More bio preprint discussion sites ...

Another Bio-related preprint discussion site has popped up: Connecting the Dots: Warburg's Lens: A pre-print discussion forum for the mathematical oncology community.  From my friend and colleague Jacob Scott.  A good addition to Haldane's Sieve.  Seems to me preprints are the next wave in open access in biology ...

Re-reading this on "Why women leave academia and why universities should be worried"

Been reading some somewhat old material out there on women in academia.  I am getting more and more interested in this issue especially as I have become more involved in the UC Davis ADVANCE Program.  The ADVANCE program from the National Science Foundation "aims to increase the participation and advancement of women in academic science and engineering careers."

I was pointed to this Guardian article from 2012 today based on "The chemistry PhD: the impact on women's retention": Why women leave academia and why universities should be worried | Higher Education Network | Guardian Professional.   This Guardian article has a lot of detail and links to other information.  Definitely worth checking out if you had not seen it or forgotten it.

The human microbiome never looked so good

Another week, another microbial art project --- this one is from Erno-Erik Raitanen who is creating self portrait "bacteriograms" using his own microbiome.  See stories at Petapixel: Photographer Erno-Erik Raitanen Creates 'Self-Portraits' Using His Own Bacteria and CoCreate: INSTAGERMS: SEE A PHOTOGRAPHER’S STRANGELY BEAUTIFUL PORTRAITS OF HIS OWN BACTERIA. 

From CoCreate

“The process itself is pretty much a replication of the processes used in microbiology to cultivate bacteria on agar in petri dishes,” Raitenan says. “Instead of agar, I just used the film gelatin as my growth medium. As the bacteria grows, it consumes the gelatin layers that together make all the colors in a color photograph, and creates all these random patterns and colors.”

The human microbiome never looked so good ...

Is the New York Times microbial diversity centric?

The answer to the question in the title - I think - is yes.  Here are some recent stories in the Times on topics of relevance to microbial diversity.

• Getting to Know Our Microbial Roommates 5/27/13 Peter Andrey Smith
• Microbes Hitch a Ride on the Subway 5/27/13 by Peter Andrey Smith
• Behind the Cover Story: Michael Pollan on Why Bacteria Aren't the Enemy ... 5/20/13 by Rachel Nolan
• Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome 5/15/13 by Michael Pollen
• The Hidden World of Soil Under Our Feet 5/111/13 by Jim Robbins
• Sucking Your Child's Pacifier Clean May Have Benefits - NYTimes ...- 5/6/13 by Anahad O' Connor
• Eggs, Too, May Provoke Bacteria to Raise Heart Risk - 4/24/13 by Gina Kolata
• Prognosis: Circumcision and AIDS - 4/18/13 by Nicholas Bakalar
• The Boy With a Thorn in His Joints 2/1/13 - by Susannah Meadows
• Malnourished Gain Lifesaver in Antibiotics 1/30/13 by Denise Grady
• Antibiotics Are a Gift to Be Handled With Care - 11/12/12 by Perri Klass
• Fermentation Guru Seeks Out New (and Old) Flavors - 9/17/12 by Jeff Gordinier
• WELL - Vital Signs - Risks - Weight Implications for Infant Antibiotics ... 8/28/12 by Nicholas Bakalar

Plus - of course - there is a continuous stream of information on microbes from Carl Zimmer who writes frequently for the NY Times.  Perhaps the best example of this is his coverage of the Human Microbiome Project papers: Studies of Human Microbiome Yield New Insights June 18, 2012.  But there have been and I am sure will be others. 

Sure - the NY Times is not the only place with a bunch of stories about microbial diversity and microbiomes. But they do seem tto have a good ratio of "diversity" themed coverage vs. germoophobia themed topics which are common in many other places.

Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

Well, this is one of the bigger screw ups in terms of evolution I have seen at a major journal in a while.  See the following paper in Nature: The catalytic mechanism for aerobic formation of methane by bacteria : Nature. The paper discusses some functions of "the ocean-dwelling bacterium Nitrosopumilus maritimus." Some of what is reported in the paper is perhaps interesting (alas I do not have access).  But painfully, there is one big big big big mistake - you see Nitrosopumilus maritimus is not a bacterium.  It is an archaeon (see for example this paper on its genome).


I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter)  Sure - some people debate the structure of the tree of life.  But I am pretty certain the authors here  (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are.  They just made what seems to be a colossal screw up.  And Nature not only let them, but added to it with things like their "Editors Summary":

Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.

