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Debora Marks, Ph.D.

TitleInstructor in Systems Biology
InstitutionHarvard Medical School
DepartmentSystems Biology
AddressHarvard Medical School
Alpert 536, Systems Biology
200 Longwood Ave
Boston MA 02115
Phone000/000-0000

 Biography 
 awards and honors
2010 - PhD

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Biotechnol. 2012 Nov; 30(11):1072-80.
    View in: PubMed
  2. Jeggari A, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012 Aug 1; 28(15):2062-3.
    View in: PubMed
  3. Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012 Jun 22; 149(7):1607-21.
    View in: PubMed
  4. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. PLoS One. 2011; 6(12):e28766.
    View in: PubMed
  5. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011 Dec 6; 108(49):E1293-301.
    View in: PubMed
  6. Schultz N, Marenstein DR, De Angelis DA, Wang WQ, Nelander S, Jacobsen A, Marks DS, Massagué J, Sander C. Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-ß pathway and reveal microRNA regulation of TGFBR2. Silence. 2011; 2:3.
    View in: PubMed
  7. Jacobsen A, Wen J, Marks DS, Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res. 2010 Aug; 20(8):1010-9.
    View in: PubMed
  8. Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol. 2010 Apr 20; 6:363.
    View in: PubMed
  9. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 2009 Jun; 27(6):549-55.
    View in: PubMed
  10. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 2008 Jan; 36(Database issue):D149-53.
    View in: PubMed
  11. Betel D, Sheridan R, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol. 2007 Nov; 3(11):e222.
    View in: PubMed
  12. John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods Mol Biol. 2006; 342:101-13.
    View in: PubMed
  13. Monticelli S, Ansel KM, Xiao C, Socci ND, Krichevsky AM, Thai TH, Rajewsky N, Marks DS, Sander C, Rajewsky K, Rao A, Kosik KS. MicroRNA profiling of the murine hematopoietic system. Genome Biol. 2005; 6(8):R71.
    View in: PubMed
  14. Leaman D, Chen PY, Fak J, Yalcin A, Pearce M, Unnerstall U, Marks DS, Sander C, Tuschl T, Gaul U. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell. 2005 Jul 1; 121(7):1097-108.
    View in: PubMed
  15. Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev. 2005 Jun 1; 19(11):1288-93.
    View in: PubMed
  16. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004 Nov; 2(11):e363.
    View in: PubMed
  17. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003; 5(1):R1.
    View in: PubMed
  18. Murray AW, Marks D. Can sequencing shed light on cell cycling? Nature. 2001 Feb 15; 409(6822):844-6.
    View in: PubMed
  19. Bichenkova EV, Marks D, Dobrikov MI, Vlassov VV, Morris GA, Douglas KT. Refined high-field NMR solution structure of a binary-addressed pyrene/perfluoro-azide complementary DNA oligonucleotide system shows extensive distortion in the central nick region. J Biomol Struct Dyn. 1999 Oct; 17(2):193-211.
    View in: PubMed
  20. Cole C, Marks DS, Jaffar M, Stratford IJ, Douglas KT, Freeman S. A similarity model for the human angiogenic factor, thymidine phosphorylase/platelet derived-endothelial cell growth factor. Anticancer Drug Des. 1999 Oct; 14(5):411-20.
    View in: PubMed
  21. Marks DS, Gregory CA, Wallis GA, Brass A, Kadler KE, Boot-Handford RP. Metaphyseal chondrodysplasia type Schmid mutations are predicted to occur in two distinct three-dimensional clusters within type X collagen NC1 domains that retain the ability to trimerize. J Biol Chem. 1999 Feb 5; 274(6):3632-41.
    View in: PubMed
  22. Brockwell DJ, Marks DS, Barber J. Structural investigations of kirromycin bound to bacterial elongation factor Tu by NMR and molecular dynamics. Biochem Soc Trans. 1997 Nov; 25(4):S612.
    View in: PubMed
  23. Bichenkova EV, Marks DS, Lokhov SG, Dobrikov MI, Vlassov VV, Douglas KT. Structural studies by high-field NMR spectroscopy of a binary-addressed complementary oligonucleotide system juxtaposing pyrene and perfluoro-azide units. J Biomol Struct Dyn. 1997 Oct; 15(2):307-20.
    View in: PubMed
  24. Marks DS, Vita JA, Folts JD, Keaney JF, Welch GN, Loscalzo J. Inhibition of neointimal proliferation in rabbits after vascular injury by a single treatment with a protein adduct of nitric oxide. J Clin Invest. 1995 Dec; 96(6):2630-8.
    View in: PubMed
  25. Wibley JE, McKie JH, Embrey K, Marks DS, Douglas KT, Moore MH, Moody PC. A homology model of the three-dimensional structure of human O6-alkylguanine-DNA alkyltransferase based on the crystal structure of the C-terminal domain of the Ada protein from Escherichia coli. Anticancer Drug Des. 1995 Jan; 10(1):75-95.
    View in: PubMed
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