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Debora Marks, PhD - Publications

Affiliations: 
2014- Systems Biology Harvard Medical School 
Area:
computational biology
Website:
https://www.deboramarkslab.com/
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77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Fram B, Su Y, Truebridge I, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler MA, Marks DS, Bahl CD, Khan AR, et al. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature Communications. 15: 5141. PMID 38902262 DOI: 10.1038/s41467-024-49119-x  0.51
2024 Notin P, Rollins N, Gal Y, Sander C, Marks D. Machine learning for functional protein design. Nature Biotechnology. 42: 216-228. PMID 38361074 DOI: 10.1038/s41587-024-02127-0  0.472
2024 Peidli S, Green TD, Shen C, Gross T, Min J, Garda S, Yuan B, Schumacher LJ, Taylor-King JP, Marks DS, Luna A, Blüthgen N, Sander C. scPerturb: harmonized single-cell perturbation data. Nature Methods. PMID 38279009 DOI: 10.1038/s41592-023-02144-y  0.399
2023 Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS. Learning from prepandemic data to forecast viral escape. Nature. 622: 818-825. PMID 37821700 DOI: 10.1038/s41586-023-06617-0  0.443
2023 Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, et al. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Biorxiv : the Preprint Server For Biology. PMID 37214973 DOI: 10.1101/2023.05.09.539914  0.509
2023 Placido D, Yuan B, Hjaltelin JX, Zheng C, Haue AD, Chmura PJ, Yuan C, Kim J, Umeton R, Antell G, Chowdhury A, Franz A, Brais L, Andrews E, Marks DS, et al. A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories. Nature Medicine. PMID 37156936 DOI: 10.1038/s41591-023-02332-5  0.361
2021 Shin JE, Riesselman AJ, Kollasch AW, McMahon C, Simon E, Sander C, Manglik A, Kruse AC, Marks DS. Protein design and variant prediction using autoregressive generative models. Nature Communications. 12: 2403. PMID 33893299 DOI: 10.1038/s41467-021-22732-w  0.501
2020 Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Systems. PMID 33373583 DOI: 10.1016/j.cels.2020.11.013  0.403
2020 Shen J, Yuan B, Luna A, Korkut A, Marks D, Ingraham J, Sander C. Abstract 2102: Interpretable machine learning for perturbation biology Cancer Research. 80: 2102-2102. DOI: 10.1158/1538-7445.Am2020-2102  0.409
2019 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 Systems. PMID 31838147 DOI: 10.1016/J.Cels.2019.11.008  0.521
2019 Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Inferring protein 3D structure from deep mutation scans. Nature Genetics. PMID 31209393 DOI: 10.1038/S41588-019-0432-9  0.501
2019 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 in Enzymology. 614: 363-392. PMID 30611430 DOI: 10.1016/Bs.Mie.2018.11.004  0.502
2018 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. Advances in Experimental Medicine and Biology. 1105: 153-169. PMID 30617828 DOI: 10.1007/978-981-13-2200-6_10  0.513
2018 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, et al. The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics (Oxford, England). PMID 30304492 DOI: 10.1093/Bioinformatics/Bty862  0.523
2018 Brock K, Sander C, Marks D. Using evolutionary couplings to predict contacts and build structures Acta Crystallographica Section A. 74. DOI: 10.1107/S2053273318094536  0.431
2018 Sander C, Marks D. Solutions to the computational protein folding problem The Faseb Journal. 32. DOI: 10.1096/Fasebj.2018.32.1_Supplement.377.1  0.44
2017 Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nature Biotechnology. PMID 28092658 DOI: 10.1038/Nbt.3769  0.466
2017 Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nature Biotechnology. PMID 28092658 DOI: 10.1038/Nbt.3769  0.466
2016 Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell. 167: 158-170.e12. PMID 27662088 DOI: 10.1016/J.Cell.2016.09.010  0.483
2016 Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell. 167: 158-170.e12. PMID 27662088 DOI: 10.1016/J.Cell.2016.09.010  0.483
2016 Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell. PMID 27087444 DOI: 10.1016/J.Cell.2016.03.030  0.513
2016 Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell. PMID 27087444 DOI: 10.1016/J.Cell.2016.03.030  0.513
