Publications

Journal Articles

Xianli Jiang, Emmanuel Martinez-Ledesma, Faruck Morcos. Revealing protein networks and gene-drug connectivity in cancer from direct information. Scientific Reports. 7:3739, 2017.

 
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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 PLoS ONE. 12(4): e0175796. 2017

 

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Fang Bai, Faruck Morcos, Ryan R. Cheng, Hualiang Jiang and José N. Onuchic.Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis. Proc Natl Acad Sci USA. 113 (5) E8051–E8058. 2016

 

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Ryan R. Cheng, Olle Nordesjö, Ryan L. Hayes, Herbert Levine, Samuel C. Flores, José N. Onuchic, Faruck Morcos Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes Molecular Biology and Evolution. 33 (12): 3054-3064. 2016

[Science Daily] [NSF news]

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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 J. Bacteriol. 198:18 2439-2447. 2016

 
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Alessandro Pandini, Faruck Morcos and Shahid Khan. The gearbox of the bacterial flagellar motor switch Structure. 24, 1209–1220 2016.

 
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Jeffrey K. Noel, Faruck Morcos and Jose N. Onuchic. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics F1000Research 5(F1000 Faculty Rev):106. 5:13652, 2016.

 
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Ricardo N. dos Santos*, Faruck Morcos*, Biman Jana, Adriano D. Andricopulo and Jose N. Onuchic. Dimeric interactions and complex formation using direct coevolutionary couplings. Scientific Reports. 5:13652, 2015. (* equivalent contribution)

 
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F.Bai*, Faruck Morcos*, Y.S. Sohn, M. Darash-Yahana, C.O. Rezende, C.H. Lipper, M.L. Paddock, L. Song, Y. Luo, S.H. Holt, S. Tamir, E.A. Theodorakis, P.A. Jennings, J.N. Onuchic, R. Mittler and R. Nechushtai. The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer. Proc Natl Acad Sci USA. 112(12) 3698-3703, 2015.
Highlighted in Mammalian Cell News

 
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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. Biochim. Biophys. Acta, 1853(6) 1294-1315, 2015

 
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Faruck Morcos, Nicholas P. Schafer, Ryan R. Cheng, Jose N. Onuchic and Peter G. Wolynes. Coevolutionary Information, Protein Folding Landscapes and the Thermodynamics of Natural Selection. Proc Natl Acad Sci USA 111(34): 12408-12413, 2014
Press Highlight in ScienceNewsline: From Eons to Seconds, Proteins Exploit the Same Forces

 
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S. Tamir, S. Rotem, C. Katz , Faruck Morcos, K. Hailey, J. Zuris, C. Wang, A. Conlan, C. Lipper, M. Paddock, R. Mittler, J.N. Onuchic, P.A. Jennings, A. Frieddler, R. Nechushtai. An Integrated Strategy Reveals the Protein Interface between the Cancer Targets Bcl-2 and NAF-1. Proc Natl Acad Sci USA. 111(14) 5177-5182, 2014

 
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Biman Jana, Faruck Morcos and Jose N. Onuchic. From Structure to Function: the Convergence of Structure Based Models and Co-evolutionary Information. Physical Chemistry Chemical Physics. Vol. 16, No. 14, Pages 6496-507, 2014

 
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Ryan Cheng, Faruck Morcos, Herbert Levine and Jose N. Onuchic. Towards rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci USA . 111(5): E563-71, 2014
Press Highlight in Phys.org: Researchers tune in to protein pairs: Team quanti es how mutations a ffect cell signaling in bacteria

 
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Faruck Morcos, Biman Jana, Terence Hwa and Jose N. Onuchic. Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci USA. Vol 110, No. 51, p. 20533-20538. 2013
Press Highlight in ScienceDaily: Proteins' passing phases revealed

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

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

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

 
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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. Physical Biology. Vol. 8, No. 2, 2011.

 
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Faruck Morcos, R. Lopez, S. Chatterjee, P. Brenner, C. McClendon, J. Zintsmaster, M. Ercsey-Ravasz, C.R. Sweet,
M. Jacobson, J. Peng and J. Izaguirre. Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Computational Biology. 6(12): e1001015, 2010.

 
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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. IEEE Transactions on Information Theory. Vol. 56, No. 2, p. 742-755, 2010.

 
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Zaher Dawy, Faruck Morcos, Johanna Weindl and Jakob C. Mueller. Translation initiation modeling and mutational analysis based on the 3-end of the Escherichia coli 16S rRNA sequence. Elsevier BioSystems. 96 (1), p. 58-64, 2009

 
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Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre. Cytoprophet: a Cytoscape plug-in for the protein and domain interaction networks inference. Bioinformatics , Vol. 24, Issue 19, pp. 2265-2266, 2008

 
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S. Flores, K. Keating, J. Painter, F. Morcos, K. Nguyen, E. Merrit, L. Kuhn and M. Gerstein. HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins: Structure, Function, and Bioinformatics. Vol. 73, Issue 2, Pages 299-319, Nov, 2008

 
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Zaher Dawy, Pavol Hanus, Johanna Weindl, Janis Dingel, Faruck Morcos. On genomic coding theory. European Transactions on Telecommunications , John Wiley & Sons, Ltd. Vol. 18, Issue 8, pp. 873-879, 2007

 
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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. IEEE/ACM Transactions on Computational Biology and Bioinformatics , Vol. 4 pp. 78-87, 2007

 
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Book Chapters

Faruck Morcos, Terence Hwa, Jose N. Onuchic and Martin Weigt. Direct Coupling Analysis for protein contact prediction. Protein Structure Prediction, Methods in Molecular Biology, 3rd Edition. Springer Science+Business Media. 2014

 
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Peer-reviewed Conference Articles

Faruck Morcos, Marcin Sikora, Dale Kaiser, Mark Alber and Jesus Izaguirre. Estimation of protein and domain interactions in the switching motility system of Myxococcus xanthus. Pacific Symposium of Biocomputing (PSB). 157-65, January, 2010.

 
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Faruck Morcos, Charles Lamanna, Nitesh V. Chawla and Jesus Izaguirre. Determination of Specificity Residues in Two Component Systems using Graphlets. International Conference on Bioinformatics and Computational Biology (BIOCOMP). July, 2009.

 
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