Publications

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• M. Ruiz Ortega, M.V. Pogorelyy, A.A. Minervina, P.G. Thomas, A.M. Walczak, T. Mora
  Learning predictive signatures of HLA type from T-cell repertoires

  bioRxiv (2024)

• M.-F. Abbate, T. Dupic, E. Vigne, M.A. Shahsavarian, A.M. Walczak, T. Mora
  Computational detection of antigen specific B cell receptors following immunization

  bioRxiv (2023)

• V. Karnaukhov, A. Le Gac., L. Bilonda, T. Mora, A. M. Walczak, O. Lantz
  TCR repertoire analysis indicates TCR-independent lineage choice of MAIT cells

  PNAS (2024)

• X. Chen, M. Winiarski, A. Puścian, E. Knapska, T. Mora, A. M. Walczak
  Modelling collective behavior in groups of mice housed under semi-naturalistic conditions

  elife (2024)

  bioRxiv (2023)

• G. Isacchini, V. Quiniou, H. Vantomme, P. Stys, E. Mariotti-Ferandiz, D. Klatzmann, A.M. Walczak, T. Mora, A. Nourmohammad
  Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

  PRX Life (2024)

  arXiv (2023)

• B. Meynard-Piganeau, C. Feinauer, M. Weigt, A. M. Walczak, T. Mora
  TULIP - a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes

  PNAS (2024) bioRxiv (2023)

• F. Camaglia, I. Nemenman, T. Mora, A.M. Walczak
  Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors

  PRE (2024)

  arXiv (2023)

• T. Mora, A.M. Walczak
  Quantitative theory of viral-immune coevolution may be within reach

  PRX Life 1 (2023) [pdf] [arXiv]

• V. Chardès, A. Mazzolini, T. Mora, A.M. Walczak
  Evolutionary stability of antigenically escaping viruses

  arXiv (2023) PNAS (2023)

• T. Mora and A. M. Walczak, Towards a quantitative theory of tolerance

  [arxiv]Trends in Immunology (2023)

• L. Hahn, A. M. Walczak and T. Mora, Dynamical information synergy in biochemical signaling networks

  [arxiv] PRL (2023)

• J. Crocker, J. L. Payne, A. M. Walczak and P. J. Wittkopp, Interdisciplinary approaches to predicting evolutionary biology

  [Phil. Trans. B (2023) ]

• N. Spisak, T. Dupic, T. Mora and A. M. Walczak, Combining mutation and recombination statistics to infer clonal families in antibody repertoires

  [biorxiv]

• C. Metoikidou, V. Karnaukhov, B. Boeckx, E.Timperi, P.E. Bonte, L. Wang, M. Espenel, B. Albaut, D. Loirat, X. Wang, C. Sotiriou, P. Aftimos, K. Punie, Hans Wildiers, V. Labroska. M.W. Wang, O. Lantz, T. Mora, A.M Walczak, J.J. Waterfall, L. Buisseret, D. Lambrechts, S. Amigorena, E.Romano Tissue resident CD8+ T cell clonal expansion in advanced triple negative breast cancer is associated with response to chemoimmunotherapy,

  submitted (2023)

• P. Meysman, J. Barton, B. Bravi, L. Cohen-Lavi, V. Karnaukhov, E. Lilleskov, A. Montemurro, M. Nielsen, T. Mora,P.Pereira,A.Postovskaya,M.RodriguezMartinez,J.Fernandez-de-Cossio-Diaz,A.Vujkovic,A.M. Walczak, A. Weber, R. Yin, A. Eugster, V. Sharma Benchmarking solutions to the T-cell receptor epitope prediction problem : IMMREP22 workshop report,

  [biorxiv] ImmunoInformatics (2023)

• A. Mazzolini, T. Mora*, A. M. Walczak* Inspecting the interaction between HIV and the immune system through genetic turnover,

  [biorxiv] Phil. Trans. B (2023)

• X. Chen, M. Winiarski, A. Puscian, E. Knapska, A. M. Walczak*, T. Mora* Generalized Glauber dynamics for inference in biology,

  PRX (2023) [arxiv]

• X. Chen, F. Ginoux, T. Mora*, A. M. Walczak*, C. Wyart* Granger causality analysis for calcium transients in neuronal networks : challenges and improvements,

  [biorxiv] eLife (2023)