And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted "Twisted Tree of Life Award #16".

UPDATE 5/28 7AM

I love the ad that came up while I was writing this post and searching for some information.  I think Nature could use the services from this ad:

I so want a few 1000 of these: Mobile Robotic Laboratory from MBARI

Thanks to Michael Ferrari for pointing me to this:: Mobile Robotic Laboratory Will Track Ocean Toxins - Popular Mechanics.  The article discusses some developments at MBARI for mobile sensor / sampler devices that could be used for various marine microbiology studies.  A few years ago I got a tour of MBARI from Alex Worden (see pics below) and got to see some of their toys but many of the developments in this article are new to me.  I can't wait until it is possible to deploy a few hundred thousand of these and get massive amounts of data ...

ASM2013 - One of the best parts - meeting the "Young Ambassadors"

I attended the American Society for Microbiology (ASM) meeting in Denver last week.  It was a bit overwhelming as usual, with the 1000s of people there.  One surprise for me was an invitation to a after dinner party hosted by Nathan Wolfe and others from Metabiota.  I am not really a big fan of parties (as many who know me know) but this was small and even better it was mostly populated by the recipients of the ASM International Young Ambassador Award winners.  Wolfe was one of the keynote speakers at the ASM Meeting and I think he was hosting this party in part as a reception for the Young Ambassador's.

For more on the winners see

• Engaging Tomorrow’s Leaders: ASM Appoints 30 Young Ambassadors
• ASM Young Ambassador Program

Anyway - it was very interesting to talk to many of them.  And I even got a picture with one of them - Yu Xia from Hong Kong (we were trying to form some sort of Tree of Life with our fingers).

All societies have their good and bad parts.  Sponsoring Young Ambassadors from other countries is definitely one of the very good things ASM does.

Worth a look: PhyloFacts FAT-CAT web server: ortholog identification & function prediction

Quick post.  This seems like a potentially useful resource and tool: The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Abstract:
The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

Story behind the paper: from Jeremy Barr on "Bacteriophage and mucus. Two unlikely entities, or an exceptional symbiosis? "

I am pleased to have a guest post in my "Story behind the paper" series.  This one is from Jeremy Barr in Forest Rohwer's lab about a new PNAS paper. 

Bacteriophage and mucus. Two unlikely entities, or an exceptional symbiosis?

By Jeremy J. Barr

Our recent research at The Rohwer Lab at San Diego State University investigates a new symbiosis formed between bacteriophage, viruses that only infect and kill bacteria, and mucus, that slimy stuff coating your mouth, nose, lungs and gut.

Bacteriophage, or phage for short are ubiquitous throughout nature. They are found everywhere. So it shouldn’t surprise you to learn that these phage are also found within mucus. In fact, if you actually sat down and thought about the best place you would look for phage, you might have picked mucus as a great starting point. Mucus is loaded with bacteria, and like phage, is found everywhere. Almost every animal uses mucus, or a mucus-like substance, to protect its environmentally exposed epithelium from the surrounding environment. Phage in mucus is nothing novel.

But what if there were more phage in mucus? What if the phage, immotile though they may be, were actually sticking within it?

It turns out that there are more phage in mucus, over four times more phage, and this appears true across extremely divergent animal mucosa. But this apparent increase in phage could very simply be explained by increased replication due to access to increased bacterial hosts residing within mucus layers. But this assumption alone doesn’t hold up. Applying phage T4 to sterile tissue culture cells resulted in significantly more phage sticking to the cell lines that produced a mucus layer, compared to those that did not. There were no bacterial hosts for phage replication in these experiments. Yet still, more phage accumulated in mucus.

Surely the law of mass-action could explain this apparent accumulation. The more phage we apply to an aqueous external environment, the more phage will diffuse into and enter the mucus layer, being slowed in the process due to the gel-like properties, and eventually resulting in an apparent accumulation of phage in mucus. But when we removed mass-action from the equation, and simply coated mucus-macromolecules onto a surface, still more phage stuck. Our assumptions were too simple.
Phage are ingenious. They have evolved, traded, and disseminated biological solutions to almost every biological problem, whether we are aware of it or not. So in order to solve the phage-mucus quandary, we needed to look to one of the most ubiquitous and populous families of proteins found in nature: the immunoglobulin superfamily. This protein fold is so ubiquitous that it appears in almost every form of life. Within our own bodies, it is the protein that affords us immunological protection. Bacteria utilize the protein fold to adhere to each other, to surfaces, and as a form of communication. And as it would turn out, phage make an innovative use of the same protein fold to stick to mucus.

