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Items: 1 to 50 of 52

1.

The evolution of the temporal program of genome replication.

Agier N, Delmas S, Zhang Q, Fleiss A, Jaszczyszyn Y, van Dijk E, Thermes C, Weigt M, Cosentino-Lagomarsino M, Fischer G.

Nat Commun. 2018 Jun 6;9(1):2199. doi: 10.1038/s41467-018-04628-4.

2.

Meet-U: Educating through research immersion.

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A.

PLoS Comput Biol. 2018 Mar 15;14(3):e1005992. doi: 10.1371/journal.pcbi.1005992. eCollection 2018 Mar.

3.

[From sequence variability to structural and functional prediction: modeling of homologous protein families].

Barrat-Charlaix P, Weigt M.

Biol Aujourdhui. 2017;211(3):239-244. doi: 10.1051/jbio/2017030. Epub 2018 Feb 7. Review. French.

PMID:
29412135
4.

How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?

Figliuzzi M, Barrat-Charlaix P, Weigt M.

Mol Biol Evol. 2018 Apr 1;35(4):1018-1027. doi: 10.1093/molbev/msy007. Erratum in: Mol Biol Evol. 2018 Jul 1;35(7):1821.

PMID:
29351669
5.

Inverse statistical physics of protein sequences: a key issues review.

Cocco S, Feinauer C, Figliuzzi M, Monasson R, Weigt M.

Rep Prog Phys. 2018 Mar;81(3):032601. doi: 10.1088/1361-6633/aa9965. Review.

PMID:
29120346
6.

Inter-residue, inter-protein and inter-family coevolution: bridging the scales.

Szurmant H, Weigt M.

Curr Opin Struct Biol. 2018 Jun;50:26-32. doi: 10.1016/j.sbi.2017.10.014. Epub 2017 Nov 5. Review.

7.

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria.

Couce A, Caudwell LV, Feinauer C, Hindré T, Feugeas JP, Weigt M, Lenski RE, Schneider D, Tenaillon O.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E9026-E9035. doi: 10.1073/pnas.1705887114. Epub 2017 Oct 10.

8.

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis.

Uguzzoni G, John Lovis S, Oteri F, Schug A, Szurmant H, Weigt M.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2662-E2671. doi: 10.1073/pnas.1615068114. Epub 2017 Mar 13.

9.

Improving landscape inference by integrating heterogeneous data in the inverse Ising problem.

Barrat-Charlaix P, Figliuzzi M, Weigt M.

Sci Rep. 2016 Nov 25;6:37812. doi: 10.1038/srep37812.

10.

Direct coevolutionary couplings reflect biophysical residue interactions in proteins.

Coucke A, Uguzzoni G, Oteri F, Cocco S, Monasson R, Weigt M.

J Chem Phys. 2016 Nov 7;145(17):174102.

PMID:
27825220
11.

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.

Gueudré T, Baldassi C, Zamparo M, Weigt M, Pagnani A.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12186-12191. Epub 2016 Oct 11.

12.

Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

Feinauer C, Szurmant H, Weigt M, Pagnani A.

PLoS One. 2016 Feb 16;11(2):e0149166. doi: 10.1371/journal.pone.0149166. eCollection 2016.

13.

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.

Figliuzzi M, Jacquier H, Schug A, Tenaillon O, Weigt M.

Mol Biol Evol. 2016 Jan;33(1):268-80. doi: 10.1093/molbev/msv211. Epub 2015 Oct 6.

14.

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.

De Leonardis E, Lutz B, Ratz S, Cocco S, Monasson R, Schug A, Weigt M.

Nucleic Acids Res. 2015 Dec 2;43(21):10444-55. doi: 10.1093/nar/gkv932. Epub 2015 Sep 29.

15.

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani A.

PLoS One. 2014 Mar 24;9(3):e92721. doi: 10.1371/journal.pone.0092721. eCollection 2014.

16.

Direct coupling analysis for protein contact prediction.

Morcos F, Hwa T, Onuchic JN, Weigt M.

