Aleksandra Walczak, PhD - Publications

Affiliations: 
CNRS, Paris, Île-de-France, France 

78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Minervina AA, Pogorelyy MV, Komech EA, Karnaukhov VK, Bacher P, Rosati E, Franke A, Chudakov D, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones. Elife. 9. PMID 32081129 DOI: 10.7554/eLife.53704  1
2020 Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines. 8. PMID 31906351 DOI: 10.3390/vaccines8010013  1
2019 Marchi J, Galpern EA, Espada R, Ferreiro DU, Walczak AM, Mora T. Size and structure of the sequence space of repeat proteins. Plos Computational Biology. 15: e1007282. PMID 31415557 DOI: 10.1371/journal.pcbi.1007282  1
2019 Marchi J, Lässig M, Mora T, Walczak AM. Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems. Pathogens (Basel, Switzerland). 8. PMID 31362404 DOI: 10.3390/pathogens8030115  1
2019 Nourmohammad A, Otwinowski J, Łuksza M, Mora T, Walczak AM. Fierce selection and interference in B-cell repertoire response to chronic HIV-1. Molecular Biology and Evolution. PMID 31209469 DOI: 10.1093/molbev/msz143  1
2019 Pogorelyy MV, Minervina AA, Shugay M, Chudakov DM, Lebedev YB, Mora T, Walczak AM. Detecting T cell receptors involved in immune responses from single repertoire snapshots. Plos Biology. 17: e3000314. PMID 31194732 DOI: 10.1371/journal.pbio.3000314  1
2019 Mayer A, Balasubramanian V, Walczak AM, Mora T. How a well-adapting immune system remembers. Proceedings of the National Academy of Sciences of the United States of America. PMID 30988203 DOI: 10.1073/pnas.1812810116  1
2019 Bradde S, Mora T, Walczak AM. Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 374: 20180095. PMID 30905281 DOI: 10.1098/rstb.2018.0095  1
2019 Dupic T, Marcou Q, Walczak AM, Mora T. Genesis of the αβ T-cell receptor. Plos Computational Biology. 15: e1006874. PMID 30830899 DOI: 10.1371/journal.pcbi.1006874  1
2019 Sethna Z, Elhanati Y, Callan CG, Walczak AM, Mora T. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. Bioinformatics (Oxford, England). PMID 30657870 DOI: 10.1093/bioinformatics/btz035  1
2018 Adams RM, Kinney JB, Walczak AM, Mora T. Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Systems. PMID 30611676 DOI: 10.1016/j.cels.2018.12.004  1
2018 Rossi NA, Mora T, Walczak AM, Dunlop MJ. Active degradation of MarA controls coordination of its downstream targets. Plos Computational Biology. 14: e1006634. PMID 30589845 DOI: 10.1371/journal.pcbi.1006634  1
2018 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. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30459272 DOI: 10.1073/pnas.1809642115  1
2018 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. Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination. Frontiers in Immunology. 9: 2115. PMID 30319606 DOI: 10.3389/fimmu.2018.02115  1
2018 Tran H, Desponds J, Perez Romero CA, Coppey M, Fradin C, Dostatni N, Walczak AM. Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern. Plos Computational Biology. 14: e1006513. PMID 30307984 DOI: 10.1371/journal.pcbi.1006513  1
2018 Toledano A, Elhanati Y, Benichou JIC, Walczak AM, Mora T, Louzoun Y. Evidence for Shaping of Light Chain Repertoire by Structural Selection. Frontiers in Immunology. 9: 1307. PMID 29988361 DOI: 10.3389/fimmu.2018.01307  1
2018 Elhanati Y, Sethna Z, Callan CG, Mora T, Walczak AM. Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination. Immunological Reviews. 284: 167-179. PMID 29944757 DOI: 10.1111/imr.12665  1
2018 Pogorelyy MV, Minervina AA, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Method for identification of condition-associated public antigen receptor sequences. Elife. 7. PMID 29533178 DOI: 10.7554/eLife.33050  1
2018 Marcou Q, Mora T, Walczak AM. High-throughput immune repertoire analysis with IGoR. Nature Communications. 9: 561. PMID 29422654 DOI: 10.1038/s41467-018-02832-w  1
2018 Marcou Q, Carmi-Levy I, Trichot C, Soumelis V, Mora T, Walczak A. A model for the integration of conflicting exogenous and endogenous signals by dendritic cells. Physical Biology. PMID 29360100 DOI: 10.1088/1478-3975/aaaa0a  1
