Quick post here. There is a really nice piece on in the New York Times Sunday Magazine by Michael Pollan on the human microbiome: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome. In it he discusses how he had his microbiome typed by the American Gut Project and he discusses browsing through the output. He also discusses a diversity of issues in the microbiome and work of various folks. People featured include Justin Sonnenburg, Rob Knight, Burce German, Catherine Lozupone, Stanley Falkow, Jeffrey Gordon, Michael Fischback, Maria Gloria Dominguez-Bello, Martin Blaser, Ruth Ley, Andrew Gewirtz, Patrice Cani, Erica Sonnenburg, and Stephen O'Keefe. The article does a really good job of highlighting why the microbiome is important yet does not oversell what we know at this point.
I note - Pollan came to UC Davis as part of his research for the article a little while back. Below are some pics of him getting a tour of the UC Davis LEED Platinum brewing facility. Anyway the article is definitely worth a look. And just in time for the ASM 2013 Meeting which I am about to head to this AM.
The Tree of Life
Blog by Jonathan Eisen, Prof. at UC Davis. More info at: Lab Page , Profile , or Twitter. Go to fancy "dynamic" views here .
Just in time for #ASM2013 - FDA adding regulations for fecal transplants #microbiome
Well, I guess this could be good news or bad news or both. The FDA has sniffed the winds of microbiome studies and decided that it wants some more regulation on fecal transplants (aka fecal bacteriotherapy). See for example Fecal Transplant: FDA Wants Regulation. Fecal transplants are spreading like crazy these days and every where I go in real life and online I hear and see more about them. For more on fecal transplants see some of my previous posts such as More (you know you wanted it) on fecal transplants and the microbiome and Fecal transplants in the news and Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively.
I guess the FDA feels like they have to do something given the spread of FT. Given how many scam artists and oversellers of the microbiome are out there I think some sort of increased protection or regulation is probably a good thing. But I am not sure what the best way to do this is. Clearly some are unhappy with the FDA sticking their noses into fecal transplants (e.g., see here). But given how little we know about FTs other than as treatment for Clostridium dificile infections it seems like one could make a reasonable argument for more regulation or caution. It seems strange though that we can do just about anything and everything we want to kill all the microbes around us with very little regulation and yet attempting to manipulate the microbes in and on us or add a few here and there is being regulated more.
What do others think? Do we need more regulation from the FDA on fecal transplants?
UPDATE - some links to other discussions of this:
What do others think? Do we need more regulation from the FDA on fecal transplants?
UPDATE - some links to other discussions of this:
- The kibosh (from Controversies in hospital infection prevention)
- Fecal transplants to treat C. diff now need FDA approval
- FDA halts US poop transplants pending further review (Raw Story).
- FDA: Fecal Transplants Need Investigational New Drug Application ... (JWatch blog)
- Oversight for Fecal Transplants | The Daily Scan | GenomeWeb
- Many Years Young: Fecal Transplant: FDA Wants Regulation
- FDA Declares Stool a Drug -- Not kidding! @ TigerDroppings.com
- Fecal Transplant: FDA Wants Regulation - Digestive Health Center - Everyday Health - EverydayHealth.com
Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis
Quick post here. Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network. It was a major success. For those who don't know Software Carpentry's mission is is to build basic computing skills among researchers. From their web site:
Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn't rare.A great idea and done really well. Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site. See for example their videos and their reading list and their lessons. They really do great things ...
ICG Europe starts w/ "Omics & the future of man" & sticks to men the rest of the time
Fun. Another day. Another YAMMGM (yet another mostly male genomics meeting). This one is the International Conference on Genomics Europe 2013. I have copied the program as it is now here and then highlighted the men and women as far as I can tell. And, well, it is not very balanced. It starts off, ironically, with "Omics and the future of man" and then stays on both omics and alas, men, for most of the meeting. The first woman does not talk until 5 pm on the first day. Nothing against BGI per se. But they seem to be repeat offenders in having meetings with mostly male speakers. A difference between countries? Perhaps. But unfortunate and unpleasant nevertheless.
