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Faculty Profile

Libusha Kelly, Ph.D.

Dr. Libusha Kelly
 

Professional Interests

Our lab is geared toward extracting insights into the structure and dynamics of interacting microbial populations from genomics datasets. 

The metabolic capacity of communities of microbes can be selected for by environmental conditions and is accelerated by the ability of microbes to exchange genes with each other and with viruses. A major question, therefore, is: How does variability at the gene level affect the functional capacity and potential social interactions between members of microbial populations? 

We use network analysis, information theory, and dynamical modeling to 1) predict gene exchange and population evolution in microbial ecosystems in response to changing environmental conditionsand 2) define the organization and distribution of functions in microbial communities

Visit our lab website: http://www.kellylab.org/

 

Selected Publications

Primary author publications:

Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW. Genetic diversity in cultured and wild marinecyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME J. 2013 May 9. doi:10.1038/ismej.2013.58. [Epub ahead of print] 

Kelly L†, Huang KH†, Ding H, Chisholm SW. ProPortal: A resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40.

Kelly L†, Fukushima H†, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hotspots revealed by mutational, evolutionary, and structural characterization of ABC transporters. Protein Sci. 2010 Nov;19(11):2110-21. 

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 α–helical membrane proteins. J Struct Funct Genomics. 2009 Dec;10(4):269-80.

Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput. 2007:51-63.

Collaborations:

Cyanophage and cyanobacterial genomics and metagenomics

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. Environ Microbiol. 2013 May;15(5):1356-76.

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. ISME J. 2012 Aug 16. [Epub ahead of print].

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. Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):E757-64.

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. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10430-5.

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, Osburne MS, Henn MR, Chisholm SW. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol. 2010 Nov;12(11):3035-56.

Osburne MS, Holmbeck BM, Frias-Lopez J, Steen R, Huang K, Kelly L, Coe A, Waraska K, Gagne A, Chisholm SW. Environ Microbiol. UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase. 2010 Jul;12(7):1978-88. 

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, Birren BW, Chisholm SW. Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS One. 2010 Feb 5;5(2):e9083.

Computational sequence and structure analysis of membrane proteins

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 Sci. 2010 Mar;19(3):412-28.

Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol. 2009 Jan 23;385(3):820-30.

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. J Struct Funct Genomics. 2009 Mar;10(1):9-16.

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 Res. 2009 Jan;37 (Database issue):D347-54.

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 Res. 2006 Jan 1;34(Database issue):D291-5.

Computational analysis of human genetic variation 

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. 2007 Apr;48(4):674-83.

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. Pharmacol Rev. 2006 Mar;58(1):1-2.

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. 2005 Jun 15;21(12):2814-20.

Karchin R, Kelly L, Sali A. Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput. 2005:397-408. 

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, Cox DR. Complex High-Resolution Linkage Disequilibrium and Haplotype Patterns of Single-Nucleotide Polymorphisms in 2.5 Mb of Sequence on Human Chromosome 21 Genomics. 2001 Nov;78(1-2):64-72.

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, Foster BD, Freudenberg RW, Hadley D, Hamilton LR, Jeffrey TJ, Kelly L, Lazzeroni L, Levy MR, Lewis SC, Liu X, Lopez FJ, Louie B, Marquis JP, Martinez RA, Matsuura MK, Misherghi NS, Norton JA, Olshen A, Perkins SM, Perou AJ, Piercy C, Piercy M, Qin F, Reif T, Sheppard K, Shokoohi V, Smick GA, Sun WL, Stewart EA, Fernando J, Tejeda, Tran NM, Trejo T, Vo NT, Yan SC, Zierten DL, Zhao S, Sachidanandam R, Trask BJ, Myers RM, Cox DR. A High-Resolution Radiation Hybrid Map of the Human Genome Draft Sequence. Science. 2001 Feb 16;291(5507):1298-302. 

† Indicates that authors contributed equally to the publication

 
 

More Information About Dr. Libusha Kelly

http://www.kellylab.org/

Material in this section is provided by individual faculty members who are solely responsible for its accuracy and content.

Contact

Albert Einstein College of Medicine
Michael F. Price Center
1301 Morris Park Avenue , Room 553B
Bronx, NY 10461

Tel: 718.678.1148
Fax: 718.678.1022
libusha.kelly@einstein.yu.edu

 
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