29 posts · 27,113 views
Blog of Jonathan A. Eisen, evolutionary biologist, microbial genomics researchers, and Open Access advocate, Professor at UC Davis and Academic Editor in Chief of PLoS Biology.
Jonathan Eisen
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- August 9, 2010
- 08:47 PM
- 7,471 views
Lack of neutrality in bacteria and where pseudogenes go when they die
by Jonathan Eisen in The Tree of Life
Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland's neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are........ Read more »
Kuo, C., & Ochman, H. (2010) The Extinction Dynamics of Bacterial Pseudogenes. PLoS Genetics, 6(8). DOI: 10.1371/journal.pgen.1001050
- October 13, 2006
- 12:00 AM
- 1,243 views
World's Smallest Genome of a Cellular Organism?
by Jonathan Eisen in The Tree of Life
Discussion of Science paper on a very small genome... Read more »
Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006) The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science, 314(5797), 267-267. DOI: 10.1126/science.1134196
- February 3, 2010
- 10:53 AM
- 1,091 views
Story behind the science: #PLoS Genetics "Evolutionary mirages" paper
by Jonathan Eisen in The Tree of Life
So there is this cool new paper out in PLoS Genetics: Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. and I have wanted to write about it for a week or so. You see, the paper is about something I have been interested in for most of my career - how the particular processes by which mutations occur can sometimes be biased (i.e., some types of mutations are more common than others) and that these biases can create high........ Read more »
Lusk, R., & Eisen, M. (2010) Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. PLoS Genetics, 6(1). DOI: 10.1371/journal.pgen.1000829
- August 21, 2010
- 04:53 AM
- 1,006 views
More (you know you wanted it) on fecal transplants and the microbiome
by Jonathan Eisen in The Tree of Life
Image fromI Heart Guts blogThere is an interesting mini review in the Journal of Clinical Gastroenterology's September issue that may be of interest to some out there. It is entitled "Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome" by Martin Floch and well, the title is indicative of the article.Yes, the fecal transplant meme is here to stay. Sure, the cognoscenti already knew about fecal transplants. Perhaps they had read Tara Smith's discussion of it in her Aetiology blog in 20........ Read more »
Floch, M. (2010) Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome. Journal of Clinical Gastroenterology, 44(8), 529-530. DOI: 10.1097/MCG.0b013e3181e1d6e2
Grehan, M., Borody, T., Leis, S., Campbell, J., Mitchell, H., & Wettstein, A. (2010) Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora. Journal of Clinical Gastroenterology, 44(8), 551-561. DOI: 10.1097/MCG.0b013e3181e5d06b
Khoruts, A., Dicksved, J., Jansson, J., & Sadowsky, M. (2009) Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea. Journal of Clinical Gastroenterology, 1. DOI: 10.1097/MCG.0b013e3181c87e02
Yoon, S., & Brandt, L. (2010) Treatment of Refractory/Recurrent C. difficile-associated Disease by Donated Stool Transplanted Via Colonoscopy. Journal of Clinical Gastroenterology, 44(8), 562-566. DOI: 10.1097/MCG.0b013e3181dac035
- December 29, 2009
- 02:03 PM
- 994 views
Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
by Jonathan Eisen in The Tree of Life
Today is a fun day for me. A paper on which I am the senior author is being published in Nature (yes, the Academic Editor in Chief of PLoS Biology is publishing a paper in Nature, more on that below ..). This paper, entitled, "A phylogeny driven genomic encyclopedia of bacteria and archaea" represents a culmination of years of work by many people from multiple institutions. Today in this blog I am going to do my best to tell the story behind the paper - about the people and t........ Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- December 29, 2009
- 01:43 AM
- 979 views
More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"
by Jonathan Eisen in The Tree of Life
Additional discussion of recent paper... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- November 15, 2010
- 07:52 AM
- 969 views
One of my new favorite things: paleovirology
by Jonathan Eisen in The Tree of Life
Just a quick post here about a paper that came out about a month or so ago: PLoS Biology: Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
This paper, by Clément Gilbert, Cédric Feschotte is quite cool. In it they describe their work on "Paleovirology" where they look for viruses than have "endogenized" by inserting into the genome of some host species. This endogenization is important in particular when the endogenous form becomes inactive and thus, i........ Read more »
Gilbert, C., & Feschotte, C. (2010) Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biology, 8(9). DOI: 10.1371/journal.pbio.1000495
- January 6, 2010
- 12:32 PM
- 954 views
#PLoSOne paper keywords revealing: (#Penis #Microbiome #Circumcision #HIV); press release misleading
by Jonathan Eisen in The Tree of Life
UPDATE - READ COMMENTS - LEAD AUTHOR HAS GOTTEN PRESS RELEASE CHANGED
A new paper just showed up on PLoS One and it has some serious potential to be important The paper (PLoS ONE: The Effects of Circumcision on the Penis Microbiome) reports on analyses that show differences in the microbiota (which they call the microbiome - basically what bacterial species were present) in men before and after circumcision. And they found some significant differences. It is a nice study of a relatively poo........ Read more »
Price, L., Liu, C., Johnson, K., Aziz, M., Lau, M., Bowers, J., Ravel, J., Keim, P., Serwadda, D., Wawer, M.... (2010) The Effects of Circumcision on the Penis Microbiome. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008422
- October 12, 2010
- 10:00 PM
- 858 views
Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper
by Jonathan Eisen in The Tree of Life
Just a quick post here. A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search
In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers. The system is available through their webserver "Ask Hermes".
