So – I have been enjoying all the Fake Scientific Publishing Posts on Twitter from @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj and others. Now I understand why some people think I am behind some of these (e.g., here are some of my Fake Science News posts). But alas though I WISH I was behind some of these accounts, I am not. Anyway – I created a storification of the beginning of some of these postings if you want to see some of the origins of the fakery.
http://storify.com/phylogenomics/fake-scientific-publishing.js[<a href=”http://storify.com/phylogenomics/fake-scientific-publishing” target=”_blank”>View the story “Fake Scientific Publishing” on Storify</a>]
Author: Jonathan Eisen
I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis
Hmm … City of Davis definition of microorganism needs work
From City of Davis Guide to Composting
MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.
Gonna have to get them to work on this …
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One of the coolest things I discovered at Science Online 2012: Science Scout Stickers #scio12
Love this concept: Science Scout Stickers | Hydra Creations | Hydra Creations
They were giving some out at Science Online 2012 and I really like them. They had texture and look very cool on my laptop (computer that is). Pondering getting some more. Wondering how I convince them to make some other kinds …
Here are scans of the handout from Science Online 2012
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Microbial metaomics discussion group this week: metatranscriptomics and biogeography
A visiting student at my lab Lea Benedicte Skov Hansen will be leading our “metaomics” discussion group this week. We will be discussing a combination of metatranscriptomics and biogeography and the papers of the week are:
Metatranscriptomics paper:
Microbial community gene expression in ocean surface waters. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.
Some related papers of potential interest from DeLong
- Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre.
- Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.
- Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean.
- Microbial metatranscriptomics in a permanent marine oxygen minimum zone.
- Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.
We are also discussing:
Drivers of bacterial beta-diversity depend on spatial scale. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC.
Proc Natl Acad Sci U S A. 108(19):7850-4. (NOTE I am an author on this one – but the meat of the ideas/work was done by Jen Martiny, Claire Horner-Devine and others).
Related papers of possible interest by Jen Martiny and Claire Horner-Divine include:
- Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.
- Patterns of fungal diversity and composition along a salinity gradient.
- The biogeography of ammonia-oxidizing bacterial communities in soil.
- Phylogenetic clustering and overdispersion in bacterial communities.
- Microbial biogeography: putting microorganisms on the map.
- An ecological perspective on bacterial biodiversity.
- A taxa-area relationship for bacteria.
- A comparison of taxon co-occurrence patterns for macro- and microorganisms.
Will let everyone know how the discussions go.
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Hard to tell if this is a SPAM conference or not "4th Intntl. Science in Society Conference"
Hard to tell if this is email I just got is about a SPAM Conference or not.
Dear Colleague,
On behalf of the Conference Organizing Committee, I would like to inform you of the:
FOURTH INTERNATIONAL CONFERENCE ON SCIENCE IN SOCIETY
University of California, Berkeley, USA
17 – 19 November 2012
http://science-society.com/conference-2012/
This conference addresses the social impacts, values, pedagogies, politics and economics of science. It is an inclusive forum that welcomes a breadth of perspectives on science from practitioners, teachers and researchers representing a wide range of academic disciplines.
The Science in Society Conference is held annually in different locations around the world. The Inaugural Science in Society Conference was held at the University of Cambridge United Kingdom, in 2009. The Conference was held at the Universidad Carlos III de Madrid, Madrid, Spain in 2010; and the Catholic University of America, Washington DC, USA in 2011.
In addition to Plenary Presentations from leading speakers in the field, the Science in Society Conference includes parallel presentations by practitioners, teachers and researchers. We invite you to respond to the conference Call-for-Papers. Presenters submit their written papers for publication in the peer refereed “International Journal of Science in Society”. If you are unable to attend the conference in person, virtual registrations are also available which allow you to submit a paper for refereeing and possible publication in the journal as well as the option of uploading a video presentation to our YouTube channel.
