A.A. Minervina, M.V. Pogorelyy, K. Mayer-Blackwell, R. Tirtakusuma, S.A. Schattgen, A. Fiore-Gartland, A.M. Walczak, T. Mora, P. Bradley, P.G. Thomas
Uneven TCR chain pairing constraints govern epitope recognition
D.P.G.H. Wong, A.M. Walczak, T. Mora
Surveying the adaptive landscapes of 10,000 antibodies
M. Milighetti, Z. Sethna, S. Martis, C. Reiche, Y. Elhanati, V.P. Balachandran, B.D. Greenbaum, A.M. Walczak, T. Mora
Unbiased identification of responding T cell clones from longitudinal repertoire sequencing with CloneSearch
H. Alston, T. Mora, A.M. Walczak
Neutralization titers reveal the structure of polyclonal antibody responses
A.G. Kline, M. Koch-Janusz, A.M. Walczak, T. Mora, S.E. Palmer
Coarse-graining reveals collective predictive information in a sensory population
L. Di Bari, T. Mora, A. Pagnani, A.M. Walczak, F. Zamponi, S. Rossi
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
M. Dhanasekar, K. Fidelin, M. Greco, E.T. Lunsford, M. Carbo-Tano, C. Deleuze, L. Moisan, T. Mora, A.M. Walczak, C. Wyart
Noradrenaline prolongs the state of motor arrest via cerebrospinal fluid signaling
G. Athènes, A. Woolfe, T. Mora, A.M. Walczak
Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics
A. Mazzolini, A.M. Walczak, T. Mora
Dynamics of memory B cells and plasmablasts in healthy individuals
L. Gieselmann, A.T. DeLaitsch, M. Rohde, H. Gruell, C. Kreer, M. Seda Ercanoglu, H.B. Gristick, P. Schommers, E. Ahmadov, C. Radford, A. Mazzolini, L. Zhang, A.P. West Jr, J. Worczinski, A. Momot, M.L. Reichwein, J. Knüfer, R. Stumpf, N.N. Mkhize, H. Kaldine, S. Bhebhe, S. Deshpande, F. Giovannoni, E. Stefanutti, F. Benigni, C. Havenar-Daughton, D. Corti, A. Kroidl, A. Adhikari, A.J. Nanfack, G.E. Ambada, R. Duerr, L. Maganga, W. William, N.E. Ntinginya, T. Wolf, C. Geldmacher, M. Hoelscher, C. Lehmann, P.L. Moore, T. Mora, A.M. Walczak, P.B. Gilbert, N.A. Doria-Rose, Y. Huang, J.D. Bloom, M.S. Seaman, P.J. Bjorkman, F. Klein
Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy
H. Alston, M. Rouches, A. Murugan, A.M. Walczak, T. Mora
Theoretical limits for sensing through phase separation
D. Porter, C. Collins, A. Mazzolini, L. Jouneau, V. Mhanna, C. Coiffier, M. Peruzzi, Y. Jaszczyszyn, E. Mariotti-Ferrandiz, F. Huetz, B. Collet, T. Mora, A.M. Walczak, B. Verrier, P. Boudinot
Divergent B-cell repertoire remodelling by mRNA, DNA and live attenuated vaccines in fish
T. Tohme, M. Vergassola, T. Mora, A.M. Walczak
Fast decisions with biophysically constrained gene promoter architectures
M.-F. Abbate, P. Toxe, N. Maestrali, M. Gagnaire, E. Vigne, M.A. Shahsavarian, T. Mora, A.M. Walczak
Integrating computational detection and experimental validation for rapid GFRAL-specific antibody discovery
D.S. Banerjee, M.J. Falk, M.L. Gardel, A.M. Walczak, T. Mora, S. Vaikuntanathan
Learning via mechanosensitivity and activity in cytoskeletal networks
A. Aragon, A. Lambert, T. Mora, A.M. Walczak
Learning evolutionary parameters from genealogies using allelic trees
C. Metoikidou, V.K. Karnaukhov, B. Boeckx, E. Timperi, P.E. Bonté, L. Wang, M. Espenel, B. Albaud, D. Loirat, X. Wang, C. Sotiriou, P. Aftimos, K. Punie, H. Wildiers, V. Labroska, M.-W. Wang, J.J. Waterfall, M. Piccart-Gebhart, T. Mora, A.M. Walczak, O. Lantz, L. Buisseret, D. Lambrechts, S. Amigorena, E. Romano
Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer
X. Chen, K. Crocker, S. Kuehn, A.M. Walczak, T. Mora
Inferring resource competition in microbial communities from time series
M. Nielsen, A. Eugster, M. Fynbo Jensen, M. Goel, A. Tiffeau-Mayer, A. Pelissier, S. Valkiers, M. Rodríguez Martínez, B. Meynard-Piganeeau, V. Greiff, T. Mora, A.M. Walczak, G. Croce, D.L. Moreno, D. Gfeller, P. Meysman, J. Barton
Lessons learned from the IMMREP23 TCR-epitope prediction challenge
P. Pereira, H. Minoux, A.M. Walczak, T. Mora
Energy-based generative models for monoclonal antibodies
M. Kramar, L. Hahn, A.M. Walczak, T. Mora, M. Coppey
Single cells can resolve graded stimuli
N. Blot, C. Brooks, D.W. Swartz, E. Abdelaleem, M. Garic, A. Iglesias-Ramas, M. Pasek, T. Mora, A.M. Walczak
How host mobility patterns shape antigenic escape during viral-immune co-evolution