2017 Mayer A, Mora T, Rivoire O, Walczak AM. Transitions in optimal adaptive strategies for populations in fluctuating environments. Physical Review. E. 96: 032412. PMID 29346942 DOI: 10.1103/PhysRevE.96.032412  1
2017 Mayer A, Rivoire O, Mora T, Walczak A. [Evolutionary explanation of the diversity of immune strategies]. Medecine Sciences : M/S. 33: 593-595. PMID 28990557 DOI: 10.1051/medsci/20173306012  1
2017 Pogorelyy MV, Elhanati Y, Marcou Q, Sycheva AL, Komech EA, Nazarov VI, Britanova OV, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. Plos Computational Biology. 13: e1005572. PMID 28683116 DOI: 10.1371/journal.pcbi.1005572  1
2017 Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Inferring repeat-protein energetics from evolutionary information. Plos Computational Biology. 13: e1005584. PMID 28617812 DOI: 10.1371/journal.pcbi.1005584  1
2017 Fisher CK, Mora T, Walczak AM. Variable habitat conditions drive species covariation in the human microbiota. Plos Computational Biology. 13: e1005435. PMID 28448493 DOI: 10.1371/journal.pcbi.1005435  1
2017 Sethna Z, Elhanati Y, Dudgeon CS, Callan CG, Levine AJ, Mora T, Walczak AM. Insights into immune system development and function from mouse T-cell repertoires. Proceedings of the National Academy of Sciences of the United States of America. PMID 28196891 DOI: 10.1073/pnas.1700241114  1
2016 Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. Elife. 5. PMID 28035901 DOI: 10.7554/eLife.23156  1
2016 Desponds J, Tran H, Ferraro T, Lucas T, Perez Romero C, Guillou A, Fradin C, Coppey M, Dostatni N, Walczak AM. Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos. Plos Computational Biology. 12: e1005256. PMID 27942043 DOI: 10.1371/journal.pcbi.1005256  1
2016 Mora T, Walczak AM, Castello LD, Ginelli F, Melillo S, Parisi L, Viale M, Cavagna A, Giardina I. Local equilibrium in bird flocks. Nature Physics. 12: 1153-1157. PMID 27917230 DOI: 10.1038/nphys3846  1
2016 Mayer A, Mora T, Rivoire O, Walczak AM. Diversity of immune strategies explained by adaptation to pathogen statistics. Proceedings of the National Academy of Sciences of the United States of America. PMID 27432970 DOI: 10.1073/pnas.1600663113  1
2016 Mora T, Walczak AM. Rényi entropy, abundance distribution, and the equivalence of ensembles. Physical Review. E. 93: 052418. PMID 27300934 DOI: 10.1103/PhysRevE.93.052418  1
2016 Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics (Oxford, England). PMID 27153709 DOI: 10.1093/bioinformatics/btw112  1
2016 Mugler A, Kittisopikul M, Hayden L, Liu J, Wiggins CH, Süel GM, Walczak AM. Noise Expands the Response Range of the Bacillus subtilis Competence Circuit. Plos Computational Biology. 12: e1004793. PMID 27003682 DOI: 10.1371/journal.pcbi.1004793  1
2016 Sokolowski TR, Walczak AM, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review. E. 93: 022404. PMID 26986359 DOI: 10.1103/PhysRevE.93.022404  1
2016 Ferraro T, Lucas T, Clémot M, De Las Heras Chanes J, Desponds J, Coppey M, Walczak AM, Dostatni N. New methods to image transcription in living fly embryos: the insights so far, and the prospects. Wiley Interdisciplinary Reviews. Developmental Biology. PMID 26894441 DOI: 10.1002/wdev.221  1
2015 Desponds J, Mora T, Walczak AM. Fluctuating fitness shapes the clone-size distribution of immune repertoires. Proceedings of the National Academy of Sciences of the United States of America. PMID 26711994 DOI: 10.1073/pnas.1512977112  1
2015 Espada R, Parra RG, Sippl MJ, Mora T, Walczak AM, Ferreiro DU. Repeat proteins challenge the concept of structural domains. Biochemical Society Transactions. 43: 844-9. PMID 26517892 DOI: 10.1042/BST20150083  1
2015 Bagnara D, Squillario M, Kipling D, Mora T, Walczak AM, Da Silva L, Weller S, Dunn-Walters DK, Weill JC, Reynaud CA. A Reassessment of IgM Memory Subsets in Humans. Journal of Immunology (Baltimore, Md. : 1950). 195: 3716-24. PMID 26355154 DOI: 10.4049/jimmunol.1500753  1
2015 Elhanati Y, Sethna Z, Marcou Q, Callan CG, Mora T, Walczak AM. Inferring processes underlying B-cell repertoire diversity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26194757 DOI: 10.1098/rstb.2014.0243  1
