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The Structure of Genealogies in the Presence of Purifying Selection: An Effective Coalescent Theory

 Michael M. Desai , Aleksandra M. Walczak , Lauren E. Nicolaisen , Joshua B. Plotkin
2010
Pré-publication, Document de travail hal-00547405v1

Evolution and folding of repeat proteins

 Ezequiel Galpern , Jacopo Marchi , Thierry Mora , Aleksandra Walczak , Diego Ferreiro
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (31), ⟨10.1073/pnas.2204131119⟩
Article dans une revue hal-03854601v1

Dynamical Information Synergy in Biochemical Signaling Networks

 Lauritz Hahn , Walczak Aleksandra , Thierry Mora
Physical Review Letters, 2023, 131 (12), pp.128401. ⟨10.1103/PhysRevLett.131.128401⟩
Article dans une revue hal-04252238v1
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RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles

 Barbara Bravi , Jérôme Tubiana , Simona Cocco , Rémi Monasson , Thierry Mora , et al.
Cell Systems, 2021, 12 (2), pp.195-202.e9. ⟨10.1016/j.cels.2020.11.005⟩
Article dans une revue hal-03153691v1

Granger causality analysis for calcium transients in neuronal networks, challenges and improvements

 Xiaowen Chen , Faustine Ginoux , Martin Carbo-Tano , Thierry Mora , Aleksandra Walczak , et al.
eLife, 2023, 12, ⟨10.7554/eLife.81279⟩
Article dans une revue hal-04252210v1
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Contribution of resident and circulating precursors to tumor-infiltrating CD8 + T cell populations in non-small cell lung cancer patients

 Paul Gueguen , Christina Metoikidou , Thomas Dupic , Myriam Lawand , Christel Goudot , et al.
Science Immunology, 2021, 6 (55), pp.eabd5778. ⟨10.1126/sciimmunol.abd5778⟩
Article dans une revue hal-02988498v1
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Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

 Natanael Spisak , Aleksandra Walczak , Thierry Mora
Nucleic Acids Research, 2020, 48, pp.10702 - 10712. ⟨10.1093/nar/gkaa825⟩
Article dans une revue hal-02988489v1
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Evidence for Shaping of Light Chain Repertoire by Structural Selection

 Adar Toledano , Yuval Elhanati , Jennifer I C Benichou , Aleksandra M Walczak , Thierry Mora , et al.
Frontiers in Immunology, 2018, 9, pp.1307. ⟨10.3389/fimmu.2018.01307⟩
Article dans une revue hal-01833908v1

The structure of allelic diversity in the presence of purifying selection

 Michael M. Desai , Aleksandra M. Walczak , Joshua B. Plotkin
2010
Pré-publication, Document de travail hal-00547402v1
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Deep generative selection models of T and B cell receptor repertoires with soNNia

 Giulio Isacchini , Aleksandra M Walczak , Thierry Mora , Armita Nourmohammad
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (14), pp.e2023141118. ⟨10.1101/2020.11.05.370346⟩
Article dans une revue hal-02991468v2

What are the current driving questions in immune repertoire research?

 Victor Greiff , Eline Luning Prak , Tim O’donnell , Francesca Finotello , Sai Reddy , et al.
Cell Systems, 2022, 13 (9), pp.683-686. ⟨10.1016/j.cels.2022.08.006⟩
Article dans une revue hal-03854592v1
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Optimal prediction with resource constraints using the information bottleneck

 Vedant Sachdeva , Thierry Mora , Aleksandra Walczak , Stephanie Palmer
PLoS Computational Biology, 2021, 17 (3), pp.e1008743. ⟨10.1371/journal.pcbi.1008743⟩
Article dans une revue hal-03367851v2
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Antigenic waves of virus–immune coevolution

 Jacopo Marchi , Michael Lässig , Aleksandra M Walczak , Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (27), pp.e2103398118. ⟨10.1073/pnas.2103398118⟩
Article dans une revue hal-03367761v1
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Generative models of T-cell receptor sequences

 Giulio Isacchini , Zachary Sethna , Yuval Elhanati , Armita Nourmohammad , Aleksandra Walczak , et al.
Physical Review E , 2020, 101 (6), ⟨10.1103/PhysRevE.101.062414⟩
Article dans une revue hal-02988458v1

Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination

 Susana Magadan , Luc Jouneau , Maximilian Puelma Touzel , Simon Marillet , Wahiba Chara , et al.
Frontiers in Immunology, 2018, 9
Article dans une revue hal-01968155v1
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How many different clonotypes do immune repertoires contain?

