{"id":370,"date":"2016-06-24T13:10:59","date_gmt":"2016-06-24T13:10:59","guid":{"rendered":"http:\/\/44.196.76.129\/?page_id=370"},"modified":"2025-07-14T21:21:27","modified_gmt":"2025-07-14T21:21:27","slug":"research-molecular-evolution","status":"publish","type":"page","link":"https:\/\/morcoslaboratory.org\/?page_id=370","title":{"rendered":"Research- Molecular Evolution"},"content":{"rendered":"
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\"BPevolution\"<\/a><\/p>\n<\/div>\n<\/div><\/div><\/div><\/div>

Divyanshu Shukla, Jonathan Martin, Faruck Morcos, Davit A Potoyan
\nThermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis<\/span> Journal of Chemical Theory and Computation.<\/em> 21 (6), 3277-3287, 2025. <\/p>\n<\/div><\/div><\/div><\/div>

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Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G Wolynes. The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.<\/span> Proceedings of the National Academy of Sciences.<\/em> 121(21), e2322428121, 2024. (Perspective)<\/p>\n<\/div><\/div><\/div><\/div>

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Sophia Alvarez, Charisse M Nartey, Nicholas Mercado, Jose Alberto de la Paz, Tea Huseinbegovic, Faruck Morcos. In vivo functional phenotypes from a computational epistatic model of evolution.<\/span> Proceedings of the National Academy of Sciences.<\/em> 121(6), e2308895121, 2024. (Perspective)<\/p>\n<\/div><\/div><\/div><\/div>

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Faruck Morcos Characterizing the landscape of evolvability<\/span> Nature Ecology & Evolution.<\/em> 1-2, 2022. (Perspective)<\/p>\n<\/div><\/div><\/div><\/div>

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Jose A. De la Paz, Charisse M. Nartey, Monisha Yuvaraj and Faruck Morcos Epistatic contributions promote the unification of incompatible models of neutral molecular evolution<\/span> Proceedings of the National Academy of Sciences <\/em> Vol. 117 (11), 5873-5882, 2020. <\/p>\n<\/div><\/div><\/div><\/div>

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Ryan R. Cheng, Olle Nordesj\u00f6, Ryan L. Hayes, Herbert Levine, Samuel C. Flores, Jos\u00e9 N. Onuchic, Faruck Morcos. Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes<\/span> Molecular Biology and Evolution.<\/em> 2016<\/p>\n

[Science Daily<\/a>] [NSF news<\/a>]
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Faruck Morcos, Nicholas P. Schafer, Ryan R. Cheng, Jos\u0013e N. Onuchic and Peter G. Wolynes. Coevolutionary Information, Protein Folding Landscapes and the Thermodynamics of Natural Selection.<\/span> Proc Natl Acad Sci\u00a0USA<\/em> 111(34): 12408-12413, 2014
Press Highlight in ScienceNewsline: From Eons to Seconds, Proteins Exploit the Same Forces<\/a><\/p>\n<\/div><\/div><\/div><\/div>

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Ryan Cheng, Faruck Morcos, Herbert Levine and Jos\u0013e N. Onuchic. Towards rationally redesigning bacterial\u00a0two-component signaling systems using coevolutionary information. <\/span> Proc Natl Acad Sci USA <\/em>. 111(5): E563-71,\u00a02014
Press Highlight in Phys.org: Researchers tune in to protein pairs: Team quanti\fes how mutations a\u000bffect cell signaling in bacteria<\/a><\/p>\n<\/div><\/div><\/div><\/div>

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Faruck Morcos, Biman Jana, Terence Hwa and Jos\u0013e N. Onuchic. Coevolutionary signals across protein lineages help capture multiple protein conformations.<\/span> Proc Natl Acad Sci USA.<\/em> Vol 110, No. 51, p. 20533-20538. 2013
Press Highlight in ScienceDaily: Proteins' passing phases revealed<\/a><\/p>\n<\/div><\/div><\/div><\/div>

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Joanna I. Sulkowska*, Faruck Morcos*, Martin Weigt, Terence Hwa and Jose N. Onuchic. Genomics-aided structure prediction.<\/span> Proc Natl Acad Sci USA.<\/em> Vol. 109, No. 26, p. 10340-45, 2012. (*equivalent contribution)
\nProtein residues kiss, don't tell: Genomes reveal contacts, scientists refine methods for protein-folding prediction<\/a><\/p>\n<\/div><\/div><\/div><\/div>

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Faruck Morcos*, Andrea Pagnani*, Bryan Lunt, Arianna Bertolino, Debora S. Marks, Chris Sander, Riccardo Zecchina,
\nJose N. Onuchic, Terence Hwa and Martin Weigt. Direct-coupling analysis of residue coevolution captures native contacts across many protein families.<\/span> Proc Nat Acad Sci USA.<\/em> Vol. 108, No. 49, E1293-E1301, 2011. (*equivalent contribution) <\/p>\n<\/div><\/div><\/div><\/div>

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<\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"

Divyanshu Shukla, Jonathan Martin, Faruck Morcos, Davit A Potoyan Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis Journal of Chemical Theory and Computation. 21 (6), 3277-3287, 2025. [PDF]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":38,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"full-width-page.php","meta":{"footnotes":""},"class_list":["post-370","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/370","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=370"}],"version-history":[{"count":46,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/370\/revisions"}],"predecessor-version":[{"id":1772,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/370\/revisions\/1772"}],"up":[{"embeddable":true,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/38"}],"wp:attachment":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=370"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}