2015 Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Capturing coevolutionary signals inrepeat proteins. Bmc Bioinformatics. 16: 207. PMID 26134293 DOI: 10.1186/s12859-015-0648-3  1
2015 Desai MM, Walczak AM. Microbiology. Flexible gene pools. Science (New York, N.Y.). 348: 977-8. PMID 26023126 DOI: 10.1126/science.aab3957  1
2015 Mayer A, Balasubramanian V, Mora T, Walczak AM. How a well-adapted immune system is organized. Proceedings of the National Academy of Sciences of the United States of America. 112: 5950-5. PMID 25918407 DOI: 10.1073/pnas.1421827112  1
2015 Cappuccio A, Zollinger R, Schenk M, Walczak A, Servant N, Barillot E, Hupé P, Modlin RL, Soumelis V. Combinatorial code governing cellular responses to complex stimuli. Nature Communications. 6: 6847. PMID 25896517 DOI: 10.1038/ncomms7847  1
2015 Walczak AM. Tiling solutions for optimal biological sensing Comptes Rendus Physique. 16: 761-772. DOI: 10.1016/j.crhy.2015.09.004  1
2015 Mancini F, Marsili M, Walczak AM. Trade-Offs in Delayed Information Transmission in Biochemical Networks Journal of Statistical Physics. DOI: 10.1007/s10955-015-1332-8  1
2014 Elhanati Y, Murugan A, Callan CG, Mora T, Walczak AM. Quantifying selection in immune receptor repertoires. Proceedings of the National Academy of Sciences of the United States of America. 111: 9875-80. PMID 24941953 DOI: 10.1073/pnas.1409572111  1
2014 Cavagna A, Giardina I, Ginelli F, Mora T, Piovani D, Tavarone R, Walczak AM. Dynamical maximum entropy approach to flocking. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 042707. PMID 24827278 DOI: 10.1103/PhysRevE.89.042707  1
2014 Bialek W, Cavagna A, Giardina I, Mora T, Pohl O, Silvestri E, Viale M, Walczak AM. Social interactions dominate speed control in poising natural flocks near criticality. Proceedings of the National Academy of Sciences of the United States of America. 111: 7212-7. PMID 24785504 DOI: 10.1073/pnas.1324045111  1
2014 Good BH, Walczak AM, Neher RA, Desai MM. Genetic diversity in the interference selection limit. Plos Genetics. 10: e1004222. PMID 24675740 DOI: 10.1371/journal.pgen.1004222  1
2014 Cavagna A, Del Castello L, Giardina I, Grigera T, Jelic A, Melillo S, Mora T, Parisi L, Silvestri E, Viale M, Walczak AM. Flocking and Turning: a New Model for Self-organized Collective Motion Journal of Statistical Physics. 158: 601-627. DOI: 10.1007/s10955-014-1119-3  1
2013 Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Frontiers in Immunology. 4: 413. PMID 24348479 DOI: 10.3389/fimmu.2013.00413  1
2013 Mancini F, Wiggins CH, Marsili M, Walczak AM. Time-dependent information transmission in a model regulatory circuit. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 022708. PMID 24032865 DOI: 10.1103/PhysRevE.88.022708  1
2013 Mora T, Walczak AM. Effect of phenotypic selection on stochastic gene expression. The Journal of Physical Chemistry. B. 117: 13194-205. PMID 23795617 DOI: 10.1021/jp403231f  1
2013 Desai MM, Walczak AM, Fisher DS. Genetic diversity and the structure of genealogies in rapidly adapting populations. Genetics. 193: 565-85. PMID 23222656 DOI: 10.1534/genetics.112.147157  1
2012 Walczak AM, Mugler A, Wiggins CH. Analytic methods for modeling stochastic regulatory networks. Methods in Molecular Biology (Clifton, N.J.). 880: 273-322. PMID 23361990 DOI: 10.1007/978-1-61779-833-7_13  1
2012 Burger A, Walczak AM, Wolynes PG. Influence of decoys on the noise and dynamics of gene expression. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 041920. PMID 23214628 DOI: 10.1103/PhysRevE.86.041920  1
2012 Murugan A, Mora T, Walczak AM, Callan CG. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proceedings of the National Academy of Sciences of the United States of America. 109: 16161-6. PMID 22988065 DOI: 10.1073/pnas.1212755109  1
2012 Tkačik G, Walczak AM, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 041903. PMID 22680494 DOI: 10.1103/PhysRevE.85.041903  1
2012 Mora T, Walczak AM, Zamponi F. Transition path sampling algorithm for discrete many-body systems. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 036710. PMID 22587212 DOI: 10.1103/PhysRevE.85.036710  1