 Thierry Mora , Aleksandra Walczak
Current Opinion in Systems Biology, 2019, 18, pp.104-110. ⟨10.1016/j.coisb.2019.10.001⟩
Article dans une revue hal-02569976v1

DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age

 Jos Urbanus , Jason Cosgrove , Joost Beltman , Yuval Elhanati , Rafael Moral , et al.
Nature Communications, 2023, 14 (1), pp.2184. ⟨10.1038/s41467-023-37167-8⟩
Article dans une revue hal-04252234v1

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

 Jonathan Desponds , Massimo Vergassola , Aleksandra M. Walczak
eLife, 2020, 9, pp.e49758. ⟨10.7554/eLife.49758⟩
Article dans une revue hal-02421264v1
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Physical observables to determine the nature of membrane-less cellular sub-compartments

 Mathias Heltberg , Judith Miné-Hattab , Angela Taddei , Aleksandra Walczak , Thierry Mora
eLife, 2021, 10, ⟨10.7554/eLife.69181⟩
Article dans une revue hal-03815448v1
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Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

 Mikhail V. Pogorelyy , Yuval Elhanati , Quentin Marcou , Anastasiia L. Sycheva , Ekaterina A. Komech , et al.
PLoS Computational Biology, 2017, 13 (7), pp.e1005572. ⟨10.1371/journal.pcbi.1005572⟩
Article dans une revue hal-01579464v1
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Size and structure of the sequence space of repeat proteins

 Jacopo Marchi , Ezequiel A Galpern , Rocío Espada , Diego U Ferreiro , Aleksandra M. Walczak , et al.
PLoS Computational Biology, 2019, 15 (8), pp.e1007282. ⟨10.1371/journal.pcbi.1007282⟩
Article dans une revue hal-02345012v1
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Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems

 Jacopo Marchi , Michael Lässig , Thierry Mora , Aleksandra M. Walczak
Pathogens, 2019, 8 (3), pp.115. ⟨10.3390/pathogens8030115⟩
Article dans une revue hal-02360335v1
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OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

 Zachary Sethna , Yuval Elhanati , Curtis G Callan , Aleksandra M. Walczak , Thierry Mora
Bioinformatics, 2019, 35 (17), pp.2974-2981. ⟨10.1093/bioinformatics/btz035⟩
Article dans une revue hal-02344638v1
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Immune Fingerprinting through Repertoire Similarity

 Thomas Dupic , Meriem Bensouda Koraichi , Anastasia Minervina , Mikhail Pogorelyy , Thierry Mora , et al.
2020
Pré-publication, Document de travail hal-02988485v1
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Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

 Pieter Meysman , Justin Barton , Barbara Bravi , Liel Cohen-Lavi , Vadim Karnaukhov , et al.
ImmunoInformatics, 2023, 9, pp.100024. ⟨10.1016/j.immuno.2023.100024⟩
Article dans une revue hal-03854607v1
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Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

 Angela Phillips , Katherine Lawrence , Alief Moulana , Thomas Dupic , Jeffrey Chang , et al.
eLife, 2021, 10, ⟨10.7554/eLife.71393⟩
Article dans une revue hal-03367741v1

Exotic quantum phases and phase transitions in correlated matter

 Fabien Alet , Aleksandra M. Walczak , Matthew P. A. Fisher
Physica A: Statistical Mechanics and its Applications, 2006, 369 (1), pp.122-142. ⟨10.1016/j.physa.2006.04.003⟩
Article dans une revue hal-00169454v1

Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation

 Vadim K. Karnaukhov , Anne‐laure Le Gac , Linda Bilonda Mutala , Aurelie Darbois , Laetitia Perrin , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (14), ⟨10.1073/pnas.2311348121⟩
Article dans une revue hal-04532544v1
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Population variability in the generation and thymic selection of T-cell repertoires

 Zachary Sethna , Giulio Isacchini , Thomas Dupic , Thierry Mora , Aleksandra Walczak , et al.
PLoS Computational Biology, 2020, 16 (12), pp.e1008394. ⟨10.1371/journal.pcbi.1008394⟩
Article dans une revue hal-02988471v1

Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints

 Victor Chardès , Massimo Vergassola , Aleksandra Walczak , Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (8), pp.e2113512119. ⟨10.1073/pnas.2113512119⟩
Article dans une revue hal-03854606v2
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