• C. Kreer, C. Lupo, M. S. Ercanoglu, L. Gieselmann, N. Spisak, J. Grossbach, M. Schlotz, P. Schommers, H. Gruell, L.Dold, A. Beyer, A. Nourmohammad, T. Mora*, A. M. Walczak*, F. Klein* Determining probabilities of HIV-1 bNAb development in healthy and chronically infected individuals,

  [biorxiv]Nature Comm. (2023)

• J. Urbanus, J. Cosgrove, J. Beltman, Y. Elhanati, R. de Andrade Mora, C. Conrad, J. van Heijst, E. Tubeuf, A. Velds, L. Kok, C. Merle, J. Magnusson, J. Frisen, S. Fre, A. M Walczak, T. Mora, H. Jacobs, T. N. Schumacher and L. Perie DRAG in situ barcoding reveals an increase in the number of HSPCs contributing to myelopoiesis with age,

  [biorxiv] Nature Comm. (2023)

• F. Ferretti, S. Grosse-Holz, C. Holmes, J. L. Shivers, I. Giardina, T. Mora, A. M. Walczak, Signatures of irreversibility in microscopic models of flocking,

  [arxiv] PRE (2022)

• M. Bensouda Koraichi, S. Ferri, A.M. Walczak*, T. Mora*, Inferring the T-cells repertoire dynamics of healthy individuals,

  [biorxiv] PNAS (2023)

• E. A. Galpern, J. Marchi, T. Mora, A.M. Walczak, D.U. Ferreiro, From evolution to folding of repeat proteins,

  [arxiv] PNAS (2022)

• F. Camaglia, A. Ryvkin, E. Greenstein, S. Reich-Zeliger, B. Chain, T. Mora*, A.M. Walczak*, N. Friedman, Population based selection shapes the T cell receptor repertoire during thymic development,

  [biorxiv] eLife (2023)

• M. Luksza, Z. M. Sethna, L. A. Rojas, J. Lihm, B. Bravi, Y. Elhanati, K Soares, M. Amisaki, D. Hoyos, A. Dobrin, P. Guasp, A. Zebboud, R. Yu, A. K. Chandra, T. Waters, Z. Odgerel, J. Leung, R. Kappagantula, A. Makohon-Moore, A. Johns, A. Gill, M. Gigoux, J. Wolchok, T. Merghoub, M. Sadelain, E. Patterson, C. Iacobuzio-Donahue, R. Monasson, T. Mora, A. M. Walczak, S. Cocco, B. D. Greenbaum, and V. P. Balachandran, Neoantigen quality predicts immunoediting and clonal evolution in pancreatic cancer survivors

  [biorxiv] Nature (2022)

• T. Mora, C. Poletto, M. Sales-Pardo, A.M. Walczak, Physics research against pandemics,

  European Physical Society Grand Challenges Physics for Society at the Horizon 2050 (2022)

• M. Ruiz Ortega, N. Spisak, T. Mora*, A. M. Walczak*, Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals,

  [biorxiv] PLoS Genetics (2023)

• C. Lupo, N. Spisak, A. M. Walczak*, T. Mora* Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies,

  [arxiv] PLoS CB (2022)

• G. Fernandes, H. Tran, M. Andrieu, Y. Diaw, C.A.Perez-Romero, C. Fradin, A.M. Walczak*, N. Dostatni* Synthetic deconstruction of hunchback regulation by Bicoid,

  [biorxiv] eLife (2022)

• V. Chardes, M. Vergassola, A. M. Walczak*, T. Mora*, Affinity maturation for an optimal balance bet- ween long-term immune coverage and short-term resource constraints,

  [biorxiv] PNAS (2022)

• G. Isacchini, N. Spisak, A. Nourmohammad*, T. Mora*, A.M. Walczak*, MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories,

  [arxiv] PRE (2022)

• A.M. Phillips, K.R. Lawrence, A. Moulana, T. Dupic, J. Chang, M. S. Johnson, I. Cvijovic, T. Mora, A.M. Walczak, M.M. Desai, Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies,

  [biorxiv] eLife (2021)

• M.L. Heltberg, J. Miné-Hattab, A. Taddei, A.M. Walczak*, T. Mora*, Physical observables to determine the nature of membrane-less cellular sub-compartments,

  [biorxiv] eLife (2021)

• J. Marchi, M. Laessig, T. Mora*, A. M. Walczak*, Antigenic waves of virus-immune co-evolution

  [biorxiv] PNAS (2021)

• M. Bensouda Koraichi, M. Puelma Touzel, T. Mora, A. M. Walczak, NoisET : Noise learning and Expansion detection of T-cell receptors with Python