Sessions with speakers:
Sessions with speakers:
Plenary Session 1: Omics and the future of man
Plenary Session 2 :
- 09:00-09:10: Opening ICG-Europe 2013 & Welcome: Hans Galjaard, Chairman of the Department of Clinical Genetics at Erasmus University
- 09:10-09:55: Talk 1: Huanming Yang, BGI, China
- 9:55-10:25: Talk 2: Jeremy Nicholsen, Head of the Department of Surgery and Cancer, Imperial College London, UK
- Topic: Molecular Phenotyping and Systems Medicine Approaches in Personalised and Public Healthcare
Plenary Session 2 :
- 11:00-11:30: Talk 1 (30 min): Jun Wang, CEO, BGI, China
- 11:30-12:00: Talk 2 (30 min): Karsten Kristiansen, Head of the Department of Biology, University of Copenhagen, Denmark
- 12:00-12:30: Talk 3 (30 min): Nils Brunner, Director of the Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Denmark
- Topic: Docetaxel resistance in vitro: Known mechanisms and novel pathways in breast cancer
- Chairman: Prof. Jun Wang, BGI, China
- 13:30-13.55: Talk 1: Rajeev K. Varshney, Director-Centre of Excellence in Genomics, ICRISA, Hyderabad, India
- Topic: “Little” is “more” for chickpea and pigeonpea
- 13.55-14.20: Talk 2: Michael Bevan, Genomics and Functional Genomics of Bread Wheat for Crop Improvement, John Innes Centre, Norwich, UK
- Topic: Genomics and Functional Genomics of Bread Wheat for Crop Improvement
- 14.20-14.45: Talk 3: Michel Georges, Unit of Animal Genomics, University of Liège, Belgium
- 14.45-15.15: Talk 4: Tomas Marques, ICREA Research Professor, Universitat Pompeu Fabra, Spain
- Topic: Great Ape genetic diversity
- 15.15-15.35: Talk 5: TBC
- Chairman: Prof. Marc Van Montagu , VIB, Belgium
- 16:00-16:20: Talk 1(20 min): Stein Aerts, Heading the Laboratory of Computational Biology, K.U.Leuven, Belgium
- Topic: Probing into the genome, transcriptome, and regulatory network of T-cell acute lymphoblastic leukemia
- 16:20-16:40: Talk 2(20 min): Lars Bullinger, Assistant Professor, University of Ulm, Germany
- Topic: Genomics in acute myeloid leukemia (AML) – clinical translation of findings
- 16:40-17:00: Talk 3(20 min): Diether Lambrechts, Assistant Professor, K.U.Leuven & VIB, Belgium
- Topic: Mutation signatures of mismatch repair deficiency in cancer genomes
- 17:00-17:20: Talk 4(20 min): Lynnette Fernandez-Cuesta, University of Cologne, Germany
- Topic: Characterization of lung neuroendocrine tumors
- 17:20-17:40: Talk 5(20 min): Henrik Ditzel, University of Southern Denmark, Denmark
- Chairman: Dr. Jan Cools (K.U.Leuven, VIB)
- 14:30-14:50: Talk 1 (20 min): Boo Edgar, Program Director, Innovation and entrepreneurship; The Sahlgrenska Academy, University of Gothenburg
- 14:50-15:10: Talk 2 (20 min): Martin Bonde, Chairman of Danish Biotech association
- 15:10-15:30: Talk 3 (20 min): Søren Møller, Managing Investment Director, Novo Seeds
- Chairman: Johan Cardoen
- 16:00-16:20: Talk 1(20 min): Johan Cardoen, Managing Director VIB
- 16:20-16:40: Talk 2(20 min): Patrick Van Beneden, GIMV
- 16:40-17:00: Talk 3(20 min): Ann De Beuckelaer, Flanders Bio
- 09:00-09:30: Talk 1 (30 min): Wigard Kloosterman, UMC Utrecht, The Netherlands
- Topic: Cause and Consequence of Complex Genomic Rearrangements
- 09:30-10:00: Talk 2 (30 min): Michael Talkowski, Instructor, MGH, Harvard University, USA
- Topic: Sequencing unique human genomes reveals novel loci in autism and predictive phenotypes in prenatal diagnostics
- 10:00-10:30: Talk 3 (30 min): Thierry Voet, K.U.Leuven
- Chairman: Prof. Edwin Cuppen , Hubrecht Institute
- 09:00-09:30: Talk 1 (30 min): Hui Wang, The Centre for Ecology & Hydrology, UK
- Topic: Virus discovery by using deep sequencing data
- 09.30-10:00: Talk 2 (30 min): TBC
- 10:00-10:30: Talk 3 (30 min): Bjoern Textor, New England Biolabs GmbH
- Topic: Direct Selection of Microbiome DNA from Host DNA
- 11:00-11:30: Talk 1 (30 min): Jeroen Raes, Scientific Collaborator, VUB&VIB
- 11:30-12:00: Talk 2 (30 min): Rob Knight, Associate Professor, Colorado University
- Topic: Characterizing microbial effects of family structure, including our furry family members?