2012 Bialek W, Cavagna A, Giardina I, Mora T, Silvestri E, Viale M, Walczak AM. Statistical mechanics for natural flocks of birds. Proceedings of the National Academy of Sciences of the United States of America. 109: 4786-91. PMID 22427355 DOI: 10.1073/pnas.1118633109  1
2012 Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB. The structure of allelic diversity in the presence of purifying selection. Theoretical Population Biology. 81: 144-57. PMID 22198521 DOI: 10.1016/j.tpb.2011.12.002  1
2012 Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM. The structure of genealogies in the presence of purifying selection: a fitness-class coalescent. Genetics. 190: 753-79. PMID 22135349 DOI: 10.1534/genetics.111.134544  1
2012 Walczak A, Šlusarski T, Lehmann-Szweykowska A, Kamieniarz G. Structural and magnetic properties of Co thin films on Au(111) substrates Acta Physica Polonica A. 121: 653-659.  1
2011 Tkačik G, Walczak AM. Information transmission in genetic regulatory networks: a review. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 23: 153102. PMID 21460423 DOI: 10.1088/0953-8984/23/15/153102  1
2010 Mugler A, Walczak AM, Wiggins CH. Information-optimal transcriptional response to oscillatory driving. Physical Review Letters. 105: 058101. PMID 20867954 DOI: 10.1103/PhysRevLett.105.058101  1
2010 Walczak AM, Tkacik G, Bialek W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 041905. PMID 20481751 DOI: 10.1103/PhysRevE.81.041905  1
2010 Mora T, Walczak AM, Bialek W, Callan CG. Maximum entropy models for antibody diversity. Proceedings of the National Academy of Sciences of the United States of America. 107: 5405-10. PMID 20212159 DOI: 10.1073/pnas.1001705107  1
2010 Burger A, Walczak AM, Wolynes PG. Abduction and asylum in the lives of transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 107: 4016-21. PMID 20160109 DOI: 10.1073/pnas.0915138107  1
2010 HoŁderna-Natkaniec K, Jurga K, Woźniak-Braszak A, Walczak A. Molecular reorientations of N-n-hexyltetrachlorophthalimide Studied by 1H NMR Acta Physica Polonica A. 117: 537-548.  1
2009 Mugler A, Walczak AM, Wiggins CH. Spectral solutions to stochastic models of gene expression with bursts and regulation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 041921. PMID 19905356 DOI: 10.1103/PhysRevE.80.041921  1
2009 Tkacik G, Walczak AM, Bialek W. Optimizing information flow in small genetic networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 031920. PMID 19905159 DOI: 10.1103/PhysRevE.80.031920  1
2009 Walczak AM, Wolynes PG. Gene-gene cooperativity in small networks. Biophysical Journal. 96: 4525-41. PMID 19486675 DOI: 10.1016/j.bpj.2009.03.005  1
2009 Walczak AM, Mugler A, Wiggins CH. A stochastic spectral analysis of transcriptional regulatory cascades. Proceedings of the National Academy of Sciences of the United States of America. 106: 6529-34. PMID 19351901 DOI: 10.1073/pnas.0811999106  1
2008 Schultz D, Walczak AM, Onuchic JN, Wolynes PG. Extinction and resurrection in gene networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 19165-70. PMID 19033463 DOI: 10.1073/pnas.0810366105  1
2008 Stevenson JD, Walczak AM, Hall RW, Wolynes PG. Constructing explicit magnetic analogies for the dynamics of glass forming liquids. The Journal of Chemical Physics. 129: 194505. PMID 19026064 DOI: 10.1063/1.3009827  1
2008 Ferreiro DU, Walczak AM, Komives EA, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. Plos Computational Biology. 4: e1000070. PMID 18483553 DOI: 10.1371/journal.pcbi.1000070  1
2005 Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG. Self-regulating gene: an exact solution. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 051907. PMID 16383645 DOI: 10.1103/PhysRevE.72.051907  1
2005 Walczak AM, Onuchic JN, Wolynes PG. Absolute rate theories of epigenetic stability. Proceedings of the National Academy of Sciences of the United States of America. 102: 18926-31. PMID 16361441 DOI: 10.1073/pnas.0509547102  1
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