, Albert Faye, Mathie Lorrot, Grégoire Benoist, Nelly Briand, Marie Courbebaisse, Roland Martin, Peter Van Endert, Jean-Sébastien Hulot, Anne Blanchard, Eric Tartour, Maria C Leite-de-Moraes, Guillaume Lezmi, Mickael Ménager, Marine Luka, Claude-Agnès Reynaud, Jean-Claude Weill, Laetitia Languille, Marc Michel, Pascal Chappert, Thierry Mora, Aleksandra M Walczak, Marc Eloit, Petra Bacher, Alexander Scheffold, Matthieu Mahevas, Isabelle Sermet-Gaudelus, Simon Fillatreau
Preschool-age children maintain a distinct memory CD4 + T cell and memory B cell response after SARS-CoV-2 infection. Science translational medicine 16 (765) (2024)
Barthelemy Meynard-Piganeau, Christoph Feinauer, Martin Weigt, Aleksandra M Walczak, Thierry Mora
TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes. Proceedings of the National Academy of Sciences of the United States of America 121 (24) (2024)
Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody A Shahsavarian, Aleksandra M Walczak, Thierry Mora
Computational detection of antigen-specific B cell receptors following immunization. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Vadim K Karnaukhov, Anne-Laure Le Gac, Linda Bilonda Mutala, Aurelie Darbois-Delahousse, Laetitia Perrin, Francois Legoux, Aleksandra M Walczak, Thierry Mora, Olivier Lantz
Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proceedings of the National Academy of Sciences of the United States of America 121 (14) (2024)
Barthelemy Meynard-Piganeau, Christoph Feinauer, Martin Weigt, Aleksandra M Walczak, Thierry Mora
TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes. Proceedings of the National Academy of Sciences of the United States of America 121 (24) (2024)
Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody A Shahsavarian, Aleksandra M Walczak, Thierry Mora
Computational detection of antigen-specific B cell receptors following immunization. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Natanael Spisak, Gabriel Athènes, Thomas Dupic, Thierry Mora, Aleksandra M Walczak
Combining mutation and recombination statistics to infer clonal families in antibody repertoires. eLife 13 (2024)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Victor Chardès, Andrea Mazzolini, Thierry Mora, Aleksandra M Walczak
Evolutionary stability of antigenically escaping viruses. Proceedings of the National Academy of Sciences of the United States of America 120 (44) (2023)
María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra M Walczak
Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals. PLoS genetics 19 (2) (2023)
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Inferring the T cell repertoire dynamics of healthy individuals. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Inferring the T cell repertoire dynamics of healthy individuals. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Jos Urbanus, Jason Cosgrove, Joost B Beltman, Yuval Elhanati, Rafael A Moral, Cecile Conrad, Jeroen W van Heijst, Emilie Tubeuf, Arno Velds, Lianne Kok, Candice Merle, Jens Peter Magnusson, Léa Guyonnet, Jonas Frisén, Silvia Fre, Aleksandra M Walczak, Thierry Mora, Heinz Jacobs, Ton N M Schumacher, Leïla Perié
DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age. Nature communications 14 (1) (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra M Walczak, Claire Wyart
Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 12 (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra M Walczak, Claire Wyart
Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 12 (2023)
Andrea Mazzolini, Thierry Mora, Aleksandra M Walczak
Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 378 (1877) (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra M Walczak, Claire Wyart
Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 12 (2023)
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Inferring the T cell repertoire dynamics of healthy individuals. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Justin Crocker, Joshua L Payne, Aleksandra M Walczak, Patricia J Wittkopp
Interdisciplinary approaches to predicting evolutionary biology. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 378 (1877) (2023)
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra M Walczak, Claire Wyart
Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 12 (2023)
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra M Walczak, Claire Wyart
Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 12 (2023)
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Inferring the T cell repertoire dynamics of healthy individuals. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Inferring the T cell repertoire dynamics of healthy individuals. Proceedings of the National Academy of Sciences of the United States of America 120 (4) (2023)
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benjamin M Chain, Thierry Mora, Aleksandra M Walczak, Nir Friedman
Quantifying changes in the T cell receptor repertoire during thymic development. eLife 12 (2023)
Barbara Bravi, Andrea Di Gioacchino, Jorge Fernandez-de-Cossio-Diaz, Aleksandra M Walczak, Thierry Mora, Simona Cocco, Remi Monasson
