Frank W. Larimer Adjunct Professor, Genome Science & Technology http://genome.ornl.gov/~fwl/ PhD: Genetics, Florida State University MS: Genetics, Florida State University BS: Biology, Albion College Oak Ridge National Laboratory PO Box 2008 MS6164 Oak Ridge, TN 37831-6164 larimerfw@ornl.gov

Keywords:
Bioinformatics, genomics, genome annotation, proteomics, protein engineering

Research Area:
Research interests include microbial genomics, genome annotation, and bioinformatics, as well as proteomics and microbial physiology. He retired from ORNL in 2005, where he was a Distinguished Scientist and Group Leader in the Genome Analysis Group of the Life Sciences Division. He was formerly the Deputy Director of the Center for Molecular and Cellular Systems, and remains a member of the Computational Biology Institute.

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. Earlier research in the Protein Engineering Program centered on studies of enzymatic mechanisms in a number of critcal Calvin cycle enzymes including ribulose-bisphosphate carboxylase/oxygenase, phosphoribulokinase (and it's activator, thioredoxin), phosphoribulose epimerase, and phosphoribose isomerase. Initial work in the genetic control of mutagenesis and DNA repair lead to early adoption of cloning and sequencing technologies, which in turn were critical to the establishment of the Protein Engineering Program at ORNL.

Selected Publications:

• Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L.-A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, III, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje (2005). Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. Proc Nat Acad Sci USA. 102(6): 2099-2105.
  


• Verberkmoes, N. C., W. J. Hervey, M. Shah, M. Land, L. Hauser, F. W. Larimer, G. J. Van Berkel, and D. E. Goeringer (2005). Evaluation of shotgun proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations.. Anal Chem. 77(6): 923-932.
  


• Feil, H., W. S. Feil, P. Chain, F. Larimer, G. DiBartolo, A. Copeland, A. Lykidis, S. Trong, M. Nolan, E. Goltsman, J. Thiel, S. Malfatti, J. E. Loper, A. Lapidus, J. C. Detter, M. Land, P. M. Richardson, N. C. Kyrpides, N. Ivanova, and S. E. Lindow (2005). Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Nat Acad Sci USA. 102(31): 11064-11069.
  


• Oren, A., Larimer, F., Richardson, P., Lapidus, A., Csonka, L. N. (2005). How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles. 9(4): 275-9.
  


• Chain PS, Comerci DJ, Tolmasky ME, Larimer FW, Malfatti SA, Vergez LM, Aguero F, Land ML, Ugalde RA, Garcia E (2005). Whole-genome analyses of speciation events in pathogenic brucellae. Infect. Immun.. 73(12): 8353-61. PubMed
  


• Larimer, FW, P Chain, L Hauser, J Lamerdin, S Malfatti, L Do, M Land, DA Pelletier, JT Beatty, AS Lang, FR Tabita, JL Gibson, TE Hanson, C Bobst, J Torres y Torres, C Peres, F Harrison, J Gibson and CS Harwood. (2004). Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnology. 22(1): 55-61. PubMed
  


• Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology. 22(6): 695-700. PubMed
  


• Strader, MB; VerBerkmoes, NC; Tabb, DL; Connelly, HM; Barton, JW; Bruce, BD; Pelletier, DA; Davison, BH; Hettich, RL; Larimer, FW; Hurst, GB (2004). Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated Top-Down and Bottom-Up Mass Spectrometric Approach. J. Proteome Res.. 3(5): 965-78.
  


• Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E (2004). Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Nat. Acad. Sci. USA. 101(38): 13826-13831. PubMed
  


• Hendrickson, EL, R Kaul, Y Zhou, D Bovee, P Chapman, J Chung, E Conway de Macario, JA Dodsworth, W Gillett, DE Graham, M Hackett, AK Haydock, A Kang, ML Land, R Levy, TJ Lie, TA Major, BC Moore, I Porat, A Palmeiri, G Rouse, C Saenphimmachak, D Soll, S Van Dien, T Wang, WB Whitman, Q Xia, Y Zhang, FW Larimer, MV Olson, and JA Leigh. (2004). Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis. J. Bacteriol.. 186(20): 6956-6969.
  


• Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004). The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 306(5693): 79-86. PubMed
  


• Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW. (2003). Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424(6952): 1042-7. PubMed
  


• Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. (2003). The genome of a motile marine Synechococcus. Nature. 424(6952): 1037-42. PubMed
  


• Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M, Arp D. (2003). Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol.. 185(9): 2759-73. PubMed
  


• Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R. (2003). Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13(7): 1580-8. PubMed