B. Manfroi et al.
Preschool-age children maintain a distinct memory CD4+ T cell and memory B cell response after SARS-CoV-2 infection
G. Mahuas, T. Buffet, O. Marre, U. Ferrari, T. Mora
Strong, but not weak, noise correlations are beneficial for population coding
V.K. Karnaukhov, A.-L. Le Gac, L. Bilonda Mutala, A. Darbois, L. Perrin, F. Legoux, A.M. Walczak, T. Mora, O. Lantz
Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation
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
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
Proc Natl Acad Sci 121(35) e2401058121 (2024) [pdf] [bioRxiv]
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
G. Isacchini, V. Quiniou, P. Barennes, V. Mhanna, H. Vantomme, P. Stys, E. Mariotti-Ferrandiz, D. Klatzmann, A.M. Walczak, T. Mora, A. Nourmohammad
Local and Global Variability in Developing Human T-Cell Repertoires
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
Proc Natl Acad Sci 121(24) e2316401121 (2024) [pdf] [bioRxiv]
R. Assmann, D. Caldwell, G. Cerullo, H. Chapman, D. Cialla-May, M. Durante, A. Faus-Golfe, J. Hellwage, S. Hellwage, C. Krafft, T. Mappes, T.G. Mayerhöfer, T. Mora, A. Peters, C. Poletto, J. Popp, F. Ritort, P. Rösch, L. Rossi, M. Sales-Pardo, I. Schie, M. Schmitt, F. Simmel, A.M. Walczak
Physics for health
Chapter 5 in EPS Grand Challenges: Physics for Society in the Horizon 2050 (IOP Publishing, 2024)
F. Camaglia, I. Nemenman, T. Mora, A.M. Walczak
Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors
T. Mora, A.M. Walczak
Quantitative theory of viral-immune coevolution may be within reach
V. Chardès, A. Mazzolini, T. Mora, A.M. Walczak
Evolutionary stability of antigenically escaping viruses
T. Mora, A.M. Walczak
Towards a quantitative theory of tolerance
L. Hahn, A.M. Walczak, T. Mora
Dynamical information synergy in biochemical signaling networks
N. Spisak, G. Athenes, T. Mora, A.M. Walczak
Combining mutation and recombination statistics to infer clonal families in antibody repertoires
J. Urbanus, J. Cosgrove, J. Beltman, Y. Elhanati, R. de Andrade Moral, C. Conrad, J.W. van Heijst, E. Tubeuf, A. Velds, L. Kok, C. Merle, J.P. Magnusson, J. Frisén, S. Fre, A.M. Walczak, T. Mora, H. Jacobs, T.N. Schumacher, Leila Perié
DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age
B. Bravi, A. Di Gioacchino, J. Fernandez-de-Cossio-Diaz, A.M. Walczak, T. Mora, S. Cocco, R. Monasson
Learning the differences: a transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
G. Mahuas, O. Marre, T. Mora, U. Ferrari
A small-correlation expansion to quantify information in noisy sensory systems
P. Meysman, J. Barton, B. Bravi, L. Cohen-Lavi, V.K. Karnaukhov, E. Lilleskov, A. Montemurro, M. Nielsen, T. Mora, P. Pereira, A. Postovskaya, M. Rodríguez Martínez, 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
X. Chen, M. Winiarski, A. Puścian, E. Knapska, A.M. Walczak, T. Mora
Generalized Glauber dynamics for inference in biology
A. Mazzolini, T. Mora, A.M. Walczak
Inspecting the interaction between HIV and the immune system through genetic turnover
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
Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals
X. Chen, F. Ginoux, T. Mora, A.M. Walczak, C. Wyart
Granger causality analysis for calcium transients in neuronal networks: challenges and improvements
M. Łuksza, Z. Sethna, L.A. Rojas, J. Lihm, B. Bravi, Y. Elhanati, K. Soares, M. Amisaki, A. Dobrin, D. Hoyos, P. Guasp, A. Zebboudj, R. Yu, A. Kaya 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, R. Monasson, T. Mora, A.M. Walczak, S. Cocco, C. Iacobuzio-Donahue, B.D. Greenbaum, V.P. Balachandran
Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
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
M. Bensouda Koraichi, S. Ferri, A.M. Walczak, T. Mora
Inferring the T-cells repertoire dynamics of healthy individuals
Proc Natl Acad Sci 120(4) e2207516120 (2023) [pdf] [bioRxiv]
