29 posts · 37,127 views
I am an evolutionary biologist, open access advocate, and professor at the University of California, Davis.
The Tree of Life
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- May 12, 2012
- 11:10 AM
- 417 views
Oh the irony - new #OpenAccess #PLoSOne paper on Research Blogs doesn't share data behind analyses.
by Jonathan Eisen in The Tree of Life
Interesting new paper: PLoS ONE: Research Blogs and the Discussion of Scholarly Information. All about the new world of science blogging. Much of the context here relates to openness. Yet as far as I can tell, the data collected that make up the meat of the analyses in the paper, are not shared. Uggh.
Is there something I am missing here? Shouldn't a prerequisite of publishing this kind of paper be sharing the information / data used in the analyses? Shouldn........ Read more »
Shema, H., Bar-Ilan, J., & Thelwall, M. (2012) Research Blogs and the Discussion of Scholarly Information. PLoS ONE, 7(5). DOI: 10.1371/journal.pone.0035869
- May 12, 2012
- 10:34 AM
- 465 views
Nice use of PacBio sequencing to characterize methyltransferase specificity
by Jonathan Eisen in The Tree of Life
Figure 1.
Rich Roberts just pointed me to this cool paper on which he is a co-author: Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. The paper was published in Nucleic Acids Research and is from Robert's group at New England Biolabs and Jonas Korlach's and others at Pacific Biosciences. What is cool is that they used the timing of the real time DNA sequencing to identify bases in particular DNA fragments that were methylated........ Read more »
Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research, 40(4). DOI: 10.1093/nar/gkr1146
- May 12, 2012
- 10:31 AM
- 421 views
Quick post - new paper of interest on "The Infinitely Many Genes Model ..."
by Jonathan Eisen in The Tree of Life
This paper seems of potential interest: The Infinitely Many Genes Model for the Distributed Genome of Bacteria by Franz Baumdicker, Wolfgang R. Hess, and Peter Pfaffelhuber
Abstract:
The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these........ Read more »
Baumdicker, F., Hess, W., & Pfaffelhuber, P. (2012) The Infinitely Many Genes Model for the Distributed Genome of Bacteria. Genome Biology and Evolution, 4(4), 443-456. DOI: 10.1093/gbe/evs016
- May 12, 2012
- 10:27 AM
- 446 views
'Danger and Evolution in the Twilight Zone': Guest post by Randen Patterson and Gaurav Bhardwaj
by Jonathan Eisen in The Tree of Life
Figure 1. PHYRN concept and work flow.
'Danger and Evolution in the twilight zone'
I have been communicating with Randen Patterson on and off over the last five years or so about his efforts to try and study the evolution of gene families when the sequence similarity in the gene family is so low that making multiple sequence alignments are very difficult. Recently, Randen moved to UC Davis so I have been talking / emailing with jim more and more about this issue. Of note, Randen........ Read more »
Bhardwaj, G., Ko, K., Hong, Y., Zhang, Z., Ho, N., Chintapalli, S., Kline, L., Gotlin, M., Hartranft, D., Patterson, M.... (2012) PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0034261
- September 3, 2011
- 02:59 AM
- 1,103 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
- August 21, 2011
- 02:16 PM
- 1,023 views
Hydrogen as a fuel? No this is not about cars, this is about animals and their symbionts in the deep sea
by Jonathan Eisen in The Tree of Life
As many of you know, I generally avoid writing about non open access publications here. But occasionally I make exceptions. And I am making one today. There is a wicked cool paper out in Nature today. Entitled "Hydrogen is an energy source for hydrothermal vent symbioses" comes from Nicole Dubilier, Jillian Petersen and others. It is about my favorite ecosystem(s) on the planet - hydrothermal vents. I became interested in these vents in 1989 when I met Colleen Cavan........ Read more »
Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V.... (2011) Hydrogen is an energy source for hydrothermal vent symbioses. Nature, 476(7359), 176-80. PMID: 21833083
- August 21, 2011
- 02:14 PM
- 1,111 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
- August 21, 2011
- 02:09 PM
- 1,048 views
Get to know Jack & the story behind the paper by @gilbertjacka "Defining seasonal marine microbial community dynamics"
by Jonathan Eisen in The Tree of Life
A few days ago I became aware of the publication of a cool new paper: "Defining seasonal marine microbial community dynamics" by Jack A. Gilbert, Joshua A Steele, J Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Alice C McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A Fuhrman and Dawn Field. The paper was published in the ISME Journal and is freely available using the ISME Open option.
If you want to know more about Jack (in case you don't k........ Read more »
Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I.... (2011) Defining seasonal marine microbial community dynamics. The ISME journal. PMID: 21850055
- March 18, 2011
- 05:48 PM
- 924 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
- February 4, 2011
- 05:04 PM
- 1,041 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 24, 2011
- 03:36 AM
- 1,150 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
- November 15, 2010
- 07:52 AM
- 1,278 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
- October 12, 2010
- 10:00 PM
- 1,113 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
- August 21, 2010
- 04:53 AM
- 1,380 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
- August 9, 2010
- 08:47 PM
- 9,745 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
- May 3, 2010
- 03:33 PM
- 821 views
Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran
by Jonathan Eisen in The Tree of Life
As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids -- Moran and Jarvik 328 (5978): 624 -- ScienceI first found out about this from Ed Yong's blog post here (just........ Read more »
Moran, N., & Jarvik, T. (2010) Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. Science, 328(5978), 624-627. DOI: 10.1126/science.1187113
, . (2010) Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biology, 8(2). DOI: 10.1371/journal.pbio.1000313
- February 3, 2010
- 10:53 AM
- 1,291 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
- January 26, 2010
- 06:29 PM
- 1,075 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
- January 26, 2010
- 12:32 PM
- 966 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
- January 20, 2010
- 06:57 AM
- 957 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
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