Cold Spring Harbor presents the men's only view on the evolution of sequencing

On June 5 I posted a guest blog post by an anonymous person writing about the Programming for Biology workshop at Cold Spring Harbor Labs: Guest post on Yet Another Mostly Male Meeting (YAMMM) - Programming for Biology 

And this post generated some responses including yesterday a series of responses from whomever is behind the Cold Spring Harbor Meetings Twitter account.

@phylogenomics @mike_schatz We do have a role. Course instructors develop speaker lists but we work with them, especially on diversity. 1/5

— CSHL Meetings (@cshlmeetings) June 23, 2015

@phylogenomics @mike_schatz Gender, race/ethnicity, U.S. representation, and geographic region are some ways we look at diversity. 2/5

— CSHL Meetings (@cshlmeetings) June 23, 2015

@phylogenomics @mike_schatz The gender skew in the 2014 Programming course came up last year and we talked to Simon and Sofia about it. 3/5

— CSHL Meetings (@cshlmeetings) June 23, 2015

@phylogenomics @mike_schatz Simon & Sofia teach a great course that is always very well received and evaluated by its students. 4/5

— CSHL Meetings (@cshlmeetings) June 23, 2015

@phylogenomics @mike_schatz They'll teach a great course again this year and ensure its list of guest lecturers includes more women. 5/5

— CSHL Meetings (@cshlmeetings) June 23, 2015

Sounds great.  And I retweeted all of these.

And then I got an email invite to a new Cold Spring Harbor Meeting: The Evolution of Sequencing Technology: A Half Century of Progress

With a long long list of speakers.  Alas, the gender ratio here of speakers is abyssmal.  I have highlighted men in yellow and women in green (with the caveat that I always try to giver that assigning gender from names or appearance or records is not always accurate)

1. Mark Adams, J. Craig Venter Institute
2. Gillian Air, University of Oklahoma
3. Shankar Balasubramanian, University of Cambridge, UK
4. Hagan Bayley, Oxford Nanopore Technologies, Ltd.
5. David Bentley, Illumina Cambridge, Ltd
6. Sydney Brenner, Salk Institute for Biological Studies
7. Nigel Brown, University of Edinburgh, UK
8. George Brownlee, University of Oxford, UK 
9. Graham Cameron, Bioinformatics Resource, Australia EMBL
10. Piero Carninci, RIKEN Ctr.for Life Science Technologies, Japan
11. Norman Dovichi, University of Notre Dame
12. J. William Efcavitch, Molecular Assemblies, Inc.
13. Miguel Garcia-Sancho, University of Edinburgh, UK
14. Mark Gerstein, Yale University 
15. Jack Gilbert, University of Chicago
16. Walter Gilbert, Harvard University
17. Philip Green, University of Washington
18. Leroy Hood, Institute for Systems Biology
19. Clyde Hutchison, J. Craig Venter Institute
20. James Kent, University of California, Santa Cruz
21. Jonas Korlach, Pacific Biosciences
22. Victor Ling, BC Cancer Agency, Canada
23. David Lipman, NCBI/NLM National Instiutes of Health 
24. James Lupski, Baylor College of Medicine
25. Thomas Maniatis, Columbia University Medical Center
26. W. Richard McCombie, Cold Spring Harbor Laboratory
27. Joachim Messing, Waksman Institute, Rutgers University
28. Gene Myers, Max Planck Institute of Molecular Cell Biology & Genetics, Germany
29. Richard Myers, HudsonAlpha Institute for Biotechnology
30. Debbie Nickerson, University of Washington
31. James Ostell, NLM/NCBI
32. Stephen Quake, Stanford University/HHMI
33. Charles Richardson, Harvard Medical School
34. Richard Roberts, New England BioLabs
35. Jane Rogers, The Genome Analysis Centre, UK
36. Mostafa Ronaghi, Illumina, Inc.
37. Yoshiyuki Sakaki, University of Tokyo
38. Jay Shendure, University of Washington
39. Melvin Simon, Caltech
40. Hamilton Smith, J. Craig Venter Institute
41. Lloyd Smith, University of Wisconsin-Madison
42. J. Craig Venter, J. Craig Venter Institute
43. Robert Waterston, University of Washington
44. James Watson, Cold Spring Harbor Laboratory 
45. Jean Weissenbach, Genoscope, France
46. Barbara Wold, Caltech
47. Huanming Yang, Beijing Genomics Institute, China

