The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures. - Diego U. Ferreiro; Aleksandra M. Walczak; Elizabeth A. Komives; Peter G. Wolynes (PLoS Comput. Biol., 2008)

Flocking and turning: a new model for self-organized collective motion. - Andrea Cavagna; Lorenzo Del Castello; Irene Giardina; Tomas Grigera; Asja Jelic; Stefania Melillo; Thierry Mora; Leonardo Parisi; Edmondo Silvestri; Massimiliano Viale; Aleksandra M. Walczak (CoRR, 2014)

Capturing coevolutionary signals inrepeat proteins. - Rocío Espada; R. Gonzalo Parra; Thierry Mora; Aleksandra M. Walczak; Diego U. Ferreiro (BMC Bioinform., 2015)

repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. - Yuval Elhanati; Quentin Marcou; Thierry Mora; Aleksandra M. Walczak (Bioinform., 2016)

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos. - Jonathan Desponds; Huy Tran; Teresa Ferraro; Tanguy Lucas; Carmina Perez Romero; Aurelien Guillou; Cecile Fradin; Mathieu Coppey; Nathalie Dostatni; Aleksandra M. Walczak (PLoS Comput. Biol., 2016)

Noise Expands the Response Range of the Bacillus subtilis Competence Circuit. - Andrew Mugler; Mark Kittisopikul; Luke Hayden; Jintao Liu; Chris H. Wiggins 001; Gürol M. Süel; Aleksandra M. Walczak (PLoS Comput. Biol., 2016)

Inferring repeat-protein energetics from evolutionary information. - Rocío Espada; R. Gonzalo Parra; Thierry Mora; Aleksandra M. Walczak; Diego U. Ferreiro (PLoS Comput. Biol., 2017)

Variable habitat conditions drive species covariation in the human microbiota. - Charles K. Fisher; Thierry Mora; Aleksandra M. Walczak (PLoS Comput. Biol., 2017)

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 Komech; Vadim I. Nazarov; Olga V. Britanova; Dmitry M. Chudakov; Ilgar Z. Mamedov; Yuri B. Lebedev; Thierry Mora; Aleksandra M. Walczak (PLoS Comput. Biol., 2017)

Active degradation of MarA controls coordination of its downstream targets. - Nicholas A. Rossi; Thierry Mora; Aleksandra M. Walczak; Mary J. Dunlop (PLoS Comput. Biol., 2018)

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern. - Huy Tran; Jonathan Desponds; Carmina Perez Romero; Mathieu Coppey; Cecile Fradin; Nathalie Dostatni; Aleksandra M. Walczak (PLoS Comput. Biol., 2018)

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. - Zachary Sethna; Yuval Elhanati; Curtis G. Callan Jr.; Aleksandra M. Walczak; Thierry Mora (Bioinform., 2019)

Dissipation in Non-Steady State Regulatory Circuits. - Paulina Szymanska-Rozek; Dario Villamaina; Jacek Miekisz; Aleksandra M. Walczak (Entropy, 2019)

Genesis of the αβ T-cell receptor. - Thomas Dupic; Quentin Marcou; Aleksandra M. Walczak; Thierry Mora (PLoS Comput. Biol., 2019)

Size and structure of the sequence space of repeat proteins. - Jacopo Marchi; Ezequiel A. Galpern; Rocío Espada; Diego U. Ferreiro; Aleksandra M. Walczak; Thierry Mora (PLoS Comput. Biol., 2019)

SOS: online probability estimation and generation of T-and B-cell receptors. - Giulio Isacchini; Carlos Olivares; Armita Nourmohammad; Aleksandra M. Walczak; Thierry Mora (Bioinform., 2020)

Population variability in the generation and selection of T-cell repertoires. - Zachary Sethna; Giulio Isacchini; Thomas Dupic; Thierry Mora; Aleksandra M. Walczak; Yuval Elhanati (PLoS Comput. Biol., 2020)

Inferring the immune response from repertoire sequencing. - Maximilian Puelma Touzel; Aleksandra M. Walczak; Thierry Mora (PLoS Comput. Biol., 2020)

The Connection between Discrete- and Continuous-Time Descriptions of Gaussian Continuous Processes. - Federica Ferretti; Victor Chardès; Thierry Mora; Aleksandra M. Walczak; Irene Giardina (CoRR, 2021)

MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories. - Giulio Isacchini; Natanael Spisak; Armita Nourmohammad; Thierry Mora; Aleksandra M. Walczak (CoRR, 2021)

Probing T-cell response by sequence-based probabilistic modeling. - Barbara Bravi; Vinod P. Balachandran; Benjamin D. Greenbaum; Aleksandra M. Walczak; Thierry Mora; Rémi Monasson; Simona Cocco (PLoS Comput. Biol., 2021)

Optimal prediction with resource constraints using the information bottleneck. - Vedant Sachdeva; Thierry Mora; Aleksandra M. Walczak; Stephanie E. Palmer (PLoS Comput. Biol., 2021)

Disorder and the Neural Representation of Complex Odors. - Kamesh Krishnamurthy; Ann M. Hermundstad; Thierry Mora; Aleksandra M. Walczak; Vijay Balasubramanian (Frontiers Comput. Neurosci., 2022)

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies. - Cosimo Lupo; Natanael Spisak; Aleksandra M. Walczak; Thierry Mora (PLoS Comput. Biol., 2022)

Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors. - Francesco Camaglia; Ilya Nemenman; Thierry Mora; Aleksandra M. Walczak (CoRR, 2023)

Learning predictive signatures of HLA type from T-cell repertoires. - María Ruiz Ortega; Mikhail V. Pogorelyy; Anastasia A. Minervina; Paul G. Thomas; Thierry Mora; Aleksandra M. Walczak (PLoS Comput. Biol., 2025)