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A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data.

Huang YJ, Brock KP, Sander C, Marks DS, Montelione GT.

Adv Exp Med Biol. 2018;1105:153-169. doi: 10.1007/978-981-13-2200-6_10.


Combining Evolutionary Covariance and NMR Data for Protein Structure Determination.

Huang YJ, Brock KP, Ishida Y, Swapna GVT, Inouye M, Marks DS, Sander C, Montelione GT.

Methods Enzymol. 2019;614:363-392. doi: 10.1016/bs.mie.2018.11.004. Epub 2018 Dec 23.


Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.

Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS.

Nat Microbiol. 2019 Feb;4(2):328-338. doi: 10.1038/s41564-018-0309-1. Epub 2018 Dec 3.


Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis.

Ramírez-Guadiana FH, Rodrigues CDA, Marquis KA, Campo N, Barajas-Ornelas RDC, Brock K, Marks DS, Kruse AC, Rudner DZ.

PLoS Genet. 2018 Nov 7;14(11):e1007753. doi: 10.1371/journal.pgen.1007753. eCollection 2018 Nov.


Cryo-electron microscopy structure of the lipid droplet-formation protein seipin.

Sui X, Arlt H, Brock KP, Lai ZW, DiMaio F, Marks DS, Liao M, Farese RV Jr, Walther TC.

J Cell Biol. 2018 Dec 3;217(12):4080-4091. doi: 10.1083/jcb.201809067. Epub 2018 Oct 16.


The EVcouplings Python framework for coevolutionary sequence analysis.

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.

Bioinformatics. 2018 Oct 9. doi: 10.1093/bioinformatics/bty862. [Epub ahead of print]


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

Riesselman AJ, Ingraham JB, Marks DS.

Nat Methods. 2018 Oct;15(10):816-822. doi: 10.1038/s41592-018-0138-4. Epub 2018 Sep 24.


Magnetically Controlled Growing Rods: The Experience of Mechanical Failure from a Single Center Consecutive Series of 28 Children with a Minimum Follow-up of 2 Years.

Beaven A, Gardner AC, Marks DS, Mehta JS, Newton-Ede M, Spilsbury JB.

Asian Spine J. 2018 Oct;12(5):794-802. doi: 10.31616/asj.2018.12.5.794. Epub 2018 Sep 10.


A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.

Kotler E, Shani O, Goldfeld G, Lotan-Pompan M, Tarcic O, Gershoni A, Hopf TA, Marks DS, Oren M, Segal E.

Mol Cell. 2018 Sep 6;71(5):873. doi: 10.1016/j.molcel.2018.08.013. No abstract available.


Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.

Maddamsetti R, Johnson DT, Spielman SJ, Petrie KL, Marks DS, Meyer JR.

Evolution. 2018 Oct;72(10):2234-2243. doi: 10.1111/evo.13586. Epub 2018 Sep 11.


A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.

Kotler E, Shani O, Goldfeld G, Lotan-Pompan M, Tarcic O, Gershoni A, Hopf TA, Marks DS, Oren M, Segal E.

Mol Cell. 2018 Jul 5;71(1):178-190.e8. doi: 10.1016/j.molcel.2018.06.012. Erratum in: Mol Cell. 2018 Sep 6;71(5):873.


Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli.

Zheng S, Sham LT, Rubino FA, Brock KP, Robins WP, Mekalanos JJ, Marks DS, Bernhardt TG, Kruse AC.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6709-6714. doi: 10.1073/pnas.1802192115. Epub 2018 Jun 11.


Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.

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.

Nature. 2018 Apr 5;556(7699):118-121. doi: 10.1038/nature25985. Epub 2018 Mar 28.


Genetic variation in human drug-related genes.

Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS.

Genome Med. 2017 Dec 22;9(1):117. doi: 10.1186/s13073-017-0502-5.


Long-Term Outcomes of Patent Foramen Ovale Closure or Medical Therapy after Stroke.

Saver JL, Carroll JD, Thaler DE, Smalling RW, MacDonald LA, Marks DS, Tirschwell DL; RESPECT Investigators.