Immunoglobulin, phage and mucus, are all pervasive throughout environments. The interaction between these three entities forms a new symbiosis between phage and their animal hosts. This symbiosis contributes a previously unrecognized immune system that reduces bacterial numbers in mucus, and protects the animal host from attack. We call this symbiosis/immunity, Bacteriophage Adherence to Mucus, or BAM for short.

Our work is open access and available through PNAS .

If you would like to read further about BAM and its implications see these two commentaries by Carl Zimmer at National Geographic  and by Ed Yong at Nature News

Cool bacterial art makes gizmodo #MicrobialArt

Quick post - cool bacterial art project has made Gizmodo.  See Bacteria Never Looked So Beautiful.  From an Art of Science competition at Princeton.  I wonder what Artologica - my favorite microbial art artist - thinks of this.

For some other posts about microbial art see:

• Germophobia: wanna get people in the mood for "Contagion" movie about killer virus - grow harmless microbes in public #microbialart
• My new microbial art for my office: salt evaporation ponds and goethermal spring stamps
• Microbial art for the holidays from the J. Craig Venter Institute
• Guest post on "The phone microbiome" from Georgia Barguil in Jack Gilbert's lab
• Microbes, art and a bit of satire all in one place - Design Interactions at the RCA
• Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"
• What to do - what to do - cool microbial art w/ a #badomics word --- must resist purchasing -- must resist ...
• My new microbe art corner w/ three works by @artologica
• Microbial & Evolution art by @artologica has whole new meaning now that I met her at @scio12

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note - I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad - covering all microbes - all the time - everywhere. But much of it is due to a growing interest in the microbes closer to us - those that live in and on us (the human microbiome) - those that live in and on plants and animals and other organisms we care about - and those that live in the places where we spend much of our time (the microbes of the built environment). I mean - come on - everyone is talking about fecal transplants now in public - in cover stories of the NY Times Magazine and in Ted talks.

• Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too. 
• The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology. 
• Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com). 
• Crowdsourcing (not the same thing as Citizen Science - more on this another time perhaps) is also growing in leaps and bounds. 
• Crowdfunding is providing new ways to fund scientific activities. 
• Sensors of all kinds are getting cheaper and easier to use and are being deployed widely. 
• Many people are becoming more and more interesting in recording information about themselves and sharing it with others. 
• The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research. 
• Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used. 

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include 

• Germophobia is rampant and fueled by media hype and marketing forces. 
• We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on 
• Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know - claiming that probiotics will cure all ailments for example. 
• Some information about microbes that is out there on the web is, well, less that ideal 
• The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most. 

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

• Ethics 
• Funding 
• Openness and sharing 
• Visualization 
• Analysis tools 
• Communication 
• Outreach 

And of course - the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project - well - why not? Get your act together.

Anyway - got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

-------------------------
Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

---

UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

Excellent piece in the NY Times Magazine by @michaelpollan "Some of my best friends are germs" #ASM2013

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.

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:

• 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:

Plenary Session 1: Omics and the future of man

• 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

Chairman: Prof.Huanming Yang, BGI, China

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

Plenary Session 3: Plant and Animal Genomics

• 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

Session 4: Cancer genomics and Transcriptional Regulation

• 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)

Workshop：Innovation-Entrepreneurship and Venture creation-1

• 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

Session 5: Human Disease- Structural Genomic Variation and Function

• 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

Session 6: Metagenomics

• 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)

Session 7(3 talks: include Q&A 5 mins): Human Disease - Clinical Genetics

• 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

Session 8: Health and Translational Medicine-1

• 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

Session 9: Human disease

• 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

Session 10: Health and Translational Medicine-2

• 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

Workshop: Ethical, Legal and Social Implications (ELSI)

• 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

Session 11: Biobanks

• 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

Workshop: Use of Omics Technology for Personalized Medicine

• 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

Session 12: Bioinformatics

• 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.

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:

• 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.

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.

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.

• 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:

• 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.

The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuks from Jonathan Eisen

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

I love this ... "Dr. Eleanor's Book of Common Ants" based in part on citizen science data

This is really cool:  Dr. Eleanor's Book of Common Ants.  Free to download.  With incredible pics from Alex Wild.  And based in part on data from the School of Ants citizen science project.  You can download the PDF or the iBook from iTunes.  From the folks at "Your Wild Life" including Holly Menninger and Rob Dunn and others.  Definitely worth checking out.