  [arxiv] J. Chem. Phys . (2022)

• B. Bravi, V.P. Balachandran, B.D. Greenbaum, A.M. Walczak, T. Mora, R. Monasson, S. Cocco, Probing T-cell response by sequence-based probabilistic modeling

  [bioarxiv]
  PLoS Comp. Biol. (2021)

• F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, T. Giardina, The Connection between Discrete- and Continuous-Time Descriptions of Gaussian Continuous Processes

  [arxiv]PRE (2022)

• G. Isacchini, A.M Walczak, T. Mora, Armita Nourmohammad, Deep generative selection models of T and B cell receptor repertoires with soNNia

  [bioarxiv]
  PNAS (2021)

• P. Gueguen, C. Metoikidou, T. Dupic, M. Lawand, C. Goudot, S. Baulande, S. Lameiras, O. Lantz, N. Girard, A. Seguin-Givelet, M. Lefevre, T. Mora, A. M. Walczak, J. Waterfall, and S. Amigorena, Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in non-small cell lung cancer patients

  [bioarxiv] Science Immunology (2021)

• N. Spisak, A. M. Walczak, T. Mora, Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

  [bioarxiv] Nucleic Acids Research 48 (19) 10702-10712 (2020)

• T. Dupic, M. Bensouda Koraichi, A. A. Minervina, M. V. Pogorelyy, T. Mora, A. M. Walczak, Immune fingerprinting

  [arxiv] PLoS Computational Biology 16(12) e1008394 (2020)

• J. Mine-Hattab, M. Heltberg, M. Villemeur, C. Guedj, T. Mora, A. M. Walczak, M. Dahan, A. Taddei, Single molecule microscopy reveals key physical features of repair foci in living cells

  [bioarxiv] eLife (2021)

• A. A. Minervina, E. A. Komech, A. Titov, M. Bensouda Koraichi, E. Rosati, I. Z. Mamedov, A. Franke, G. A. Efimov, D. M. Chudakov, T. Mora, A. M. Walczak, Y. B. Lebedev, M. V. Pogorelyy, Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection

  [bioarxiv] eLife (2021)

• V. Sachdeva, T. Mora, A. M. Walczak, S. E. Palmer, Optimal prediction with resource constraints using the information bottleneck

  [bioarxiv] PloS Computational Biology (2021)

• B. Bravi, J. Tubiana, S. Cocco, R. Monasson, T. Mora, A. M. Walczak, Flexible machine learning prediction of antigen presentation for rare and common HLA-I alleles

  [bioarxiv] Cell Systems 12 1-8 (2020)

• G. Isacchini, C. Olivares, A. Nourmohammad, A. M. Walczak, T. Mora, SOS : Online probability estimation and generation of T and B cell receptors

  [arxiv] Bioinformatics (2020)

• Z. Sethna, G. Isacchini, T. Dupic, T. Mora, A. M. Walczak, Y. Elhanati,, Population variability in the generation and thymic selection of T-cell repertoires

  [bioarxiv] PLoS Computational Biology 16(12) e1008394 (2020)

• F. Ferretti, V. Chardes, T. Mora, A. M. Walczak, I. Giardina, Building general Langevin models from discrete data sets

  [arxiv] PRX (2020)

• M. Puelma Touzel, A.M. Walczak*, T. Mora*, Inferring the immune response from repertoire sequencing

  [arxiv] PloS Computational Biology (2020)

• C. Kreer , H. Gruell , T. Mora , A.M. Walczak, Florian Klein, Exploiting B cell receptor analyses to inform on HIV-1 vaccination strategies.

  Vaccines (2020)

• A. A. Minervina, M. V. Pogorelyy, E. A. Komech, V. K. Karnaukhov, P. Bacher, E. Rosati, A. Franke, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev, T. Mora*, A. M. Walczak*, Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell level

  [arxiv] eLife 9:e53704 (2020)

• P. Szymanska-Rozek, D. Villamaina, J. Miekisz, A.M. Walczak, Dissipation in non-steady state regulatory circuits

  [arxiv] Entropy (2019)

• G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak and T. Mora, On generative models of T-cell receptor sequences

  [biorxiv] PRE (2020)

• H. Tran, A. M. Walczak, N. Dostatni, Constraints and limitations on decoding positional information : the Bicoid case-study.

  [biorxiv] Current Topics in Developmental Biology (2019)

• T. Mora* and A.M. Walczak*, How many different clonotypes do immune repertoires contain?