That is right.  47 speakers.  4 of which are female.  For a whopping 7.8 % female speakers.  This is one of the most extreme skews I have seen for any meeting.  This truly makes me sick to my stomach.   Since there are plenty of women who have had and still have fundamentally important roles in the field of sequencing and sequencing technology I infer that this most likely reflects some type of bias in the meeting organization and planning process.

The meeting page lists the organizers as

• Mark Adams, J. Craig Venter Institute       
• Nigel Brown, University of Edinburgh, UK
• Mila Pollock, Cold Spring Harbor Laboratory     
• Robert Waterston, University of Washington

And one of the major sponsors as Illumina.

I think they all have some explaining to do.

One last note - the meeting description says "The opening session will include a tribute to Frederick Sanger, the father of DNA sequencing, and will cover the early efforts in protein, RNA and DNA sequencing."  Really?  The father of DNA sequencing?  Seems perfect for this meeting I guess.

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UPDATE 6/29/15 7 PM PST

Apparently this meeting is part of a series on the history of molecular biology.  The meeting page says

The CSHL/Genentech Center Conferences on the History of Molecular Biology & Biotechnology (http://library.cshl.edu/hosted-meetings) aim to explore important themes of discovery in the biological sciences, bringing together scientists who made many of the seminal discoveries that began the field with others whose interests may include the current status of the field, the historical progress of the field, and/or the application of these techniques and approaches in biotechnology and medicine. Previous meetings in the series have included:  

Biotechnology: Past, Present & Future (2008)
History of Restriction Enzymes (2013)
Messenger RNA: From Discovery to Synthesis and Regulation in Bacteria and Eukaryotes (2014)
Plasmids: History & Biology (2014)

So I decided to take a peek at these meetings I started with Biotechnology: Past, Present & Future (2008).

Organizers

1. Mila Pollock 
2. Jan Witkowski

Advisors

1. Sydney Brenner
2. Peter Feinstein
3. Lee Hood
4. Tom Maniatis
5. Richard Roberts 

Speakers are listed below:

1. Garen Bohlin
2. Robert Bud 
3. Don Comb 
4. Peter Feinstein
5. Maryann Feldman 
6. Herbert Heyneker 
7. John H. Leamon
8. Yuk-Lam Lo 
9. Alan McHughen 
10. Stelios Papadopoulos 
11. Rich Roberts
12. Robert Steinbrook
13. Kenneth Thibodeau 
14. Marc Van Montagu
15. Charles Weissmann 
16. Julie Xing

For speakers that comes to 14:2 male:female or 12.5 % female

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Next I went to History of Restriction Enzymes (2013).

Organizers

1. Herb Boyer, University of California, San Francisco
2. Stu Linn, University of California, Berkeley
3. Mila Pollock, Cold Spring Harbor Laboratory
4. Richard Roberts, New England BioLabs

Speakers are listed below:

1. Aneel Aggarwal, Mount Sinai School of Medicine
2. Werner Arber, University of Basel, Switzerland
3. Tom Bickle, University of Basel, Switzerland
4. Herb Boyer, University of California, San Francisco
5. Jack Chirikjian, Georgetown University
6. Steve Halford, Bristol University, United Kingdom
7. Ken Horiuchi, The Rockefeller University
8. Clyde Hutchison, J. Craig Venter Institute
9. Arvydas Janulaitis, Institute of Biotechnology, Lithuania
10. Stu Linn, University of Califoria, Berkeley
11. Bill Linton, Promega
12. Arvydas Lubys, Institute of Biotechnology, Lithuania
13. Matthew Meselson, Harvard University
14. Rick Morgan, New England BioLabs
15. Andrzej Piekarowicz, Warsaw University, Poland
16. Alfred Pingoud, Institute of Biochemistry - Giessen, Germany
17. Mila Pollock, Cold Spring Harbor Laboratory
18. Rich Roberts, New England BioLabs
19. John Rosenberg, University of Pittsburgh
20. Ham Smith, J. Craig Venter Institute
21. Bruno Strasser, Yale University & University of Geneva
22. Geoff Wilson, New England BioLabs

