Journal Articles
Jonathan Martin, Marcos Lequerica Mateos, José N Onuchic, Ivan Coluzza, Faruck MorcosMachine learning in biological physics: From biomolecular prediction to design Proceedings of the National Academy of Sciences. 121 (27), e2311807121, 2024.
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Rachel Nechushtai, Linda Rowland, Ola Karmi, Henri-Baptiste Marjault, Thi Thao Nguyen, Shubham Mittal, Raheel S Ahmed, DeAna Grant, Camila Manrique-Acevedo, Faruck Morcos, José N Onuchic, Ron MittlerCISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance Proceedings of the National Academy of Sciences. 121 (22), e2405123121, 2024.
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Hana Jaafari, Carlos Bueno, Nicholas P Schafer, Jonathan Martin, Faruck Morcos, Peter G WolynesThe physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes Proceedings of the National Academy of Sciences. 121 (21), e2322428121, 2024.
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Sophia Alvarez, Charisse M Nartey, Nicholas Mercado, Jose Alberto de la Paz, Tea Huseinbegovic, Faruck MorcosIn vivo functional phenotypes from a computational epistatic model of evolution Proceedings of the National Academy of Sciences. 121 (6), e2308895121, 2024.
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Charisse M Nartey, Hyun Jo Koo, Caroline Laurendon, Hana Z Shaik, Paul O’maille, Joseph P Noel, Faruck Morcos Coevolutionary Information Captures Catalytic Functions and Reveals Divergent Roles of Terpene Synthase Interdomain Connections Biochemistry. 63 (3), 355-366, 2024.
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Faruck Morcos, Paul C Whitford, Margaret S Cheung Biography of José N. Onuchic The Journal of Physical Chemistry B. 127 (35), 7556-7557, 2023.
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Faruck Morcos, Paul C Whitford, Margaret S Cheung Tribute to José N. Onuchic The Journal of Physical Chemistry B. 127 (35), 7553-7555, 2023.
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Cheyenne Ziegler, Jonathan Martin, Claude Sinner, Faruck Morcos Latent generative landscapes as maps of functional diversity in protein sequence space Nature Communications. 14 (1), 2222, 2023.
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Aishwarya Krishnamohan, George L Hamilton, Rajen Goutam, Hugo Sanabria, Faruck Morcos Coevolution and smfret enhances conformation sampling and fret experimental design in tandem pdz1–2 proteins The Journal of Physical Chemistry B. 127 (4), 884-898, 2023.
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Faruck Morcos Evolutionary entrenchment in immune proteins selects against stabilizing mutations Proceedings of the National Academy of Sciences. 119 (49), e2216087119, 2022.
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Krithika Ravishankar, Xianli Jiang, Emmett M Leddin, Faruck Morcos, G Andrés Cisneros Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation Biophysical Journal. 121 (19), 3663-3673, 2022.
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Hsichuan Chi, Qin Zhou, Jasmine N. Tutol, Shelby M. Phelps, Jessica Lee, Paarth Kapadia, Faruck Morcos*, and Sheel C. Dodani* Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor ACS Synthetic Biology. Vol. 11, (4), 1627–1638, 2022. (*Co-corresponding)
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Faruck Morcos Characterizing the landscape of evolvability Nature Ecology & Evolution. 1-2, 2022. (Perspective)
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Ola Karmi, Henri-Baptiste Marjault, Fang Bai, Susmita Roy, Yang-Sung Sohn, Merav Darash Yahana, Faruck Morcos, Konstantinos Ioannidis, Yaakov Nahmias, Patricia A Jennings, Ron Mittler, José N Onuchic, Rachel Nechushtai A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics Proceedings of the National Academy of Sciences. Vol. 119 (7), e2121491119, 2022.
Amit Gaba, Mark A Hix, Sana Suhail, Ben Flath, Brock Boysan, Danielle R Williams, Tomas Pelletier, Michael Emerman, Faruck Morcos, G Andrés Cisneros, Linda Chelico Divergence in dimerization and activity of primate APOBEC3C Journal of Molecular Biology. Vol. 433 (24), 167306, 2021.
