Aleksandra M. Walczak

发表

repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data

Yuval Elhanati, Quentin Marcou, Thierry Mora, 2015, bioRxiv.

Flocking and Turning: a New Model for Self-organized Collective Motion

Thierry Mora, Aleksandra M. Walczak, Andrea Cavagna, 2014, ArXiv.

Immune fingerprinting through repertoire similarity

Thierry Mora, Aleksandra M. Walczak, Thomas Dupic, 2021, PLoS genetics.

Information processing in small gene regulatory networks and cascades

Aleksandra M. Walczak, 2010 .

Trade-Offs in Delayed Information Transmission in Biochemical Networks

Aleksandra M. Walczak, Matteo Marsili, Francesca Mancini, 2015, 1504.03637.

Noise Expands the Response Range of the Bacillus subtilis Competence Circuit

Aleksandra M. Walczak, Chris Wiggins, Andrew Mugler, 2015, PLoS Comput. Biol..

Quantitative Immunology for Physicists.

Thierry Mora, Aleksandra M. Walczak, Grégoire Altan-Bonnet, 2019, 1907.03891.

Physical constraints in biological collective behaviour

Thierry Mora, Aleksandra M. Walczak, Andrea Cavagna, 2018, Current Opinion in Systems Biology.

Noise Induced Biological Adaptation Differs between Analogous Differentiation Circuits

Aleksandra M. Walczak, Andrew Mugler, Mark Kittisopikul, 2011 .

Generative models of T-cell receptor sequences.

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2020, Physical review. E.

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

Aleksandra M. Walczak, Peter G. Wolynes, Diego U. Ferreiro, 2008, PLoS Comput. Biol..

Optimizing Information Flow in Small Genetic Networks. II. Feed-forward Interactions

Aleksandra M. Walczak, William Bialek, Gašper Tkačik, 2010 .

Predicting the spectrum of TCR repertoire sharing with a data‐driven model of recombination

Yuval Elhanati, Aleksandra M. Walczak, Zachary Sethna, 2018, bioRxiv.

Predicting the future from the past in visual object motion: optimal representations of mixed stochastic/deterministic trajectories

Thierry Mora, Aleksandra M. Walczak, Stephanie E. Palmer, 2020 .

hunchback Promoters Can Readout Morphogenetic Positional Information in Less Than a Minute

Aleksandra M. Walczak, Massimo Vergassola, Jonathan Desponds, 2019, bioRxiv.

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

Yuval Elhanati, Quentin Marcou, Thierry Mora, 2016, bioRxiv.

Genesis of the αβ T-cell receptor

Quentin Marcou, Aleksandra M. Walczak, Thomas Dupic, 2019, PLoS Comput. Biol..

Optimal prediction with resource constraints using the information bottleneck

Thierry Mora, Aleksandra M. Walczak, Vedant Sachdeva, 2020, bioRxiv.

Capturing coevolutionary signals inrepeat proteins

Thierry Mora, Aleksandra M. Walczak, R. Gonzalo Parra, 2014, BMC Bioinformatics.

Quantitative Immunology for Physicists

Thierry Mora, Aleksandra M. Walczak, Gr'egoire Altan-Bonnet, 2019, bioRxiv.

Organization of an optimal adaptive immune system

Thierry Mora, Aleksandra M. Walczak, Vijay Balasubramanian, 2017 .

On generative models of T-cell receptor sequences

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2019, bioRxiv.

Inferring repeat-protein energetics from evolutionary information

Thierry Mora, Aleksandra M. Walczak, R. Gonzalo Parra, 2017, PLoS Comput. Biol..

High-throughput immune repertoire analysis with IGoR

Quentin Marcou, Thierry Mora, Aleksandra M. Walczak, 2017, Nature Communications.

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos

Aleksandra M. Walczak, Huy Tran, Mathieu Coppey, 2016, PLoS Comput. Biol..

Building General Langevin Models from Discrete Datasets

Thierry Mora, Aleksandra M. Walczak, Irene Giardina, 2019, 1912.10491.

Size and structure of the sequence space of repeat proteins

Aleksandra M. Walczak, Diego U. Ferreiro, Thierry Mora, 2019, bioRxiv.

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2018 .

Tiling solutions for optimal biological sensing

Aleksandra M. Walczak, A. Walczak, 2015, 1507.01963.

Variable habitat conditions drive species covariation in the human microbiota

Thierry Mora, Aleksandra M. Walczak, Charles K. Fisher, 2017, PLoS Comput. Biol..

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern

Aleksandra M. Walczak, Mathieu Coppey, Jonathan Desponds, 2018, bioRxiv.

