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Publications 2001 2019

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2019
1 Citation (Scopus)

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs

Guthrie, L., Wolfson, S. & Kelly, L., Jun 11 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
Biotransformation
Toxicity
Metabolism
Food
Biochemistry
2018
37 Citations (Scopus)

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

Kauffman, K. M., Hussain, F. A., Yang, J., Arevalo, P., Brown, J. M., Chang, W. K., Vaninsberghe, D., Elsherbini, J., Sharma, R. S., Cutler, M. B., Kelly, L. & Polz, M. F., Feb 1 2018, In : Nature. 554, 7690, p. 118-122 5 p.

Research output: Contribution to journalArticle

DNA Viruses
Viruses
Bacteria
DNA
Caudovirales
7 Citations (Scopus)

Data descriptor: Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Berube, P. M., Biller, S. J., Hackl, T., Hogle, S. L., Satinsky, B. M., Becker, J. W., Braakman, R., Collins, S. B., Kelly, L., Berta-Thompson, J., Coe, A., Bergauer, K., Bouman, H. A., Browning, T. J., De Corte, D., Hassler, C., Hulata, Y., Jacquot, J. E., Maas, E. W., Reinthaler, T. & 5 others, Sintes, E., Yokokawa, T., Lindell, D., Stepanauskas, R. & Chisholm, S. W., Jan 1 2018, In : Scientific data. 5, 180154.

Research output: Contribution to journalArticle

Descriptors
Genome
Genes
Cell
Oceanography
2 Citations (Scopus)

Data Descriptor: Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses

Kauffman, K. M., Brown, J. M., Sharma, R. S., VanInsberghe, D., Elsherbini, J., Polz, M. & Kelly, L., Jul 3 2018, In : Scientific data. 5, 180114.

Research output: Contribution to journalArticle

Viruses
Descriptors
Virus
interaction
time series
2017
21 Citations (Scopus)

Human microbiome signatures of differential colorectal cancer drug metabolism

Guthrie, L., Gupta, S., Daily, J. P. & Kelly, L., Dec 1 2017, In : npj Biofilms and Microbiomes. 3, 1, 27.

Research output: Contribution to journalArticle

irinotecan
Microbiota
Colorectal Neoplasms
Pharmaceutical Preparations
Glucuronidase
2015
2 Citations (Scopus)

Microbiology and ecology are vitally important to premedical curricula

Smith, V. H., Rubinstein, R. J., Park, S., Kelly, L. & Klepac-Ceraj, V., Jan 1 2015, In : Evolution, Medicine and Public Health. 2015, 1, p. 179-192 14 p., eov014.

Research output: Contribution to journalArticle

Microbiota
microbiology
curriculum
Microbiology
Ecology
64 Citations (Scopus)

Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity

Wallace, B. D., Roberts, A. B., Pollet, R. M., Ingle, J. D., Biernat, K. A., Pellock, S. J., Venkatesh, M. K., Guthrie, L., O'Neal, S. K., Robinson, S. J., Dollinger, M., Figueroa, E., McShane, S. R., Cohen, R. D., Jin, J., Frye, S. V., Zamboni, W. C., Pepe-Ranney, C., Mani, S., Kelly, L. & 1 others, Redinbo, M. R., Jun 22 2015, In : Chemistry and Biology. 22, 9, p. 1238-1249 12 p.

Research output: Contribution to journalArticle

Microbiota
Glucuronidase
Drug-Related Side Effects and Adverse Reactions
Toxicity
irinotecan
2014
46 Citations (Scopus)

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

Biller, S. J., Berube, P. M., Berta-Thompson, J. W., Kelly, L., Roggensack, S. E., Awad, L., Roache-Johnson, K. H., Ding, H., Giovannoni, S. J., Rocap, G., Moore, L. R. & Chisholm, S. W., Sep 30 2014, In : Scientific data. 1, 140034.

Research output: Contribution to journalArticle

Prochlorococcus
Cyanobacteria
ecology
Genome
Genes
2013
48 Citations (Scopus)

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

Malmstrom, R. R., Rodrigue, S., Huang, K. H., Kelly, L., Kern, S. E., Thompson, A., Roggensack, S., Berube, P. M., Henn, M. R. & Chisholm, S. W., Jan 2013, In : ISME Journal. 7, 1, p. 184-198 15 p.

