Computational Chemistry Shared Resource – Publications

Contact Information

Sivanesan Dakshanamurthy, PhD, MBA
Director of CCSR
Telephone: (202) 687-2347
Office: New Research Building E401

Selected Publications

  1. Wathieu H, Issa NT, Fernandez AI, Mohandoss M, Tiek DM, Franke JL, Byers SW, Riggins RB, Dakshanamurthy S. Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. Oncotarget. 2017 Oct 9;8(54):92926-92942. doi: 10.18632/oncotarget.21669. eCollection 2017 Nov 3. PubMed PMID: 29190967; PubMed Central PMCID: PMC5696233.

  2. Simbulan-Rosenthal CM, Dakshanamurthy S, Gaur A, Chen YS, Fang HB, Abdussamad M, Zhou H, Zapas J, Calvert V, Petricoin EF, Atkins MB, Byers SW, Rosenthal DS. The repurposed anthelmintic mebendazole in combination with trametinib suppresses refractory NRASQ61K melanoma. Oncotarget. 2017 Feb 21;8(8):12576-12595. doi: 10.18632/oncotarget.14990. PubMed PMID: 28157711; PubMed Central PMCID: PMC5355037.

  3. Wathieu H, Issa NT, Mohandoss M, Byers SW, Dakshanamurthy S. MSD-MAP: A Network-Based Systems Biology Platform for Predicting Disease-Metabolite Links. Comb Chem High Throughput Screen. 2017;20(3):193-207. doi: 10.2174/1386207319666161214111254. PubMed PMID: 28024464.

  4. Issa NT, Kruger J, Wathieu H, Raja R, Byers SW, Dakshanamurthy S. DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. BMC Bioinformatics. 2016 May 5;17(1):202. doi:10.1186/s12859-016-1065-y. PubMed PMID: 27151405; PubMed Central PMCID:

  5. Wathieu H, Issa NT, Byers SW, Dakshanamurthy S. Harnessing Polypharmacology with Computer-Aided Drug Design and Systems Biology. Curr Pharm Des. 2016;22(21):3097-108. Review. PubMed PMID: 2690794

  6. Issa NT, Peters OJ, Byers SW, Dakshanamurthy S. RepurposeVS: A Drug Repurposing-Focused Computational Method for Accurate Drug-Target Signature Predictions. Comb Chem High Throughput Screen. 2015;18(8):784-94. PubMed PMID: 26234515; PubMed Central PMCID: PMC5848469.

  7. Petrini I, Meltzer PS, Kim IK, Lucchi M, Park KS, Fontanini G, Gao J, Zucali PA, Calabrese F, Favaretto A, Rea F, Rodriguez-Canales J, Walker RL, Pineda M, Zhu YJ, Lau C, Killian KJ, Bilke S, Voeller D, Dakshanamurthy S, Wang Y, Giaccone G. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors. Nat Genet. 2014 Aug;46(8):844-9. doi: 10.1038/ng.3016. Epub 2014 Jun 29. PubMed PMID: 24974848; PubMed Central PMCID: PMC5705185.

  8. Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, Baudry J. Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer. Concurr Comput. 2014 Apr 25;26(6):1268-1277. PubMed PMID: 24729746; PubMed Central PMCID: PMC3979631.

  9. Assefnia S, Dakshanamurthy S, Guidry Auvil JM, Hampel C, Anastasiadis PZ, Kallakury B, Uren A, Foley DW, Brown ML, Shapiro L, Brenner M, Haigh D, Byers SW. Cadherin-11 in poor prognosis malignancies and rheumatoid arthritis: common target, common therapies. Oncotarget. 2014 Mar 30;5(6):1458-74. PubMed PMID: 24681547; PubMed Central PMCID: PMC4039224.

  10. Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, Byers SW. Predicting new indications for approved drugs using a proteochemometric method. J Med Chem. 2012 Aug 9;55(15):6832-48. doi: 10.1021/jm300576q. Epub 2012 Jul 25. PubMed PMID: 22780961; PubMed Central PMCID: PMC3419493.

  11. Erkizan HV, Kong Y, Merchant M, Schlottmann S, Barber-Rotenberg JS, Yuan L, Abaan OD, Chou TH, Dakshanamurthy S, Brown ML, Uren A, Toretsky JA. A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing’s sarcoma. Nat Med. 2009 Jul;15(7):750-6. doi: 10.1038/nm.1983. Epub 2009 Jul 5. PubMed PMID: 19584866; PubMed Central PMCID: PMC2777681.

  12. Mi L, Xiao Z, Hood BL, Dakshanamurthy S, Wang X, Govind S, Conrads TP, Veenstra TD, Chung FL. Covalent binding to tubulin by isothiocyanates. A mechanism of cell growth arrest and apoptosis. J Biol Chem. 2008 Aug 8;283(32):22136-46. doi: 10.1074/jbc.M802330200. Epub 2008 Jun 3. PubMed PMID: 18524779; PubMed Central PMCID: PMC2494917.

  13. Veselik DJ, Divekar S, Dakshanamurthy S, Storchan GB, Turner JM, Graham KL, Huang L, Stoica A, Martin MB. Activation of estrogen receptor-alpha by the anion nitrite. Cancer Res. 2008 May 15;68(10):3950-8. doi: 10.1158/0008-5472.CAN-07-2783. PubMed PMID: 18483281; PubMed Central PMCID: PMC3676890.

  14. Dakshanamurthy S, Kim M, Brown ML, Byers SW. In-silico fragment-based identification of novel angiogenesis inhibitors. Bioorg Med Chem Lett. 2007 Aug 15;17(16):4551-6. Epub 2007 Jun 15. PubMed PMID: 17591441.

  15. VandenBussche CJ, Dakshanamurthy S, Posch PE, Hurley CK. A single polymorphism disrupts the killer Ig-like receptor 2DL2/2DL3 D1 domain. J Immunol. 2006 Oct 15;177(8):5347-57. PubMed PMID: 17015720.