Marks Lab Selected Publications



Debbie's Google Scholar Page

2018

Deep generative models of genetic variation capture the effects of mutations.

AJ Riesselman, JB Ingraham, DS Marks

Nature Methods 2018 Published 24 Sep 2018
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Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli

Sanduo Zheng, Lok-To Sham, Frederick A Rubino, Kelly P Brock, William P Robins, John J Mekalanos, Debora S Marks, Thomas G Bernhardt, Andrew C Kruse

PNAS 2018 Published 11 June 2018
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3D protein structure from genetic epistasis experiments

Nathan J Rollins, Kelly P Brock, Frank J Poelwijk, Michael A Stiffler, Nicholas P Gauthier, Chris Sander, Debora S Marks

bioRxiv 2018 Published 11 May 2018
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Population-specific design of de-immunized protein biotherapeutics

Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas Hopf, Debora Marks, Oliver Kohlbacher

PLOS Comp Bio 2018 Published 2 March 2018
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Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis

Megan Sjodt, Kelly Brock, Genevieve Dobihal, Patricia DA Rohs, Anna G Green, Thomas A Hopf, Alexander J Meeske, Veerasak Srisuknimit, Daniel Kahne, Suzanne Walker, Debora S Marks, Thomas G Bernhardt, David Z Rudner, Andrew C Kruse

Nature 2018 Published 5 April 2018
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Genome-wide discovery of epistatic loci affecting antibiotic resistance using evolutionary couplings

Benjamin Schubert, Rohan Maddamsetti, Jackson Nyman, Maha R Farhat, Debora S Marks

bioRxiv 2018 Published 1 January 2018
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2017

Deep generative models of genetic variation capture mutation effects

Adam J Riesselman *, John B Ingraham *, Debora Susan Marks
* Joint first authors
arXiv preprint 2017 Available on arXiv 18 December 2017
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Population-specific design of de-immunized protein biotherapeutics

B Schubert, C Schärfe, P Dönnes, T Hopf, D Marks, O Kohlbacher
arXiv preprint 2017 Available on arXiv 28 June 2017
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Variational Inference for Sparse and Undirected Models

J Ingraham & D Marks
ICML 2017 Available on arXiv 14 June 2017
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Genetic variation in human drug-related genes

CPI Scharfe, R Tremmel, M Schwab, O Kohlbacher & DS Marks
bioRxiv Web 7 June 2017
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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
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EV Mutation Homepage

2016

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
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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)
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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
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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
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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
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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
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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
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Evolutionary Couplings and Protein 3D Structure Prediction

R Sheridan, RJ Fieldhouse, S Hayat, Y Sun, Y Antipin, L Yang, TA Hopf & DS Marks
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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
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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
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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
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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.
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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.
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Human microRNA Targets

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