Methods Mol Biol. 2014;1137:55-70. doi: 10.1007/978-1-4939-0366-5_5.

PMID:
24573474
17.

Perturbation biology: inferring signaling networks in cellular systems.

Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C.

PLoS Comput Biol. 2013;9(12):e1003290. doi: 10.1371/journal.pcbi.1003290. Epub 2013 Dec 19.

18.

From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction.

Cocco S, Monasson R, Weigt M.

PLoS Comput Biol. 2013;9(8):e1003176. doi: 10.1371/journal.pcbi.1003176. Epub 2013 Aug 22.

19.

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models.

Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012707. Epub 2013 Jan 11.

PMID:
23410359
20.

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.

Li N, You X, Chen T, Mackowiak SD, Friedländer MR, Weigt M, Du H, Gogol-Döring A, Chang Z, Dieterich C, Hu Y, Chen W.

Nucleic Acids Res. 2013 Apr 1;41(6):3619-34. doi: 10.1093/nar/gkt072. Epub 2013 Feb 8.

21.

Genomics-aided structure prediction.

Sułkowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10340-5. doi: 10.1073/pnas.1207864109. Epub 2012 Jun 12.

22.

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis.

Dago AE, Schug A, Procaccini A, Hoch JA, Weigt M, Szurmant H.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1733-42. doi: 10.1073/pnas.1201301109. Epub 2012 Jun 5.

23.

Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1293-301. doi: 10.1073/pnas.1111471108. Epub 2011 Nov 21.

24.

Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.

Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M.

PLoS One. 2011 May 9;6(5):e19729. doi: 10.1371/journal.pone.0019729.

25.

Structure-activity relationships of flavonoids as inhibitors of breast cancer resistance protein (BCRP).

Pick A, Müller H, Mayer R, Haenisch B, Pajeva IK, Weigt M, Bönisch H, Müller CE, Wiese M.

Bioorg Med Chem. 2011 Mar 15;19(6):2090-102. doi: 10.1016/j.bmc.2010.12.043. Epub 2010 Dec 30.

PMID:
21354800
26.

Computational modeling of phosphotransfer complexes in two-component signaling.

Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H.

Methods Enzymol. 2010;471:43-58. doi: 10.1016/S0076-6879(10)71003-X. Epub 2010 Mar 1.

PMID:
20946841
27.

Inference of direct residue contacts in two-component signaling.

Lunt B, Szurmant H, Procaccini A, Hoch JA, Hwa T, Weigt M.

Methods Enzymol. 2010;471:17-41. doi: 10.1016/S0076-6879(10)71002-8. Epub 2010 Mar 1.

PMID:
20946840
28.

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.

Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R.

BMC Bioinformatics. 2010 Jun 29;11:355. doi: 10.1186/1471-2105-11-355.

29.

High-resolution protein complexes from integrating genomic information with molecular simulation.

Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22124-9. doi: 10.1073/pnas.0912100106. Epub 2009 Dec 17.

30.

3D-QSAR with the aid of pharmacophore search and docking-based alignments for farnesyltransferase inhibitors.

Vaidya M, Weigt M, Wiese M.

Eur J Med Chem. 2009 Oct;44(10):4070-82. doi: 10.1016/j.ejmech.2009.04.045. Epub 2009 May 8.

PMID:
19515462
31.

Identification of direct residue contacts in protein-protein interaction by message passing.

Weigt M, White RA, Szurmant H, Hoch JA, Hwa T.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):67-72. doi: 10.1073/pnas.0805923106. Epub 2008 Dec 30.

32.

Clustering by soft-constraint affinity propagation: applications to gene-expression data.

Leone M, Sumedha, Weigt M.

Bioinformatics. 2007 Oct 15;23(20):2708-15. Epub 2007 Sep 25.

PMID:
17895277
33.

Propagation of external regulation and asynchronous dynamics in random Boolean networks.

Mahmoudi H, Pagnani A, Weigt M, Zecchina R.

Chaos. 2007 Jun;17(2):026109.