  Current Opinion in Systems Biology (2019)

• G. Altan-Bonnet*, T. Mora*, A.M. Walczak*, Quantitative Immunology for Physicists

  [arxiv] Physics Reports (2020)

• J. Desponds, M. Vergassola, A.M. Walczak, hunchback Promoters Can Readout Morphogenetic Positional Information in Less Than a Minute

  [biorxiv] eLife (2020)

• T. Mora, A.M. Walczak, O. Rivoire, Dynamics in fluctuating and evolving environments

  to appear in Physical Biology (2020)

• J. Marchi, M. Laessig, T. Mora*, A. M. Walczak*, Multi-lineage evolution in viral populations driven by host immune systems

  [biorxiv] Pathogens (2019)

• J. Marchi, E.A. Galpern, R. Espada, D.U. Ferreiro, A.M. Walczak*, T.Mora*, Size and structure of the sequence space of repeat proteins

  [biorxiv] PloS Computational Biology (2019)

• M.V. Pogorelyy, A.A. Minervina, M. Shugay, D.M. Chudakov, Y.B. Lebedev, T. Mora, A. M. Walczak, Detecting T-cell receptors involved in immune responses from single repertoire snapshots

  [arxiv] PloS Biology (2019)

• Z. Sethna, Y. Elhanati, G. G. Callan Jr., T. Mora, A. M. Walczak, OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

  [arxiv] Bioinformatics (2019)

• T. Dupic, Q. Marcou, T. Mora, A. M. Walczak, Genesis of the alpha-beta T-cell receptor

  [arxiv] PloS Computational Biology (2019)

• A. Mayer, V. Balasubramanian, T. Mora, A.M. Walczak, How a well-adapting immune system remembers

  [bioarxiv] PNAS (2019)

• S. Bradde, T. Mora*, A. M. Walczak*, Cost and benefits of CRISPR spacer acquisition

  [arxiv] Philosophical Transactions B (2019)

• H. Tran, J. Desponds, C.A. Perez-Romero, M. Coppey, C. Fradin, N. Dostatni, A.M Walczak, Precision in a rush: trade-offs between positioning and steepness of the hunchback expression pattern

  [bioarxiv] PloS Computational Biology (2018)

• T. Lucas, H. Tran, C.A. Perez-Romero, A. Guillou, M. Coppey, C. Fradin, A.M Walczak, N. Dostatni, 3 minutes to precisely measure morphogen concentration

  [bioarxiv] PloS Genetics (2018)

• R.A. Neher and A. M. Walczak, Progress and open problems in evolutionary dynamics

  [arxiv] Proceedings of the 24th Solvay Conference in Physics -- The Physics of Living Matter : Space, Time and Information in Biology, Worldpress (2018)

• M. V. Pogorelyy, A. A. Minervina, M. Puelma Touzel, A. L. Sycheva, E. A. Komech, E. I. Kovalenko, G. G. Karganova, E. S. Egorov, A. Yu. Komkov, D. M. Chudakov, I. Z. Mamedov, T. Mora*, A. M. Walczak*, Y. B. Lebedev* , Precise tracking of vaccine-responding T-cell clones reveals convergent and personalized response in identical twins

  [arxiv ] PNAS (2019)

• A. Cavagna, I. Giardina, T. Mora, A. M. Walczak, Physical constraints in biological collective behaviour

  [Current Opinion in Systems Biology (2018)]

• Y. Elhanati, Z. Sethna, G. G. Callan Jr., T. Mora*, A.M. Walczak* , Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

  [arxiv ] Immunological Reviews (2018)

• R. N. Germain, B. D. Greenbaum, A. Hoffmann, K. Miller-Jensen, T. Mora, A. M. Walczak, E. Segal, T. Vogl, S. Klompus, S. Peled-Liviatan, A. Weinberger, S. T. Smale, J. S. Tsang , How Can Systems Biology Test Principles and Tools Using Immune Cells as a Model?

  [Trends in Immunology Systems (2018)]

• R. N. Germain, B. D. Greenbaum, A. Hoffmann, K. Miller-Jensen, T. Mora, A. M. Walczak, E. Segal, T. Vogl, S. Klompus, S. Peled-Liviatan, A. Weinberger, S. T. Smale, J. S. Tsang , How Can Systems Biology Test Principles and Tools Using Immune Cells as a Model?