Research output: Contribution to journalArticle

Prochlorococcus
Genomics
Ecology
genomics
genome
33 Citations (Scopus)

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

Kelly, L., Ding, H., Huang, K. H., Osburne, M. S. & Chisholm, S. W., Sep 2013, In : ISME Journal. 7, 9, p. 1827-1841 15 p.

Research output: Contribution to journalArticle

Phosphorus
phosphorus
genetic variation
gene
Genes
54 Citations (Scopus)

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

Labrie, S. J., Frois-Moniz, K., Osburne, M. S., Kelly, L., Roggensack, S. E., Sullivan, M. B., Gearin, G., Zeng, Q., Fitzgerald, M., Henn, M. R. & Chisholm, S. W., May 2013, In : Environmental Microbiology. 15, 5, p. 1356-1376 21 p.

Research output: Contribution to journalArticle

genome
Genome
bacteriophages
Bacteriophages
gene
2012
24 Citations (Scopus)

ProPortal: A resource for integrated systems biology of Prochlorococcus and its phage

Kelly, L., Huang, K. H., Ding, H. & Chisholm, S. W., Jan 2012, In : Nucleic Acids Research. 40, D1

Research output: Contribution to journalArticle

Prochlorococcus
Systems Biology
Bacteriophages
Synechococcus
Genome
2011

Letter to the editor

Kelly, L., Fukushima, H., Karchin, R., Gow, J. M., Chinn, L. W., Pieper, U., Segal, M. R., Kroetz, D. L. & Sali, A., Jan 2011, In : Protein Science. 20, 1, p. 4-5 2 p.

Research output: Contribution to journalArticle

151 Citations (Scopus)

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

Thompson, L. R., Zeng, Q., Kelly, L., Huang, K. H., Singer, A. U., Stubbe, J. & Chisholm, S. W., Sep 27 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 39

Research output: Contribution to journalArticle

Bacteriophages
Carbon
Transaldolase
Pentose Phosphate Pathway
Genes
2010
56 Citations (Scopus)

Analysis of high-throughput sequencing and annotation strategies for phage genomes

Henn, M. R., Sullivan, M. B., Stange-Thomann, N., Osburne, M. S., Berlin, A. M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S. K., Nusbaum, C., Birren, B. W. & Chisholm, S. W., Feb 5 2010, In : PLoS One. 5, 2, e9083.

Research output: Contribution to journalArticle

Bacteriophages
bacteriophages
Genes
Throughput
Genome
138 Citations (Scopus)

Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria

Li, B., Sher, D., Kelly, L., Shi, Y., Huang, K., Knerr, P. J., Joewono, I., Rusch, D., Chisholm, S. W. & Van Der Donk, W. A., Jun 8 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 23, p. 10430-10435 6 p.

Research output: Contribution to journalArticle

Cyclic Peptides
Cyanobacteria
Prochlorococcus
Bacteria
Oceans and Seas
64 Citations (Scopus)

Comparison of human solute carriers

Schlessinger, A., Matsson, P., Shima, J. E., Pieper, U., Yee, S. W., Kelly, L., Apeltsin, L., Stroud, R. M., Ferrin, T. E., Giacomini, K. M. & Sali, A., Mar 2010, In : Protein Science. 19, 3, p. 412-428 17 p.

Research output: Contribution to journalArticle

Substrates
Substrate Specificity
Membrane Proteins
Organ Specificity
Aptitude
13 Citations (Scopus)

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains

Kelly, L., Fukushima, H., Karchin, R., Gow, J. M., Chinn, L. W., Pieper, U., Segal, M. R., Kroetz, D. L. & Sali, A., Nov 2010, In : Protein Science. 19, 11, p. 2110-2121 12 p.

Research output: Contribution to journalArticle

ATP-Binding Cassette Transporters
Polymorphism
Single Nucleotide Polymorphism
Nucleotides
Membrane Transport Proteins
177 Citations (Scopus)

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

Sullivan, M. B., Huang, K. H., Ignacio-Espinoza, J. C., Berlin, A. M., Kelly, L., Weigele, P. R., DeFrancesco, A. S., Kern, S. E., Thompson, L. R., Young, S., Yandava, C., Fu, R., Krastins, B., Chase, M., Sarracino, D., Osburne, M. S., Henn, M. R. & Chisholm, S. W., Nov 2010, In : Environmental Microbiology. 12, 11, p. 3035-3056 22 p.