OK that is 21:1 or 4.5 % women. Well, I guess this makes the meeting on sequencing look good.

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So then I went to "Messenger RNA: From Discovery to Synthesis and Regulation in Bacteria and Eukaryotes (2014)".  Speakers are below:

Organizers:

1. James Darnell, The Rockefeller University
2. Adrian Krainer, Cold Spring Harbor Laboratory
3. Mila Pollock, Cold Spring Harbor Laboratory

Speakers

1. Arnold Berk, University of California, Los Angeles
2. Douglas Black, HHMI, University of California, Los Angeles
3. George Brawerman, Tufts University School of Medicine
4. Sydney Brenner, Janelia Farm Research Campus, HHMI
5. Stephen Buratowski, Harvard Medical School
6. Louise Chow, University of Alabama
7. Juan Pablo Couso, University of Sussex, UK
8. James Darnell, The Rockefeller University
9. Gideon Dreyfuss, HHMI, University of Pennsylvania
10. Grigorii Georgiev, Russian Academy of Sciences, Russia
11. Adrian Krainer, Cold Spring Harbor Laboratory
12. Tom Maniatis, Columbia University Medical Center
13. James Manley, Columbia University
14. Lynne Maquat, University of Rochester Medical Center
15. Matthew Meselson, Harvard University
16. Melissa Moore, University of Massachusetts Medical School
17. Bernard Moss, National Institute of Allergy & Infectious Diseases
18. Arthur Pardee, Dana Farber Cancer Institute
19. Mila Pollock, Cold Spring Harbor Laboratory
20. Rich Roberts, New England BioLabs
21. Robert Roeder, The Rockefeller University
22. Mike Rosbash, Brandeis University
23. Robert Schleif, John Hopkins University
24. Robert Singer, Albert Einstein College of Medicine
25. Nahum Sonenberg, McGill University, Montré, Quéc, Canada
26. Joan Steitz, Yale University/ HHMI
27. David Tollervey, Wellcome Center for Cell Biology; University of Edinburgh, UK
28. Jonathan Warner, Albert Einstein College of Medicine
29. James Watson, Cold Spring Harbor Laboratory

So so much better no? 24:5 Male: Female or 17% female (for the speakers).

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Finally I checked out Plasmids: History & Biology (2014)

Organizers

1. Dhruba Chattoraj, National Cancer Institute, Bethesda, MD
2. Stanley N. Cohen, Stanford University
3. Stanley Falkow, Stanford University
4. Richard Novick, New York University
5. Chris Thomas, University of Birmingham, UK
6. Jan Witkowski, Cold Spring Harbor Laboratory, NY

