{"id":325,"date":"2015-11-25T20:20:43","date_gmt":"2015-11-25T20:20:43","guid":{"rendered":"http:\/\/44.196.76.129\/?page_id=325"},"modified":"2025-07-11T16:29:51","modified_gmt":"2025-07-11T16:29:51","slug":"research-biomolecular-interactions-and-networks","status":"publish","type":"page","link":"https:\/\/morcoslaboratory.org\/?page_id=325","title":{"rendered":"Research – Biomolecular Interactions and Networks"},"content":{"rendered":"

\"Phosphoglucose_Isomerase\"<\/a>One of the most important concepts\u00a0in modern biology is the fact that the complexity of life is encoded in the interaction of its units. Understanding and uncovering this network of interactions is a fundamental goal for systems biology and to our laboratory. We are interested in characterizing interactions at several scales: including\u00a0amino acid or nucleotide interactions, \u00a0physical interactions of functional domains, \u00a0protein-protein, protein-rna\/dna, \u00a0macro molecular interactions, drug-molecule, gene and signaling\u00a0networks as well as cellular interactions. Our focus has been traditionally to uncover hidden interactions but we are also dedicated to create predictive models and to study\u00a0complexity\u00a0in biological networks.<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Qin Zhou, Jose Alberto de la Paz, Alexander D Stanowick, Xingcheng Lin, Faruck Morcos
\nCharacterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing<\/span> Nucleic Acids Research.<\/em> 53 (12), gkaf592, 2025.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>
\n[PDF<\/a>]
\n<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, Jos\u00e9 N Onuchic, Ron MittlerCISD3\/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance<\/span> Proceedings of the National Academy of Sciences.<\/em> 121 (22), e2405123121, 2024. <\/p>\n<\/div><\/div><\/div><\/div>

<\/span>
\n[PDF<\/a>]
\n<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

Amit Gaba, Mark A Hix, Sana Suhail, Ben Flath, Brock Boysan, Danielle R Williams, Tomas Pelletier, Michael Emerman, Faruck Morcos, G Andr\u00e9s Cisneros, Linda Chelico Divergence in dimerization and activity of primate APOBEC3C<\/span> Journal of Molecular Biology. <\/em> Vol. 433 (24), 167306, 2021.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>
\n[PDF<\/a>]
\n<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

Faruck Morcos and Jose N. Onuchic The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes<\/span> Current opinion in structural biology.<\/em> 56, 179-186. 2019 <\/p>\n<\/div><\/div><\/div><\/div>

<\/span>
\n[PDF<\/a>]
\n<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

Ricardo N dos Santos, Shahid Khan, Faruck Morcos. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution.<\/span> Royal Society Open Science<\/em>.5 (5), 171854, 2018. <\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

O. Karmi, S.H. Holt, L. Song, S. Tamir, Y. Luo, F. Bai, A. Adenwalla, M. Darash-Yahana, Y. Sohn, P.A. Jennings, R. K. Azad, J. N. Onuchic, F. Morcos, R. Nechushtai, R. Mittler Interactions between mitoNEET and NAF-1 in cells<\/span> PLoS ONE.<\/em> 12(4): e0175796. 2017<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Joseph S. Boyd, Ryan R. Cheng, Mark L. Paddock, Cigdem Sancar, Faruck Morcos*, Susan S. Golden* A Combined Computational and Genetic Approach Uncovers Network Interactions of the Cyanobacterial Circadian Clock<\/span> Journal of Bacteriology<\/em>. 198:2439 \u20132447. 2016.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Ricardo N. dos Santos*, Faruck Morcos*, Biman Jana, Adriano D. Andricopulo and Jose N. Onuchic. Dimeric interactions and complex formation using direct coevolutionary couplings.<\/span> Scientic Reports<\/em>. 5:13652, 2015. (* equivalent contribution)<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

S. Tamir, M.L. Paddock, M. Darash-Yahana-Baram, S.H. Holt, Y.S. Sohn, L. Agranat, D. Michaeli, J.T. Sto-
eth, C.H. Lipper, Faruck Morcos, I.Z. Cabantchik, J.N. Onuchic, P.A. Jennings, R. Mittler, R. Nechushtai.
Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease.<\/span> Biochim. Biophys. Acta<\/em>, 1853(6) 1294-1315, 2015<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

S. Tamir, S. Rotem, C. Katz , Faruck Morcos, K. Hailey, J. Zuris, C. Wang, A. Conlan, C. Lipper, M. Paddock,\u00a0R. Mittler, J.N. Onuchic, P.A. Jennings, A. Frieddler, R. Nechushtai. An Integrated Strategy Reveals the\u00a0Protein Interface between the Cancer Targets Bcl-2 and NAF-1.<\/span> Proc Natl Acad Sci USA<\/em>. 111(14) 5177-5182,\u00a02014<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

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>

<\/span>
\n[PDF<\/a>]
\n<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

Ramy Mourad, Zaher Dawy and Faruck Morcos. Designing Pooling Systems for Noisy High-Throughput Protein-Protein Interaction Experiments using Boolean Compressed Sensing. <\/span> IEEE\/ACM Transactions on Computational Biology and Bioinformatics.<\/em> 10(6): 1478-1490, 2013.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

C. Harvey, Faruck Morcos, C. Sweet, D. Kaiser, S. Chatterjee, X. Liu, D. Chen and M. Alber. Study of elastic collisions of Myxococcus xanthus in swarms.<\/span> Physical Biology.<\/em> Vol. 8, No. 2, 2011.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Faruck Morcos, Marcin Sikora, Mark Alber, Dale Kaiser and Jesus A. Izaguirre. Belief Propagation Estimation of Protein and Domain Interactions using the Sum-Product Algorithm.<\/span> IEEE Transactions on Information Theory.<\/em> Vol. 56, No. 2, p. 742-755, 2010.<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre. Cytoprophet: a Cytoscape plug-in for the protein and domain interaction networks inference. <\/span> Bioinformatics <\/em>, Vol. 24, Issue 19, pp. 2265-2266, 2008<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesus A. Izaguirre. Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. <\/span> IEEE\/ACM Transactions on Computational Biology and Bioinformatics <\/em>, Vol. 4 pp. 78-87, 2007<\/p>\n<\/div><\/div><\/div><\/div>

<\/span>\u00a0
[PDF<\/a>]
<\/span>\u00a0<\/p>\n<\/div><\/div><\/div><\/div><\/div>

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

One of the most important concepts\u00a0in modern biology is the fact that the complexity of life is encoded in the interaction of its units. Understanding and uncovering this network of interactions is a fundamental goal for systems biology and to our laboratory. We are interested in characterizing interactions at several scales: including\u00a0amino acid or nucleotide Read More …<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"full-width-page.php","meta":{"footnotes":""},"class_list":["post-325","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/325","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=325"}],"version-history":[{"count":21,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/325\/revisions"}],"predecessor-version":[{"id":1765,"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=\/wp\/v2\/pages\/325\/revisions\/1765"}],"wp:attachment":[{"href":"https:\/\/morcoslaboratory.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=325"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}