Marks Lab Selected Publications



Debbie's Google Scholar Page

2016

Mutation effects predicted from sequence co-variation

TA Hopf *, JB Ingraham *, FJ Poelwijk, CP Schärfe, M Springer, C Sander & DS Marks
* Joint first authors
Nature Biotechnology Web 16 Jan 2017
View on Journal Website
EV Mutation Homepage

Structured States of Disordered Proteins from Genomic Sequences

A Toth-Petroczy *, P Palmedo *, JB Ingraham, TA Hopf, B Berger, C Sander & DS Marks
* Joint first authors
Cell, Volume 167, 158-170
View on Journal Website | PubMed

Genomic Epidemiology of Gonococcal Resistance to Extended Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the US, 2000-2013

YH Grad, SR Harris, RD Kikcaldy, AG Green, DS Marks, SD Bentley, D Trees & M Lipsitch
J Infect Dis. (2016)
View on Journal Website | PubMed

Antiparallel Protocadherin Homodimers Use Distinct Affinity and Specificity-Mediating Regions in Cadherin Repeats 1-4

JM Nicoludis, BE Vogt, AG Green, CP Shärfe, DS Marks & R Gaudet
eLife 2016;5:e18449
View on Journal Website | PubMed

3D RNA and Functional Interactions from Evolutionary Couplings

C Weinrab, AJ Riesselman, JB Ingraham, T Gross, C Sander & DS Marks
Cell, Volume 165, 1-13
View on Journal Website | PubMed

Bayesian Sparsity for Intractable Distibutions

JB Ingraham & DS Marks
View on arXiv Website

2015

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

JM Nicoludis, S-Y Lau, CP Schärfe, DS Marks, WA Weihofen & R Gaudet
Cell Press Vol. 23 no. 11 pp. 2087-2098
View on Journal Website | PubMed

Quantification of the Effect of Mutations Using a Global Probability Model of Natural Sequence Variation

TA Hopf *, JB Ingraham *, FJ Peolwijk, M Springer, C Sander & DS Marks
* Joint first authors
View on arXiv Website

Protein Structure Determination by Combining Sparse NMR Data with Evolutionary Couplings

Y Tang, Y Janet Huang, TA Hopf, C Sander *, DS Marks * & GT Montelione *
* Corresponding authors
Nature Methods 12, 751-754
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Inferring Pariwise Interactions from Biological Data Using Maximum-Entropy Probability Models

RR Stein, DS Marks & C Sander
PLoS Comput Biol 11(7): e1004182
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All-atom 3D Structure Prediction of Transmembrane β-barrel proteins from sequences

S Hayat, C Sander, DS Marks & A Elofsson
PNAS Vol. 112 no. 17 pp. 5413-5418
View on Journal Website | PubMed

MicroRNA Control of Protein Expression Noise

JM Schmiedel, SL Klemm, Y Zheng, A Sahay, N Blüthgen, DS Marks & A van Oudenaarden
Science Vol. 348 no. 6230 pp.128-132
View on Journal Website | PubMed

Evolutionary Couplings and Protein 3D Structure Prediction

R Sheridan, RJ Fieldhouse, S Hayat, Y Sun, Y Antipin, L Yang, TA Hopf & DS Marks
View on bioRxiv Website

2014

Amino Acid Coevolution Reveals Three-Dimensional Structure and Functional Domains of Insect Odorant Receptors

TA Hopf, S Morinaga, S Ihara, K Touhara, DS Marks & R Benton
Nature Communications 6, Article number: 6077
View on Journal Website | PubMed

Sequence Co-Evolution Gives 3D Contacts and Structures of Protein Complexes

TA Hopf *, C Schärfe *, J Rodrigues, AG Green, O Kohlbacher, C Sander, A Bonvin & DS Marks
* Joint first authors
eLife 2014;3:e03430
View on Journal Website | PubMed

2012

Protein Structure Prediction from Sequence Variation

DS Marks, TA Hopf & C Sander
Nature Biotechnology 30, 1072-1080 (2012)
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Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

TA Hopf, JL Colwell, R Sheridan, B Rost, C Sander & DS Marks
Cell, Vol. 149, Issue 7, pp. 1607-1621
View on Journal Website | PubMed

2011 and earlier

Protein 3D Structure Computed from Evolutionary Sequence Variation

DS Marks*, LJ Colwell*, R Sheridan, TA Hopf, A Pagnani, R Zecchina & C Sander
*Joint first authors
PLoS One 2011 June 12 :e28766. Epub 2011 Dec 7.
View on Journal Website | PubMed

Target mRNA Abundance Dilutes microRNA and siRNA Activity

A Arvey, E Larsson, C Sander, CS Leslie & DS Marks
Molecular Systems Biology 6 (2010): 363. PMC. Web. 13 Oct. 2016
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Transfection of Small RNAs Globally Perturbs Gene Regulation by Endogenous microRNAs

AA Khan, D Betel, ML Miller, C Sander, CS Leslie & DS Marks
Nature Biotechnology, 2009:27(6):549-55.
View on Journal Website | PubMed

Human microRNA Targets

B John, AJ Enright, A Aravin, T Tuschl, C Sander & DS Marks
PLoS Biology :e363. Epub2004
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