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  1. 1.   Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics
  2. Eren, Meryem; Tuncbag, Nurcan; Jang,Hyunbum; Nussinov,Ruth; Gursoy, Attila; Keskin, Ozlem
  3. The journal of physical chemistry. B. 2021, May 27; 125(20): 5210-5221.
  1. 2.   A genome-wide association study of bladder cancer identifies a new susceptibility locus within SLC14A1, a urea transporter gene on chromosome 18q12.3
  2. Garcia-Closas, M.; Ye, Y. Q.; Rothman, N.; Figueroa, J. D.; Malats, N.; Dinney, C. P.; Chatterjee, N.; Prokunina-Olsson, L.; Wang, Z. M.; Lin, J.; Real, F. X.; Jacobs, K. B.; Baris, D.; Thun, M.; De Vivo, I.; Albanes, D.; Purdue, M. P.; Kogevinas, M.; Kamat, A. M.; Lerner, S. P.; Grossman, H. B.; Gu, J.; Pu, X.; Hutchinson, A.; Fu, Y. P.; Burdett, L.; Yeager, M.; Tang, W.; Tardon, A.; Serra, C.; Carrato, A.; Garcia-Closas, R.; Lloreta, J.; Johnson, A.; Schwenn, M.; Karagas, M. R.; Schned, A.; Andriole, G.; Grubb, R.; Black, A.; Jacobs, E. J.; Diver, W. R.; Gapstur, S. M.; Weinstein, S. J.; Virtamo, J.; Hunter, D. J.; Caporaso, N.; Landi, M. T.; Fraumeni, J. F.; Silverman, D. T.; Chanock, S. J.; Wu, X. F.
  3. Human Molecular Genetics. 2011, Nov; 20(21): 4282-4289.
  1. 3.   Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
  2. Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O.
  3. Nature Protocols. 2011, Sep; 6(9): 1341-1354.
  1. 4.   The landscape of recombination in African Americans
  2. Hinch, A. G.; Tandon, A.; Patterson, N.; Song, Y. L.; Rohland, N.; Palmer, C. D.; Chen, G. K.; Wang, K.; Buxbaum, S. G.; Akylbekova, E. L.; Aldrich, M. C.; Ambrosone, C. B.; Amos, C.; Bandera, E. V.; Berndt, S. I.; Bernstein, L.; Blot, W. J.; Bock, C. H.; Boerwinkle, E.; Cai, Q. Y.; Caporaso, N.; Casey, G.; Cupples, L. A.; Deming, S. L.; Diver, W. R.; Divers, J.; Fornage, M.; Gillanders, E. M.; Glessner, J.; Harris, C. C.; Hu, J. J.; Ingles, S. A.; Isaacs, W.; John, E. M.; Kao, W. H. L.; Keating, B.; Kittles, R. A.; Kolonel, L. N.; Larkin, E.; Le Marchand, L.; McNeill, L. H.; Millikan, R. C.; Murphy, A.; Musani, S.; Neslund-Dudas, C.; Nyante, S.; Papanicolaou, G. J.; Press, M. F.; Psaty, B. M.; Reiner, A. P.; Rich, S. S.; Rodriguez-Gil, J. L.; Rotter, J. I.; Rybicki, B. A.; Schwartz, A. G.; Signorello, L. B.; Spitz, M.; Strom, S. S.; Thun, M. J.; Tucker, M. A.; Wang, Z. M.; Wiencke, J. K.; Witte, J. S.; Wrensch, M.; Wu, X. F.; Yamamura, Y.; Zanetti, K. A.; Zheng, W.; Ziegler, R. G.; Zhu, X. F.; Redline, S.; Hirschhorn, J. N.; Henderson, B. E.; Taylor, H. A.; Price, A. L.; Hakonarson, H.; Chanock, S. J.; Haiman, C. A.; Wilson, J. G.; Reich, D.; Myers, S. R.