If you want to learn more about the system I suggest you read the paper. &n........ Read more »
Yu, H., Liu, F., & Ramesh, B. (2010) Automatic Figure Ranking and User Interfacing for Intelligent Figure Search. PLoS ONE, 5(10). DOI: 10.1371/journal.pone.0012983
- January 24, 2011
- 03:36 AM
- 845 views
Phylogeny rules:
by Jonathan Eisen in The Tree of Life
I am a coauthor on a new paper in PLoS Computational Biology I thought I would promote here. The full citation for the paper is:
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data (doi:10.1371/journal.pcbi.1001061).
The paper discusses a new software program "phylOTU" which is for phylogenetic-based identification of "operational taxonomic units", which are also known as OTUs. What are OTUs? ........ Read more »
Sharpton, T., Riesenfeld, S., Kembel, S., Ladau, J., O'Dwyer, J., Green, J., Eisen, J., & Pollard, K. (2011) PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. PLoS Computational Biology, 7(1). DOI: 10.1371/journal.pcbi.1001061
- January 26, 2010
- 06:29 PM
- 834 views
Wanted:Feedback on Importance of Finishing (Microbial) Genomes
by Jonathan Eisen in The Tree of Life
To allI am writing because I am working on a project to evaluate the importance of finishing microbial genomes. I know there has been lots of talk about this out there on the web and in papers, etc but I think a fresh discussion is useful. To get people up to speed below is a summary of the issue as I see it.Shotgun sequencing: Genome sequencing relies generally on the shotgun method at the beginning of a project where DNA fragments from an organism of interest are sequenced in a highly random........ Read more »
Blakesley, R., Hansen, N., Gupta, J., McDowell, J., Maskeri, B., Barnabas, B., Brooks, S., Coleman, H., Haghighi, P., Ho, S.... (2010) Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates. BMC Genomics, 11(1), 21. DOI: 10.1186/1471-2164-11-21
Fraser, C., Eisen, J., Nelson, K., Paulsen, I., & Salzberg, S. (2002) The Value of Complete Microbial Genome Sequencing (You Get What You Pay For). Journal of Bacteriology, 184(23), 6403-6405. DOI: 10.1128/JB.184.23.6403-6405.2002
Chain, P., & et al. (2009) Genome Project Standards in a New Era of Sequencing. Science, 326(5950), 236-237. DOI: 10.1126/science.1180614
- November 30, 1999
- 12:00 AM
- 798 views
Most important paper ever in microbiology?
by Jonathan Eisen in The Tree of Life
Discussion of papers reporting discovery of the archaea... Read more »
Woese CR, & Fox GE. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 74(11), 5088-90. PMID: 270744
Fox GE, Magrum LJ, Balch WE, Wolfe RS, & Woese CR. (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proceedings of the National Academy of Sciences of the United States of America, 74(10), 4537-4541. PMID: 16592452
Balch WE, Magrum LJ, Fox GE, Wolfe RS, & Woese CR. (1977) An ancient divergence among the bacteria. Journal of molecular evolution, 9(4), 305-11. PMID: 408502
- December 24, 2009
- 08:04 AM
- 785 views
Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
by Jonathan Eisen in The Tree of Life
Discussion of the background to a recent Nature paper ... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- January 26, 2010
- 12:32 PM
- 757 views
Cool paper, & winner of "worst new omics word award": Predatosome
by Jonathan Eisen in The Tree of Life
And the bad new omics words keep streaming in. Today's winner of the "Worst New Omics Word Award" is going to Carey Lambert, Chien-Yi Chang, Michael J. Capeness and R. Elizabeth Sockett from Nottingham for their use/ invention of "Predatosome". They use this term in the title of their new PLoS One paper: The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. Here is the very long sentence where the define it:The gene products required for the initial invasive predat........ Read more »
Lambert, C., Chang, C., Capeness, M., & Sockett, R. (2010) The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008599
- February 4, 2011
- 05:04 PM
- 754 views
IQ Test for bacteria
by Jonathan Eisen in The Tree of Life
Social IQ of bacteria
Another quick one here. Interesting paper out in BMC Genomics: Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments
The paper is from Eshel-Ben Jacob and colleagues from many institutions around the world.
