| Year |
Citation |
Score |
| 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 |
0.363 |
|
| 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 |
0.373 |
|
| 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 |
0.762 |
|
| 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 |
0.427 |
|
| 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 |
0.423 |
|
| 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 |
0.767 |
|
| 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 |
0.627 |
|
| 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 |
0.689 |
|
| 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 |
0.755 |
|
| 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 |
0.669 |
|
| 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 |
0.595 |
|
| 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 |
0.429 |
|
| 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 |
0.665 |
|
| 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 |
0.582 |
|
| 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 |
0.529 |
|
| 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 |
0.676 |
|
| 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 |
0.507 |
|
| 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 |
0.697 |
|
| 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 |
0.548 |
|
| 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 |
0.581 |
|
| 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 |
0.484 |
|
| 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 |
0.511 |
|
| 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 |
0.435 |
|
| 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 |
0.417 |
|
| 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 |
0.435 |
|
| 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 |
0.48 |
|
| 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 |
0.456 |
|
| 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 |
0.507 |
|
| 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 |
0.383 |
|
| 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 |
0.369 |
|
| 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 |
0.448 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2019 |
Guthrie L, Wolfson S, Kelly L. The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. Elife. 8. PMID 31184303 DOI: 10.7554/Elife.42866 |
0.28 |
|
| 2022 |
Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L. Resolving the structure of phage-bacteria interactions in the context of natural diversity. Nature Communications. 13: 372. PMID 35042853 DOI: 10.1038/s41467-021-27583-z |
0.277 |
|
| 2023 |
Kelly L, Flamholz Z, Biller S. Large language models improve annotation of viral proteins. Research Square. PMID 37205395 DOI: 10.21203/rs.3.rs-2852098/v1 |
0.27 |
|
| 2015 |
Wallace BD, Roberts AB, Pollet RM, Ingle JD, Biernat KA, Pellock SJ, Venkatesh MK, Guthrie L, O'Neal SK, Robinson SJ, Dollinger M, Figueroa E, McShane SR, Cohen RD, Jin J, ... ... Kelly L, et al. Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity. Chemistry & Biology. 22: 1238-49. PMID 26364932 DOI: 10.1016/J.Chembiol.2015.08.005 |
0.251 |
|
| 2019 |
Hitchings R, Kelly L. Drug Metabolism as a Community Effort. Cell Metabolism. 30: 235-237. PMID 31390549 DOI: 10.1016/J.Cmet.2019.07.005 |
0.25 |
|
| 2021 |
Yang JY, Fang W, Miranda-Sanchez F, Brown JM, Kauffman KM, Acevero CM, Bartel DP, Polz MF, Kelly L. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Systems. PMID 34143976 DOI: 10.1016/j.cels.2021.05.019 |
0.247 |
|
| 2019 |
Hitchings R, Kelly L. Predicting and Understanding the Human Microbiome's Impact on Pharmacology. Trends in Pharmacological Sciences. 40: 495-505. PMID 31171383 DOI: 10.1016/J.Tips.2019.04.014 |
0.244 |
|
| 2019 |
Guthrie L, Kelly L. Bringing microbiome-drug interaction research into the clinic. Ebiomedicine. PMID 31151933 DOI: 10.1016/J.Ebiom.2019.05.009 |
0.239 |
|
| 2015 |
Smith VH, Rubinstein RJ, Park S, Kelly L, Klepac-Ceraj V. Microbiology and ecology are vitally important to premedical curricula. Evolution, Medicine, and Public Health. 2015: 179-92. PMID 26198190 DOI: 10.1093/Emph/Eov014 |
0.239 |
|
| 2019 |
Guthrie L, Wolfson S, Kelly L. Author response: The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs Elife. DOI: 10.7554/Elife.42866.022 |
0.226 |
|
| 2019 |
Kelly L. Harnessing the Microbiome to Improve Drug Therapy. Clinical Pharmacology and Therapeutics. 106: 287-289. PMID 31355459 DOI: 10.1002/Cpt.1510 |
0.196 |
|
| 2023 |
Feng M, Namanja-Magliano H, Rajagopalan S, Mishra T, Ducati RG, Hirsch BM, Kelly L, Szymczak W, Fajardo JE, Sidoli S, Fiser A, Jacobs WR, Schramm VL. MAT Gain of Activity Mutation in Is Associated with Resistance to MTAN Transition State Analogues. Acs Infectious Diseases. PMID 36920074 DOI: 10.1021/acsinfecdis.2c00644 |