2015 Stein RR, Marks DS, Sander C. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. Plos Computational Biology. 11: e1004182. PMID 26225866 DOI: 10.1371/Journal.Pcbi.1004182  0.504
2015 Stein RR, Marks DS, Sander C. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. Plos Computational Biology. 11: e1004182. PMID 26225866 DOI: 10.1371/Journal.Pcbi.1004182  0.504
2015 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, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/Nmeth.3440  0.404
2015 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, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/Nmeth.3440  0.404
2015 Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nature Methods. PMID 26121406 DOI: 10.1038/Nmeth.3455  0.492
2015 Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nature Methods. PMID 26121406 DOI: 10.1038/Nmeth.3455  0.492
2015 Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proceedings of the National Academy of Sciences of the United States of America. 112: 5413-8. PMID 25858953 DOI: 10.1073/Pnas.1419956112  0.512
2015 Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proceedings of the National Academy of Sciences of the United States of America. 112: 5413-8. PMID 25858953 DOI: 10.1073/Pnas.1419956112  0.512
2015 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, et al. Pathway and network analysis of cancer genomes Nature Methods. 12: 615-621. DOI: 10.1038/nmeth.3440  0.356
2014 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. 3. PMID 25255213 DOI: 10.7554/Elife.03430  0.526
2014 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. 3. PMID 25255213 DOI: 10.7554/Elife.03430  0.526
2014 Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/Bioinformatics/Btu458  0.473
2014 Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/Bioinformatics/Btu458  0.473
2014 Hopf TA, Schärfe CPI, Rodrigues JPGLM, Green AG, Kohlbacher O, Sander C, Bonvin AMJJ, Marks DS. Author response: Sequence co-evolution gives 3D contacts and structures of protein complexes Elife. DOI: 10.7554/Elife.03430.032  0.468
2013 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Potential miRNA Target Sites in the 3′ UTRs of Selected Genes Plos Biology. DOI: 10.1371/Journal.Pbio.0020363.G004  0.45
2012 Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nature Biotechnology. 30: 1072-80. PMID 23138306 DOI: 10.1038/Nbt.2419  0.54
2012 Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 149: 1607-21. PMID 22579045 DOI: 10.1016/J.Cell.2012.04.012  0.536
2012 Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 149: 1607-21. PMID 22579045 DOI: 10.1016/J.Cell.2012.04.012  0.536
2012 Morcos F, Pagnini A, Lunt B, Bertolino A, Marks D, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families Biophysical Journal. 102: 250a. DOI: 10.1016/J.Bpj.2011.11.1378  0.5
2011 Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. Plos One. 6: e28766. PMID 22163331 DOI: 10.1371/Journal.Pone.0028766  0.542
2011 Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. Plos One. 6: e28766. PMID 22163331 DOI: 10.1371/Journal.Pone.0028766  0.542
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: E1293-301. PMID 22106262 DOI: 10.1073/Pnas.1111471108  0.537
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: E1293-301. PMID 22106262 DOI: 10.1073/Pnas.1111471108  0.537
2011 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-β pathway and reveal microRNA regulation of TGFBR2. Silence. 2: 3. PMID 21401928 DOI: 10.1186/1758-907X-2-3  0.5
2011 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-β pathway and reveal microRNA regulation of TGFBR2. Silence. 2: 3. PMID 21401928 DOI: 10.1186/1758-907X-2-3  0.5
2010 Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Molecular Systems Biology. 6: 433. PMID 21081925 DOI: 10.1038/Msb.2010.89  0.469
2010 Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Molecular Systems Biology. 6: 433. PMID 21081925 DOI: 10.1038/Msb.2010.89  0.469
2010 Jacobsen A, Wen J, Marks DS, Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Research. 20: 1010-9. PMID 20508147 DOI: 10.1101/Gr.103259.109  0.325
2010 Jacobsen A, Wen J, Marks DS, Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Research. 20: 1010-9. PMID 20508147 DOI: 10.1101/Gr.103259.109  0.325
