Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Login and Edit functionality is currently unavailable.

Debora Marks, Ph.D.

Title
Institution
Department
Address
Profile Picture

Biography

Bibliographic
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.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. Elife. 2020 09 01; 9. PMID: 32870157.
    Citations:    Fields:    
  2. Sjodt M, Rohs PDA, Gilman MSA, Erlandson SC, Zheng S, Green AG, Brock KP, Taguchi A, Kahne D, Walker S, Marks DS, Rudner DZ, Bernhardt TG, Kruse AC. Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex. Nat Microbiol. 2020 06; 5(6):813-820. PMID: 32152588.
    Citations: 1     Fields:    
  3. Stiffler MA, Poelwijk FJ, Brock KP, Stein RR, Riesselman A, Teyra J, Sidhu SS, Marks DS, Gauthier NP, Sander C. Protein Structure from Experimental Evolution. Cell Syst. 2020 01 22; 10(1):15-24.e5. PMID: 31838147.
    Citations: 2     Fields:    
  4. Nicoludis JM, Green AG, Walujkar S, May EJ, Sotomayor M, Marks DS, Gaudet R. Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. Proc Natl Acad Sci U S A. 2019 09 03; 116(36):17825-17830. PMID: 31431536.
    Citations: 2     Fields:    Translation:HumansCells
  5. Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Inferring protein 3D structure from deep mutation scans. Nat Genet. 2019 07; 51(7):1170-1176. PMID: 31209393.
    Citations: 9     Fields:    Translation:HumansCells
  6. Hopf TA, Green AG, Schubert B, Mersmann S, Schärfe CPI, Ingraham JB, Toth-Petroczy A, Brock K, Riesselman AJ, Palmedo P, Kang C, Sheridan R, Draizen EJ, Dallago C, Sander C, Marks DS. The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics. 2019 05 01; 35(9):1582-1584. PMID: 30304492.
    Citations: 7     Fields:    
  7. Huang YJ, Brock KP, Ishida Y, Swapna GVT, Inouye M, Marks DS, Sander C, Montelione GT. Combining Evolutionary Covariance and NMR Data for Protein Structure Determination. Methods Enzymol. 2019; 614:363-392. PMID: 30611430.
    Citations: 1     Fields:    Translation:HumansCells
  8. Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS. Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nat Microbiol. 2019 02; 4(2):328-338. PMID: 30510172.
    Citations: 4     Fields:    Translation:HumansCells
  9. Ramírez-Guadiana FH, Rodrigues CDA, Marquis KA, Campo N, Barajas-Ornelas RDC, Brock K, Marks DS, Kruse AC, Rudner DZ. Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis. PLoS Genet. 2018 11; 14(11):e1007753. PMID: 30403663.
    Citations:    Fields:    Translation:Cells
  10. Sui X, Arlt H, Brock KP, Lai ZW, DiMaio F, Marks DS, Liao M, Farese RV, Walther TC. Cryo-electron microscopy structure of the lipid droplet-formation protein seipin. J Cell Biol. 2018 12 03; 217(12):4080-4091. PMID: 30327422.
    Citations: 14     Fields:    Translation:AnimalsCells
  11. Riesselman AJ, Ingraham JB, Marks DS. Deep generative models of genetic variation capture the effects of mutations. Nat Methods. 2018 10; 15(10):816-822. PMID: 30250057.
    Citations: 9     Fields:    Translation:Humans
  12. Maddamsetti R, Johnson DT, Spielman SJ, Petrie KL, Marks DS, Meyer JR. Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature. Evolution. 2018 10; 72(10):2234-2243. PMID: 30152871.
    Citations:    Fields:    Translation:Cells
  13. Kotler E, Shani O, Goldfeld G, Lotan-Pompan M, Tarcic O, Gershoni A, Hopf TA, Marks DS, Oren M, Segal E. A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. Mol Cell. 2018 09 06; 71(5):873. PMID: 30193102.
    Citations: 5     Fields:    
  14. Kotler E, Shani O, Goldfeld G, Lotan-Pompan M, Tarcic O, Gershoni A, Hopf TA, Marks DS, Oren M, Segal E. A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. Mol Cell. 2018 07 05; 71(1):178-190.e8. PMID: 29979965.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  15. Zheng S, Sham LT, Rubino FA, Brock KP, Robins WP, Mekalanos JJ, Marks DS, Bernhardt TG, Kruse AC. Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli. Proc Natl Acad Sci U S A. 2018 06 26; 115(26):6709-6714. PMID: 29891673.
    Citations: 9     Fields:    Translation:Cells
  16. Sjodt M, Brock K, Dobihal G, Rohs PDA, Green AG, Hopf TA, Meeske AJ, Srisuknimit V, Kahne D, Walker S, Marks DS, Bernhardt TG, Rudner DZ, Kruse AC. Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis. Nature. 2018 04 05; 556(7699):118-121. PMID: 29590088.
    Citations: 11     Fields:    Translation:Cells
  17. Huang YJ, Brock KP, Sander C, Marks DS, Montelione GT. A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data. Adv Exp Med Biol. 2018; 1105:153-169. PMID: 30617828.
    Citations: 1     Fields:    Translation:Cells
  18. Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS. Genetic variation in human drug-related genes. Genome Med. 2017 12 22; 9(1):117. PMID: 29273096.
    Citations: 10     Fields:    Translation:Humans
  19. 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 01; 9(4):1072-1083. PMID: 28379360.
    Citations: 6     Fields:    
  20. Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol. 2017 02; 35(2):128-135. PMID: 28092658.
    Citations: 62     Fields:    Translation:HumansCells
  21. 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.
    Citations: 30     Fields:    Translation:HumansCells
  22. 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 11 15; 214(10):1579-1587. PMID: 27638945.
    Citations: 57     Fields:    Translation:HumansCells
  23. 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 07 29; 5. PMID: 27472898.
