Lab and computational methods development

The Eisen Lab has a long interest in laboratory and computational methods development especially as it relates to microbes and/or sequencing.  Example areas on this topic are discussed below.

Computational Methods Development

The lab has had a major focus on computational methods development with an emphasis on using phylogeny (in diverse ways) as a tool in studies of microbial diversity.  Example publications on this topic is below

  • Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. 2015. Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLOS Computational Biology 11(11): e1004573.  PMID: 26565399. PMCID: PMC4643905.
  • Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243. PMID: 24482762. PMC3897386.
  • 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: e77033. PMCID: PMC3798382.
  • Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.PLoS ONE 8: e62510. PMID: 23638103. PMCID: PMC3636077.
  • 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.
  • 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: e1002743. PMID: 23133348. PMCID: PMC3486904. 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. PMID: 23061897. PMCID: PMC3481395. 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: e43866. PMID: 23049741. PMCID: PMC3445553. PDF.
  • Tritt A, Eisen JA, Facciotti M, Darling A. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7: e42304. PMID: 23028432. PMCID: PMC3441570. PDF.
  • Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7: e30288. PMID: 22272325. PMCID: PMC3260272. PDF.
  • Darling A, Tritt A, Eisen JA, Facciotti M. 2011. Mauve assembly metrics. Bioinformatics 27: 2756-2757. PMID: 21810901. PMCID: PMC3179657. PDF.
  • Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6: e23214. PMID: 21912589. PDF.
  • Sharpton TJ, Risenfeld 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: e1001061. PMID: 21283775. PMCID: PMC3024254. PDF.
  • Langille MGI, Eisen JA. 2010.BioTorrents: a file sharing service for scientific data. PLoS ONE 5: e10071. PMID: 20418944. PDF.
  • 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 11: 317. PMID: 20540779. 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: R151. PMID: 18851752.
  • Wu D, Hartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3: e2566. PMID: 18596968. PDF.
  • Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008. PDF.
  • Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5: e82. PMID: 17355177. PDF.
  • Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538
  • Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8: 163-167. PMID: 952191
  • Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078. PMID: 9334711. PMCID: PMC315595. PDF.
  • Eisen JA. 1997. The genetic data environment: a user modifiable and expandable multiple sequence analysis package, In Methods in Molecular Biology vol 70: Sequence Data Analysis Guidebook (SR Swindell, ed), Humana, Totowa, NJ, pp. 13-38. PMID: 90896. PDF.
  • Eisen JA. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. Journal of Molecular Evolution 41: 1105-1123. PMID: 8587109. PMCID: PMC3188426. PDF.
  • Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723. PMID: 7651832. PMCID: PMC307096. PDF.

Lab Methods for Microbial Diversity Studies

  • Horng KR, Ganz HH, Eisen JA, Marks SL. 2018. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6: e4827.
  • Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. Swabs to genomes: a comprehensive workflow. PeerJ 3: e960. PMID: 26020012. PMCID: PMC4435499.
  • Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2: e415. PMID: 24918035. PMCID: PMC4045339.
  • Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5: e10209. PMID: 20419134. PDF. Data available here.
  • Pollock DD, Eisen JA, Doggett NA, Cummings MP. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular Biology and Evolution 7: 1776-1788. PMID: 11110893. PDF.

Standards and Guidelines

  • Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35(8): 725-731. doi: 10.1038/nbt.3893. PMID: 2878742.
  • 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. 2010. Meeting Report. The Terabase Metagenomics workshop and the vision of an Earth Microbiome Project. Standards in Genomic Sciences 3: 243-248. PMID: 21304727. PDF.
  • Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. 2013. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME Journal 8: 1-3. PMID: 24152717. PMCID: PMC3869023.
  • Leebens-Mac J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, DePamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin, EV, Mishler BD, Philippe H, Pirer JC, Qiu Y-L, Rheee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the first steps towards a phylogenetic reporting standard: minimal information about a phylogenetic analysis (MIAPA). OMICS 10: 231-238. PMID: 16901231. PMCID: PMC3167193. PDF.
  • Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. 2002. The value of complete microbial genome sequencing (You get what you pay for). Journal of Bacteriology 184: 6403-6405. PMID: 12426324. PDF.
  • Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527. PDF.
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