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All microbes, all the time. May the microbes be ever in your favor.

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      • Data from Wu et al. 2011 Stalking 4th Domain paper
    • Other
      • 16S PCR Protocol
      • Gut Check: The Microbiome Game
      • Jonathan Eisen’s Figshare
  • Misc.
    • Retroblogging Meetings and Seminars: Posting Scans of Notes
    • Miscellaneous Notes and Scans
Jonathan Eisen's Lab

Tag: function

Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet:

Some new papers that may be of interest to people:

  • FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. 
  • Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis from Pookhao, Naruekamol 
  • Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data
  • Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization 
  • MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data   
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–
Author Jonathan EisenPosted on October 1, 2014Categories Misc.Tags annotation, function, HMMs, metagenomics, Misc., vFAMS, virusesLeave a comment on Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

RSS Lab Blog

  • New paper from Eisen lab and others … on challenges with relic RNA in SARS-CoV-2 environmental surveys April 27, 2022
    New paper out from my lab and other labs. Zuniga-Montanez R, Coil DA, Eisen JA, Pechacek R, Guerrero RG, Kim M, Shapiro K, Bischel HN. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA? PLoS One. 2022 Apr 22;17(4):e0267212. doi: 10.1371/journal.pone.0267212. PMID: 35452479; PMC […]
  • New preprint out from my lab and others about environmental monitoring for SARS-CoV-2 in schools and in part about how difficult this is November 18, 2021
    New preprint out on from the Eisen Lab and others. This is from a collaboration between David Coil, Heather Bischel, Karen Shapiro,  Randi Pechacek, Roque G. Guerrero, Minji Kim, and Rogelio Zuniga-Montanez (first author) at University of California, Davis.   It is about environmental monitoring for SARS-CoV-2 in schools and, well, in part about how difficul […]
  • Article about Dr. Connie Rojas getting UC Davis Chancellor’s Postdoctoral Fellow Award November 10, 2021
    See Researcher Studying the Microbiome and Chemical Communication of Cats Named a Chancellor’s Postdoctoral Fellow for an article by Greg Watry about Dr. Connie Rojas who is a post-doc in my lab. Dr. Rojas got a UC Davis Chancellor’s Postdoctoral Fellow Award to come to UC Davis to work on cats and the role of … Continue reading "Article about Dr. Conni […]

RSS The Tree of Life Blog

  • Best pics from Trip to Monterey - Day 1 - May 25, 2022
  • Videos about using the UCSC Genome Browser for analysis of SarsCOV2
  • Endosymbiosis Animations for "Biodiversity and the Tree of Life"

RSS microBEnet blog

  • 2022 Microbiology of the Built Environment Gordon Research Meeting
  • BioBE Preprint: Controlled Chamber COVID Study

Lab Blog Archives

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  • Home
  • About
    • Disclosures
    • Jonathan Eisen Bio
    • Funding
    • Questions for Jonathan Eisen (Advice, Background, Projects, etc)
    • Eisen CV (Google Doc)
    • More About Jonathan Eisen
  • People
  • Projects
    • Istmobiome
    • Seagrass Microbiomes
  • Past Projects
    • microBEnet
    • SWAN (Studies of Women’s Health Across the Nation) Microbiome
    • Corn Microbiome
    • Genomic Encyclopedia of Bacteria and Archaea (GEBA)
  • Publications
    • Publications Table
    • Publications by Topic
      • Publications: Animal-Microbe Interactions
      • Publications: Phylogenomic and Computational Methods and Tools
      • Publications – Marine Symbioses and Microbiology
      • Publications – Phylogenetic Diversity of Genomes
      • Publications: Plants and Associated Microbes
    • Eisen Pubs on Google Scholar
    • Publications – Pubmed
    • Publications List w/ notes
    • Evolution Textbook
  • Social Media
    • Eisen Lab Blog
    • Eisen’s Tree of Life Blog
    • microBEnet Blog
    • Eisen’s Twitter
    • Eisen Lab on Twitter
  • Education/Outreach
    • Space Microbes
    • Eisen Lab in the News
    • Gut Check: The Microbiome Game
    • Bodega Applied Phylogenetics Course
    • UC Davis Courses
    • Undergrad Genome Project
    • Eisen Talks and Presentations
    • Jonathan Eisen’s TED Talk on “Meet Your Microbes”
    • Jonathan Eisen Talks on Youtube
    • Eisen talks on Slideshare
  • Products
    • Software
      • A5 Assembly Pipeline
      • AMPHORA
      • APIS
      • Biotorrents
      • ComboDB
      • CompostBin
      • Mauve Assembly Metrics
      • PhyloSift
      • phylOTU
      • Pique
      • STAP
      • OTU Hunter
      • WATERS
      • Zorro
    • Lab Data
      • Lab Sequence Data
      • Eisen Lab Data at Figshare
      • Sifting Families: SFams
      • Darwin’s Finch Genome Data at Figshare
      • Data from Morgan et al. metagenomic simulation
      • Haloarchaea Data from Lynch et al. 2012
      • Data from Wu et al. 2011 Stalking 4th Domain paper
    • Other
      • 16S PCR Protocol
      • Gut Check: The Microbiome Game
      • Jonathan Eisen’s Figshare
  • Misc.
    • Retroblogging Meetings and Seminars: Posting Scans of Notes
    • Miscellaneous Notes and Scans
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