  [Cell Systems (2018)]

• A. Nourmohammad, J. Otwinowski, M. Łuksza, T. Mora*, A.M Walczak* , Clonal competition in B-cell repertoires during chronic HIV-1 infection

  [arxiv] Molecular Biology and Evolution (2019)

• N.A. Rossi, T. Mora, A.M. Walczak, M.J. Dunlop, Active degradation of a regulator controls coordination of downstream genes

  [bioarxiv] PloS Computational Biology (2018)

• R.M. Adams, J.B. Kinney, A.M. Walczak, T. Mora, Physical epistatic landscape of antibody binding affinity

  [arxiv] Cell Systems (2018)

• M. V. Pogorelyy, A. A. Minervina, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev, T. Mora, A. M. Walczak, Method for identification of condition-associated public antigen receptor sequences

  [arxiv] eLife (2018)

• H. Tran, C.A. Perez-Romero, T. Ferraro, C. Fradin, N. Dostatni, M. Coppey, A.M Walczak, LiveFly - a toolbox for the analysis of transcription dynamics in live Drosophila embryos

  Methods in Molecular Biology (2018)

• C.A. Perez-Romero, H. Tran, M. Coppey, A.M. Walczak, C. Fradin, N. Dostatni, Live imaging of mRNA transcription in Drosophila Embryos

  Methods in Molecular Biology (2018)

• S. Magadan, L. Jouneau, M. Puelma Touzel, S. Marillet, W. Chara, A. Six, E. Quillet, T. Mora, A.M. Walczak, F. Cazals, O. Sunyer, S. Fillatreau, P. Boudinot, Origin of the public memory antibody response induced upon antiviral vaccination in fish

  Frontiers in Immunology (2018)

• A. Toledano, Y. Elhanati, J. I. C. Benichou, A. M. Walczak, T. Mora, Y. Louzoun, Evidence for shaping of L chain repertoire by structural selection

  Frontiers in Immunology (2018)

• K. Krishnamurthy, A. M. Hermundstad, T. Mora, A. M. Walczak, V. Balasubramanian, Disorder and the neural representation of complex odors : smelling in the real world

  [arxiv]

• Q. Marcou, T. Mora, A. M. Walczak, IGoR : a tool for high-throughput immune repertoire analysis

  [arxiv] Nature Communications (2018)

• J. W. Larkin, X. Zhai, K. Kikuchi, S. Redford, A. Prindle, J. Liu, A. M. Walczak, J. Garcia-Ojalvo, A. Mugler and G. M. Suel, Signal Percolation within a Bacterial Community

  [arxiv] Cell Systems (2018) [abstract]

• A. Mayer, T. Mora, O. Rivoire, A. M. Walczak, Transitions in optimal adaptive strategies for populations in fluctuating environments

  PRE (2017) [arxiv]

• J. Desponds, A. Mayer, T. Mora and A. M. Walczak, Population dynamics of immune repertoires

  (2017) [arxiv] Mathematical, Computational and Experimental T Cell Immunology - Springer volume (2018)

• A. Mayer, T. Mora, O. Rivoire, A. M. Walczak, Explication evolutive de la diversite des strategies immunitaires

  Medecine/Sciences (2017)

• R. Espada, RG Parra, T Mora, AM Walczak, DU Ferreiro , Inferring repeat protein energetics from evolutionary information

  PLoS Computational Biology (2017) [arxiv] [biorxiv] [pdf]

• Z.Sethna, Y.Elhanati, C.S.Dudgeon, C.G.Callan,Jr., A.Levine, T.Mora and A.M.Walczak, Mouse T-cell repertoires as statistical ensembles: overall characterization and age dependence

  PNAS (2017) [arxiv]

• M. Laessig, V. Mustonen and A. M. Walczak, Predicting evolution

  Nature Ecology & Evolution (2017) [pdf]

• C. G. Callan Jr., T. Mora and A. M. Walczak, Repertoire sequencing and the statistical ensemble approach to adaptive immunity

  Current Opinion in Systems Biology (2017)

• J. Desponds, H. Tran, T. Ferraro, T. Lucas, C. Perez Romero, A. Guillou, C. Fradin, M. Coppey, N. Dostatni, A. M. Walczak, Precision of readout at the hunchback gene

  PLoS Comp. Biol. (2016) [arxiv] [biorxiv] [pdf]

• Q. Marcou, I. Carmi-Levy, C. Trichot, V. Soumelis, T. Mora, A. M. Walczak, A model for the integration of conflicting exogenous and endogenous signals by dendritic cells

  Physical Biology (2018) [arxiv] [biorxiv] [pdf]