Inferring the immune response from repertoire sequencing

Thierry Mora, Aleksandra M. Walczak, Maximilian Puelma Touzel, 2019, bioRxiv.

SOS: online probability estimation and generation of T-and B-cell receptors

Thierry Mora, Aleksandra M. Walczak, Armita Nourmohammad, 2020, Bioinform..

How a well-adapting immune system remembers

Thierry Mora, Aleksandra M. Walczak, Vijay Balasubramanian, 2018 .

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2018, bioRxiv.

Dissipation in Non-Steady State Regulatory Circuits

Aleksandra M. Walczak, Jacek Miekisz, Dario Villamaina, 2019, Entropy.

repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data

Yuval Elhanati, Quentin Marcou, Thierry Mora, 2015 .

Constraints and limitations on decoding positional information: the Bicoid case-study

Aleksandra M. Walczak, Nathalie Dostatni, Huy Tran, 2019, bioRxiv.

Optimal prediction with resource constraints using the information bottleneck

Thierry Mora, Aleksandra M. Walczak, Stephanie E. Palmer, 2021, PLoS Comput. Biol..

Probing T-cell response by sequence-based probabilistic modeling

Simona Cocco, Rémi Monasson, Thierry Mora, 2021, PLoS Comput. Biol..

MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories pdf

Thierry Mora, Aleksandra M. Walczak, Armita Nourmohammad, 2021, ArXiv.

Modeling antigen presentation and immune recognition with Restricted Boltzmann Machines

Simona Cocco, Rémi Monasson, Thierry Mora, 2021 .

Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems

Thierry Mora, Aleksandra M. Walczak, Michael Lässig, 2019, bioRxiv.

New methods to image transcription in living fly embryos: the insights so far, and the prospects

Aleksandra M. Walczak, Mathieu Coppey, Teresa Ferraro, 2016, Wiley interdisciplinary reviews. Developmental biology.

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

Thierry Mora, Aleksandra M. Walczak, Dmitriy M. Chudakov, 2018, Proceedings of the National Academy of Sciences.

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Thierry Mora, Aleksandra M. Walczak, Curtis G. Callan, 2012, Proceedings of the National Academy of Sciences.

Detecting T-cell receptors involved in immune responses from single repertoire snapshots

Thierry Mora, Aleksandra M. Walczak, Mikhail Shugay, 2018, bioRxiv.

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

Aleksandra M. Walczak, Mathieu Coppey, Teresa Ferraro, 2013, Current Biology.

Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition

Thierry Mora, Aleksandra M. Walczak, Serena Bradde, 2019, Philosophical Transactions of the Royal Society B.

Diversity of immune strategies explained by adaptation to pathogen statistics

Thierry Mora, Aleksandra M. Walczak, Olivier Rivoire, 2015 .

Local equilibrium in bird flocks

Thierry Mora, Aleksandra M. Walczak, Andrea Cavagna, 2015, Nature Physics.

Quantifying lymphocyte receptor diversity

Thierry Mora, Aleksandra M. Walczak, 2016 .

Evidence for Shaping of Light Chain Repertoire by Structural Selection

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2018, Front. Immunol..

Questioning the activity of active matter in natural flocks of birds

Thierry Mora, Aleksandra M. Walczak, Andrea Cavagna, 2015 .

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

Thierry Mora, Aleksandra M. Walczak, Wahiba Chaara, 2013, Front. Immunol..

Cost and benefits of CRISPR spacer acquisition

Thierry Mora, Aleksandra M. Walczak, Serena Bradde, 2018, 1811.03674.

Precision in a rush: trade-offs between positioning and steepness of the hunchback expression pattern

Aleksandra M. Walczak, Mathieu Coppey, Jonathan Desponds, 2018 .

Repertoire sequencing and the statistical ensemble approach to adaptive immunity

Thierry Mora, Aleksandra M. Walczak, Curtis G. Callan, 2017 .

Physical epistatic landscape of antibody binding affinity

Thierry Mora, Aleksandra M. Walczak, Justin B. Kinney, 2017, bioRxiv.

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

Thierry Mora, Aleksandra M. Walczak, Frédéric Cazals, 2018, Front. Immunol..

Population variability in the generation and thymic selection of T-cell repertoires

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2020, bioRxiv.

Population dynamics of immune repertoires

Thierry Mora, Aleksandra M. Walczak, Jonathan Desponds, 2017, bioRxiv.

Quantifying selection in immune receptor repertoires

Yuval Elhanati, Thierry Mora, Aleksandra M. Walczak, 2014 .

Predicting evolution

Ville Mustonen, Aleksandra M. Walczak, Michael Lässig, 2017, Nature Ecology &Evolution.