A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity. eLife 12 (2023)
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra M Walczak
NoisET: Noise Learning and Expansion Detection of T-Cell Receptors. The journal of physical chemistry. A 126 (40) (2022)
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra M Walczak, Joshua J Waterfall, Sebastian Amigorena
Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer. Science immunology 6 (55) (2022)
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra M Walczak, Nathalie Dostatni
Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription. eLife 11 (2022)
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies. PLoS computational biology 18 (6) (2022)
Victor Chardès, Massimo Vergassola, Aleksandra M Walczak, Thierry Mora
Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints. Proceedings of the National Academy of Sciences of the United States of America 119 (8) (2022)
Ezequiel A Galpern, Jacopo Marchi, Thierry Mora, Aleksandra M Walczak, Diego U Ferreiro
Evolution and folding of repeat proteins. Proceedings of the National Academy of Sciences of the United States of America 119 (31) (2022)
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra M Walczak, Maxime Dahan, Angela Taddei
Single molecule microscopy reveals key physical features of repair foci in living cells. eLife 10 (2021)
Angela M Phillips, Katherine R Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo S Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra M Walczak, Michael M Desai
Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. eLife 10 (2021)
Arvind Murugan, Kabir Husain, Michael J Rust, Chelsea Hepler, Joseph Bass, Julian M J Pietsch, Peter S Swain, Siddhartha G Jena, Jared E Toettcher, Arup K Chakraborty, Kayla G Sprenger, T Mora, Aleksandra M Walczak, Olivier Rivoire, Shenshen Wang, Kevin B Wood, Antun Skanata, Edo Kussell, Rama Ranganathan, Hong-Yan Shih, Nigel Goldenfeld
Roadmap on biology in time varying environments. Physical biology 18 (4) (2021)
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
Antigenic waves of virus-immune coevolution. Proceedings of the National Academy of Sciences of the United States of America 118 (27) (2021)
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Deep generative selection models of T and B cell receptor repertoires with soNNia. Proceedings of the National Academy of Sciences of the United States of America 118 (14) (2021)
Anastasia A Minervina, Ekaterina A Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z Mamedov, Andre Franke, Grigory A Efimov, Dmitriy M Chudakov, Thierry Mora, Aleksandra M Walczak, Yury B Lebedev, Mikhail V Pogorelyy
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection. eLife 10 (2021)
Thomas Dupic, Meriem Bensouda Koraichi, Anastasia A Minervina, Mikhail V Pogorelyy, Thierry Mora, Aleksandra M Walczak
Immune fingerprinting through repertoire similarity. PLoS genetics 17 (1) (2021)
Mathias L Heltberg, Judith Miné-Hattab, Angela Taddei, Aleksandra M Walczak, Thierry Mora
Physical observables to determine the nature of membrane-less cellular sub-compartments. eLife 10 (2021)
Vedant Sachdeva, Thierry Mora, Aleksandra M Walczak, Stephanie E Palmer
Optimal prediction with resource constraints using the information bottleneck. PLoS computational biology 17 (3) (2021)
Jonathan Desponds, Massimo Vergassola, Aleksandra M Walczak
A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute. eLife 9 (2020)
Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M Walczak, Yuval Elhanati
Population variability in the generation and selection of T-cell repertoires. PLoS computational biology 16 (12) (2020)
Anastasia A Minervina, Mikhail V Pogorelyy, Ekaterina A Komech, Vadim K Karnaukhov, Petra Bacher, Elisa Rosati, Andre Franke, Dmitriy M Chudakov, Ilgar Z Mamedov, Yury B Lebedev, Thierry Mora, Aleksandra M Walczak
Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones. eLife 9 (2020)
Mikhail V Pogorelyy, Anastasia A Minervina, Mikhail Shugay, Dmitriy M Chudakov, Yury B Lebedev, Thierry Mora, Aleksandra M Walczak
Detecting T cell receptors involved in immune responses from single repertoire snapshots. PLoS biology 17 (6) (2019)
Tanguy Lucas, Huy Tran, Carmina Angelica Perez Romero, Aurélien Guillou, Cecile Fradin, Mathieu Coppey, Aleksandra M Walczak, Nathalie Dostatni
3 minutes to precisely measure morphogen concentration. PLoS genetics 14 (10) (2018)
Huy Tran, Jonathan Desponds, Carmina Angelica Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M Walczak
Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern. PLoS computational biology 14 (10) (2018)
Mikhail V Pogorelyy, Anastasia A Minervina, Dmitriy M Chudakov, Ilgar Z Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak
Method for identification of condition-associated public antigen receptor sequences. eLife 7 (2018)
Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Angelica Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M Walczak
Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos. PLoS computational biology 12 (12) (2016)
Rhys M Adams, Thierry Mora, Aleksandra M Walczak, Justin B Kinney
Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 5 (2016)