Speakers

1. Peter Barth, Helsby, Cheshire UK
2. Susana Brom, Universidad Nacional Autonóma de México, Cuernavaca, Morelos Mexico
3. Ananda Chakrabarty, University of Illinois
4. Mike Chandler, Université Sabatier, Toulouse, France
5. Dhruba Chattoraj, National Cancer Institute, Bethesda, MD
6. Don Clewell, University of Michigan, Ann Arbor, MI
7. Stanley N. Cohen, Stanford University
8. Fernando de la Cruz, Universidad de Cantabria, Spain
9. R. Curtiss III, Arizona State University, Tempe, AZ
10. Julian Davies, University of British Columbia, Canada
11. Stanley Falkow, Stanford University
12. Laura Frost, University of Alberta, Edmonton, Alberta, Canada
13. Barbara Funnell, University of Toronto, Toronto, Ontario, Canada
14. Mathias Grote, Technische Universität Berlin, Germany
15. George A. Jacoby, Lahey Clinic, Burlington, MA
16. Mark Jones, Life Sciences Foundation, San Francisco, CA
17. Saleem Khan, University of Pittsburgh
18. Bruce Levin, Emory University, Atlanta, GA
19. John Mekalanos, Harvard Medical School
20. Marc van Montagu, Ghent University, Belgium
21. Richard Novick, New York University
22. David Sherratt, University of Oxford, UK
23. David Summers, University of Cambridge, UK
24. Chris Thomas, University of Birmingham, UK
25. Eva Top, University of Idaho, Moscow, ID
26. Gerhart Wagner, Uppsala University, Sweden
27. Michael Yarmolinsky, National Cancer Institute, Bethesda MD
28. Peter Young, University of York, UK

That comes to 24:4 for speakers or 14% female.

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Notice any patterns?  The totals for these meetings come to 17 women out of 142 speakers.  Or ~12 %.  That is a dismal record for Cold Spring Harbor Labs and certainly does not convince me that they are trying at all to have diversity represented at their meetings.  I note - I truly love many things about CSHL.  This is definitely not one of them.

UPDATE 2 - Some discussion of this post on Twitter

@nl_brown @phylogenomics wrote 'plenty of women who have had & still have fundamentally important roles in the field of sequencing&seqtech'

— Geertje van Keulen (@DrGvanK) June 27, 2015

@DrGvanK Sadly, it is correct as the history of sequencing is male-dominated. Original phiX paper had 1/9 women authors and... (1/2)

— Nigel Brown (@nl_brown) June 27, 2015

@DrGvanK (2/2) ...Gillian Air is on list. There will be 1 further replacement female/male. Not proud & could have done better on new techs

— Nigel Brown (@nl_brown) June 27, 2015

@DrGvanK Would be good if they were named and could be invited to speak.

— Nigel Brown (@nl_brown) June 27, 2015

@phylogenomics @DrGvanK Attempt was to represent the history of DNA sequencing. This is why I sought names we might have missed. (1/2)

— Nigel Brown (@nl_brown) June 27, 2015

@phylogenomics @DrGvanK (2/2) Taking diversity over actual history is both token & revisionist. Would have loved more equality in 1900s

— Nigel Brown (@nl_brown) June 27, 2015

@nl_brown @DrGvanK I don't buy it; there are always different angles on history and technology and your appears severely skewed towards men

— Jonathan Eisen (@phylogenomics) June 27, 2015

@nl_brown @DrGvanK for example, though I love @gilbertjacka what role exactly did he have in history of DNA sequencing? (sorry Jack)

— Jonathan Eisen (@phylogenomics) June 27, 2015

@nl_brown @DrGvanK @gilbertjacka and if the meeting includes applications of sequencing I can think of dozens of women who could be there

— Jonathan Eisen (@phylogenomics) June 27, 2015

@nl_brown @DrGvanK @gilbertjacka many on speaker list who don't do sequencing technology per se; if include those could include many others

— Jonathan Eisen (@phylogenomics) June 27, 2015

UPDATE 3: Made a Storify w/ some of the discussions

Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM

Well, got an email invite to one of these Oxford Global Meetings. Sadly the gender ratio of listed speakers is awful. I highlighted the list below (men in yellow, women in green).  Ratio of 17:3.  (See below).  No thanks Oxford Global.