    Citations: 13     Fields:    Translation:HumansCells
  24. 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.
    Citations: 28     Fields:    Translation:Cells
  25. 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.
    Citations: 25     Fields:    Translation:AnimalsCells
  26. 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.
    Citations: 16     Fields:    Translation:Cells
  27. Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD. Pathway and network analysis of cancer genomes. Nat Methods. 2015 Jul; 12(7):615-621. PMID: 26125594.
    Citations: 77     Fields:    Translation:HumansCells
  28. 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.
    Citations: 25     Fields:    Translation:HumansCells
  29. 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.
    Citations: 15     Fields:    Translation:Cells
  30. 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.
    Citations: 96     Fields:    Translation:AnimalsCells
  31. 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.
    Citations: 30     Fields:    Translation:Animals
  32. 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.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  33. 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.
    Citations: 9     Fields:    Translation:AnimalsCells
  34. 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.
    Citations: 122     Fields:    Translation:Cells
  35. 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.
    Citations: 34     Fields:    Translation:Cells
  36. 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.
    Citations: 49     Fields:    Translation:Cells
  37. Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Biotechnol. 2012 Nov; 30(11):1072-80. PMID: 23138306.
    Citations: 167     Fields:    Translation:Cells
  38. 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.
    Citations: 180     Fields:    Translation:Cells
  39. 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.
    Citations: 166     Fields:    Translation:HumansAnimalsCells
  40. 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.
    Citations: 289     Fields:    Translation:HumansAnimalsCells
  41. 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.
    Citations: 301     Fields:    Translation:Cells
  42. 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.
    Citations: 39     
  43. 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.
    Citations: 61     Fields:    Translation:HumansCells
  44. 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.
    Citations: 159     Fields:    Translation:HumansCells
  45. 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.
    Citations: 212     Fields:    Translation:HumansCells
  46. 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.
    Citations: 1019     Fields:    Translation:HumansAnimalsCells
  47. 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.
    Citations: 37     Fields:    Translation:AnimalsCells
  48. John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods Mol Biol. 2006; 342:101-13. PMID: 16957370.
    Citations: 47     Fields:    Translation:HumansCells
  49. 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.
    Citations: 163     Fields:    Translation:Animals
  50. 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.
    Citations: 116     Fields:    Translation:AnimalsCells
  51. 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.
    Citations: 115     Fields:    Translation:AnimalsCells
  52. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004 Nov; 2(11):e363. PMID: 15502875.
    Citations: 1341     Fields:    Translation:HumansAnimalsCells
  53. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003; 5(1):R1. PMID: 14709173.
    Citations: 1009     Fields:    Translation:AnimalsCells
  54. Murray AW, Marks D. Can sequencing shed light on cell cycling? Nature. 2001 Feb 15; 409(6822):844-6. PMID: 11237006.
    Citations: 28     Fields:    Translation:HumansAnimalsCells
  55. 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.
    Citations:    Fields:    Translation:Cells
  56. 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.
    Citations:    Fields:    Translation:HumansCells
  57. 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.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  58. 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.
    Citations:    Fields:    Translation:Cells
  59. 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.
    Citations: 1     Fields:    Translation:Cells
  60. 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.
    Citations: 38     Fields:    Translation:HumansAnimalsCells
  61. 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.
    Citations: 4     Fields:    Translation:HumansCells
Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile: HMS/HSDM faculty should contact feedbackcatalyst.harvard.edu. For faculty or fellow appointment updates and changes, please ask your appointing department to contact HMS. For fellow personal and demographic information, contact HMS Human Resources at human_resourceshms.harvard.edu. For faculty personal and demographic information, contact HMS Office for Faculty Affairs at facappthms.harvard.edu.
Marks's Networks
Click the
Explore
buttons for more information and interactive visualizations!
Concepts (256)
Explore
_
Co-Authors (29)
Explore
_
Similar People (60)
Explore
_
Same Department 
Explore
_
Physical Neighbors
_
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.