Publications

Publications from iSEEM 2

2013

• 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. PMID = 24146954.
• Ladau, J., T.J. Sharpton, M.M. Finucane, G. Jospin, S.W. Kembel, J. O’Dwyer, A.F. Koeppel, J.L. Green, K.S. Pollard. 2013. Global marine bacterial diversity peaks at high latitudes in winter. ISME 7(9):1669-77. doi: 10.1038/ismej.2013.37. PMID = 23514781.
• 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. PMID: 23851394.
• Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. 110(3):1053-8. doi: 10.1073/pnas.1217107110. PMID = 23277585.

2012

• 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.
• 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. PMID: 23133348. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.100 2743
• Eisen JA. 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.
• Jiang X, Langille MGI, Neches RY, Elliot MA, Levin SA, Eisen JA, Weitz JS, Dushoff J. 2012. Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scales. PLoS ONE 7(9): e43866. doi:10.1371/journal.pone.0043866. PMID: 23049741

 

Publications from iSEEM 1

2011

• Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. 2011. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol. doi: 10.1111/j.1462-2920.2011.02576.x.
• Eisen JA. 2011. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes, Frans J. de Bruijn, (ed),Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, Vol. 1.. Wiley Press.
• Wu M and ‘Eisen JA. 2011. Towards Automated Phylogenomic Inference, Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, Wiley Press.
• Chandler JA, Morgan Lang J, Bhatnagar S, Eisen JA, Kopp A (2011) Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System. PLoS Genet 7(9): e1002272. doi:10.1371/journal.pgen.1002272.
• Kembel SW, Eisen JA, Pollard KS, Green JL. 2011. The Phylogenetic diversity of metagenomes. PLoS ONE 6(8): e23214.
• Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. 2011. Aggregating, tagging and integrating biodiversity research. PLoS One 6(8): e19491.
• Sharpton TJ, Riesenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PhylOTU: A High-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology, 7(1): e1001061PMCID 3024254.
• Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7850-4. Epub 2011 Apr 25. PMCID 3093525.
• Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One. 2011 Mar 18;6(3):e18011. PMCID 3060911.
• Hubisz MJ, Pollard KS, Siepel A (2011). PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in Bioinformatics, (12)1: 41-51PMCID 3030812. Open Access.

2010

• Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2011. Meeting Report. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Standards in Genomic Sciences, 3(3): 243-248.PMCID 3035311.
• Langille MGI, Eisen JA. 2010. BioTorrents: A File Sharing Service for Scientific Data. PLoS One. 2010 Apr 14;5(4):e10071. PMCID 2854681.
• Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. 2010. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics. 2010 Jun 12;11:317. PMCID 2898799.
• O’Dwyer JP, Green JL (2010). Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecol Lett 13:87 – 95.
• Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463-1464.

2009

• 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. 2009 Dec 24;462(7276):1056-60. PMCID 3073058
• O’Dwyer JP, Lake JK, Ostling A, Savage VM, Green JL. 2009. An integrative framework for stochastic, size-structured community assembly. Proc Natl Acad Sci 106:6170-6175.
• Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2009. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Research, 20: 110-121 PMCID 2798823.

2008

• Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13;9(10):R151.. PMCID 2760878. Open access.
• Wu D, Hartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One. 2008 Jul 2;3(7):e2566. . PMCID 2432038. Open access.
• Green J, Bohannan B, Whitaker R. 2008. Microbial biogeography: from taxonomy to traits. Science. 2008 320:1039-43.