The deadline for the next round in the call for papers (a title and short abstract) is 21 February 2012. Future deadlines will be announced on the conference website after this date. Proposals are reviewed within two weeks of submission. Full details of the conference, including an online proposal submission form, may be found at the conference website: http://science-society.com/conference-2012/ .
We look forward to receiving your proposal and hope you will be able to join us in Berkeley, USA in August.
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EVE198 / EVE161 Microbial Phylogenomics Course Spring 2012
EVE 198 – Spring Quarter 2012 – CRN 74485 – 3 units P/NP grading
Microbial Phylogenomics: The Evolutionary Diversification of Microbes and their Genomes
Professor Jonathan Eisen
TR 1:40-3:00pm
Room 1344 Storer Hall
Prerequisites for this EVE 198 / Jonathan Eisen course are BIS 2ABC (or its equivalent, for transfer students). (This course is moving through the course approval process, and will eventually be EVE 161!)
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New #openaccess paper in G3 from my lab w/ many others on ‘Programmed DNA elimination in Tetrahymena’ #CiliatesRule
A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core (Joseph Fass and Dawei Lin). The paper is in G3, an open access journal from the Genetics Society.
This stems from the project I coordinated on the sequencing and analysis of the macronuclear genome of the single-celled ciliate Tetrahymena thermophila. This organism, like other ciliates, has two nuclei – one called the micronucleus and one called the micronucleus macronucleus. In essence you can view the micronucleus as the germ line for this single-celled creature and the micronucleus macronucleus is akin to somatic cells. The micronucleus is reserved mostly for reproduction. And the micronucleus macronucleus is used for gene expression. In sexual reproduction, haploid versions of the micronuclear genomes from two lineages merge together just like in sexual reproduction for other eukaryotes. After sex the offspring then create a macronuclear genome by taking the micronuclear genome and processing it in a variety of ways – going from 5 chromosomes for example to hundreds. Plus many regions of the micronuclear genome are “spliced” out and never make it into the macronuclear genome. Our new paper focuses on trying to better characterize which regions of the micronuclear genome get eliminated.
For more on our past work on Tetrhymena genomics see here which includes links to much more information including to my 2006 blog post about our first paper on the project.
Note – the work in my lab on the sequencing was supported by grants from NSF and NIH-NIGMS.
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New paper from lab: Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila
A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophil a. It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core. The paper is in G3, an open access journal from the Genetics Society.
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New publication from members of my lab (e.g., @ryneches) & lab of Marc Facciotti on ChIP-seq based mapping of archaeal transcription factors
New publication from members of my lab and the lab of Marc Facciotti on a workflow for ChIP-seq based mapping of archaeal transcription factors. The paper includes a description of new software from Russell Neches in my lab called pique for peak calling.
See: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq
Russell’s pique software is available on github here: https://github.com/ryneches/pique.
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The Pique software package processes ChIP-seq coverage data to predict protein-binding sites. Strand-specific coverage data are output as tracks for the Gaggle Genome Browser, and putative-binding sites (peaks) are output as ‘bookmark files’. (A) Screenshot of data browsing in the Gaggle Genome Browser. Green box outlines the navigation window for clicking through bookmarks of predicted binding sites. Details of each site can be displayed (inset). The Gaggle toolbar (shown with black arrow) can be used to broadcast selected data to other ‘geese’ in the gaggle package, programs such as R, cytoscape, BLAST or KEGG. (B) Schematic overview of bioinformatics workflow.
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Wilbanks, E., Larsen, D., Neches, R., Yao, A., Wu, C., Kjolby, R., & Facciotti, M. (2012). A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq Nucleic Acids Research DOI: 10.1093/nar/gks063
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New publication from Lizzy Wilbanks, Russell Neches, et al
New publication from members of the lab in Nucleic Acids Research:
A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.
Congrats. Gonna have to make some new jam …
Jonathan Eisen's Lab 