• T. Mora and A. M. Walczak, Quantifying lymphocyte receptor diversity

  Systems Immunology Eds.J. Das and C. Jayaprakash (2017) [arxiv] [biorxiv] [pdf]

• T. Mora and A. M. Walczak, Renyi entropy, abundance distribution and the equivalence of ensembles

  PRE (2016) [arxiv] [pdf]

• M. Pogorelyy, Y. Elhanati, Q. Marcou, A. Sycheva, E. Komech, V. Nazarov, O. Britanova, D. Chudakov, I. Mamedov,Y. Lebedev, T. Mora, A. M. Walczak, Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

  PloS Comp. Biol. (2017) [arxiv] [biorxiv] [pdf]

• R.M. Adams, J.B. Kinney, T. Mora, A. M. Walczak, Diversity of immune strategies explained by adaptation to pathogen statistics

  eLife (2017) [arxiv] [biorxiv] [pdf]

• A. Mayer, T. Mora, O. Rivoire, A. M. Walczak, Diversity of immune strategies explained by adaptation to pathogen statistics

  PNAS 113 8630(2016) [arxiv] [biorxiv] [pdf]

• T. Mora, A. M. Walczak, L. Del Castello, F. Ginelli, S. Melillo, L. Parisi, M. Viale, A. Cavagna and I. Giardina, Questioning the activity of active matter in natural flocks of birds

  Nature Physics (2016) [arxiv] [pdf]

• Y. Elhanati, Q. Marcou, T. Mora and A. M. Walczak
  repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data

  Bioinformatics (2016) [arxiv] [biorxiv] [pdf]

• C. K. Fisher, T. Mora and A. M. Walczak,
  Habitat Fluctuations Drive Species Covariation in the Human Microbiota

  PLoS Comp. Biol. (2016) [arxiv] [pdf]

• A. Mugler, M. Kittisopikul, L. Hayden, J. Liu, C. H. Wiggins, G. M. Suel and A. M. Walczak,
  Noise expands the response range of the Bacillus subtilis competence circuit

  PLoS Comp. Biol. (2016) [ abs] [arxiv] [pdf]

• T. R. Sokolowski, A. M. Walczak, W. Bialek, and G. Tkacik,
  Extending the dynamic range of transcription factor action by translational regulation

  Phys. Rev. E 93 022404(2016) [arxiv] [pdf]

• J. Desponds, T. Mora and A. M. Walczak,
  Fluctuating fitness shapes the clone size distribution of immune repertoires

  PNAS 113 274(2016) [arxiv] [biorxiv] [pdf]

• T. Ferraro, T. Lucas, M. Clemot, J. De Las Heras Chanes, J. Despond, M. Coppey, A. M. Walczak and N. Dostatni, New methods to image transcription in living fly embryos : the insights so far, and the prospects.

  WIREs Developmental Biology 10 221(2016) [pdf]

• T. Ferraro, E. Esposito, L. Mancini, N. Sam, T. Lucas, M. Coppey, N. Dostatni, A. M. Walczak, M. Levine and M. Lagha, Transcriptional memory in the Drosophila embryo.

  Current Biology 26 1(2015) [abs] [pdf]

• M. M. Desai and A. M. Walczak, Flexible gene pools

  Science 348 977 (2015) [abs] [pdf]

• R. Espada, R. Gonzalo Parra, M. J. Sippl, T. Mora, A. M. Walczak and D. U. Ferreiro
  Repeat Proteins challenge the concept of structural domains.

  Biochemical Society Transactions 43 844 (2015) [abs]

• Y. Elhanati, Z. Sethna, Q. Marcou, C. G. Callan Jr., T. Mora and A. M. Walczak
  Inferring processes underlying B-cell repertoire diversity

  Philosophical Transactions B 370 20140243 (2015) [arxiv] [biorxiv] [abs] [pdf]

• F. Mancini, M. Marsili and A. M. Walczak, Trade-offs in delayed information transmission in biochemical networks.

  J. Stat. Phys (2015) [arxiv] [pdf]

• A. M. Walczak
  Tiling solutions for optimal biological sensing

  Comptes Rendus Physique (2015)

  [arxiv] [pdf]

• D. Bagnara, M. Squillario, D. Kipling, T. Mora, A. M. Walczak, L. Da Silva, S. Weller, D. Dunn-Walters, J.-C. Weill, C.-A. Reynaud, A redefinition of IgM memory subsets in humans

  Journal of Immunology (2015)

• A. Mayer, V. Balasubramanian, T. Mora, A.M. Walczak
  How a well-adapted immune system is organized.

  Proc Natl Acad Sci USA 112 5950 (2015)

  [arxiv] [abs] [pdf]

  featured in [phys.org|medicalxpress ]

• R. Espada, R.G. Parra, T. Mora, A.M. Walczak, D. Ferreiro
  Capturing coevolutionary signals in repeat proteins.

  BMC Bioinformatics 16 207 (2015)

  [arxiv] [abs] [pdf]

• A. Cappuccio, R. Zollinger, M. Schenk, A.M. Walczak, N. Servant, E. Barillot, P. Hupe, R. Modlin, V. Soumelis, The combinatorial code governing innate immune cell response to complex stimuli

  Nature Comm. 6 6847 (2015) [abs] [pdf]

• Y. Elhanati, A. Murugan, C. G. Callan, T. Mora and A. M. Walczak, Quantifying selection in immune receptor repertoires

  Proc Natl Acad Sci USA 111(27) 9875-9880 (2014) [arxiv] [biorxiv] [abs] [pdf]

• A. Cavagna, L. Del Castello, I. Giardina, T. Grigera, A. Jelic, S. Melillo, T. Mora, L. Parisi, E. Silvestri, M. Viale, A. M. Walczak, Flocking and turning : a new model for self-organized collective motion.

  J. Stat. Phys 158(3) 601-627 (2014) [arxiv] [abs] [pdf]

• A. Cavagna, I. Giardina, F. Ginelli, T. Mora, D. Poviani, R. Tavarone, A. M. Walczak, Dynamical Maximum Entropy Approach to Flocking.

  Phys. Rev. E 89 042707(2014) [arxiv] [abs] [pdf]

• A. Six, E. Mariotti-Ferrandiz, W. Chaara, S. Magadan, H.-P. Pham, M.-P. Lefranc, T. Mora, V. Thomas- Vaslin, A. M. Walczak, P. Boudinot, The past, present and future of immune repertoire biology - the rise of next-generation repertoire analysis.

  Frontiers in Immunology 4 413(2013) [abs] [pdf]

• T. Lucas, T. Ferraro, B. Roelens, J. De Las Heras Chanes, A. M. Walczak, M. Coppey, N. Dostatni, Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos.

  Current Biology 23 1(2013) [abs] [pdf]

  featured in Development [abs][pdf]

• W. Bialek, A. Cavagna, I. Giardina, T. Mora, O. Pohl, E. Silvestri, M. Viale, A. Walczak, Social interactions dominate speed control in driving natural flocks toward criticality.

  Proc Natl Acad Sci USA (2014) [arxiv] [abs] [pdf]

• B. Good, A. M. Walczak, R. Neher and M. M. Desai, Genetic Diversity in the Interference Selection Limit.

  PLoS Genetics 10 e1004222(2014) [arxiv] [abs] [pdf]

• T. Mora and A. M. Walczak, Effect of Phenotypic Selection on Stochastic Gene Expression.

  J. Phys. Chem. 117 13194 (2013) [arxiv] [abs] [pdf]

• F. Mancini, C. H. Wiggins, M. Marsili and A. M. Walczak, Time-dependent information transmission in a model regulatory circuit.

  Phys. Rev. E 88 022708 (2013) [arxiv] [pdf]

• A. Murugan, T. Mora, A. M. Walczak and C. G. Callan, Statistical inference of the mechanisms of T-cell receptor diversity generation from sequence repertoires.

  Proc Natl Acad Sci USA 109 16161 (2012) [arxiv] [abs] [pdf]

• M. M. Desai, A. M. Walczak and D. F. Fisher, Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations.

  Genetics 193 565 (2013) [arxiv] [abs] [pdf]

• A. Burger, A. M. Walczak and P. G. Wolynes, Abduction and asylum in the lives of transcription factors.

  Phys. Rev. E 86 041920(2012) [arxiv] [pdf]

• T. Mora, A. M. Walczak and F. Zamponi, Transition path sampling algorithm for discrete many-body systems.

  Phys. Rev. E 85 036710(2012) [arxiv] [abs] [pdf]

• G. Tkacik, A. M. Walczak and W. Bialek, Optimizing information flow in small genetic networks. III: A self-interacting gene.

  Phys. Rev. E 85 041903(2012) [arxiv] [abs] [pdf]

• W Bialek, A Cavagna, I Giardina, T Mora, E Silvestri, M Viale and A. M. Walczak, Statistical mechanics for natural flocks of birds.