E.A. Galpern, J. Marchi, T. Mora, A.M. Walczak, D.U. Ferreiro
Evolution and folding of repeat proteins
F. Camaglia, A. Ryvkin, E. Greenstein, S. Reich-Zeliger, B. Chain, T. Mora, A.M. Walczak, N. Friedman
Quantifying changes in the T cell receptor repertoire during thymic development
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
C. Lupo, N. Spisak, A.M. Walczak, T. Mora
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
M.A. Goldin, B. Lefebvre, S. Virgili, A. Ecker, T. Mora, U. Ferrari, O. Marre
Context-dependent selectivity to natural scenes in the retina
V. Chardès, M. Vergassola, A.M. Walczak, T. Mora
Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
G. Isacchini, N. Spisak, A. Nourmohammad*, T. Mora*, A.M. Walczak*
Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
V. Greiff, E.T. Luning Prak, T. O'Donnell, F. Finotello, S.T. Reddy, A.M. Walczak, T. Mora
What are the current driving questions in immune repertoire research?
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
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
M. Bensouda Koraichi, M. Puelma Touzel, T. Mora*, A.M. Walczak*
NoisET: Noise Learning and Expansion Detection of T-Cell Receptors
J. Marchi, M. Lässig, A.M. Walczak*, T. Mora*
Antigenic waves of virus-immune co-evolution
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.J. Waterfall, S. Amigorena
Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer
F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, I. Giardina
Renormalization group approach to connect discrete-and continuous-time descriptions of Gaussian processes
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
A. Murugan, K. Husain, M.J. Rust, C. Hepler, J. Bass, J.M.J. Pietsch, P.S. Swain, S.G. Jena, J.E. Toettcher, A.K. Chakraborty, K.G. Sprenger, T. Mora, A.M. Walczak, O. Rivoire, S. Wang, K.B. Wood, A. Skanata, E. Kussell, R. Ranganathan, H.-Y. Shih, N. Goldenfeld
Roadmap on biology in time varying environments
D. Conti, T. Mora
Non-equilibrium dynamics of adaptation in sensory systems
G. Isacchini, A.M. Walczak, T. Mora, A. Nourmohammad
Deep generative selection models of T and B cell receptor repertoires with soNNia
N. Spisak, A.M. Walczak, T. Mora
Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Nucleic Acids Research 48(19) 10702-10712 (2020) [pdf] [arXiv]
T. Dupic, M. Bensouda Koraichi, A.A. Minervina, M.V. Pogorelyy, T. Mora, A.M. Walczak
Immune fingerprinting through repertoire similarity
G. Mahuas, G. Isacchini, O. Marre, U. Ferrari, T. Mora
A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons
J. Miné-Hattab, M.L. 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
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
V. Sachdeva, T. Mora, A.M. Walczak, S.E. Palmer
Optimal prediction with resource constraints using the information bottleneck
B. Bravi, J. Tubiana, S. Cocco, R. Monasson, T. Mora, A.M. Walczak
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles
G. Isacchini, C. Olivares, A. Nourmohammad, A.M. Walczak, T. Mora
SOS: Online probability estimation and generation of T and B cell receptors
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
C. Kreer, H. Gruell, T. Mora, A.M. Walczak, F. Klein
Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, I. Giardina
Building general Langevin models from discrete data sets
M. Puelma Touzel, A.M. Walczak, T. Mora
Inferring the immune response from repertoire sequencing
G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak, T. Mora
Generative models of T-cell receptor sequences
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
T. Mora, I. Nemenman
Physical limit to concentration sensing in a changing environment
Phys. Rev. Lett. 123 198101 (2019) [pdf] [arXiv]
See also the synopsis in Physics:
A Biological Cell As a Chemical Sensor
T. Mora, A.M. Walczak
How many different clonotypes do immune repertoires contain?