2010 Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Molecular Systems Biology. 6: 363. PMID 20404830 DOI: 10.1038/Msb.2010.24  0.481
2010 Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Molecular Systems Biology. 6: 363. PMID 20404830 DOI: 10.1038/Msb.2010.24  0.481
2010 Larsson E, Sander C, Marks D. Erratum: mRNA Turnover Rate Limits siRNA and microRNA Efficacy Molecular Systems Biology. DOI: 10.1038/Msb.2010.113  0.389
2009 Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology. 27: 549-55. PMID 19465925 DOI: 10.1038/Nbt.1543  0.497
2009 Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology. 27: 549-55. PMID 19465925 DOI: 10.1038/Nbt.1543  0.497
2009 Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Corrigendum: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs Nature Biotechnology. 27: 671-671. DOI: 10.1038/Nbt0709-671A  0.4
2007 Betel D, Wilson M, Gabow AP, Marks DS, Sander C. The microRNA.org resource: targets and expression Nucleic Acids Research. 36: 149-153. PMID 18158296 DOI: 10.1093/Nar/Gkm995  0.505
2007 Betel D, Wilson M, Gabow AP, Marks DS, Sander C. The microRNA.org resource: targets and expression Nucleic Acids Research. 36: 149-153. PMID 18158296 DOI: 10.1093/Nar/Gkm995  0.505
2006 John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods of Molecular Biology. 342: 101-113. PMID 16957370 DOI: 10.1385/1-59745-123-1:101  0.508
2006 John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods of Molecular Biology. 342: 101-113. PMID 16957370 DOI: 10.1385/1-59745-123-1:101  0.508
2005 Betel D, Sheridan RP, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. Plos Computational Biology. 3. PMID 17997596 DOI: 10.1371/Journal.Pcbi.0030222  0.474
2005 Betel D, Sheridan RP, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. Plos Computational Biology. 3. PMID 17997596 DOI: 10.1371/Journal.Pcbi.0030222  0.474
2005 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 Biology. 6: R71. PMID 16086853 DOI: 10.1186/Gb-2005-6-8-R71  0.469
2005 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 Biology. 6: R71. PMID 16086853 DOI: 10.1186/Gb-2005-6-8-R71  0.469
2005 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. 121: 1097-108. PMID 15989958 DOI: 10.1016/J.Cell.2005.04.016  0.47
2005 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. 121: 1097-108. PMID 15989958 DOI: 10.1016/J.Cell.2005.04.016  0.47
2005 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 & Development. 19: 1288-93. PMID 15937218 DOI: 10.1101/Gad.1310605  0.485
2005 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 & Development. 19: 1288-93. PMID 15937218 DOI: 10.1101/Gad.1310605  0.485
2005 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Correction: Human MicroRNA Targets Plos Biology. 3: e264. DOI: 10.1371/Journal.Pbio.0030264  0.447
2004 Chang J, Nicolas E, Marks D, Sander C, Lerro A, Buendia MA, Xu C, Mason WS, Moloshok T, Bort R, Zaret KS, Taylor JM. miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. Rna Biology. 1: 106-13. PMID 17179747 DOI: 10.4161/Rna.1.2.1066  0.446
2004 Chang J, Nicolas E, Marks D, Sander C, Lerro A, Buendia MA, Xu C, Mason WS, Moloshok T, Bort R, Zaret KS, Taylor JM. miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. Rna Biology. 1: 106-13. PMID 17179747 DOI: 10.4161/Rna.1.2.1066  0.446
2004 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. Plos Biology. 2: e363. PMID 15502875 DOI: 10.1371/Journal.Pbio.0020363  0.525
2004 John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. Plos Biology. 2: e363. PMID 15502875 DOI: 10.1371/Journal.Pbio.0020363  0.525
2004 Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T. Identification of virus-encoded microRNAs. Science (New York, N.Y.). 304: 734-6. PMID 15118162 DOI: 10.1126/Science.1096781  0.457
2004 Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T. Identification of virus-encoded microRNAs. Science (New York, N.Y.). 304: 734-6. PMID 15118162 DOI: 10.1126/Science.1096781  0.457
2003 Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biology. 5: R1. PMID 14709173 DOI: 10.1186/Gb-2003-5-1-R1  0.514
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