Skip to content


[1]   R. R. Cheng, F. Morcos, H. Levine, and J. N. Onuchic, “Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information,” Proc Natl Acad Sci U S A, vol. 111, no. 5, pp. E563–71, 2014. Feb 4; Epub 2014 Jan 21.

[2]   S. Cocco, R. Monasson, and M. Weigt, “From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction,” PLoS Comput Biol, vol. 9, no. 8, p. e1003176, 2013. Epub 2013 Aug 22.

[3]   A. E. Dago, A. Schug, A. Procaccini, J. A. Hoch, M. Weigt, and H. Szurmant, “Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis,” Proc Natl Acad Sci U S A, vol. 109, no. 26, pp. E1733–42, 2012. Epub 2012 Jun 5.

[4]   D. de Juan, F. Pazos, and A. Valencia, “Emerging methods in protein co-evolution,” Nat Rev Genet, vol. 14, no. 4, pp. 249–61, 2013. Epub 2013 Mar 5.

[5]   K. A. Dill and J. L. MacCallum, “The protein-folding problem, 50 years on,” Science, vol. 338, no. 6110, pp. 1042–1046, 2012.

[6]   M. Ekeberg, C. Lovkvist, Y. H. Lan, M. Weigt, and E. Aurell, “Improved contact prediction in proteins: Using pseudolikelihoods to infer potts models,” Physical Review E, vol. 87, no. 1, 2013. 079DY Times Cited:4 Cited References Count:53.

[7]   B. K. Ho, D. Perahia, and A. M. Buckle, “Hybrid approaches to molecular simulation,” Curr Opin Struct Biol, vol. 22, no. 3, pp. 386–93, 2012. Epub 2012 May 25.

[8]   B. Lunt, H. Szurmant, A. Procaccini, J. Hoch, T. Hwa, and M. Weigt, “Inference of direct residue contacts in two-component signaling,” Methods in Enzymology, vol. 471, pp. 17–41, 2010.

[9]   D. S. Marks, T. A. Hopf, and C. Sander, “Protein structure prediction from sequence variation,” Nat Biotechnol, vol. 30, no. 11, pp. 1072–80, 2012.

[10]   F. Morcos, T. Hwa, J. N. Onuchic, and M. Weigt, Direct Coupling Analysis for protein contact prediction, vol. 1137, ch. 5. Springer Science+Buisiness Media, 2014.

[11]   F. Morcos, B. Jana, T. Hwa, and J. N. Onuchic, “Coevolutionary signals across protein lineages help capture multiple protein conformations,” Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. 20533–8, 2013. Epub 2013 Dec 2.

[12]   F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. S. Marks, C. Sander, R. Zecchina, J. N. Onuchic, T. Hwa, and M. Weigt, “Direct-coupling analysis of residue coevolution captures native contacts across many protein families,” Proc Natl Acad Sci U S A, vol. 108, no. 49, pp. E1293–301, 2011. Epub 2011 Nov 21.

[13]   A. Procaccini, B. Lunt, H. Szurmant, T. Hwa, and M. Weigt, “Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.,” PLoS one, vol. 6, p. e19729, 2011.

[14]   A. Schug, M. Weigt, J. N. Onuchic, T. Hwa, and H. Szurmant, “High-resolution protein complexes from integrating genomic information with molecular simulation.,” Proc Natl Acad Sci USA, vol. 106, pp. 22124–22129, 2009.

[15]   J. I. Sułkowska, F. Morcos, M. Weigt, T. Hwa, and J. N. Onuchic, “Genomics-aided structure prediction,” Proc Natl Acad Sci U S A, vol. 109, no. 26, pp. 10340–5, 2012. Jun 26, Epub 2012 Jun 12.

[16]   H. Szurmant and J. A. Hoch, “Statistical analyses of protein sequence alignments identify structures and mechanisms in signal activation of sensor histidine kinases,” Mol Microbiol, vol. 87, no. 4, pp. 707–12, 2013. Epub 2012 Dec 28.

[17]   M. Weigt, R. A. White, H. Szurmant, J. A. Hoch, and T. Hwa, “Identification of direct residue contacts in protein-protein interaction by message passing.,” Proc Natl Acad Sci USA, vol. 106, pp. 67–72, 2009.

Copyright 2013 Bryan Lunt, Faruck Morcos, All rights reserved.