- 12:00-12:30: Talk 3 (30 min): Ruth Ley, Cornell University
- Topic: Host control of the microbiome
- Chairman: Dr. Jeroen Raes (VUB, VIB)
- 11:00-11:35: Talk 1(35 min): Han Brunner, Department of Human Genetics, Radboud University Nijmegen Medical Centre, The Netherlands
- Topic: Clinical Genetic Diagnostics by Genome Sequencing.
- 11:35-12:05: Talk 2(30 min): Wang Wei, BGI Health, Shenzhen, China
- Topic: Non-invasive prenatal testing (NIPT): Current clinical application and future outlook
- 12:05-12:45: Talk 3(30 min): Gabor Vajta, BGI Europe, Copenhagen, Denmark and Central Queensland University, Rockhampton, Australia in concert with Du Yutao, BGI Health, Shenzhen, China
- Topic: Pre-implantation Diagnostics by Blastocyst Biopsy, Vitrification and Genome Sequencing
- Chairman: Prof. Lars Bolund, Aarhus University
- 13:30-13:55: Talk 1(25 min): Vince Gao, BGI
- Topic: Development of Clinical Service at BGI Health
- 13.55-14:20: Talk 2(25 min): Attila Lorincz, UK
- Topic: Clinical Validation of Genomic and Epigenomic Biomarker Panels
- 14:20-14:45: Talk 3(25 min): Maurizio Ferrari, Director of Clinical Molecular Biology and Cytogenetics Laboratory, and Head of Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele, Milan, Italian
- Topic: From bench to bedside: new advanced molecular techniques for genetic diagnosis
- 14:45-15:10: Talk 4(25 min): Carlos Simón Vallés, Board Certified and Full Professor of Obstetrics and Gynecology at the University of Valencia,Spain
- Topic: Clinical Application of the endometrial receptivity array
- 15:10-15:35: Talk 5(20 min): To be selected from submitted abstracts
- Chairman: Dr. Vince Gao , BGI
- 13:30-13:55: Talk 1(25 min): Lars Bolund, Professor of Clinical Genetics at Aarhus University, Denmark, and Adjunct Professor of Human Genetics at Copenhagen University, Denmark
- Topic: Chronic Disorders, Rare Genetic Variants and Pig Models of Degenerative Disease Processes
- 13:55-14:20: Talk 2(25 min): Tao Dong, Head of anti-viral T cell immunology group, MRC Human Immunology Unit, Oxford University, UK
- 14:20-14:45: Talk 3(25 min): Hartmut Wekerle, Honorary Professor, Max Planck Institute of Neurobiology, Martinsried, Germany
- 14:45-15:10: Talk 4(20 min): Ramneek Gupta, The Technical University of Denmark, Danmark
- 15:10-15:30: Talk 5(20 min): Anders Børglum, Professor, Aarhus University, Denmark
- Chairman: TBC
- 16:00-16:20: Talk 1(20 min): Diana M Eccles, Academic Vice President of the Clinical Genetics Society, Southampton General Hospital, UK
- 16:20-16:40: Talk 2(20 min): E. Gomez Garcia, Maastricht University, the Netherlands
- 16:40-17:00: Talk 3(20 min): Pascal Pujol , Chu Montpellier, France
- 17:00-17:20: Talk 4(20 min): Atocha Romero, Hospital Clinico San Carlos, Spain
- 17:20-17:40: Talk 5(20 min): Ian Campbell, Peter MacCallum Cancer Centre, Australia
- Topic: Identification and validation of familial cancer susceptibility genes using massively parallel sequencing
- Chairman: Prof. Yves-Jean Bignon, Centre Jean Perrin
- 16:00-16:20: Talk 1(20 min): Lone Frank, Denmark
- 16:20-16:40: Talk 2(20 min): Pascal Borry, K.U.Leuven, Belgium
- 16:40-17:00: Talk 3(20 min): TBC
- Chairman: Prof. Huanming Yang, BGI
- 08:00-08:30: Talk 1 (30 min): Zhang Yong, BGI, China
- 08:30-09:00: Talk 2 (30 min): Kristian Hveem, Chief Scientific Officer, Nord-Trondelag County, Norway