Research output: Contribution to journalArticle

genomics
gene
Genes
genes
genome
15 Citations (Scopus)

UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase

Osburne, M. S., Holmbeck, B. M., Frias-Lopez, J., Steen, R., Huang, K., Kelly, L., Coe, A., Waraska, K., Gagne, A. & Chisholm, S. W., Jul 2010, In : Environmental Microbiology. 12, 7, p. 1978-1988 11 p.

Research output: Contribution to journalArticle

Prochlorococcus
Deoxyribodipyrimidine Photo-Lyase
Pyrimidine Dimers
operon
Operon
2009
13 Citations (Scopus)

A survey of integral α-helical membrane proteins

Kelly, L., Pieper, U., Eswar, N., Hays, F. A., Li, M., Roe-Zurz, Z., Kroetz, D. L., Giacomini, K. M., Stroud, R. M. & Sali, A., Dec 2009, In : Journal of Structural and Functional Genomics. 10, 4, p. 269-280 12 p.

Research output: Contribution to journalArticle

Membrane Proteins
Genome
Genes
Multidrug Resistance-Associated Proteins
Molecular Sequence Annotation
131 Citations (Scopus)

MODBASE, a database of annotated comparative protein structure models and associated resources

Pieper, U., Eswar, N., Webb, B. M., Eramian, D., Kelly, L., Barkan, D. T., Carter, H., Mankoo, P., Karchin, R., Marti-Renom, M. A., Davis, F. P. & Sali, A., 2009, In : Nucleic Acids Research. 37, SUPPL. 1

Research output: Contribution to journalArticle

Databases
Single Nucleotide Polymorphism
Proteins
Binding Sites
Ligands
9 Citations (Scopus)

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination

Hays, F. A., Roe-Zurz, Z., Li, M., Kelly, L., Gruswitz, F., Sali, A. & Stroud, R. M., Mar 2009, In : Journal of Structural and Functional Genomics. 10, 1, p. 9-16 8 p.

Research output: Contribution to journalArticle

Membrane Proteins
Pipelines
Saccharomyces cerevisiae
Inosine Monophosphate
Membranes
42 Citations (Scopus)

Selecting Optimum Eukaryotic Integral Membrane Proteins for Structure Determination by Rapid Expression and Solubilization Screening

Li, M., Hays, F. A., Roe-Zurz, Z., Vuong, L., Kelly, L., Ho, C. M., Robbins, R. M., Pieper, U., O'Connell, J. D., Miercke, L. J. W., Giacomini, K. M., Sali, A. & Stroud, R. M., Jan 23 2009, In : Journal of Molecular Biology. 385, 3, p. 820-830 11 p.

Research output: Contribution to journalArticle

Membrane Proteins
Saccharomyces cerevisiae
Proteome
Saccharomycetales
Protein S
23 Citations (Scopus)

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

Pieper, U., Chiang, R., Seffernick, J. J., Brown, S. D., Glasner, M. E., Kelly, L., Eswar, N., Sauder, J. M., Bonanno, J. B., Swaminathan, S., Burley, S. K., Zheng, X., Chance, M. R., Almo, S. C., Gerlt, J. A., Raushel, F. M., Jacobson, M. P., Babbitt, P. C. & Sali, A., Apr 2009, In : Journal of Structural and Functional Genomics. 10, 2, p. 107-125 19 p.

Research output: Contribution to journalArticle

Amidohydrolases
Phosphopyruvate Hydratase
Genomics
mandelate racemase
Isomerases
81 Citations (Scopus)

The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial 'mobilome'

Sullivan, M. B., Krastins, B., Hughes, J. L., Kelly, L., Chase, M., Sarracino, D. & Chisholm, S. W., Nov 2009, In : Environmental Microbiology. 11, 11, p. 2935-2951 17 p.

Research output: Contribution to journalArticle

Proteome
proteome
Oceans and Seas
genome
oceans
2007
24 Citations (Scopus)

Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy

Soranzo, N., Kelly, L., Martinian, L., Burley, M. W., Thom, M., Sali, A., Kroetz, D. L., Goldstein, D. B. & Sisodiya, S. M., Apr 2007, In : Epilepsia. 48, 4, p. 674-683 10 p.

