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

Pogorelyy MV, Minervina AA, Touzel MP, Sycheva AL, Komech EA, Kovalenko EI, Karganova GG, Egorov ES, Komkov AY, Chudakov DM, Mamedov IZ, Mora T, Walczak AM, Lebedev YB.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12704-12709. doi: 10.1073/pnas.1809642115. Epub 2018 Nov 20.


3 minutes to precisely measure morphogen concentration.

Lucas T, Tran H, Perez Romero CA, Guillou A, Fradin C, Coppey M, Walczak AM, Dostatni N.

PLoS Genet. 2018 Oct 26;14(10):e1007676. doi: 10.1371/journal.pgen.1007676. eCollection 2018 Oct.


Rational Design of Noncovalent Diamondoid Microporous Materials for Low-Energy Separation of C6-Hydrocarbons.

Bury W, Walczak AM, Leszczyński MK, Navarro JAR.

J Am Chem Soc. 2018 Nov 7;140(44):15031-15037. doi: 10.1021/jacs.8b09522. Epub 2018 Oct 23.


LiveFly: A Toolbox for the Analysis of Transcription Dynamics in Live Drosophila Embryos.

Tran H, Perez-Romero CA, Ferraro T, Fradin C, Dostatni N, Coppey M, Walczak AM.

Methods Mol Biol. 2018;1863:183-195. doi: 10.1007/978-1-4939-8772-6_11.


Live Imaging of mRNA Transcription in Drosophila Embryos.

Perez-Romero CA, Tran H, Coppey M, Walczak AM, Fradin C, Dostatni N.

Methods Mol Biol. 2018;1863:165-182. doi: 10.1007/978-1-4939-8772-6_10.


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

Magadan S, Jouneau L, Puelma Touzel M, Marillet S, Chara W, Six A, Quillet E, Mora T, Walczak AM, Cazals F, Sunyer O, Fillatreau S, Boudinot P.

Front Immunol. 2018 Sep 27;9:2115. doi: 10.3389/fimmu.2018.02115. eCollection 2018.


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

Tran H, Desponds J, Perez Romero CA, Coppey M, Fradin C, Dostatni N, Walczak AM.

PLoS Comput Biol. 2018 Oct 11;14(10):e1006513. doi: 10.1371/journal.pcbi.1006513. eCollection 2018 Oct.


Signal Percolation within a Bacterial Community.

Larkin JW, Zhai X, Kikuchi K, Redford SE, Prindle A, Liu J, Greenfield S, Walczak AM, Garcia-Ojalvo J, Mugler A, Süel GM.

Cell Syst. 2018 Aug 22;7(2):137-145.e3. doi: 10.1016/j.cels.2018.06.005. Epub 2018 Jul 25.


Evidence for Shaping of Light Chain Repertoire by Structural Selection.

Toledano A, Elhanati Y, Benichou JIC, Walczak AM, Mora T, Louzoun Y.

Front Immunol. 2018 Jun 22;9:1307. doi: 10.3389/fimmu.2018.01307. eCollection 2018.


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

Elhanati Y, Sethna Z, Callan CG Jr, Mora T, Walczak AM.

Immunol Rev. 2018 Jul;284(1):167-179. doi: 10.1111/imr.12665.


Method for identification of condition-associated public antigen receptor sequences.

Pogorelyy MV, Minervina AA, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM.

Elife. 2018 Mar 13;7. pii: e33050. doi: 10.7554/eLife.33050.


High-throughput immune repertoire analysis with IGoR.

Marcou Q, Mora T, Walczak AM.

Nat Commun. 2018 Feb 8;9(1):561. doi: 10.1038/s41467-018-02832-w.


A model for the integration of conflicting exogenous and endogenous signals by dendritic cells.

Marcou Q, Carmi-Levy I, Trichot C, Soumelis V, Mora T, Walczak AM.

Phys Biol. 2018 May 16;15(5):056001. doi: 10.1088/1478-3975/aaaa0a.


Transitions in optimal adaptive strategies for populations in fluctuating environments.

Mayer A, Mora T, Rivoire O, Walczak AM.

Phys Rev E. 2017 Sep;96(3-1):032412. doi: 10.1103/PhysRevE.96.032412. Epub 2017 Sep 21.


Predicting evolution.

Lässig M, Mustonen V, Walczak AM.

Nat Ecol Evol. 2017 Feb 21;1(3):77. doi: 10.1038/s41559-017-0077.


