The Tree of Life

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

By Jonathan Eisen .. 5/23/2013 08:59:00 AM

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? "

By Jonathan Eisen .. 5/22/2013 10:30:00 AM

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

By Jonathan Eisen .. 5/20/2013 07:45:00 PM

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:

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

By Jonathan Eisen .. 5/19/2013 11:24:00 AM

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

By Jonathan Eisen .. 5/19/2013 06:41:00 AM

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

By Jonathan Eisen .. 5/18/2013 01:59:00 PM

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

By Jonathan Eisen .. 5/18/2013 01:08:00 AM

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

By Jonathan Eisen .. 5/14/2013 07:32:00 AM

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

No need to oversell the human microbiome with studies like these ...

By Jonathan Eisen .. 5/14/2013 02:10:00 AM

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"

By Jonathan Eisen .. 5/13/2013 12:52:00 AM

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: