All posts; Tags Include "open access"
- February 3, 2010
- 10:53 AM
- 433 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
- 12:32 PM
- 324 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
- 253 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 12, 2010
- 12:26 AM
- 282 views
Why research articles should be publicly accessible (Shulenburger 2009, PLoS Biology)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
I cannot even count the number of times when I have been denied access to a journal article I needed. Oftentimes, it was while I was working on a paper in college and couldn’t read the paper that all the other scholars cited, or the paper that supported an argument I was trying to make. [...]... Read more »
Shulenburger, D. (2009) University Public-Access Mandates Are Good for Science. PLoS Biology, 7(11). DOI: 10.1371/journal.pbio.1000237
- January 6, 2010
- 12:32 PM
- 415 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
- 412 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
- 361 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
- 317 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
- 246 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
- December 10, 2009
- 02:12 AM
- 220 views
A PLoS ONE Success Story--Taxol Crystals Masquerading as Microtubules
by Steve Koch in Steve Koch Science
Andy Maloney, a Ph.D. student in our lab, recently read and summarized a very interesting paper in his open lab notebook. The paper, "Taxol Crystals Can Masquerade as Stabilized Microtubules," was published in PLoS ONE in January of 2008 by Margit Foss, Buck W. L. Wilcox, G. Bradley Alsop, and Dahong Zhang1. Since our lab is now heavily involved in experiments involving kinesin and microtubules, and because it addresses something that had been a mystery to us, the paper really caught my intere........ Read more »
Foss M, Wilcox BW, Alsop GB, & Zhang D. (2008) Taxol crystals can masquerade as stabilized microtubules. PloS one, 3(1). PMID: 18213384
- October 29, 2009
- 01:24 PM
- 201 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
- 186 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
- 327 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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