  Proc Natl Acad Sci USA 109 4786(2012) [arxiv] [abs] [pdf]

• G. Tkacik and A. M. Walczak, Information transmission in genetic regulatory networks: a review.

  J. Phys. : Condens. Matter 23 153102 (2011) [arxiv] [abs] [pdf]

• A. M. Walczak, L. E. Nicolaisen, J. B. Plotkin and M. M. Desai The Structure of Genealogies in the Presence of Purifying Selection: An Effective Coalescent Theory.

  Genetics 190 753 (2011) [arxiv] [abs] [pdf] [Supplement]

• M. M. Desai, L. E. Nicolaisen, A. M. Walczak and J. B. Plotkin, The Structure of Allelic Diversity in the Presence of Purifying Selection.

  Theoretical Population Biology 81 144 (2011) [arxiv] [abs] [pdf]

• A. M. Walczak, A. Mugler and C. H. Wiggins, Analytic methods for modeling stochastic regulatory networks.

  appeared as a chapter in "Methods in Molecular Biology" Eds. M. Betterton and X. Liu, Springer Verlag [arxiv] [abs] [pdf]

• A. Mugler, A. M. Walczak and C. H. Wiggins, Telling time with an intrinsically noisy clock.

  Phys. Rev. Lett. 105 058101 (2010) [arxiv] [abs] [pdf]

• A. M. Walczak, G. Tkacik and W. Bialek, Optimizing information flow in small genetic networks. II: Feed forward interactions.

  Phys. Rev. E 81 041905 (2010) [arxiv] [abs] [pdf]

• T. Mora, A. M. Walczak, W. Bialek, C. G. Callan, Maximum entropy models for antibody diversity.

  Proc Natl Acad Sci USA 107(12) 5405-5410 (2010) [arxiv] [abs] [pdf]

• A. Burger, A. M. Walczak and P. G. Wolynes, Abduction and asylum in the lives of transcription factors.

  Proc Natl Acad Sci USA 107 4016 (2010) [abs] [pdf]

• A. Mugler, A. M. Walczak and C. H. Wiggins, Spectral solutions to stochastic models of gene expression with bursts and regulation.

  Phys. Rev. E 80 041921 (2009) [arxiv] [abs] [pdf]

• G. Tkacik, A. M. Walczak and W. Bialek, Optimizing information flow in small genetic networks.

  Phys. Rev. E 80 031920 (2009) [arxiv] [abs] [pdf]

• A. M. Walczak, A. Mugler and C. H. Wiggins, A stochastic spectral analysis of transcriptional regulatory cascades.

  Proc Natl Acad Sci USA 106 6529 (2009) [arxiv] [abs] [pdf]

• A. M. Walczak and P. G. Wolynes, Gene-gene cooperativity in small networks.

  Biophys. J. 96 4525 (2009) [arxiv] [abs] [pdf]

• D. Schultz, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Absolute rate theories of epigenetic stability.

  Proc Natl Acad Sci USA 105 19165 (2008) [abs] [pdf]

• J. D. Stevenson, A. M. Walczak, R. W. Hall and P. G. Wolynes,

  Journal of Chemical Physics 129 194505 (2008) [arxiv] [abs] [pdf]

• A. M. Walczak, D. U. Ferreiro, E. A. Komives and P. G. Wolynes, The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity and the Folding Funnels of One-Dimensional Architectures.

  PLoS Computational Biology 4 e1000070(2008) [abs] [pdf]

• A. M. Walczak, F. Alet and M. P. A. Fisher, Exotic quantum phase transitions in correlated matter.

  Physica A 369 122 (2006) [arxiv] [abs] [pdf]

• A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Absolute rate theories of epigenetic stability.

  Proc Natl Acad Sci USA 102 18926 (2005) [arxiv] [abs] [pdf]

• J. E. M. Hornos, D. Schultz, G. C. P. Innocentini, J. Wang, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Self-regulating gene: an exact solution.

  Phys. Rev. E 72 51907 (2005) [abs] [pdf]

• A. M. Walczak, M. Sasai and P.G. Wolynes, Self-Consistent Proteomic Field Theory of Stochastic Gene Switches.

  Biophys. J. 88 828 (2005) [arxiv] [abs] [pdf]

• A. M. Walczak and J. M. Antosiewicz, Langevin Dynamics of Proteins at Constant pH.

  Phys. Rev. E 66 051911 (2002) [abs] [pdf]