- 09:00-09:30: Talk 3 (30 min): Shaoliang Peng, National University of Defense Technology, China
- Topic: Bioinformatics and Computational Biology on TianHe Supercomputer
- Chairman: Dr. Zhang Yong, BGI
- 08:00-08:30: Talk 1 (30 min): Jenny Wei, R&D Information China, AstraZeneca global R&D
- Topic: Genomics for Personalized Medicine: From Discovery to Clinic
- 08:30-09:00:Talk 2 (30 min):André Rosenthal, CEO, Signature Diagnostics AG
- Topic: Next-Gen Sequencing Tests for Prognosis and Prediction of Response to Therapy of Patients with Colorectal Cancer Using Somatic Mutation Signatures
- 09:00-09:30: Talk 3 (30 min):Radoje Drmanac, Complete Genomics, Inc. Mountain View, California, U.S.A.
- Topic: Accurate whole genome sequencing as the ultimate genetic test enabling personalized disease prevention and treatment
- Chairman: TBC
- 10:00-10:30: Talk 1 (30 min): Nathaniel Street, Assistant professor, Umea University
- Topic: Sequencing the Norway spruce genome reveals a unique history of repeat expansion
- 10:30-11:00: Talk 2 (30 min): Sofie Van Landeghem, Ghent University, VIB, Belgium
- Topic: Mining the literature to enhance integrative network biology
- 11:00-11:30: Talk 3 (30 min): Mario Caccamo, Acting Director at The Genome Analysis Centre, Norwich, UK
- Topic: Next Generation Genomics for Complex Crops
- Chairman: Prof. Yves Van De Peer (U.Ghent, VIB)
For related posts see
- YAMMGM: Yet another mostly male genomics meeting #2: Beyond the Genome 2013
- YAMMGM: Yet another mostly male genomics meeting
- Crosspost from PLOS Biologue: Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members
- Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12
- Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don't take a XX
- Winner of the "genome conference speakers should be male" award ...
- "Genomics: the Power and the Promise" meeting - could be called "Men Studying Genomics" instead
- Diversity (of speakers, participants) at meetings: do something about it
No need to oversell the human microbiome with studies like these ...
I know I complain all the time about news stories and people "overselling the microbiome". Mind you, I believe microbial communities are likely to be found to have very very important roles in the biology of the plants and animals and other organisms on which they live, but I worry about overhyping the possibilities. But thankfully, there are some good researchers at work out there documenting just what the microbiome can and does do. And the results continue to be promising.
Here is the one that caught my eye most recently: BBC News - 'Weight loss gut bacterium' found about this PNAS paper. While the study is in mice and it is what one could call "limited" in some ways, it is really fascinating and has much promise. Basically, they isolated a new bacterium (with the awkward name of Akkermansia muciniphila, and did a series of experiments in mice looking at the role this bacterium can play in many mouse gut properties. But most interesting, treatment of mice with this bacterium (and only when the bacterium was alive) led to a reduction in high fat induced metabolic disorders and obesity. I am still re-reading the paper but the result seems solid. And exciting.
So - there is no need to oversell the microbiome when the results coming in sell themselves ...
