Category Archives: Lab Publications

New EisenLab paper: PhyloSift: phylogenetic analysis of genomes and metagenomes [PeerJ]

New paper from people in the Eisen lab (and some others): PhyloSift: phylogenetic analysis of genomes and metagenomes [PeerJ].  This project was coordinated by Aaron Darling, who was a Project Scientist in my lab and is now a Professor at the … Continue reading

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New paper from Eisen lab: Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG-I project

A new paper of possible interest discussing one of the new phases of the GEBA Genomic Encyclopedia of Bacteria and Archaea project. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG-I project | Kyrpides | Standards in … Continue reading

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New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my … Continue reading

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New papers from people in the lab …

A lot of new papers from people in the lab in the last month or so.  See below for details of some of them: PLOS ONE: Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices from Jenna Morgan Lang, Aaron … Continue reading

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Email from Biomed Central pointing to ways to get #altmetrics for recent sFAMS paper

Just received from Biomed Central and thought some people might be interested in some of the ways they try to help you gather metrics about your papers. Dear Prof Eisen, We thought you might be interested to know how many … Continue reading

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New paper: MicrobeDB: a locally maintainable database of microbial genomic sequences

New paper out involving the lab.  The lead author is Morgan Langille, who was a post doc in the lab and is now at Dalhausie Dalhousie University.  The paper describes a tool for creation and maintenance of a local genome sequence … Continue reading

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New paper from lab: Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila

A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophil a.  It was a collaboration between Kathy Collins, … Continue reading

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New publication from Lizzy Wilbanks, Russell Neches, et al

New publication from members of the lab in Nucleic Acids Research: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. Congrats.  Gonna have to make some new jam …

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New paper: PLoS ONE: Accounting For Alignment Uncertainty in Phylogenomics

A new paper is out from the lab: PLoS ONE: Accounting For Alignment Uncertainty in Phylogenomics. It describes the “Zorro” software for automated alignment masking. Abstract: Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been … Continue reading

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New publication from the lab: Assemblathon 1: A competitive assessment of de novo short read assembly methods

Aaron Darling from the lab is an author on a new paper just published: Assemblathon 1: A competitive assessment of de novo short read assembly methods.

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