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

Pogorelyy MV, Elhanati Y, Marcou Q, Sycheva AL, Komech EA, Nazarov VI, Britanova OV, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM.

PLoS Comput Biol. 2017 Jul 6;13(7):e1005572. doi: 10.1371/journal.pcbi.1005572. eCollection 2017 Jul.


Inferring repeat-protein energetics from evolutionary information.

Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU.

PLoS Comput Biol. 2017 Jun 15;13(6):e1005584. doi: 10.1371/journal.pcbi.1005584. eCollection 2017 Jun.


Variable habitat conditions drive species covariation in the human microbiota.

Fisher CK, Mora T, Walczak AM.

PLoS Comput Biol. 2017 Apr 27;13(4):e1005435. doi: 10.1371/journal.pcbi.1005435. eCollection 2017 Apr.


Insights into immune system development and function from mouse T-cell repertoires.

Sethna Z, Elhanati Y, Dudgeon CS, Callan CG Jr, Levine AJ, Mora T, Walczak AM.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2253-2258. doi: 10.1073/pnas.1700241114. Epub 2017 Feb 14. Erratum in: Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2798. Dudgeon, Chrissy S [corrected to Dudgeon, Crissy R].


Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves.

Adams RM, Mora T, Walczak AM, Kinney JB.

Elife. 2016 Dec 30;5. pii: e23156. doi: 10.7554/eLife.23156.


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

Desponds J, Tran H, Ferraro T, Lucas T, Perez Romero C, Guillou A, Fradin C, Coppey M, Dostatni N, Walczak AM.

PLoS Comput Biol. 2016 Dec 12;12(12):e1005256. doi: 10.1371/journal.pcbi.1005256. eCollection 2016 Dec.


Local equilibrium in bird flocks.

Mora T, Walczak AM, Castello LD, Ginelli F, Melillo S, Parisi L, Viale M, Cavagna A, Giardina I.

Nat Phys. 2016 Dec;12(12):1153-1157. Epub 2016 Aug 15.


Diversity of immune strategies explained by adaptation to pathogen statistics.

Mayer A, Mora T, Rivoire O, Walczak AM.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8630-5. doi: 10.1073/pnas.1600663113. Epub 2016 Jul 18.


Rényi entropy, abundance distribution, and the equivalence of ensembles.

Mora T, Walczak AM.

Phys Rev E. 2016 May;93(5):052418. doi: 10.1103/PhysRevE.93.052418. Epub 2016 May 24.


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

Elhanati Y, Marcou Q, Mora T, Walczak AM.

Bioinformatics. 2016 Jul 1;32(13):1943-51. doi: 10.1093/bioinformatics/btw112. Epub 2016 Feb 26.


Noise Expands the Response Range of the Bacillus subtilis Competence Circuit.

Mugler A, Kittisopikul M, Hayden L, Liu J, Wiggins CH, Süel GM, Walczak AM.

PLoS Comput Biol. 2016 Mar 22;12(3):e1004793. doi: 10.1371/journal.pcbi.1004793. eCollection 2016 Mar.


Extending the dynamic range of transcription factor action by translational regulation.

Sokolowski TR, Walczak AM, Bialek W, Tkačik G.

Phys Rev E. 2016 Feb;93(2):022404. doi: 10.1103/PhysRevE.93.022404. Epub 2016 Feb 4.


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

Ferraro T, Lucas T, Clémot M, De Las Heras Chanes J, Desponds J, Coppey M, Walczak AM, Dostatni N.

Wiley Interdiscip Rev Dev Biol. 2016 May-Jun;5(3):296-310. doi: 10.1002/wdev.221. Epub 2016 Feb 19. Review.


Transcriptional Memory in the Drosophila Embryo.

Ferraro T, Esposito E, Mancini L, Ng S, Lucas T, Coppey M, Dostatni N, Walczak AM, Levine M, Lagha M.

Curr Biol. 2016 Jan 25;26(2):212-218. doi: 10.1016/j.cub.2015.11.058. Epub 2015 Dec 31.


Fluctuating fitness shapes the clone-size distribution of immune repertoires.

Desponds J, Mora T, Walczak AM.

Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):274-9. doi: 10.1073/pnas.1512977112. Epub 2015 Dec 28.


Repeat proteins challenge the concept of structural domains.

Espada R, Parra RG, Sippl MJ, Mora T, Walczak AM, Ferreiro DU.