UPDATE 30 minutes after posting
Of course, I should have checked to see if Ed Yong wrote anything about this. And he did: The Mucus-Lover that Stops Mice from Getting Fat. Read his post. It is excellent. With ALL sorts of links and background and other detail.
Here is the one that caught my eye most recently: BBC News - 'Weight loss gut bacterium' found about this PNAS paper. While the study is in mice and it is what one could call "limited" in some ways, it is really fascinating and has much promise. Basically, they isolated a new bacterium (with the awkward name of Akkermansia muciniphila, and did a series of experiments in mice looking at the role this bacterium can play in many mouse gut properties. But most interesting, treatment of mice with this bacterium (and only when the bacterium was alive) led to a reduction in high fat induced metabolic disorders and obesity. I am still re-reading the paper but the result seems solid. And exciting.
So - there is no need to oversell the microbiome when the results coming in sell themselves ...
UPDATE 30 minutes after posting
Of course, I should have checked to see if Ed Yong wrote anything about this. And he did: The Mucus-Lover that Stops Mice from Getting Fat. Read his post. It is excellent. With ALL sorts of links and background and other detail.
Twisted tree of life award #15: NBC News on "Junk DNA mystery"
Oh for fu$*# sake. Really MSNBC? I mean, I know perhaps I should not expect much from some in the press but this is just awful: 'Junk' DNA mystery solved: It's not needed.
Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage). This article has some complete and utter crap:
Some parts that I have issues with:
Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes. Oh and the organism is complex. Therefore, apparently, it follows that
"The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans."
And this leads us to 'Junk' DNA mystery solved: It's not needed.
So - basically - if ONE FUCKING ORGANISM DELETES SOME OF IT'S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.
Aaaaaaaaaaaaaaaaaaargh.
And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.
Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage). This article has some complete and utter crap:
Some parts that I have issues with:
- The headline: "'Junk' DNA mystery solved: It's not needed." The headline is silly but alas it is consistent with what is in the article.
- "So-called junk DNA, the vast majority of the genome that doesn't code for proteins". So - they have redefined junk DNA as all non coding DNA?
- "For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn't seem to contain genes or turn genes on or off." Apparently there is an entity out there known as "The Genome".
And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.
- "At least for a plant, junk DNA really is just junk — it's not required." Except that they did not show this - they just showed that one plant can have a small genome and not have a lot of "junk" as they call it, which of course does not really say anything about what "junk" does or does not do in other organisms.
- "Nobody's really known what junk DNA does or doesn't do" apparently calling into question the some 10,000 plus papers on the topic.
"The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans."
And this leads us to 'Junk' DNA mystery solved: It's not needed.
So - basically - if ONE FUCKING ORGANISM DELETES SOME OF IT'S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.
Aaaaaaaaaaaaaaaaaaargh.
And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.
Past winners:
- Twisted tree of life award #14: @nytimes and Nathaniel Rich on Immortal Jellyfish
- Twisted tree of Life Award #13: Press release from U. Oslo on new protozoan
- Twisted Tree of Life Award #12: Billion Year Old Smart Bacteria That Perfectly Treat Cancer
- Twisted tree of life award #11: National Geographic for emphasizing Five Kingdoms & no Bacteria/Archaea
- Twisted tree of life award #10: @Discovermag for article on Lynne Margulis
- Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus
- Twisted Tree of Life Award #8: Alroy on "Changing the rules of evolution"
- Twisted Tree of Life Award #7: NPR on the Evolution of Crying
- Twisted tree of life award #6: Scientific American Origins piece for dissing microbes
- Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc
- Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals
- Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria
- Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms
- Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases
UPDATE 5/17/13
Some other discussions of this paper and related to my critique (though not always agreeing with me)
- Knight School of Journalism: A Weird Little Plant is Nearly Free of Junk DNA. Big Contentions Underlie Seemingly Cute Story
- From T. Ryan Gregory Genome reduction in bladderworts vs. leg loss in snakes ...
- Deconstructing Nature's “plant without junk DNA” story | Genetic ...
- From Dan Graur: The Logical Fallacy of Jonathan Eisen (a.k.a. @phylogenomics) and the Theological Implications of the Bladderwort Genome
Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes
Crossposting this from the microBEnet blog.
Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes project:
- Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 1(3):e00172-13. doi:10.1128/genomeA.00172-13.
- Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria). Genome Announc. 1(3):e00197-13. doi:10.1128/genomeA.00197-13.
These go with two previously published ones:
- Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13
- Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria). Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13.
And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling. Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.
YAMMGM: Yet another mostly male genomics meeting #2: Beyond the Genome 2013
Well, the "winner" of this months YAMMGM award is Beyond the Genome 2013 | Mission Bay | San Francisco
Alas, YAMMGM stands for "Yet another mostly male genomics meeting" so it is not an award to covet.
This meetings listed speakers are below with women highlighted in green.
That comes to 16.6% if you count all listed. If you exclude session chairs the numbers are a little different but still pretty low.
Certainly this does not prove any bias on the part of the meeting organizers. But it certainly suggests to me they might want to think about why the ratio is skewed.
Alas, YAMMGM stands for "Yet another mostly male genomics meeting" so it is not an award to covet.
This meetings listed speakers are below with women highlighted in green.
- Nicholas Navin -The University of Texas MD Anderson Cancer Center
- Sunney Xie – Harvard
- Xu Xun – BGI
- James Hicks -CSHL
- Fuchou Tang – Peking
- Itai Yanai – Israel
- Thierry Voet - Sanger
- Jacob Kitzman – Plasma cell free DNA sequencing
- Stephen Quake – Stanford and Fluidigm
- Mario Caccamo – Genome Analysis Centre
- Rob Martienssen – CSHL
- Ryan Lister – University of Westerm Australia
- Neelima Sinha – UC davis
- Jorge Dubcovsky – UC Davis
- Robert Schmitz (Salk) – 1001 Arabidopsis project and CHiP-Seq
- Marja Timmermans (CSHL)
- Magnus Nordborg
- Chairs Alicia Oshlack, Yingrui Li and Michael Schatz to chair the bioinformatics challenge.
- James Taylor – Emory and Galaxy
- Chris Dagdigian – Bioteam
- David Haussler -UC Santa Cruz
- Janet Kelso – Max Planck Institute for Evolutionary Anthropology
That comes to 16.6% if you count all listed. If you exclude session chairs the numbers are a little different but still pretty low.
Certainly this does not prove any bias on the part of the meeting organizers. But it certainly suggests to me they might want to think about why the ratio is skewed.
A good thing: More and more biology papers showing up in arXiv
Good to see some more papers in microbiology & genomics and related topics going to the preprint server arXiv.
If you are interested in population and evolutionary genetics a good place to keep up with papers on this topic in arXiv is Haldane's Sieve. The good folks there in essence make a separate post about each paper of interest and then people can comment there on the papers, since the commenting functions at arXiv are, well, challenged.
In areas related to this blog, here are some recent papers in arXiv:
If you are interested in population and evolutionary genetics a good place to keep up with papers on this topic in arXiv is Haldane's Sieve. The good folks there in essence make a separate post about each paper of interest and then people can comment there on the papers, since the commenting functions at arXiv are, well, challenged.
In areas related to this blog, here are some recent papers in arXiv:
- Adaptive reference-free compression of sequence quality scores
- Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
- Quorum sensing inhibitory compounds from extremophilic microorganisms isolated from a hypersaline cyanobacterial mat
- Distilled Single Cell Genome Sequencing and De Novo Assembly for Sparse Microbial Communities
- SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
- Five Statistical Questions about the Tree of Life
Am hoping more and more biologists start depositing papers in arXiv. My brother has started doing it for all papers in his lab so I guess that means I should too. And so should everyone else ...
The need for a phylogeny driven genomic encyclopedia of eukaryotes
Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis. When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically "Well, OK, but I don't really do much work on eukaryotes." And then I came up with an idea - I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences. I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing. So, well, I did. And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.
I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube. These are below.
I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known. We NEED to do this.
Related posts
I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube. These are below.
I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known. We NEED to do this.
Related posts
- The Tree of Life: Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria and archaea...
- The Tree of Life: More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia paper ...
- A phylogeny-driven genomic encyclopaedia of Bacteria and ... - Nature
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