Dear Professor Jonathan Eisen ,
 We hope you are well and we would like to invite you to speak at our forthcoming Next Generation Sequencing (NGS) USA congress (www.nextgenerationsequencingusa-congress.com) or co-located  Single Cell Analysis USA congress (www.singlecellusa-congress.com) to be held on 27th -28th October 2015 at Harvard Medical School, Boston, USA.
 Over the two days, the NGS USA congress aims to cover updates and application of NGS technologies in genomics and genetics research in the US and UK, Europe. Topics are comprised of NGS & NGS Data Analysis Technologies and Platforms, NGS for Cancer Drug Development, Microbiology and Immunotherapy as well as Clinical Applications & Diagnostics. Novel updates in Gene Synthesis, Protein Sequencing and Targeted Sequencing will also be explored The Single Cell Analysis USA congress looks at new methods in DNA sequencing, epigenomic DNA sequencing and RNA sequencing, informatics, data handling as well as application of single cell genomics in understanding cancer  other areas of cancer research such as cancer stem cells and immunotherapy. The presentations are also comprised of novel techniques in imaging and cytometry, isolation and processing of single cells. The congress also covers the applications in translational medicine and the clinic for therapeutic targeting.
 The combination of carefully researched topics and high-level networking opportunities creates a unique discussion platform for over 250 senior scientists we are expecting in attendance from research institutions and pharmaceutical companies. Confirmed Speakers for 2015 include:NGS·          Sreekumar Kodangattil, Senior Principal Scientist, Pfizer       
·          Shrikant M. Mane, Senior Research Scientist in Genetics; Director, MBB Keck Biotech laboratory; Director, Yale Center for Genome Analysis
·          Stephan Schuster, Professor of Biochemistry and Molecular Biology, Penn State University
·          Richard  McCombie, Professor, Human Genetics, Cold Spring Harbor Laboratory
·          Jingyue  Ju, Director, Center for Genome Technology and Biomolecular Engineering, Professor of Chemical Engineering and Pharmacology, Columbia University            
·          Christopher Mason, Chair, ABRF NGS Consortium, Assistant Professor, Weill Cornell Medical College. Dept. of Physiology & Biophysics; The Brain & Mind Research Institute
·          Michaela Bowden, Associate Director, Center for Molecular Oncologic Pathology, Dana Farber Cancer Institute      
·          Yuan Gao, Director, Associate Professor, Lieber Institute/Johns Hopkins University
·          Sheng Li, Instructor in Bioinformatics, Department of Neurological Surgery, Weill Cornell Medical College
·          Michael  Fraser, Associate Director, CPC-GENE Prostate Cancer Genomics Program, Princess Margaret Cancer Centre    
 Single Cell·          Daniel Chiu, Professor, University of Washington    
·          Steve Potter, Professor, Division of Developmental Biology, Cincinnati Children's Medical Center
·          Norman Dovichi, Professor, University Notre Dame 
·          Zaida Luthey-Schulten, Professor of Chemistry, University of Illinois
·          Paul Bohn, Professor of Chemical and Biomolecular Engineering, University of Notre Dame       
·          Navin Varadarajan, Assistant Professor, University of Houston
·          Alexander R., Ivanov, Director of the HSPH Proteomics Resource, Research Scientist
Harvard School of Public Health·          Viktor Adalsteinsson, Researcher, Researcher, Koch Institute at MIT, Broad Institute of MIT and Harvard Medical School
·          Xinghua Victor Pan, Research Scientist, Single Cell Genomics Group, Sherman Weissman Laboratory, Department of Genetics, Yale University School of Medicine
·          Cheng-Zhong Zhang, Computational Biologist, Department of Medical Oncology, Dana-Farber Cancer Institute

Do small organisms form species? New paper suggests not ...

Quick post here about a press release about a new paper: New mathematical theory says small organisms may not form species.  Seems that this new theoretical paper might be of interest to people out there. The paper is available openly here: http://rspb.royalsocietypublishing.org/content/280/1767/20131248.abstract.  Not sure quite what to make of this but thought it would be of interest.  The abstract is below:

The rapid advance in genetic sequencing technologies has provided an unprecedented amount of data on the biodiversity of meiofauna. It was hoped that these data would allow the identification and counting of species, distinguished as tight clusters of similar genomes. Surprisingly, this appears not to be the case. Here, we begin a theoretical discussion of this phenomenon, drawing on an individual-based ecological model to inform our arguments. The determining factor in the emergence (or not) of distinguishable genetic clusters in the model is the product of population size with mutation rate—a measure of the adaptability of the population as a whole. This result suggests that indeed one should not expect to observe clearly distinguishable species groupings in data gathered from ultrasequencing of meiofauna.