Research output: Contribution to journalArticle

Epilepsy
Drug Resistance
P-Glycoprotein
Anticonvulsants
Phenotype
1 Citation (Scopus)

Response to Janigro et al. [4]

Sisodiya, S., Thom, M., Kroetz, D. & Kelly, L., Jun 2007, In : Epilepsia. 48, 6, p. 1219-1220 2 p.

Research output: Contribution to journalArticle

2006
191 Citations (Scopus)

MODBASE: a database of annotated comparative protein structure models and associated resources.

Pieper, U., Eswar, N., Davis, F. P., Braberg, H., Madhusudhan, M. S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B. M., Eramian, D., Shen, M. Y., Kelly, L., Melo, F. & Sali, A., Jan 1 2006, In : Nucleic acids research.. 34, Database issue

Research output: Contribution to journalArticle

Protein Databases
Databases
Proteins
Single Nucleotide Polymorphism
Binding Sites
3 Citations (Scopus)

PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-binding cassette transporters to the PharmGKB network

Nguyen, T. D., Gow, J. M., Chinn, L. W., Kelly, L., Jeong, H., Huang, C. C., Stryke, D., Kawamoto, M., Johns, S. J., Carlson, E., Taylor, T., Ferrin, T. E., Sali, A., Giacomini, K. M. & Kroetz, D. L., Mar 2006, In : Pharmacological Reviews. 58, 1, p. 1-2 2 p.

Research output: Contribution to journalArticle

Molecular Sequence Data
ATP-Binding Cassette Transporters
Pharmacogenetics
2005
175 Citations (Scopus)

LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources

Karchin, R., Diekhans, M., Kelly, L., Thomas, D. J., Pieper, U., Eswar, N., Haussler, D. & Sali, A., Jun 15 2005, In : Bioinformatics. 21, 12, p. 2814-2820 7 p.

Research output: Contribution to journalArticle

Single nucleotide Polymorphism
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Annotation
2001
95 Citations (Scopus)

A high-resolution radiation hybrid map of the human genome draft sequence

Olivier, M., Aggarwal, A., Allen, J., Almendras, A. A., Bajorek, E. S., Beasley, E. M., Brady, S. D., Bushard, J. M., Bustos, V. I., Chu, A., Chung, T. R., De Witte, A., Denys, M. E., Dominguez, R., Fang, N. Y., Foster, B. D., Freudenberg, R. W., Hadley, D., Hamilton, L. R., Jeffrey, T. J. & 35 others, Kelly, L., Lazzeroni, L., Levy, M. R., Lewis, S. C., Liu, X., Lopez, F. J., Louie, B., Marquis, J. P., Martinez, R. A., Matsuura, M. K., Misherghi, N. S., Norton, J. A., Olshen, A., Perkins, S. M., Perou, A. J., Piercy, C., Piercy, M., Qin, F., Reif, T., Sheppard, K., Shokoohi, V., Smick, G. A., Sun, W. L., Stewart, E. A., Fernando Tejeda, J., Tran, N. M., Trejo, T., Vo, N. T., Yan, S. C. M., Zierten, D. L., Zhao, S., Sachidanandam, R., Trask, B. J., Myers, R. M. & Cox, D. R., Feb 16 2001, In : Science. 291, 5507, p. 1298-1302 5 p.

Research output: Contribution to journalArticle

Sequence Tagged Sites
Radiation Hybrid Mapping
Human Genome
Genome
18 Citations (Scopus)

Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21

Olivier, M., Bustos, V. I., Levy, M. R., Smick, G. A., Moreno, I., Bushard, J. M., Almendras, A. A., Sheppard, K., Zierten, D. L., Aggarwal, A., Carlson, C. S., Foster, B. D., Vo, N., Kelly, L., Liu, X. & Cox, D. R., 2001, In : Genomics. 78, 1-2, p. 64-72 9 p.

Research output: Contribution to journalArticle

Chromosomes, Human, Pair 21
Linkage Disequilibrium
Human Chromosomes
Haplotypes
Single Nucleotide Polymorphism