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Libusha Kelly - Publications

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33 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 Flamholz ZN, Biller SJ, Kelly L. Large language models improve annotation of prokaryotic viral proteins. Nature Microbiology. PMID 38287147 DOI: 10.1038/s41564-023-01584-8  0.347
2022 Fels JM, Khan S, Forster R, Skalina KA, Sirichand S, Fox AS, Bergman A, Mitchell WB, Wolgast LR, Szymczak WA, Bortz RH, Dieterle ME, Florez C, Haslwanter D, Jangra RK, ... ... Kelly L, et al. Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference. Cold Spring Harbor Molecular Case Studies. PMID 35831070 DOI: 10.1101/mcs.a006211  0.354
2021 Fels JM, Khan S, Forster R, Skalina KA, Sirichand S, Fox AS, Bergman A, Mitchell WB, Wolgast LR, Szymczak WA, Bortz RH, Dieterle ME, Florez C, Haslwanter D, Jangra RK, ... ... Kelly L, et al. Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference. Medrxiv : the Preprint Server For Health Sciences. PMID 33594384 DOI: 10.1101/2021.02.08.21250641  0.364
2018 Berube PM, Biller SJ, Hackl T, Hogle SL, Satinsky BM, Becker JW, Braakman R, Collins SB, Kelly L, Berta-Thompson J, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, et al. Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Scientific Data. 5: 180154. PMID 30179231 DOI: 10.1038/Sdata.2018.154  0.764
2018 Kauffman KM, Brown JM, Sharma RS, VanInsberghe D, Elsherbini J, Polz M, Kelly L. Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. Scientific Data. 5: 180114. PMID 29969110 DOI: 10.1038/Sdata.2018.114  0.421
2018 Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature. PMID 29364876 DOI: 10.1038/Nature25474  0.416
2014 Biller SJ, Berube PM, Berta-Thompson JW, Kelly L, Roggensack SE, Awad L, Roache-Johnson KH, Ding H, Giovannoni SJ, Rocap G, Moore LR, Chisholm SW. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Scientific Data. 1: 140034. PMID 25977791 DOI: 10.1038/Sdata.2014.34  0.769
2013 Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. The Isme Journal. 7: 1827-41. PMID 23657361 DOI: 10.1038/Ismej.2013.58  0.623
2013 Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology. 15: 1356-76. PMID 23320838 DOI: 10.1111/1462-2920.12053  0.683
2013 Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. The Isme Journal. 7: 184-98. PMID 22895163 DOI: 10.1038/Ismej.2012.89  0.756
2012 Kelly L, Huang KH, Ding H, Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Research. 40: D632-40. PMID 22102570 DOI: 10.1093/Nar/Gkr1022  0.665
2011 Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proceedings of the National Academy of Sciences of the United States of America. 108: E757-64. PMID 21844365 DOI: 10.1073/Pnas.1102164108  0.591
2011 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Letter to the editor Protein Science. 20: 4-5. DOI: 10.1002/Pro.555  0.428
2010 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Science : a Publication of the Protein Society. 19: 2110-21. PMID 20799350 DOI: 10.1002/Pro.491  0.487
2010 Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, et al. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology. 12: 3035-56. PMID 20662890 DOI: 10.1111/J.1462-2920.2010.02280.X  0.66
2010 Li B, Sher D, Kelly L, Shi Y, Huang K, Knerr PJ, Joewono I, Rusch D, Chisholm SW, van der Donk WA. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America. 107: 10430-5. PMID 20479271 DOI: 10.1073/Pnas.0913677107  0.58
2010 Osburne MS, Holmbeck BM, Frias-Lopez J, Steen R, Huang K, Kelly L, Coe A, Waraska K, Gagne A, Chisholm SW. UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase. Environmental Microbiology. 12: 1978-88. PMID 20345942 DOI: 10.1111/J.1462-2920.2010.02203.X  0.527
2010 Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, et al. Analysis of high-throughput sequencing and annotation strategies for phage genomes. Plos One. 5: e9083. PMID 20140207 DOI: 10.1371/Journal.Pone.0009083  0.673
2010 Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. Comparison of human solute carriers. Protein Science : a Publication of the Protein Society. 19: 412-28. PMID 20052679 DOI: 10.1002/Pro.320  0.508
2009 Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, Chisholm SW. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'. Environmental Microbiology. 11: 2935-51. PMID 19840100 DOI: 10.1111/J.1462-2920.2009.02081.X  0.695
2009 Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A. A survey of integral alpha-helical membrane proteins. Journal of Structural and Functional Genomics. 10: 269-80. PMID 19760129 DOI: 10.1007/S10969-009-9069-8  0.55
2009 Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics. 10: 107-25. PMID 19219566 DOI: 10.1007/S10969-008-9056-5  0.587
2009 Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. Journal of Molecular Biology. 385: 820-30. PMID 19061901 DOI: 10.1016/J.Jmb.2008.11.021  0.488
2009 Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. Journal of Structural and Functional Genomics. 10: 9-16. PMID 19031011 DOI: 10.1007/S10969-008-9046-7  0.514
2009 Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 37: D347-54. PMID 18948282 DOI: 10.1093/nar/gkn791  0.456
2007 Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 51-63. PMID 17990484  0.421
2007 Soranzo N, Kelly L, Martinian L, Burley MW, Thom M, Sali A, Kroetz DL, Goldstein DB, Sisodiya SM. Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia. 48: 674-83. PMID 17437410 DOI: 10.1111/J.1528-1167.2007.00926.X  0.432
2006 Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacological Reviews. 58: 1-2. PMID 16507877 DOI: 10.1124/Pr.58.1.1  0.478
2006 Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 34: D291-5. PMID 16381869 DOI: 10.1093/nar/gkj059  0.666
2005 Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (Oxford, England). 21: 2814-20. PMID 15827081 DOI: 10.1093/Bioinformatics/Bti442  0.506
2005 Karchin R, Kelly L, Sali A. Improving functional annotation of no n-s yno no mo us s nps with information theory Proceedings of the Pacific Symposium On Biocomputing 2005, Psb 2005. 397-408. PMID 15759645  0.384
2001 Olivier M, Bustos VI, Levy MR, Smick GA, Moreno I, Bushard JM, Almendras AA, Sheppard K, Zierten DL, Aggarwal A, Carlson CS, Foster BD, Vo N, Kelly L, Liu X, et al. Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21. Genomics. 78: 64-72. PMID 11707074 DOI: 10.1006/Geno.2001.6646  0.367
2001 Olivier M, Aggarwal A, Allen J, Almendras AA, Bajorek ES, Beasley EM, Brady SD, Bushard JM, Bustos VI, Chu A, Chung TR, De Witte A, Denys ME, Dominguez R, Fang NY, ... ... Kelly L, et al. A high-resolution radiation hybrid map of the human genome draft sequence. Science (New York, N.Y.). 291: 1298-302. PMID 11181994 DOI: 10.1126/Science.1057437  0.446
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