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.

Fermentation microbiomes part 2 from #UCDavis: American coolship ale microbiome

 From Nick Bokulich: This is an image of the "coolship" where the cooling wort
(pre-fermented beer) is left overnight and presumably where wild
microbes are introduced to kick off the fermentation. This is the
morning after, still full of wort.

Just a quick follow up to my recent post on How did I miss this? The botrytized wine microbiome ... from #UCDavis colleague David Mills.  There is a similar paper from the same group also in PLoS One from about the same time: PLOS ONE: Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale.  What a job --- microbes, ales and wines, and sequencing.  One of the few times when reading a paper where I have said "I wish that was me doing that work." ... must look into getting involved in such studies ...

Is Illumina the "duct tape" of sequencing?

Photo from Wikipedia.  Photo by Evan-Amos. 

For the last year or so I have become a big fan of Illumina sequencing.  We are using it for everything in the lab.  And many others are using it quite a lot too.  All sorts of interesting applications.  But of course -there are other sequencing systems that each have some advantages relative to Illumina.  And one of the key limitations of Illumina sequencing has been the read length (though that limitation gets less and less as read lengths get longer and longer from Illumina machines).

The UC Davis Genome Center has had Illumina sequencing systems for many years now and we use them extensively.  However, we felt for some time that we and others around town could benefit from complementary methods, especially those that could get longer reads.  So we sought funding to buy other systems.  And fortunately we got an NSF MRI grant to do just that -which we used to buy a Roche 454 Jr machine and contribute to the purchase of a Pacific Biosciences machine.  These are good to have around because they open up new windows into sequencing - not just long reads but other areas as well.  For example, the PacBio system also has the ability to use it to detect modifications to bases like methylation.

Alas, both the 454 and PacBio systems have higher error rates than the Illumina systems.  And this makes some analyses challenging and limits the benefits that come from the longer reads.  So what to do?  For a while people have been using Illumina sequencing to "correct" the errors make by 454 and PacBio sequencing.  And today Matt Herper at Forbes (For A New DNA Sequencer, A Technical Fix May Have Come Too Late - Forbes) discusses a new further improvement in the ability to do this error correction (a paper just came out on the topic from Adam Phillippy, Sergey Koren, Michael Schatz, and others).

I find this whole concept a bit funny / interesting.  Not only does Illumina sequencing have many uses but one of its uses in essence helps keep aloft the potential of some of it's competitors.  In this way - Illumina can be considered the duct tape of sequencing systems.  1001 uses.  Not sure the Illumina folks will be overly thrilled with this use but that is the way it goes ...

(As an aside - any high throughput highly accurate sequencing method could be used in the same way as Illumina in most cases - ABI solid for example.  But alas for ABI Illumina has kind of taken over this part of the market).

(An another aside - we will have to wait and see how/if the Ion Torrent systems take off in the sequencing ecosystem)

(As another aside - still waiting to see some more detail from the Oxford Nanopores folks ... I would be happy to be a beta tester if anyone from Oxford is reading this).

Elaine Mardis rocks: nice talk on "Next generation sequencing"

I wish I had seen this before I gave my first lecture on Next Gen Sequencing Methods on Monday.  I will post mine later but here is a really really nice talk by Elaine Mardis from Washington University on the same topic:

Wanted - opinions/details on online systems for annotation of genomes and metagenomes

Doing a little survey/snooping around.  Trying to compile a list of available online tools for annotating microbial genomes and metagenomes.  And I am also trying to get comments on what people think of the various tools.  There are some obvious candidates to think about

• IMG and IMG/M
• RAST and MG-RAST
• IGS annotation engine (which seems to no longer be a web server but an email the sequence to someone server).

But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.