  3. Nature. 2011, Aug; 476(7359): 170-U67.
  1. 5.   Fine mapping of a region of chromosome 11q13 reveals multiple independent loci associated with risk of prostate cancer
  2. Chung, C. C.; Ciampa, J.; Yeager, M.; Jacobs, K. B.; Berndt, S. I.; Hayes, R. B.; Gonzalez-Bosquet, J.; Kraft, P.; Wacholder, S.; Orr, N.; Yu, K.; Hutchinson, A.; Boland, J.; Chen, Q.; Feigelson, H. S.; Thun, M. J.; Diver, W. R.; Albanes, D.; Virtamo, J.; Weinstein, S.; Schumacher, F. R.; Cancel-Tassin, G.; Cussenot, O.; Valeri, A.; Andriole, G. L.; Crawford, E. D.; Haiman, C. A.; Henderson, B. E.; Kolonel, L.; Le Marchand, L.; Siddiq, A.; Riboli, E.; Key, T. J.; Kaaks, R.; Isaacs, W. B.; Isaacs, S. D.; Gronberg, H.; Wiklund, F.; Xu, J. F.; Vatten, L. J.; Hveem, K.; Njolstad, I.; Gerhard, D. S.; Tucker, M.; Hoover, R. N.; Fraumeni, J. F.; Hunter, D. J.; Thomas, G.; Chatterjee, N.; Chanock, S. J.
  3. Human Molecular Genetics. 2011, Jul; 20(14): 2869-2878.
  1. 6.   High recombination rates and hotspots in a Plasmodium falciparum genetic cross
  2. Jiang, H. Y.; Li, N.; Gopalan, V.; Zilversmit, M. M.; Varma, S.; Nagarajan, V.; Li, J.; Mu, J. B.; Hayton, K.; Henschen, B.; Yi, M.; Stephens, R.; McVean, G.; Awadalla, P.; Wellems, T. E.; Su, X. Z.
  3. Genome Biology. 2011, Apr 4; 12(4): 14.
  1. 7.   Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans
  2. Laayouni, H. L. H.; Montanucci, L.; Sikora, M.; Mele, M.; Dall'Olio, G. M.; Lorente-Galdos, B.; McGee, K. M.; Graffelman, J.; Awadalla, P.; Bosch, E.; Comas, D.; Navarro, A.; Calafell, F.; Casals, F.; Bertranpetit, J.
  3. Plos One. 2011, Mar; 6(3): 8.
  1. 8.   A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci
  2. Rothman, N.; Garcia-Closas, M.; Chatterjee, N.; Malats, N.; Wu, X. F.; Figueroa, J. D.; Real, F. X.; Van den Berg, D.; Matullo, G.; Baris, D.; Thun, M.; Kiemeney, L. A.; Vineis, P.; De Vivo, I.; Albanes, D.; Purdue, M. P.; Rafnar, T.; Hildebrandt, M. A. T.; Kiltie, A. E.; Cussenot, O.; Golka, K.; Kumar, R.; Taylor, J. A.; Mayordomo, J. I.; Jacobs, K. B.; Kogevinas, M.; Hutchinson, A.; Wang, Z. W.; Fu, Y. P.; Prokunina-Olsson, L.; Burdett, L.; Yeager, M.; Wheeler, W.; Tardon, A.; Serra, C.; Carrato, A.; Garcia-Closas, R.; Lloreta, J.; Johnson, A.; Schwenn, M.; Karagas, M. R.; Schned, A.; Andriole, G.; Grubb, R.; Black, A.; Jacobs, E. J.; Diver, W. R.; Gapstur, S. M.; Weinstein, S. J.; Virtamo, J.; Cortessis, V. K.; Gago-Dominguez, M.; Pike, M. C.; Stern, M. C.; Yuan, J. M.; Hunter, D. J.; McGrath, M.; Dinney, C. P.; Czerniak, B.; Chen, M.; Yang, H. S.; Vermeulen, S. H.; Aben, K. K.; Witjes, J. A.; Makkinje, R. R.; Sulem, P.; Besenbacher, S.; Stefansson, K.; Riboli, E.; Brennan, P.; Panico, S.; Navarro, C.; Allen, N. E.; Bueno-De-Mesquita, H. B.; Trichopoulos, D.; Caporaso, N.; Landi, M. T.; Canzian, F.; Ljungberg, B.; Tjonnel, A.; Clavel-Chapelon, F.; Bishop, D. T.; Teo, M. T. W.; Knowles, M. A.; Guarrera, S.; Polidoro, S.; Ricceri, F.; Sacerdote, C.; Allione, A.; Cancel-Tassin, G.; Selinski, S.; Hengstler, J. G.; Dietrich, H.; Fletcher, T.; Rudnai, P.; Gurzau, E.; Koppova, K.; Bolick, S. C. E.; Godfrey, A.; Xu, Z. L.; Sanz-Velez, J. I.; Garcia-Prats, M. D.; Sanchez, M.; Valdivia, G.; Porru, S.; Benhamou, S.; Hoover, R. N.; Fraumeni, J. F.; Silverman, D. T.; Chanock, S. J.