PMID:
17614696
34.

Message passing for vertex covers.

Weigt M, Zhou H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Oct;74(4 Pt 2):046110. Epub 2006 Oct 12.

PMID:
17155136
35.

Statistical mechanics of combinatorial auctions.

Galla T, Leone M, Marsili M, Sellitto M, Weigt M, Zecchina R.

Phys Rev Lett. 2006 Sep 22;97(12):128701. Epub 2006 Sep 20.

PMID:
17026006
36.

Dibenzazecine compounds with a novel dopamine/5HT2A receptor profile and 3D-QSAR analysis.

Hamacher A, Weigt M, Wiese M, Hoefgen B, Lehmann J, Kassack MU.

BMC Pharmacol. 2006 Sep 15;6:11.

37.

Core percolation and onset of complexity in boolean networks.

Correale L, Leone M, Pagnani A, Weigt M, Zecchina R.

Phys Rev Lett. 2006 Jan 13;96(1):018101. Epub 2006 Jan 4.

PMID:
16486521
38.

Cavity approach to the random solid state.

Mao X, Goldbart PM, Mézard M, Weigt M.

Phys Rev Lett. 2005 Sep 30;95(14):148302. Epub 2005 Sep 28.

PMID:
16241698
39.

Solving satisfiability problems by fluctuations: the dynamics of stochastic local search algorithms.

Barthel W, Hartmann AK, Weigt M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jun;67(6 Pt 2):066104. Epub 2003 Jun 12.

PMID:
16241301
40.

Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs.

Krzakała F, Pagnani A, Weigt M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct;70(4 Pt 2):046705. Epub 2004 Oct 29.

PMID:
15600563
41.

Polynomial iterative algorithms for coloring and analyzing random graphs.

Braunstein A, Mulet R, Pagnani A, Weigt M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Sep;68(3 Pt 2):036702. Epub 2003 Sep 3.

PMID:
14524921
42.

Computational complexity arising from degree correlations in networks.

Vázquez A, Weigt M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Feb;67(2 Pt 2):027101. Epub 2003 Feb 7.

PMID:
12636856
43.

Coloring random graphs.

Mulet R, Pagnani A, Weigt M, Zecchina R.

Phys Rev Lett. 2002 Dec 23;89(26):268701. Epub 2002 Dec 9.

PMID:
12484862
44.

Hiding solutions in random satisfiability problems: a statistical mechanics approach.

Barthel W, Hartmann AK, Leone M, Ricci-Tersenghi F, Weigt M, Zecchina R.

Phys Rev Lett. 2002 May 6;88(18):188701. Epub 2002 Apr 18.

PMID:
12005728
45.

Minimal vertex covers on finite-connectivity random graphs: a hard-sphere lattice-gas picture.

Weigt M, Hartmann AK.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 May;63(5 Pt 2):056127. Epub 2001 Apr 26.

PMID:
11414981
46.

Simplest random K-satisfiability problem.

Ricci-Tersenghi F, Weigt M, Zecchina R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Feb;63(2 Pt 2):026702. Epub 2001 Jan 23.

PMID:
11308607
47.

Typical solution time for a vertex-covering algorithm on finite-connectivity random graphs.

Weigt M, Hartmann AK.

Phys Rev Lett. 2001 Feb 19;86(8):1658-61.

PMID:
11290217
48.

Number of guards needed by a museum: a phase transition in vertex covering of random graphs.

Weigt M, Hartmann AK.

Phys Rev Lett. 2000 Jun 26;84(26 Pt 1):6118-21.

PMID:
10991138
49.

Multifractal analysis of the coupling space of feedforward neural networks.

Engel A, Weigt M.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Mar;53(3):R2064-R2067. No abstract available.

PMID:
9964608
50.

Activation of luminal Na+/H+ exchange in distal nephron of frog kidney. An early response to aldosterone.

Weigt M, Dietl P, Silbernagl S, Oberleithner H.

Pflugers Arch. 1987 May;408(6):609-14.

PMID:
3037482

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