Here is a summary of the article (from the paper)
BackgroundThe pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in deve........ Read more »
Sirota-Madi, A., Olender, T., Helman, Y., Ingham, C., Brainis, I., Roth, D., Hagi, E., Brodsky, L., Leshkowitz, D., Galatenko, V.... (2010) Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics, 11(1), 710. DOI: 10.1186/1471-2164-11-710
- January 20, 2010
- 06:57 AM
- 728 views
Confronting Intelligent Design arguments directly in the scientific literature
by Jonathan Eisen in The Tree of Life
... Read more »
FARMER, M., & HABURA, A. (2010) Using Protistan Examples to Dispel the Myths of Intelligent Design. Journal of Eukaryotic Microbiology, 57(1), 3-10. DOI: 10.1111/j.1550-7408.2009.00460.x
- September 3, 2011
- 02:59 AM
- 686 views
I think that I shall never see - metagenomic analysis as lovely as a tree #PhylogenyRules #PLoSOne
by Jonathan Eisen in The Tree of Life
Figure 2. Phylogenetic tree linking
metagenomic sequences from 31 gene
families along an oceanic depth gradient
at the HOT ALOHA site
I am a co-author on a new paper that came out in PLoS One yesterday. The paper is PLoS ONE: The Phylogenetic Diversity of Metagenomes and the full citation is Kembel SW, Eisen JA, Pollard KS, Green JL (2011) The Phylogenetic Diversity of Metagenomes. PLoS ONE 6(8): e23214. doi:10.1371/journal.pone.0023214.
The first author is Steven Kembel, a bri........ Read more »
Kembel, S., Eisen, J., Pollard, K., & Green, J. (2011) The Phylogenetic Diversity of Metagenomes. PLoS ONE, 6(8). DOI: 10.1371/journal.pone.0023214
- December 22, 2009
- 12:00 AM
- 667 views
Story behind the story for new #PLoSOne paper on Bayesian phylogenetics
by Jonathan Eisen in The Tree of Life
There is an interesting new paper in PLoS One" Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics" by Brian Kolaczkowski and Joseph Thornton. The work focuses on methods for inferring phylogenetic history and in particular two types of statistical approaches: Likelihood and Bayesian. These methods are related to each other in that both attempt to use statistical models of evolution and then test different possible phylogenetic trees related taxa by how well certain data set........ Read more »
Kolaczkowski, B., & Thornton, J. (2009) Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0007891
- March 18, 2011
- 05:48 PM
- 655 views
The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb
by Jonathan Eisen in The Tree of Life
Well, here goes.
This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled "Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees" and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I........ Read more »
Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier,, & J. Craig Venter, Jonathan A. Eisen. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One, 6(3). info:/10.1371/journal.pone.0018011
- August 21, 2011
- 02:14 PM
- 654 views
What is in a name? A case study of genomic epidemiology w/ Bacillus cereus and Bacillus anthracis
by Jonathan Eisen in The Tree of Life
There is a very interesting new paper that just came online in the Archives of Pathology: Rapidly Progressive, Fatal, Inhalation Anthrax-Like Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response
I was alerted to the paper by Eileen Choffnes of the National Academy of Sciences Institute of Medicine Forum on Microbial Threats (which I am a member of). In the paper, James Musser, Angela Wright and colleagues, the authors discuss the use of genome........ Read more »
Wright AM, Beres SB, Consamus EN, Long SW, Flores AR, Barrios R, Richter GS, Oh SY, Garufi G, Maier H.... (2011) Rapidly Progressive, Fatal, Inhalation Anthraxlike Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response. Archives of pathology . PMID: 21827220
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