Biochem Soc Trans. 2015 Oct;43(5):844-9. doi: 10.1042/BST20150083. Review.


A Reassessment of IgM Memory Subsets in Humans.

Bagnara D, Squillario M, Kipling D, Mora T, Walczak AM, Da Silva L, Weller S, Dunn-Walters DK, Weill JC, Reynaud CA.

J Immunol. 2015 Oct 15;195(8):3716-24. doi: 10.4049/jimmunol.1500753. Epub 2015 Sep 9.


Inferring processes underlying B-cell repertoire diversity.

Elhanati Y, Sethna Z, Marcou Q, Callan CG Jr, Mora T, Walczak AM.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140243. doi: 10.1098/rstb.2014.0243.


Capturing coevolutionary signals inrepeat proteins.

Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU.

BMC Bioinformatics. 2015 Jul 2;16:207. doi: 10.1186/s12859-015-0648-3.


Microbiology. Flexible gene pools.

Desai MM, Walczak AM.

Science. 2015 May 29;348(6238):977-8. doi: 10.1126/science.aab3957. No abstract available.


How a well-adapted immune system is organized.

Mayer A, Balasubramanian V, Mora T, Walczak AM.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):5950-5. doi: 10.1073/pnas.1421827112. Epub 2015 Apr 27.


Quantifying selection in immune receptor repertoires.

Elhanati Y, Murugan A, Callan CG Jr, Mora T, Walczak AM.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9875-80. doi: 10.1073/pnas.1409572111. Epub 2014 Jun 18.


Dynamical maximum entropy approach to flocking.

Cavagna A, Giardina I, Ginelli F, Mora T, Piovani D, Tavarone R, Walczak AM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Apr;89(4):042707. Epub 2014 Apr 16.


Social interactions dominate speed control in poising natural flocks near criticality.

Bialek W, Cavagna A, Giardina I, Mora T, Pohl O, Silvestri E, Viale M, Walczak AM.

Proc Natl Acad Sci U S A. 2014 May 20;111(20):7212-7. doi: 10.1073/pnas.1324045111. Epub 2014 May 1.


Genetic diversity in the interference selection limit.

Good BH, Walczak AM, Neher RA, Desai MM.

PLoS Genet. 2014 Mar 27;10(3):e1004222. doi: 10.1371/journal.pgen.1004222. eCollection 2014 Mar.


The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.

Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P.

Front Immunol. 2013 Nov 27;4:413. doi: 10.3389/fimmu.2013.00413. Review.


Live imaging of bicoid-dependent transcription in Drosophila embryos.

Lucas T, Ferraro T, Roelens B, De Las Heras Chanes J, Walczak AM, Coppey M, Dostatni N.

Curr Biol. 2013 Nov 4;23(21):2135-9. doi: 10.1016/j.cub.2013.08.053. Epub 2013 Oct 17.


Time-dependent information transmission in a model regulatory circuit.

Mancini F, Wiggins CH, Marsili M, Walczak AM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):022708. Epub 2013 Aug 12.


Effect of phenotypic selection on stochastic gene expression.

Mora T, Walczak AM.

J Phys Chem B. 2013 Oct 24;117(42):13194-205. doi: 10.1021/jp403231f. Epub 2013 Jul 19.


Analytic methods for modeling stochastic regulatory networks.

Walczak AM, Mugler A, Wiggins CH.

Methods Mol Biol. 2012;880:273-322. doi: 10.1007/978-1-61779-833-7_13. Review.


Genetic diversity and the structure of genealogies in rapidly adapting populations.

Desai MM, Walczak AM, Fisher DS.

Genetics. 2013 Feb;193(2):565-85. doi: 10.1534/genetics.112.147157. Epub 2012 Dec 5.


Influence of decoys on the noise and dynamics of gene expression.

Burger A, Walczak AM, Wolynes PG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041920. Epub 2012 Oct 31.


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

Murugan A, Mora T, Walczak AM, Callan CG Jr.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16161-6. doi: 10.1073/pnas.1212755109. Epub 2012 Sep 17.


Optimizing information flow in small genetic networks. III. A self-interacting gene.

Tkačik G, Walczak AM, Bialek W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Apr;85(4 Pt 1):041903. Epub 2012 Apr 5.


Transition path sampling algorithm for discrete many-body systems.

Mora T, Walczak AM, Zamponi F.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Mar;85(3 Pt 2):036710. Epub 2012 Mar 29.


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