Illuminating The Druggable Genome Resource Dissemination And Outreach Center

Larry A. Sklar, Ph.D.
Distinguished University Professor
Department of Pathology University of New Mexico

Previous Co-PI (Dec. 2017 - Jan. 2022)

Tudor Oprea, M.D., Ph.D.
Professor
Chief, Translational Informatics Division
Department of Internal Medicine at Health Science Center

Overview

The RDOC collaboration extends to UNM. Dr. Larry Sklar heads the Management and Administration Core (MAC), which support and coordinates across the entire IDG Consortium. Additional work will be focused on formulating policy and guidelines that will govern the collaboration and sharing of resources, data and information amongst IDG members and general scientific community. Dr. Tudor Oprea leads IDG outreach to other consortia or groups and develops training programs for PHAROS and informatics tools.

NIH grant number: 1U24TR002278-01

RDOC at UNM publications:

  1. Vidović D, Waller A, Holmes J, Sklar LA, Schürer SC. Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. Drug Discov. Today 2024 Mar 18. doi: 10.1016/j.drudis.2024.103953. PMID: 38508231
  2. Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxton C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI. How many rare diseases are there? Nat Rev Drug Discov. 2020 Feb;19(2):77-78. doi: 10.1038/d41573-019-00180-y. PMID: 32020066; PMCID: PMC7771654.
  3. Muratov EN, Bajorath J, Sheridan RP, Tetko IV, Filimonov D, Poroikov V, Oprea TI, Baskin II, Varnek A, Roitberg A, Isayev O, Curtarolo S, Fourches D, Cohen Y, Aspuru-Guzik A, Winkler DA, Agrafiotis D, Cherkasov A, Tropsha A. QSAR without borders. Chem Soc Rev. 2020 Jun 7;49(11):3525-3564. doi: 10.1039/d0cs00098a. Epub 2020 May 1. Erratum in: Chem Soc Rev. 2020 May 22;:. Curtalolo, Stefano [corrected to Curtarolo, Stefano]. PMID: 32356548; PMCID: PMC8008490.
  4. Ursu O, Holmes J, Bologa CG, Yang JJ, Mathias SL, Stathias V, Nguyen DT, Schürer S, Oprea T. DrugCentral 2018: an update. Nucleic Acids Res. 2019 Jan 8;47(D1):D963-D970. doi: 10.1093/nar/gky963. PMID: 30371892; PMCID: PMC6323925.
  5. Oprea TI. Exploring the dark genome: implications for precision medicine. Mamm Genome. 2019 Aug;30(7-8):192-200. doi: 10.1007/s00335-019-09809-0. Epub 2019 Jul 4. PMID: 31270560; PMCID: PMC6836689.
  6. Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G. Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov. 2018 May;17(5):317-332. doi: 10.1038/nrd.2018.14. Epub 2018 Mar 23. Erratum in: Nat Rev Drug Discov. 2018 Mar 23;: PMID: 29472638; PMCID: PMC6339563.
  7. Bocci G, Benet LZ, Oprea TI. Can BDDCS illuminate targets in drug design? Drug Discov Today. 2019 Dec;24(12):2299-2306. doi: 10.1016/j.drudis.2019.09.021. Epub 2019 Oct 1. PMID: 31585170; PMCID: PMC7002033.
  8. Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen DT, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, Mathé EA, Oprea TI. Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Res. 2023 Jan 6;51(D1):D1405-D1416. doi: 10.1093/nar/gkac1033. Erratum in: Nucleic Acids Res. 2023 Feb 28;51(4):1999. PMID: 36624666; PMCID: PMC9825581.
  9. Muratov EN , Amaro R , Andrade CH , Brown N , Ekins S , Fourches D , Isayev O , Kozakov D , Medina-Franco JL , Merz KM , Oprea TI , Poroikov V , Schneider G , Todd MH , Varnek A , Winkler DA , Zakharov AV , Cherkasov A , Tropsha A . A critical overview of computational approaches employed for COVID-19 drug discovery. Chem Soc Rev. 2021 Aug 21;50(16):9121-9151. doi: 10.1039/d0cs01065k. Epub 2021 Jul 2. PMID: 34212944; PMCID: PMC8371861.
  10. Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI. How to Illuminate the Druggable Genome Using Pharos. Curr Protoc Bioinformatics. 2020 Mar;69(1):e92. doi: 10.1002/cpbi.92. PMID: 31898878; PMCID: PMC7818358.
  11. Zhavoronkov A, Vanhaelen Q, Oprea TI. Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology? Clin Pharmacol Ther. 2020 Apr;107(4):780-785. doi: 10.1002/cpt.1795. Epub 2020 Mar 3. PMID: 31957003; PMCID: PMC7158211.
  12. Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI. TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res. 2021 Jan 8;49(D1):D1334-D1346. doi: 10.1093/nar/gkaa993. PMID: 33156327; PMCID: PMC7778974.
  13. Bofill A, Jalencas X, Oprea TI, Mestres J. The human endogenous metabolome as a pharmacology baseline for drug discovery. Drug Discov Today. 2019 Sep;24(9):1806-1820. doi: 10.1016/j.drudis.2019.06.007. Epub 2019 Jun 19. PMID: 31226432; PMCID: PMC7748399.
  14. Elhadad MA, Jonasson C, Huth C, Wilson R, Gieger C, Matias P, Grallert H, Graumann J, Gailus-Durner V, Rathmann W, von Toerne C, Hauck SM, Koenig W, Sinner MF, Oprea TI, Suhre K, Thorand B, Hveem K, Peters A, Waldenberger M. Deciphering the Plasma Proteome of Type 2 Diabetes. Diabetes. 2020 Dec;69(12):2766-2778. doi: 10.2337/db20-0296. Epub 2020 Sep 14. PMID: 32928870; PMCID: PMC7679779.
  15. Binder J, Ursu O, Bologa C, Jiang S, Maphis N, Dadras S, Chisholm D, Weick J, Myers O, Kumar P, Yang JJ, Bhaskar K, Oprea TI. Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. Commun Biol. 2022 Feb 11;5(1):125. doi: 10.1038/s42003-022-03068-7. PMID: 35149761; PMCID: PMC8837797.
  16. Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM; IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium; Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T. Crowdsourced mapping of unexplored target space of kinase inhibitors. Nat Commun. 2021 Jun 3;12(1):3307. doi: 10.1038/s41467-021-23165-1. PMID: 34083538; PMCID: PMC8175708.
  17. Kropiwnicki E, Binder JL, Yang JJ, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher KJ, Metzger VT, Bologa CG, Oprea TI, Ma'ayan A. Getting Started with the IDG KMC Datasets and Tools. Curr Protoc. 2022 Jan;2(1):e355. doi: 10.1002/cpz1.355. PMID: 35085427; PMCID: PMC10789444.
  18. Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G. Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov. 2018 May;17(5):377. doi: 10.1038/nrd.2018.52. Epub 2018 Mar 23. Erratum for: Nat Rev Drug Discov. 2018 May;17 (5):317-332. PMID: 29567993.

Contacts

Page reviewed on March 21, 2024