  3. Nature Genetics. 2010, Nov; 42(11): 978-U98.
  1. 9.   Comparing interfacial dynamics in protein-protein complexes: an elastic network approach
  2. Zen, A.; Micheletti, C.; Keskin, O.; Nussinov, R.
  3. Bmc Structural Biology. 2010, Aug; 10: 13.
  1. 10.   CCRXP: exploring clusters of conserved residues in protein structures
  2. Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2010, Jul; 38: W398-W401.
  1. 11.   A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33
  2. Petersen, G. M.; Amundadottir, L.; Fuchs, C. S.; Kraft, P.; Stolzenberg-Solomon, R. Z.; Jacobs, K. B.; Arslan, A. A.; Bueno-de-Mesquita, H. B.; Gallinger, S.; Gross, M.; Helzlsouer, K.; Holly, E. A.; Jacobs, E. J.; Klein, A. P.; LaCroix, A.; Li, D. H.; Mandelson, M. T.; Olson, S. H.; Risch, H. A.; Zheng, W.; Albanes, D.; Bamlet, W. R.; Berg, C. D.; Boutron-Ruault, M. C.; Buring, J. E.; Bracci, P. M.; Canzian, F.; Clipp, S.; Cotterchio, M.; de Andrade, M.; Duell, E. J.; Gaziano, J. M.; Giovannucci, E. L.; Goggins, M.; Hallmans, G.; Hankinson, S. E.; Hassan, M.; Howard, B.; Hunter, D. J.; Hutchinson, A.; Jenab, M.; Kaaks, R.; Kooperberg, C.; Krogh, V.; Kurtz, R. C.; Lynch, S. M.; McWilliams, R. R.; Mendelsohn, J. B.; Michaud, D. S.; Parikh, H.; Patel, A. V.; Peeters, P. H. M.; Rajkovic, A.; Riboli, E.; Rodriguez, L.; Seminara, D.; Shu, X. O.; Thomas, G.; Tjonneland, A.; Tobias, G. S.; Trichopoulos, D.; Van Den Eeden, S. K.; Virtamo, J.; Wactawski-Wende, J.; Wang, Z. M.; Wolpin, B. M.; Yu, H.; Yu, K.; Zeleniuch-Jacquotte, A.; Fraumeni, J. F.; Hoover, R. N.; Hartge, P.; Chanock, S. J.
  3. Nature Genetics. 2010, Mar; 42(3): 224-U29.
  1. 12.   Diversity in the Glucose Transporter-4 Gene (SLC2A4) in Humans Reflects the Action of Natural Selection along the Old-World Primates Evolution
  2. Tarazona-Santos, E.; Fabbri, C.; Yeager, M.; Magalhaes, W. C.; Burdett, L.; Crenshaw, A.; Pettener, D.; Chanock, S. J.
  3. Plos One. 2010, Mar; 5(3): 10.
  1. 13.   Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
  2. Ahmad, S.; Keskin, O.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2008 36(18): 5922-5932.
  1. 14.   The major histocompatibility complex class II alleles Mamu-DRB1*1003 and -DRB1*0306 are enriched in a cohort of simian immunodeficiency virus-infecte rhesus macaque elite controllers
  2. Giraldo-Vela, J. P.; Rudersdorf, R.; Chung, C. W.; Qi, Y.; Wallace, L. T.; Bimber, B.; Borchardt, G. J.; Fisk, D. L.; Glidden, C. E.; Loffredo, J. T.; Piaskowski, S. M.; Furlott, J. R.; Morales-Martinez, J. P.; Wilson, N. A.; Rehrauer, W. M.
