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Lucy J. Colwell, Ph.D. - Publications

Affiliations: 
2010 Harvard University, Cambridge, MA, United States 
Area:
Fluid Mechanics
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29 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
2023 Kimchi O, Brenner MP, Colwell LJ. Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the LandscapeFold Algorithm. Methods in Molecular Biology (Clifton, N.J.). 2586: 49-77. PMID 36705898 DOI: 10.1007/978-1-0716-2768-6_4  0.444
2020 Cervettini D, Tang S, Fried SD, Willis JCW, Funke LFH, Colwell LJ, Chin JW. Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase-tRNA pairs. Nature Biotechnology. PMID 32284585 DOI: 10.1038/S41587-020-0479-2  0.302
2019 Carter B, Bileschi M, Smith J, Sanderson T, Bryant D, Belanger D, Colwell LJ. Critiquing Protein Family Classification Models Using Sufficient Input Subsets. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31874057 DOI: 10.1089/Cmb.2019.0339  0.338
2019 Falk MJ, Duwel A, Colwell LJ, Brenner MP. Collagen-Inspired Self-Assembly of Twisted Filaments. Physical Review Letters. 123: 238102. PMID 31868483 DOI: 10.1103/Physrevlett.123.238102  0.449
2019 Sundar V, Colwell L. The Effect of Debiasing Protein-Ligand Binding Data on Generalization. Journal of Chemical Information and Modeling. 60: 56-62. PMID 31825609 DOI: 10.1021/Acs.Jcim.9B00415  0.352
2019 Kimchi O, Cragnolini T, Brenner MP, Colwell LJ. A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. Biophysical Journal. 117: 520-532. PMID 31353036 DOI: 10.1016/J.Bpj.2019.06.037  0.531
2019 McCloskey K, Taly A, Monti F, Brenner MP, Colwell LJ. Using attribution to decode binding mechanism in neural network models for chemistry. Proceedings of the National Academy of Sciences of the United States of America. PMID 31127041 DOI: 10.1073/Pnas.1820657116  0.491
2019 Kimchi O, Cragnolini T, Garmann R, Manoharan VN, Brenner MP, Colwell LJ. RNA Structure and Kinetics Including Pseudoknots through Complete Landscape Enumeration Biophysical Journal. 116: 353a-354a. DOI: 10.1016/J.Bpj.2018.11.1922  0.46
2018 Chow WY, Forman CJ, Bihan D, Puszkarska AM, Rajan R, Reid DG, Slatter DA, Colwell LJ, Wales DJ, Farndale RW, Duer MJ. Proline provides site-specific flexibility for in vivo collagen. Scientific Reports. 8: 13809. PMID 30218106 DOI: 10.1038/S41598-018-31937-X  0.311
2018 Mitchell LS, Colwell LJ. Analysis of nanobody paratopes reveals greater diversity than classical antibodies. Protein Engineering, Design & Selection : Peds. PMID 30053276 DOI: 10.1093/Protein/Gzy017  0.331
2018 Mitchell LS, Colwell LJ. Comparative Analysis of Nanobody Sequence and Structure Data. Proteins. PMID 29569425 DOI: 10.1002/Prot.25497  0.35
2018 Colwell LJ. Statistical and machine learning approaches to predicting protein-ligand interactions. Current Opinion in Structural Biology. 49: 123-128. PMID 29452923 DOI: 10.1016/J.Sbi.2018.01.006  0.362
2018 Qin C, Colwell LJ. Power law tails in phylogenetic systems. Proceedings of the National Academy of Sciences of the United States of America. PMID 29311320 DOI: 10.1073/Pnas.1711913115  0.356
2017 Lee AA, Brenner MP, Colwell LJ. Optimal Design of Experiments by Combining Coarse and Fine Measurements. Physical Review Letters. 119: 208101. PMID 29219382 DOI: 10.1103/Physrevlett.119.208101  0.499
2016 Lee AA, Brenner MP, Colwell LJ. Predicting protein-ligand affinity with a random matrix framework. Proceedings of the National Academy of Sciences of the United States of America. PMID 27856761 DOI: 10.1073/Pnas.1611138113  0.509
2016 Bitbol AF, Dwyer RS, Colwell LJ, Wingreen NS. Inferring interaction partners from protein sequences. Proceedings of the National Academy of Sciences of the United States of America. PMID 27663738 DOI: 10.1073/Pnas.1606762113  0.383
2015 Townsend PD, Rodgers TL, Glover LC, Korhonen HJ, Richards SA, Colwell LJ, Pohl E, Wilson MR, Hodgson DR, McLeish TC, Cann MJ. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein. The Journal of Biological Chemistry. PMID 26187469 DOI: 10.1074/Jbc.M115.669267  0.341
2015 Te?ileanu T, Colwell LJ, Leibler S. Protein sectors: statistical coupling analysis versus conservation. Plos Computational Biology. 11: e1004091. PMID 25723535 DOI: 10.1371/Journal.Pcbi.1004091  0.35
2014 Colwell LJ, Brenner MP, Murray AW. Conservation weighting functions enable covariance analyses to detect functionally important amino acids. Plos One. 9: e107723. PMID 25379728 DOI: 10.1371/Journal.Pone.0107723  0.525
2014 Colwell LJ, Qin Y, Huntley M, Manta A, Brenner MP. Feynman-Hellmann theorem and signal identification from sample covariance matrices Physical Review X. 4. DOI: 10.1103/Physrevx.4.031032  0.502
2013 Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS. Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics. 195: 443-55. PMID 23934888 DOI: 10.1534/Genetics.113.155861  0.362
2012 Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA. The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochemical Society Transactions. 40: 475-91. PMID 22616857 DOI: 10.1042/Bst20120056  0.353
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  0.386
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  0.373
2012 Beh LY, Colwell LJ, Francis NJ. A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence. Proceedings of the National Academy of Sciences of the United States of America. 109: E1063-71. PMID 22517748 DOI: 10.1073/Pnas.1118678109  0.335
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  0.386
2010 Colwell LJ, Brenner MP, Ribbeck K. Charge as a selection criterion for translocation through the nuclear pore complex. Plos Computational Biology. 6: e1000747. PMID 20421988 DOI: 10.1371/Journal.Pcbi.1000747  0.477
2010 Colwell LJ, Brenner MP, Ribbeck K. Charge as a selection criterion for translocation through the nuclear pore complex Plos Computational Biology. 6. DOI: 10.1371/journal.pcbi.1000747  0.397
2009 Colwell LJ, Brenner MP. Action potential initiation in the Hodgkin-Huxley model Plos Computational Biology. 5. PMID 19148265 DOI: 10.1371/Journal.Pcbi.1000265  0.465
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