Frank W. Larimer |
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| http://genome.ornl.gov/~fwl/ |
Ph.D., Florida State University, 1975
Frank Larimer is a Research Professor of Genome Science and Technology at the University of Tennessee, attached to the Genome Analysis Group at ORNL. His current responsibilities include research in microbial genomics, genome annotation, and bioinformatics, as well as proteomics and microbial physiology.
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OAK RIDGE NATIONAL LABORATORY
PO BOX 2008 MS6164
OAK RIDGE TN 37831-6164 |
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larimerfw@ornl.gov |
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KEYWORDS:bioinformatics, genomics, genome annotation, proteomics, protein engineering |
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DESCRIPTION OF RESEARCH: Dr. Larimer's research interests have a broad span across molecular genetics and biochemistry. Recent work is focused on microbial genomics, with emphasis on genome structure: operon, regulon, and supra-regulon organization; genome organization; and genome evolution. Other ongoing research includes microbial proteomics and high-throughput characterization of molecular machines and protein complexes.
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Selected Publications |
| Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land M, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres y Torres J, Peres C, Harrison F, Gibson J, Harwood CS. (2004). Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnology 22(1): 55-61. PubMed
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Pelletier DA, Hurst GB, Foote LJ, Lankford PK, McKeown CK, Lu TY, Schmoyer DD, Shah MB, Hervey WJ 4th, McDonald WH, Hooker BS, Cannon WR, Daly DS, Gilmore JM, Wiley HS, Auberry DL, Wang Y, Larimer FW, Kennel SJ, Doktycz MJ, Morrell-Falvey JL, Owens ET, Buchanan MV. (2008) A General System for Studying Protein-Protein Interactions in Gram-Negative Bacteria. J Proteome Res. 7(8):3319-3328. PubMed |
Weiner RM, Taylor LE, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S. (2008) Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40. PLoS Genet. 4(5):e1000087. PubMed
| Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PSG, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR. (2008). Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl. Environ. Microbiol. 74:(11): 3559-3572. PubMed
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| Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B, Bottomley PJ. (2008). The complete genome sequence of Nitrobacter hamburgensis X14 and a comparative genomic analysis of species within the Genus Nitrobacter. Appl Environ Microbiol. 74(9):2852-2863. PubMed
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| Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J; the USF Genomics Class (2008). The genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol. 74(4):1145-1156. PubMed
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| Garcia E, Worsham P, Bearden S, Malfatti S, Lang D, Larimer F, Lindler L, Chain P (2007). Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Adv Exp Med Biol. 603:17-22. PubMed
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| Stein LY, Arp DJ, Berube PM, Chain PSG, Hauser L, Jetten MSM, Klotz MG, Larimer FW, Norton JM, Op den Camp HJM, Shin M, and Wei X (2007). Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental Microbiology 9(12):2993-3007. PubMed
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| Kane SR, Chakicherla AY, Chain PSG, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, and Hristova KR. (2007). Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1. J. Bacteriol. 189(5): 1931-1945. PubMed
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| Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hügler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT. (2006). The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol. 4(12): e383. PubMed
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| Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103(42):15280-15287. PubMed
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| Tuskan GA, et al., (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793): 1596-1604. PubMed
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| Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB. (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol. 72(9): 6299-6315. PubMed
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| Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL (2006). Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen. J. Bacteriol.. 188(12): 4453-4463. PubMed
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| Mavromatis K, Doyle CK, Lykidis A, Ivanova N, Francino MP, Chain P, Shin M, Malfatti S, Larimer F, Copeland A, Detter JC, Land M, Richardson PM, Yu XJ, Walker DH, McBride JW, Kyrpides NC (2006). The genome of the obligately intracellular bacterium Ehrlichia canisi reveals themes of complex membrane structure and immune evasion strategies. J. Bacteriol.. 188(11):4015-4023. PubMed
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| Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, and Kelly DP (2006). The genome sequence of the obligately chemolithoautotrophic facultatively anaerobic bacterium Thiobacillus denitrificans. J. Bacteriol.. 188(4): 1473-1488. PubMed
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| Starkenburg SR, Chain PSG, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ. (2006) Genome sequence of the cheolithoautotrophic nitite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Appl Environ Microbiol 7(3):2050-2063. PubMed
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| VerBerkmoes NC, Shah MB, Lankford PK, Pelletier DA, Strader MB, Tabb DL, McDonald WH, Barton JW, Hurst GB, Hauser L, Davison BH, Beatty JT, Harwood CS, Tabita FR, Hettich RL, and Larimer FW (2006). Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under Its Major Metabolic States. J. Proteome Res. 5(2): 287-298. PubMed |
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