Current Opinion in Systems Biology 18 104 (2019) [pdf] [arXiv]
G. Altan-Bonnet*, T. Mora*, A.M. Walczak*
Quantitative Immunology for Physicists
J. Marchi, M. Lässig, T. Mora*, A.M. Walczak*
Multi-lineage evolution in viral populations driven by host immune systems
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
S. Bradde, T. Mora*, A.M. Walczak*
Cost and benefits of CRISPR spacer acquisition
M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman*, T. Mora*
Receptor crosstalk improves concentration sensing of multiple ligands
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 Public Memory B Cell Clones in Fish After Antiviral Vaccination
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
Z. Sethna, Y. Elhanati, C.G. Callan Jr., A.M. Walczak*, T. Mora*
OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
T. Dupic, T. Mora*, A.M. Walczak*
Genesis of the αβ T-cell receptor
C. Gardella, O. Marre*, T. Mora*
Modeling the correlated activity of neural populations: A review
A. Mayer, V. Balasubramanian, A.M. Walczak*, T. Mora*
How a well-adapting immune system remembers
A. Toledano, Y. Elhanati, J.I.C. Benichou, A.M. Walczak, T. Mora, Y. Louzoun
Evidence for Shaping of Light Chain Repertoire by Structural Selection
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
A. Cavagna, I. Giardina, T. Mora, A.M. Walczak
Physical constraints in biological collective behaviour
Y. Elhanati, Z. Sethna, C.G. Callan Jr., T. Mora*, A.M. Walczak*
Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination
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
What Can Immunologists Learn from Systems Approaches?
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?
A. Nourmohammad, J. Otwinowski, M. Łuksza, T. Mora*, A.M. Walczak*
Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
Molecular Biology and Evolution 36(10) 2184-2194 (2019) [pdf] [arXiv]
N.A. Rossi, T. Mora, A.M. Walczak, M.J. Dunlop
Active degradation of a regulator controls coordination of downstream genes
U. Ferrari, S. Deny, M. Chalk, G. Tkacik, O. Marre*, T. Mora*
Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
U. Ferrari, S. Deny, O. Marre*, T. Mora*
A simple model for low variability in neural spike trains
R.M. Adams, J.B. Kinney, A.M. Walczak*, T. Mora*
Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy
C. Gardella, O. Marre*, T. Mora*
Blindfold learning of an accurate neural metric
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
K. Krishnamurthy, A.M. Hermundstad, T. Mora, A.M. Walczak, V. Balasubramanian
Disorder and the neural representation of complex odors
Q. Marcou, T. Mora*, A.M. Walczak*
High-throughput immune repertoire analysis with IGoR
A. Mayer, T. Mora, O. Rivoire, A.M. Walczak
Transitions in optimal adaptive strategies for populations in fluctuating environments
R. Espada, R.G. Parra, T. Mora, A.M. Walczak, D.U. Ferreiro
Inferring repeat protein energetics from evolutionary information
J. Desponds, A. Mayer, T. Mora, A.M. Walczak
Population dynamics of immune repertoires
To be published as book chapter (2017) [arXiv]
M.-C. Duvernoy, T. Mora, M. Ardre, V. Croquette, D. Bensimon, C. Quilliet, J.-M. Ghigo, M. Balland, C. Beloin, S. Lecuyer, N. Desprat
Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis
U. Ferrari, C. Gardella, O. Marre*, T. Mora*
Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding
U. Ferrari, T. Obuchi, T. Mora
Random versus maximum entropy models of neural population activity
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
T. Mora, A.M. Walczak
Quantifying lymphocyte receptor diversity
in Systems Immunology: An Introduction to Modeling Methods for Scientists, eds. J. Das, and C. Jayaprakash (2018) [arXiv]
M.V. Pogorelyy, Y. Elhanati, Q. Marcou, A.L. Sycheva, E.A. Komech, V.I. Nazarov, O.V. Britanova, D.M. Chudakov, I.Z. Mamedov, Y.B. Lebedev*, T. Mora*, A.M. Walczak*
Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires
C.K. Fisher, T. Mora, A.M. Walczak
Habitat Fluctuations Drive Species Covariation in the Human Microbiota
Z. Sethna, Y. Elhanati, C.S. Dudgeon, C.G. Callan Jr., A. Levine, T. Mora, A.M. Walczak
Insights into immune system development and function from mouse T-cell repertoires
R.M. Adams, T. Mora*, A.M. Walczak*, J.B. Kinney*
Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves
C.G. Callan, T. Mora, A.M. Walczak
Repertoire sequencing and the statistical ensemble approach to adaptive immunity
C. Gardella, O. Marre*, T. Mora*
A tractable method for describing complex couplings between neurons and population rate
T. Mora, A.M. Walczak
Rényi entropy, abundance distribution and the equivalence of ensembles
A. Mayer, T. Mora, O. Rivoire, A.M. Walczak
Diversity of immune strategies explained by adaptation to pathogen statistics
T. Mora, A.M. Walczak, L. Del Castello, F. Ginelli, S. Melillo, L. Parisi, M. Viale, A. Cavagna, I. Giardina
Local equilibrium in bird flocks
Y. Elhanati, Q. Marcou, T. Mora, A.M. Walczak
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
J. Desponds, T. Mora, A.M. Walczak
Fluctuating fitness shapes the clone size distribution of immune repertoires
R. Espada, R.G. Parra, M.J. Sippl, T. Mora, A.M. Walczak, D.U. Ferreiro
Repeat proteins challenge the concept of structural domains
D. Bagnara, M. Squillario, D. Kipling, T. Mora, A.M. Walczak, L. Da Silva, S. Weller, D.K. Dunn-Walters, J.-C. Weill, C.-A. Reynaud
A Reassessment of IgM Memory Subsets in Humans
G. Tkacik, T. Mora, O. Marre, D. Amodei, S.E. Palmer, M.J. Berry, W. Bialek
Thermodynamics and signatures of criticality in a network of neurons
T. Mora
Physical limit to concentration sensing amid spurious ligands
Y. Elhanati, Z. Sethna, Q. Marcou, C.G. Callan Jr., T. Mora, A.M. Walczak
Inferring processes underlying B-cell repertoire diversity
T. Mora, S. Deny, O. Marre
Dynamical criticality in the collective activity of a population of retinal neurons
O. Marre, Vicente Botella-Soler, K.D. Simmons, T. Mora, G. Tkacik, M.J. Berry II
High accuracy decoding of dynamical motion from a large retinal population
A. Mayer, V. Balasubramanian, T. Mora, A.M. Walczak
How a well-adapted immune system is organized
R. Espada, R.G. Parra, T. Mora, A.M. Walczak, D.U. Ferreiro
Capturing coevolutionary signals in repeat proteins
M. Santolini, T. Mora, V. Hakim
A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites
A.H. Lang, C.K. Fisher, T. Mora, P. Mehta
Thermodynamics of statistical inference by cells
Y. Elhanati, A. Murugan, C.G. Callan Jr., T. Mora, A.M. Walczak
Quantifying selection in immune receptor repertoires
Proc Natl Acad Sci 111(27) 9875-9880 (2014) [pdf] [arXiv] [bioRxiv]
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
A. Cavagna, I. Giardina, F. Ginelli, T. Mora, D. Piovani, R. Tavarone, A.M. Walczak
Dynamical maximum entropy approach to flocking
W. Bialek, A. Cavagna, I. Giardina, T. Mora, O. Pohl, E. Silvestri, M. Viale, A.M. Walczak
Social interactions dominate speed control in driving natural flocks toward criticality
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
T. Mora, A.M. Walczak
Effect of Phenotypic Selection on Stochastic Gene Expression
T. Julou*, T. Mora*, L. Guillon, V. Croquette, I. Schalk, D. Bensimon, N. Desprat
Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies
G. Tkacik, O. Marre, T. Mora, D. Amodei, M.J. Berry II, W. Bialek
The simplest maximum entropy model for collective behavior in a neural network
G.J. Stephens*, T. Mora*, G. Tkacik, W. Bialek
Statistical Thermodynamics of Natural Images
Phys. Rev. Lett. 110 018701 (2013)
[pdf]
An earlier version is available on the [arxiv]
