Jeff Kimbrel

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-452
Livermore, CA 94550

email: kimbrel1@llnl.gov
phone: 925 409 6015
 

Education

Ph.D., Molecular and Cellular Biology, Oregon State University
B.S., Biological Sciences, Colorado State University

Research

My research interests focus primarily on the interactions of microbes (bacteria, archaea and bacteriophage) with other organisms and their environment. I utilize a broad range of computational biology and molecular techniques, largely focusing on improving functional annotation of prokaryotic and phage genomes, either isolated or binned from metagenomes (MAGs).

Publications

  1. Morris MM, Kimbrel JA, Geng H, Tran-Gyamfi MB, Yu ET, Sale KL, Lane, TW, Mayali X. Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salinamSphere (2022). doi:10.1128/msphere.00231-22
  2. Sokol, et al, LLNL Soil Consortium. Life and Death in the Soil Microbiome: How Ecological Processes Influence Biogeochemistry. Nature Reviews Microbiology (2022). doi:10.1038/s41579-022-00695-z
  3. Kimbrel JA, Jeffrey BM, Ward, CS. Prokaryotic Genome Annotation. Microbial Systems Biology: Methods and Protocols 2nd Edition. Springer (2022). doi:10.1007/978-1-0716-1585-0_10
  4. Nayfach, et al, IMG/M Data Consortium. A Genomic Catalog of Earthy’s Microbiomes. Nature Biotechnology (2021). doi:10.1038/s41587-020-0718-6
  5. Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome (2021). doi:10.1186/s40168-021-01154-2
  6. Kim H, Kimbrel JA, Vaiana CA, Wollard JR, Mayali X, Buie CR. Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate. ISME J (2021). doi:10.1038/s41396-021-01147-x
  7. Zhou CE, Kimbrel JA, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: code for functional annotation and comparison of phage genomes. G3|Genes|Genomes|Genetics (2021). doi: 10.1093/g3journal/jkab074
  8. Seaver, et al. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Research (2021). doi.org/10.1093/nar/gkaa746
  9. Higgins DA, Gladden J, Kimbrel JA, Simmons BA, Singer SW, Thelen MP. Bacterial guanidine riboswitch regulated SMR-type efflux transporters protect against ionic liquid toxicity. Journal of Bacteriology (2019). doi:10.1128/JB.00069-19
  10. Zhou CE, Malfatti S, Kimbrel JA, Philipson C, McNair K, Hamilton T, Edwards R, Souza B. multiPhATE: Bioinformatics Pipeline for Functional Annotation of Phage Isolates. Bioinformatics (2019). doi:10.1093/bioinformatics/btz258
  11. Fisher CL, Ward CS, Lane PD, Kimbrel JA, Stuart RK, Mayali X, Lane TW. Bacterial communities protect the alga Microchloropsis salinafrom grazing by the rotifer Brachionus plicatilisAlgal Research (2019). doi:10.1016/j.algal.2019.101500
  12. Kimbrel JA, Samo TJ, Nilson D, Thelen MP, Siccardi A, Zimba P, Lane TW, Mayali X. Host Selection and Stochastic Effects Influencing Bacterial Community Assembly on the Microalgal Phycosphere. Algal Research (2019). doi:10.1016/j.algal.2019.101489
  13. Griesemer M*, Kimbrel JA*, Zhou CE, Navid A, D'haeseleer P. Combining multiple functional annotation tools increases completeness of metabolic annotation. BMC Genomics (2018). doi:10.1186/s12864-018-5221-9
  14. Samo TJ, Kimbrel JA, Nilson D, Pett-Ridge J, Weber P, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environmental Microbiology (2018). doi:10.1111/1462-2920.14357
  15. Kimbrel JA, Ballor N, Wu Y, David M, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Frontiers in Microbiology (2018). doi:10.3389/fmicb.2018.01492
  16. Woo HL, Ballor NR, Hazen TC, Fortney JL, Simmons BA, Davenport KW, Goodwin L, Ivanova NN, Kyrpides NC, Mavromatis K, Woyke T, Jansson J, Kimbrel JA, DeAngelis KM. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Standards in Genomic Sciences (2014). doi:10.1186/1944-3277-9-19
  17. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel JA, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J (2014). doi:10.1038/ismej.2013.254
  18. Kimbrel JA, Chang JH, Arp DJ, Sayavedra-Soto LA. The draft genome sequence of Nocardioides sp. strain CF8 reveals the scope of its metabolic capabilities. Genome Announcements. August 2013. Volume 1, Issue 4. http://genomea.asm.org/content/1/4/e00439-13.short
  19. Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Applications in Plant Sciences. March 2013. Volume 1, Issue 3. http://www.bioone.org/doi/abs/10.3732/apps.1200011
  20. Kimbrel JA*, Thomas WJ*, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH. Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicumPLoS Pathogens. February 2013, Volume 9, Issue 2. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat...(*co-first authors)
  21. Di Y, Emerson SC, Shafer DW, Kimbrel JA, Chang JH. Higher Order Asymptotics for Negative Binomial Regression Inferences from RNA-Sequencing Data. Statistical Applications in Genetics and Molecular Biology. January 2013. Volume 12, Issue 1, pages 49-70. 
  22. Kimbrel JA, Di Y, Cumbie JS, Chang JC. RNA-Seq for Plant Pathogenic Bacteria. Genes. October 2011. http://www.mdpi.com/2073-4425/2/4/689
  23. Cumbie JS*, Kimbrel JA*, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences, PLoS ONE. October 2011. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00252...(*co-first authors)
  24. Sayavedra-Soto L, Hamamura N, Liu C, Kimbrel JA, Chang JH, Arp D. The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environmental Microbiology Reports. 2011. http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00239.x/full
  25. Kimbrel JA, Givan SA, Temple TN, Johnson KB, Chang JH. Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics. Molecular Plant Pathology. January, 2011. http://onlinelibrary.wiley.com/doi/10.1111/j.1364-3703.2010.00694.x/full
  26. Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics 2010, 11:522. September 28, 2010. http://www.biomedcentral.com/1471-2164/11/522/abstract
  27. International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyonNature. February 11, 2010. Kimbrel JA and Chang JH contributing authors. http://www.nature.com/nature/journal/v463/n7282/full/nature08747.html
  28. Cohu CM, Abdel-Ghany SE, Gogolin Reynolds KA, Onofrio AM, Bodecker JR, Kimbrel JA, Niyogi KK, Pilon M. Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant. October 21, 2009. http://mplant.oxfordjournals.org/content/2/6/1336.abstract
  29. Thomas WJ, Thireault CA, Kimbrel JA, Chang JH. Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. The Plant Journal. August 6, 2009. http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2009.03998.x/abst...