  3. Journal of Virology. 2008 82(2): 859-870.
  1. 15.   Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
  2. Yogurtcu, O. N.; Erdemli, S. B.; Nussinov, R.; Turkay, M.; Keskin, O.
  3. Biophysical Journal. 2008 94(9): 3475-3485.
  1. 16.   FireDock: Fast interaction refinement in molecular docking
  2. Andrusier, N.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Oct; 69(1): 139-159.
  1. 17.   Genome-wide association study of prostate cancer identifies a second risk locus at 8q24
  2. Yeager, M.; Orr, N.; Hayes, R. B.; Jacobs, K. B.; Kraft, P.; Wacholder, S.; Minichiello, M. J.; Fearnhead, P.; Yu, K.; Chatterjee, N.; Wang, Z. M.; Welch, R.; Staats, B. J.; Calle, E. E.; Feigelson, H. S.; Thun, M. J.; Rodriguez, C.; Albanes, D.; Virtamo, J.; Weinstein, S.; Schumacher, F. R.; Giovannucci, E.; Willett, W. C.; Cancel-Tassin, G.; Cussenot, O.; Valeri, A.; Andriole, G. L.; Gelmann, E. P.; Tucker, M.; Gerhard, D. S.; Fraumeni, J. F.; Hoover, R.; Hunter, D. J.; Chanock, S. J.; Thomas, G.
  3. Nature Genetics. 2007, May; 39(5): 645-649.
  1. 18.   Towards drugs targeting multiple proteins in a systems biology approach
  2. Keskin, O.; Gursoy, A.; Ma, B.; Nussinov, R.
  3. Current Topics in Medicinal Chemistry. 2007 7(10): 943-951.
  1. 19.   Association of putative concave protein-binding sites with the fluctuation behavior of residues
  2. Ertekin, A.; Nussinov, R.; Haliloglu, T.
  3. Protein Science. 2006, Oct; 15(10): 2265-2277.
  1. 20.   Increased oxidation and degradation of cytosolic proteins in alcohol-exposed mouse liver and hepatoma cells
  2. Kim, B. J.; Hood, B. L.; Aragon, R. A.; Hardwick, J. R.; Conrads, T. R.; Veenstra, T. D.; Song, B. J.
  3. Proteomics. 2006, FEB; 6(4): 1250-1260.
  1. 21.   Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
  2. Keskin, O.; Ma, B. Y.; Rogale, K.; Gunasekaran, K.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S24-S35.
  1. 22.   The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
  2. De La Vega, F. M.; Isaac, H.; Collins, A.; Scafe, C. R.; Halldorsson, B. V.; Su, X. P.; Lippert, R. A.; Wang, Y.; Laig-Webster, M.; Koehler, R. T.; Ziegle, J. S.; Wogan, L. T.; Stevens, J. F.; Leinen, K. M.; Olson, S. J.; Guegler, K. J.; You, X. Q.; Xu, L. H.; Hemken, H. G.; Kalush, F.; Itakura, M.; Zheng, Y.; de The, G.; O'Brien, S. J.; Clark, A. G.; Istrail, S.; Hunkapiller, M. W.; Spier, E. G.; Gilbert, D. A.
  3. Genome Research. 2005, APR; 15(4): 454-462.
  1. 23.   Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, MAR 15; 102(11): 3988-3993.
  1. 24.   Large-scale molecular characterization of adeno-associated virus vector integration in mouse liver
  2. Nakai, H.; Wu, X. L.; Fuess, S.; Storm, T. A.; Munroe, D.; Montini, E.; Burgess, S. M.; Grompe, M.; Kay, M. A.
  3. Journal of Virology. 2005, MAR; 79(6): 3606-3614.
  1. 25.   How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
  2. Haliloglu, T.; Keskin, O.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2005, MAR; 88(3): 1552-1559.
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