N Engl J Med. 2017 Sep 14;377(11):1022-1032. doi: 10.1056/NEJMoa1610057.


Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli.

Maddamsetti R, Hatcher PJ, Green AG, Williams BL, Marks DS, Lenski RE.

Genome Biol Evol. 2017 Apr 4. doi: 10.1093/gbe/evx064. [Epub ahead of print]


Mutation effects predicted from sequence co-variation.

Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS.

Nat Biotechnol. 2017 Feb;35(2):128-135. doi: 10.1038/nbt.3769. Epub 2017 Jan 16.


Final Fusion After Growing-Rod Treatment for Early Onset Scoliosis: Is It Really Final?

Poe-Kochert C, Shannon C, Pawelek JB, Thompson GH, Hardesty CK, Marks DS, Akbarnia BA, McCarthy RE, Emans JB.

J Bone Joint Surg Am. 2016 Nov 16;98(22):1913-1917.


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

Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M.

J Infect Dis. 2016 Nov 15;214(10):1579-1587. Epub 2016 Sep 16.


Structured States of Disordered Proteins from Genomic Sequences.

Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS.

Cell. 2016 Sep 22;167(1):158-170.e12. doi: 10.1016/j.cell.2016.09.010.


Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4.

Nicoludis JM, Vogt BE, Green AG, Schärfe CP, Marks DS, Gaudet R.

Elife. 2016 Jul 29;5. pii: e18449. doi: 10.7554/eLife.18449.


Image-based quantification of 3D morphology for bifurcations in the left coronary artery: Application to stent design.

Ellwein L, Marks DS, Migrino RQ, Foley WD, Sherman S, LaDisa JF Jr.

Catheter Cardiovasc Interv. 2016 Jun;87(7):1244-55. doi: 10.1002/ccd.26247. Epub 2015 Nov 19.


3D RNA and Functional Interactions from Evolutionary Couplings.

Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS.

Cell. 2016 May 5;165(4):963-75. doi: 10.1016/j.cell.2016.03.030. Epub 2016 Apr 14.


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

Nicoludis JM, Lau SY, Schärfe CP, Marks DS, Weihofen WA, Gaudet R.

Structure. 2015 Nov 3;23(11):2087-98. doi: 10.1016/j.str.2015.09.005. Epub 2015 Oct 15.


Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

Stein RR, Marks DS, Sander C.

PLoS Comput Biol. 2015 Jul 30;11(7):e1004182. doi: 10.1371/journal.pcbi.1004182. eCollection 2015 Jul. Review.


Pathway and network analysis of cancer genomes.

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; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium.

Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440.


Protein structure determination by combining sparse NMR data with evolutionary couplings.

Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT.

Nat Methods. 2015 Aug;12(8):751-4. doi: 10.1038/nmeth.3455. Epub 2015 Jun 29.


Benign Arterial Calcification on Screening Mammogram: A Marker for Coronary Artery Disease?

Karm D, Marks DS, Wein M, Kong AL.

J Womens Health (Larchmt). 2015 Oct;24(10):795-800. doi: 10.1089/jwh.2014.4905. Epub 2015 May 19.


All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Hayat S, Sander C, Marks DS, Elofsson A.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5413-8. doi: 10.1073/pnas.1419956112. Epub 2015 Apr 9.


Gene expression. MicroRNA control of protein expression noise.

Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N, Marks DS, van Oudenaarden A.

Science. 2015 Apr 3;348(6230):128-32. doi: 10.1126/science.aaa1738.


Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors.

Hopf TA, Morinaga S, Ihara S, Touhara K, Marks DS, Benton R.

Nat Commun. 2015 Jan 13;6:6077. doi: 10.1038/ncomms7077.


Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.

Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003976. doi: 10.1371/journal.pcbi.1003976. eCollection 2014 Dec.


Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans.

Romero-Aristizabal C, Marks DS, Fontana W, Apfeld J.

Nat Commun. 2014 Sep 29;5:5020. doi: 10.1038/ncomms6020.


Sequence co-evolution gives 3D contacts and structures of protein complexes.

Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS.

Elife. 2014 Sep 25;3. doi: 10.7554/eLife.03430.


PconsFold: improved contact predictions improve protein models.

Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A.

Bioinformatics. 2014 Sep 1;30(17):i482-8. doi: 10.1093/bioinformatics/btu458.


Deep Surgical Site Infection Following 2344 Growing-Rod Procedures for Early-Onset Scoliosis: Risk Factors and Clinical Consequences.

Kabirian N, Akbarnia BA, Pawelek JB, Alam M, Mundis GM Jr, Acacio R, Thompson GH, Marks DS, Gardner A, Sponseller PD, Skaggs DL; Growing Spine Study Group.

J Bone Joint Surg Am. 2014 Aug 6;96(15):e128.


FreeContact: fast and free software for protein contact prediction from residue co-evolution.

Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B.

BMC Bioinformatics. 2014 Mar 26;15:85. doi: 10.1186/1471-2105-15-85.


The surgical management of spinal deformity in children with a Fontan circulation: The development of an algorithm for treatment.

Evans S, Ramasamy A, Marks DS, Spilsbury J, Miller P, Tatman A, Gardner AC.

Bone Joint J. 2014 Jan;96-B(1):94-9. doi: 10.1302/0301-620X.96B1.32581.


Closure of patent foramen ovale versus medical therapy after cryptogenic stroke.

Carroll JD, Saver JL, Thaler DE, Smalling RW, Berry S, MacDonald LA, Marks DS, Tirschwell DL; RESPECT Investigators.

N Engl J Med. 2013 Mar 21;368(12):1092-100. doi: 10.1056/NEJMoa1301440.


Protein structure prediction from sequence variation.

Marks DS, Hopf TA, Sander C.

Nat Biotechnol. 2012 Nov;30(11):1072-80. doi: 10.1038/nbt.2419.


Impact of localizing general medical teams to a single nursing unit.

Singh S, Tarima S, Rana V, Marks DS, Conti M, Idstein K, Biblo LA, Fletcher KE.

J Hosp Med. 2012 Sep;7(7):551-6. doi: 10.1002/jhm.1948. Epub 2012 Jul 12.


miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.

Jeggari A, Marks DS, Larsson E.

Bioinformatics. 2012 Aug 1;28(15):2062-3. doi: 10.1093/bioinformatics/bts344. Epub 2012 Jun 19.


Three-dimensional structures of membrane proteins from genomic sequencing.

Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS.

Cell. 2012 Jun 22;149(7):1607-21. doi: 10.1016/j.cell.2012.04.012. Epub 2012 May 10.


Identification of hemodynamically optimal coronary stent designs based on vessel caliber.

Gundert TJ, Marsden AL, Yang W, Marks DS, LaDisa JF Jr.

IEEE Trans Biomed Eng. 2012 Jul;59(7):1992-2002. doi: 10.1109/TBME.2012.2196275. Epub 2012 Apr 25.


Protein 3D structure computed from evolutionary sequence variation.

Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C.

PLoS One. 2011;6(12):e28766. doi: 10.1371/journal.pone.0028766. Epub 2011 Dec 7.


Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1293-301. doi: 10.1073/pnas.1111471108. Epub 2011 Nov 21.


Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2.

Schultz N, Marenstein DR, De Angelis DA, Wang WQ, Nelander S, Jacobsen A, Marks DS, Massagué J, Sander C.

Silence. 2011 Mar 14;2:3. doi: 10.1186/1758-907X-2-3.


Acute brachial diplegia due to Lyme disease.

Gorson KC, Kolb DA, Marks DS, Hayes MT, Baquis GD.

Neurologist. 2011 Jan;17(1):24-7. doi: 10.1097/NRL.0b013e31820038cd.


Signatures of RNA binding proteins globally coupled to effective microRNA target sites.

Jacobsen A, Wen J, Marks DS, Krogh A.

Genome Res. 2010 Aug;20(8):1010-9. doi: 10.1101/gr.103259.109. Epub 2010 May 27.


Target mRNA abundance dilutes microRNA and siRNA activity.

Arvey A, Larsson E, Sander C, Leslie CS, Marks DS.

Mol Syst Biol. 2010 Apr 20;6:363. doi: 10.1038/msb.2010.24.

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