Eisen, Jonathan - University of California, Davis - College of Biological Sciences

研究领域

Research in the lab focuses on the “phylogenomics of novelty” in microbes. Major research themes include: The genomic basis for the origin and evolution of new functions. The ecology and evolution of microbial communities. The co-evolution of microbes and their carrying vessels (i.e., hosts). Variation in “evolvability.” The development of phylogeny-driven computational tools to analyze genomic and metagenomic sequence data.

近期论文

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Darling AE; Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. http://dx.doi.org/10.7717/peerj.243. Wu D, Jospin G, Eisen JA. 2013. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLOS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033 Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4:2120. doi: 10.1038/ncomms3120. PMID: 23979677. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459): 431-7. doi: 10.1038/nature12352. Lang JM, Darling AE, Eisen JA. Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510. Rands C, Darling AE, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. 2013. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 2013, 14:95 doi:10.1186/1471-2164-14-95. Eisen JA. 2012. Phylogenetic and phylogenomic approaches to analysis of microbial communities. In "The Social Biology of Microbial Communities - A Report from the National Academy of Sciences Forum on Microbial Threats." PDF. Traag B, Pugliese A, Eisen JA, Losick R. 2012. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis Journal of Bacteriology JB.01778-12 . PMID: 23123912. PDF. Kembel SW, Wu M, Eisen JA, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology 8(10): e1002743. doi:10.1371/journal.pcbi.1002743. PMID: 23133348. PDF. Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KS, Eisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics 13: 264. doi:10.1186/1471-2105-13-264. PMID: 23061897. PDF. Tritt A, Eisen JA, Facciotti M, Darling A. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7(9): e42304. doi:10.1371/journal.pone.0042304. PMID: 23028432. PDF. Chandler JA, Eisen JA, Kopp A. 2012. Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts. Applied and Environmental Microbiology 78(20): 7327-7336. PMID: 22885750. PDF. Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1:6. PDF. Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLoS Genetics 7(9): e1002272. PMID: 21966276. PDF. Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6(8): e23214. PMID: 21912589. PDF. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proceedings of the National Academy of Sciences USA 108: 7850-7854. PMID: 21518859. PDF. Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees. PLoS ONE 6(3): e18011. PMID: 21437252. PDF. Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134. PDF. Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944. PDF. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462(7276): 1056-60. PMID: 20033048. PDF. Hartman A, Lough D, Fiehn O, Barupal D, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proceedings of the National Academy of Sciences USA 106(40): 17187-17192. PMID: 19805153. PDF. Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biology 7(10): e1000224. PMID: 19855830. PDF. Eisen JA. 2009. Genomic Evolvability and the Origin of Novelty: Studying the Past, Interpreting the Present, and Predicting the Future. In Relman DA, Hamburg MA, Choffness ER, Mack A (ed), Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. The National Academies Press, Washington, DC. PDF. Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9(1): R151. PMID: 18851752. PDF. Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82. PMID: 17355177. PDF.