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profileDebora Marks, Ph.D.

TitleAssistant Professor of Systems Biology
InstitutionHarvard Medical School
DepartmentSystems Biology
AddressHarvard Medical School
Alpert 536, Systems Biology
200 Longwood Ave
Boston MA 02115
Phone000/000-0000
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2010PhD

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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. Maddamsetti R, Hatcher PJ, Green AG, Williams BL, Marks DS, Lenski RE. Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli. Genome Biol Evol. 2017 Apr 04. PMID: 28379360.
    View in: PubMed
  2. Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol. 2017 Feb; 35(2):128-135. PMID: 28092658.
    View in: PubMed
  3. Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell. 2016 Sep 22; 167(1):158-170.e12. PMID: 27662088.
    View in: PubMed
  4. Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M. Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013. J Infect Dis. 2016 Nov 15; 214(10):1579-1587. PMID: 27638945.
    View in: PubMed
  5. Nicoludis JM, Vogt BE, Green AG, Schärfe CP, Marks DS, Gaudet R. Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4. Elife. 2016 Jul 29; 5. PMID: 27472898; PMCID: PMC5001838.
  6. Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell. 2016 May 05; 165(4):963-75. PMID: 27087444; PMCID: PMC5024353 [Available on 05/05/17].
  7. Nicoludis JM, Lau SY, Schärfe CP, Marks DS, Weihofen WA, Gaudet R. Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. Structure. 2015 Nov 03; 23(11):2087-98. PMID: 26481813; PMCID: PMC4635037 [Available on 11/03/16].
  8. Stein RR, Marks DS, Sander C. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput Biol. 2015 Jul; 11(7):e1004182. PMID: 26225866; PMCID: PMC4520494.
  9. Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nat Methods. 2015 Aug; 12(8):751-4. PMID: 26121406; PMCID: PMC4521990.
  10. Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane ß-barrel proteins from sequences. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):5413-8. PMID: 25858953; PMCID: PMC4418893.
  11. Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N, Marks DS, van Oudenaarden A. Gene expression. MicroRNA control of protein expression noise. Science. 2015 Apr 03; 348(6230):128-32. PMID: 25838385.
    View in: PubMed
  12. Hopf TA, Morinaga S, Ihara S, Touhara K, Marks DS, Benton R. Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nat Commun. 2015 Jan 13; 6:6077. PMID: 25584517; PMCID: PMC4364406.
  13. Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N. Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. PLoS Comput Biol. 2014 Dec; 10(12):e1003976. PMID: 25474149; PMCID: PMC4256070.
  14. Romero-Aristizabal C, Marks DS, Fontana W, Apfeld J. Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans. Nat Commun. 2014 Sep 29; 5:5020. PMID: 25262602; PMCID: PMC4181376.
  15. Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife. 2014 Sep 25; 3. PMID: 25255213; PMCID: PMC4360534.
  16. Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics. 2014 Sep 01; 30(17):i482-8. PMID: 25161237; PMCID: PMC4147911.
  17. Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics. 2014 Mar 26; 15:85. PMID: 24669753; PMCID: PMC3987048.
  18. Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Biotechnol. 2012 Nov; 30(11):1072-80. PMID: 23138306; PMCID: PMC4319528.
  19. Jeggari A, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012 Aug 01; 28(15):2062-3. PMID: 22718787; PMCID: PMC3400968.
  20. 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. PMID: 22579045; PMCID: PMC3641781.
  21. 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. PMID: 22163331; PMCID: PMC3233603.
  22. 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 06; 108(49):E1293-301. PMID: 22106262; PMCID: PMC3241805.
  23. 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 Mar 14; 2:3. PMID: 21401928; PMCID: PMC3068080.
  24. 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. PMID: 20508147; PMCID: PMC2909566.
  25. 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. PMID: 20404830; PMCID: PMC2872614.
  26. 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. PMID: 19465925; PMCID: PMC2782465.
  27. 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. PMID: 18158296; PMCID: PMC2238905.
  28. Betel D, Sheridan R, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol. 2007 Nov; 3(11):e222. PMID: 17997596; PMCID: PMC2065894.
  29. John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods Mol Biol. 2006; 342:101-13. PMID: 16957370.
    View in: PubMed
  30. 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. PMID: 16086853; PMCID: PMC1273638.
  31. 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 01; 121(7):1097-108. PMID: 15989958.
    View in: PubMed
  32. 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 01; 19(11):1288-93. PMID: 15937218; PMCID: PMC1142552.
  33. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004 Nov; 2(11):e363. PMID: 15502875; PMCID: PMC521178.
  34. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003; 5(1):R1. PMID: 14709173; PMCID: PMC395733.
  35. Murray AW, Marks D. Can sequencing shed light on cell cycling? Nature. 2001 Feb 15; 409(6822):844-6. PMID: 11237006.
    View in: PubMed
  36. 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. PMID: 10563570.
    View in: PubMed
  37. 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. PMID: 10766296.
    View in: PubMed
  38. 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 05; 274(6):3632-41. PMID: 9920912.
    View in: PubMed
  39. 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. PMID: 9450040.
    View in: PubMed
  40. 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. PMID: 9399157.
    View in: PubMed
  41. 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. PMID: 8675628; PMCID: PMC185968.
  42. 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. PMID: 7695814.
    View in: PubMed
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