12 posts · 1,531 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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- February 3, 2010
- 10:53 AM
- 121 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
- 107 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
- 136 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
- 119 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
- January 6, 2010
- 12:32 PM
- 123 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
- December 29, 2009
- 02:03 PM
- 160 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
- 164 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
- December 24, 2009
- 08:04 AM
- 135 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
- December 22, 2009
- 12:00 AM
- 137 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
- October 29, 2009
- 01:24 PM
- 126 views
More on the PLoS Special Collection on the Genomic of Emerging Infectious Diseases
by Jonathan Eisen in The Tree of Life
Discussion of new PLoS Series on Genomics of Emerging Infectious Diseases... Read more »
Eisen, J., & MacCallum, C. (2009) Genomics of Emerging Infectious Disease: A PLoS Collection. PLoS Biology, 7(10). DOI: 10.1371/journal.pbio.1000224
- November 24, 2008
- 12:00 AM
- 104 views
Open Microbial Diversity: PLoS papers on using 454-Roche pyrosequencing for rRNA studies
by Jonathan Eisen in The Tree of Life
Discussion of two new papers on 454 sequencing and microbial diversity... Read more »
Huse, S., Dethlefsen, L., Huber, J., Welch, D., Relman, D., & Sogin, M. (2008) Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLoS Genetics, 4(11). DOI: 10.1371/journal.pgen.1000255
Dethlefsen, L., Huse, S., Sogin, M., & Relman, D. (2008) The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS Biology, 6(11). DOI: 10.1371/journal.pbio.0060280
- October 13, 2006
- 12:00 AM
- 99 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
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