Xian-Li Jiang, Rey P Dimas, Clement TY Chan*, Faruck Morcos* Coevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions Nature Communications. Vol. 12 (1), 1-8, 2021.(*Co-corresponding)
News: [UNT News]
Faruck Morcos Information Theory in Molecular Evolution: From Models to Structures and Dynamics Entropy. Vol. 23 (4), 482, 2021. (Editorial)
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Jasmine N Tutol, Jessica Lee, Hsichuan Chi, Farah N Faizuddin, Sameera S Abeyrathna, Qin Zhou, Faruck Morcos, Gabriele Meloni, Sheel C Dodani A single point mutation converts a proton-pumping rhodopsin into a red-shifted, turn-on fluorescent sensor for chloride Chemical Science. Vol. 12 (15), 5655-5663 ,2021
Jose Alberto de la Paz and Faruck Morcos Reply to Patel and Kumar: Epistasis not critical to rate distributions but key in heterotachy, overdispersion, and evolutionary Stokes shift Proceedings of the National Academy of Sciences. Vol. 118 (18), 2021. (Letter)
Nicole N Thadani, Qin Zhou, Kiara Reyes Gamas, Susan Butler, Carlos Bueno, Nicholas P Schafer, Faruck Morcos, Peter G Wolynes, Junghae Suh Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus Biophysical Journal. 120 (3), 489-503, 2021.
Claude Sinner, Cheyenne Ziegler, Yun Ho Jung, Xianli Jiang and Faruck Morcos ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators Entropy. 23 (2), 170, 2021.
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Faruck Morcos Protein conformations à la carte, a step further in de novo protein design Proceedings of the National Academy of Sciences. Vol. 117 (16), 8674-8676, 2020. (Commentary)
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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 Proceedings of the National Academy of Sciences. Vol. 117 (11), 5873-5882, 2020.
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R.N. dos Santos, G.F. Bottino, F.C. Gozzo, F. Morcos, L. Martínez. Structural complementarity of distance constraints obtained from chemical cross‐linking and amino acid coevolution Proteins: Structure, Function, and Bioinformatics. 88:625–632, 2020.
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Y. Li, J.A. De la Paz, X. Jiang, R. Liu, A.P. Pokkulandra, L. Bleris*, F. Morcos*. Coevolutionary Couplings Unravel PAM-Proximal Constraints of CRISPR-SpCas9. Biophysical Journal.117 (9), 1684-1691, 2019. (*Co-corresponding)
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Rey P Dimas, Benjamin R Jordan, Xian-Li Jiang, Catherine Martini, Joseph S Glavy, Dustin P Patterson, Faruck Morcos, Clement TY Chan Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy. Nucleic Acids Research. 2019
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Faruck Morcos and Jose N. Onuchic The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes Current opinion in structural biology. 56, 179-186. 2019
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Rey Dimas^, Xianli Jiang^, José Alberto De la Paz, Faruck Morcos* and Clement Chan* Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset Nucleic Acids Research Vol. 47 (10), 5449–5463, 2019. (* Co-corresponding)
News: [Phys.org]
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Aleksandra Jarmolinska, Qin Zhou, Joanna Ida Sulkowska*, Faruck Morcos* DCA-MOL-a PyMOL Plugin to Analyze Direct Evolutionary Couplings J. Chem. Inf. Model. 59 (2), pp 625–629. 2019 (*Co-corresponding)
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Ryan R Cheng, Ellinor Haglund, Nicholas S Tiee, Faruck Morcos, Herbert Levine, Joseph A Adams, Patricia A Jennings, José N Onuchic Designing bacterial signaling interactions with coevolutionary landscapes PloS One. 13 (8), e0201734. 2018
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Qin Zhou, Nikesh Kunder, José Alberto De la Paz, Alexandra E. Lasley, Vandita D. Bhat, Faruck Morcos* and Zachary T. Campbell* Global pairwise RNA interaction landscapes reveal core features of protein recognition Nature Communications. 9, Article number: 2511. 2018 (* Co-corresponding)
News: [EurekAlert]
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Ricardo N dos Santos, Shahid Khan, Faruck Morcos. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. Royal Society Open Science.5 (5), 171854, 2018.
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H. E. Sanchez-Ibarra, L. M. Reyes-Cortes, Xian-Li Jiang, C. M. Luna-Aguirre, D. Aguirre-Trevino, I. A. Morales-Alvarado, R. B. Leon-Cachon, F. Lavalle-Gonzalez, Faruck Morcos* and H. A. Barrera-Saldaña* Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus. Frontiers in Pharmacology. 9:320, 2018. (* Co-corresponding)
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Ricardo N dos Santos, Allan J R Ferrari, Hugo C R de Jesus, Fábio C Gozzo, Faruck Morcos, Leandro Martínez. Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics. 2018.
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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
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
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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 (* Co-corresponding)
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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
Ricardo N. dos Santos, Xianli Jiang, Leandro Martínez, Faruck Morcos Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations Computational Methods in Protein Evolution, Methods in Molecular Biology Vol. 1851. Springer Science+Business Media. 2018
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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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