• Jonathan Eisen ‏ @phylogenomics
• Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST
• Mick Watson @BioMickWatson
• @phylogenomics some microbial annotation pipelines mentioned in our review here bib.oxfordjournals.org/content/early/…
• Ewan Birney ‏ @ewanbirney 
• @phylogenomics Check out @EBImetagenomics ebi.ac.uk/metagenomics/: ORFs, Interproscan, submissions and more.
• Mick Watson ‏ @BioMickWatson 
• @ewanbirney @phylogenomics @EBImetagenomics needs illumina support, and support of assemblies :/

And from Google Plus where I asked "Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST ":

• Mary Mangan - Oh, I know some:
• Manatee: http://www.jcvi.org/cms/research/projects/annotation-service/ 
• GATU: http://athena.bioc.uvic.ca/virology-ca-tools/gatu/ 
• Apollo: http://gmod.org/wiki/Apollo
• And also from Mary
• Here's a question on that at BioStar: 
• EDIT: Another question suggests Artemis:

Cool paper from DerisiLab on viruses in unknown tropical febrile illnesses #metagenomics #viroarray

Quick post:

Figure 3. Circovirus-like
NI sequence coverage and phylogeny.

Cool new paper from Joe Derisi's lab: PLoS Neglected Tropical Diseases: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Full citation: Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, et al. (2012) Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing. PLoS Negl Trop Dis 6(2): e1485. doi:10.1371/journal.pntd.0001485

They used a combination of a viral microarray and metagenomic sequencing to characterize viruses in various samples from patients with febrile illness.  And they found some semi-novel viruses in the sample.  Definitely worth a look.

Note - here are some other posts of mine about Derisi:

• The Tree of Life: Wrap up of tweets from Joe Derisi talk
• The Tree of Life: Today at UC Davis - Joe Derisi "A Seminar in Two ...
• Joe Derisi and Open Science featured on Voice of America
• The Tree of Life: Open Access Pioneer Award #3: Joe Derisi

See some follow up discussion on Google+ here.

The story behind Pseudomonas syringae comparative genomics / pathogenicity paper; guest post by David Baltrus (@surt_lab)

More fun from the community.  Today I am very happy to have another guest post in my "Story behind the paper" series.  This one comes to us from David Baltrus, an Assistant Professor at University of Arizona.  For more on David see his lab page here and his twitter feed here.  David has a very nice post here about a paper on the "Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates" which was published in PLoS Pathogens in July.  There is some fun/interesting stuff in the paper, including analysis of the "core" and "pan" genome of this species.  Anyway - David saw my request for posts and I am very happy that he responded.  Without further ado - here is his story (I note - I added a few links and Italics but otherwise he wrote the whole thing ...).

---------------------------------------

I first want to than Jonathan for giving me this opportunity. I am a big fan of “behind the science” stories, a habit I fed in grad school by reading every Perspectives (from the journal Genetics) article that I could get a hold of. Science can be rough, but I remember finding solace in stories about the false starts and triumphs of other researchers and how randomness and luck manage to figure into any discovery. If anything I hope to use this space to document this as it is fresh in my mind so that (inevitably) when the bad science days roll around I can have something to look back on. In the very least, I'm looking forward to mining this space in the future for quotes to prove just how little I truly understood about my research topics in 2011. It took a village to get this paper published, so apologies in advance to those that I fail to mention. Also want to mention this upfront, Marc Nishimura is my co-author and had a hand in every single aspect of this paper.

Retraction - I was buzzing off about bees before my time

Recently I wrote a post about the recent study on bees associated with colony collapse disorder. After receiving a well thought out email from one of the authors on the study I have decided to retract my blog and apologize to the authors of the bee study. I rushed out my blog without really considering the evidence and the data very carefully and accept that I screwed this one up big time. The study is much more complex and comprehensive that I led people to believe. In part this was due to lack of detail in the actual manuscript but alas most of the fault lies with me - in not trying to contact the authors for more detail before mouthing off.

So I am giving myself a new award - the genomic jerk award. Hopefully there will be no more recipients.