A. Murugan, T. Mora, A.M. Walczak, C.G. Callan Jr.
Statistical inference of the generation probability of T-cell receptors from sequence repertoires
T. Mora, A.M. Walczak, F. Zamponi
Transition path sampling algorithm for discrete many-body systems
W. Bialek, A. Cavagna, I. Giardina, T. Mora, E. Silvestri, M. Viale, A.M. Walczak
Statistical mechanics for natural flocks of birds
T. Mora, W. Bialek
Are Biological Systems Poised at Criticality?
T. Mora, F. Bai, Y.-S. Che, T. Minamino, K. Namba, N.S. Wingreen
Non-genetic individuality in Escherichia coli motor switching
T. Mora, N.S. Wingreen
Limits of sensing temporal concentration changes by single cells
Phys. Rev. Lett. 104 248101 (2010) [pdf] [arXiv]
See also the viewpoint by Sima Setayeshgar:
Improving accuracy by leaps and unbounds, Physics 3 49 (2010) [pdf]
T. Mora*, A.M. Walczak*, W. Bialek, C.G. Callan
Maximum entropy models for antibody diversity
T. Mora, H. Yu, N.S. Wingreen
Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor
T. Mora, H. Yu, Y. Sowa, N.S. Wingreen
Steps in the bacterial flagellar motor
M. Mézard, T. Mora
Constraint satisfaction problems and neural networks: a statistical physics perspective
T. Mora, L. Zdeborová
Random subcubes as a toy model for constraint satisfaction problems
H. Daudé, M. Mézard, T. Mora, R. Zecchina
Pairs of SAT Assignments and Clustering in Random Boolean Formulae
T. Mora, M. Mézard
Geometrical organization of solutions to random linear Boolean equations
T. Mora, O. Rivoire
Statistical mechanics of error exponents for error-correcting codes
T. Mora, O. Rivoire
Error Exponents of Low-Density Parity-Check Codes on the Binary Erasure Channel
Information Theory Workshop 2006, ITW 06' Chengdu, IEEE, october 2006, pp. 81-85 [pdf] [arXiv]
T. Mora, A. Boudaoud
Buckling of swelling gels
M. Mézard, T. Mora, R. Zecchina
Clustering of solutions in the random satisfiability problem
T. Mora, C.M. Will
A Post-Newtonian diagnostic of quasi-equilibrium binary configurations of compact objects
T. Mora, C.M. Will
Numerically generated quasi-equilibrium orbits of black holes: Circular or eccentric?
T. Mora, A. Boudaoud
Thin elastic plates: On the core of developable cones
T. Mora
IGoR : un outil pour apprendre et simuler la génération aléatoire de récepteurs d'antigènes
T. Mora
Diversité et spécificité des récepteurs immunitaires : comment notre corps fabrique des protéines aléatoires spécialisées pour combattre les pathogènes
A. Mayer, O. Rivoire, T. Mora, A.M. Walczak
Explication évolutive de la diversité des stratégies immunitaires
T. Mora
La physique statistique : entre l'unité et le tout
TDC, no 110, L'individuel et le collectif p. 62 (2017).
Geometry and Inference in Optimization and in Information Theory (in french) [pdf]
PhD thesis (2007).
Morphogénèse de gels gonflant dans l'eau (in french) [pdf]
Intership done at the LPS in the ENS under the supervision of Arezki Boudaoud, in february 2004.
Inspiralling binary systems of compact objects: Comparison between analytical and numerical results [pdf]
Intership done at the Washington University in Saint-Louis, in the WUGRAV group, under the supervision of Clifford Will, from january till july 2002.
Plaques élastiques minces: étude du cœur des singularités (in french) [pdf]
Intership done at the LPS in the ENS under the supervision of Arezki Boudaoud, in july 2001.