0.165 |
|
| 2020 |
Chang WK, VanInsberghe D, Kelly L. Topological analysis reveals state transitions in human gut and marine bacterial communities. Npj Biofilms and Microbiomes. 6: 41. PMID 33057043 DOI: 10.1038/s41522-020-00145-9 |
0.152 |
|
| 2022 |
Wolfson SJ, Hitchings R, Peregrina K, Cohen Z, Khan S, Yilmaz T, Malena M, Goluch ED, Augenlicht L, Kelly L. Bacterial hydrogen sulfide drives cryptic redox chemistry in gut microbial communities. Nature Metabolism. 4: 1260-1270. PMID 36266544 DOI: 10.1038/s42255-022-00656-z |
0.147 |
|
| 2017 |
Downs IA, Aroniadis OC, Kelly L, Brandt LJ. Postinfection Irritable Bowel Syndrome: The Links Between Gastroenteritis, Inflammation, the Microbiome, and Functional Disease. Journal of Clinical Gastroenterology. PMID 28885302 DOI: 10.1097/MCG.0000000000000924 |
0.13 |
|
| 2023 |
Segrè D, Mitri S, Shou W, Süel GM, Mizrahi I, Kelly L, Rebolleda-Gómez M, Ratzke C, Ogbunugafor CB, Schwartzman JA, Kryazhimskiy S, Leventhal GE, Kost C, Bell T. What do you most want to understand about how collective features emerge in microbial communities? Cell Systems. 14: 91-97. PMID 36796334 DOI: 10.1016/j.cels.2023.01.001 |
0.129 |
|
| 2020 |
Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, ... ... Kelly L, et al. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends in Cancer. 6: 192-204. PMID 32101723 DOI: 10.1016/J.Trecan.2020.01.004 |
0.125 |
|
| 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 |
0.12 |
|
| 2021 |
Cohen Z, Kelly L. Bioaccumulation as a mechanism of microbiome/drug interactions. Trends in Microbiology. PMID 34952771 DOI: 10.1016/j.tim.2021.12.003 |
0.118 |
|
| 2017 |
Guthrie L, Gupta S, Daily J, Kelly L. Human microbiome signatures of differential colorectal cancer drug metabolism. Npj Biofilms and Microbiomes. 3: 27. PMID 29104759 DOI: 10.1038/s41522-017-0034-1 |
0.118 |
|
| 2020 |
Kelly L, Wolfson SJ. Finding phenazine. Elife. 9. PMID 33108273 DOI: 10.7554/eLife.62983 |
0.112 |
|
| 2020 |
Khan S, Kelly L. Multiclass Disease Classification from Microbial Whole-Community Metagenomes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 55-66. PMID 31797586 |
0.108 |
|
| 2021 |
De A, Chen W, Li H, Wright JR, Lamendella R, Lukin DJ, Szymczak WA, Sun K, Kelly L, Ghosh S, Kearns DB, He Z, Jobin C, Luo X, Byju A, et al. Bacterial Swarmers Enriched during Intestinal Stress Ameliorate Damage. Gastroenterology. PMID 33741315 DOI: 10.1053/j.gastro.2021.03.017 |
0.092 |
|
| 2023 |
Pay R, Sharrock AV, Elder R, Maré A, Bracegirdle J, Torres D, Malone N, Vorster J, Kelly L, Ryan A, Josephy PD, Allen-Vercoe E, Ackerley DF, Keyzers RA, Harvey JE. Preparation, analysis and toxicity characterisation of the redox metabolites of the azo food dye tartrazine. Food and Chemical Toxicology : An International Journal Published For the British Industrial Biological Research Association. 114193. PMID 37980979 DOI: 10.1016/j.fct.2023.114193 |
0.09 |
|
| 2020 |
Khan S, Hauptman R, Kelly L. Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities. Annual Review of Pharmacology and Toxicology. PMID 33049161 DOI: 10.1146/annurev-pharmtox-031620-031509 |
0.086 |
|
| 2022 |
Li H, Kazmi JS, Lee SK, Zhang D, Gao X, Maryanovich M, Torres LS, Verma D, Kelly L, Ginzburg YZ, Frenette PS, Manwani D. Dietary iron restriction protects against vaso-occlusion and organ damage in sickle cell disease. Blood. PMID 36315910 DOI: 10.1182/blood.2022016218 |
0.084 |
|
| 2022 |
Lasso G, Khan S, Allen SA, Mariano M, Florez C, Orner EP, Quiroz JA, Quevedo G, Massimi A, Hegde A, Wirchnianski AS, Bortz RH, Malonis RJ, Georgiev GI, Tong K, ... ... Kelly L, et al. Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes. Plos Computational Biology. 18: e1009778. PMID 35041647 DOI: 10.1371/journal.pcbi.1009778 |
0.051 |
|
| 2023 |
Peters BA, Kelly L, Wang T, Loudig O, Rohan TE. The breast microbiome in breast cancer risk and progression: a narrative review. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 37943168 DOI: 10.1158/1055-9965.EPI-23-0965 |
0.045 |
|
| 2021 |
Htwe P, Aung HH, Kywe B, Niang PT, Oo TS, Monhandas S, Kelly L, Goldman DL. Endotoxin acts synergistically with C. difficile toxin B to increase IL-1 β production: A potential role for the intestinal biome in modifying the severity of C. difficile colitis. The Journal of Infectious Diseases. PMID 33780547 DOI: 10.1093/infdis/jiab165 |
0.041 |
|
| 2019 |
Khan S, Kelly L. Fireworks: Reproducible Machine Learning and Preprocessing with PyTorch Journal of Open Source Software. 4: 1478. DOI: 10.21105/JOSS.01478 |
0.01 |
|
| Hide low-probability matches. |