Today's Spammy journal Editorial Board Offer #1

Just got this - pretty lame given that, well, I do not do anything related to this journal.

Dear Dr.Jonathan A Eisen,   

Hope this mail brings you good health and prosperity 

Fisheries and Aquaculture Journal is successfully publishing quality open access journals with the support from scientists like you. We are aware of your reputation for quality of research and trustworthiness in the field of science and thereby we request you to be an Editorial Board Member of our Fisheries and Aqua culture Journal. It would be our immense pleasure to have you as one of our editorial board member. 

Please follow the below link for more information http://omicsonline.com/open-access/editorialboard-fisheries-and-aquaculture-journal-open-access.phpIf you are interested, you are requested to send 

• A recent passport size photo (to display at our website) 
• C.V
• Biography
• Research Interests for our records 

Kindly submit your details at editor.faj@omicsonline.net, editor.faj@omicsgroup.biz We look forward to a close and long lasting scientific relationship for the benefit of scientific community.Waiting for a positive response.

With Kind Regards,XXXEditorial Assistant 

Fisheries and aqua culture Journal7 

31 Gull Ave, 

Foster City CA 94404, USA

More microbe-themed art - the Eden Project's "Human Biome"

Just got pointed to this Wired article by Katie Collins -- Eden Project's 'Human Biome' is a gross, musical microbe showcase (Wired UK)



Fascinating project that I actually don't think is gross in any way.  From the article

Invisible You: The Human Biome will explore the community of microbes that live in and on each and every one of us. Artistic and interactive displays will show bacteria, fungi and viruses, with 11 artists commissioned to create works for the exhibition.

I want to just quote the entire story but I think that is not allowed so let's just say you really should read the whole thing and look at the gallery.

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature

For many reasons I have been interested for the last few years in how agricultural practices affect microbiomes.  For example in regard to crops, how do farming practices affect the microbiomes of the plants, the microbiomes of the soil and area around the plants, and the microbiomes of organisms (including humans) who make use of the plants?

I won't go into all the detail right now for why I am interested in this topic but for some examples of my work in this area see The microbes we eat abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types and Structure, variation, and assembly of the root-associated microbiomes of rice.

Anyway, the reason I am writing this now is that tomorrow I am "testifying" to a NRC Committee about this topic and some related topics.  The presentation will be shown live online (register here).  And I thought, in the interest of openness, I would post some of what I am thinking about here before hand.

One of the key topics for tomorrow is something I have been snooping around at for a few years - how does glyphosate (the key ingredient of RoundUp and a widely used herbicide) affect microbiomes?  I am interested in this from both a scientific point of view (I think it is an interesting topic) and also from a "public policy / education" point of view.  I think this is a really good topic to have a public discussion of "microbiomes" and both the importance of microbial communities and the challenges with studying them.  So a few years ago I started thinking about working on this and developing a "Citizen Science" project around it.  And, well, I am still working on that idea and probably will be trying to launch something in the near future.  As a first start I thought it would be good to start to engage the community (researchers, teachers, the public, etc) in a discussion of this topic.  So .. this is the beginning of that I guess.

Some questions I think are interesting:

• Does glyphosate affect plant microbiomes?
• Does glyphosate affect soil microbiomes?
• Does consumption of plants treated with glyphosate affect the microbiomes of the consumer? 
• Directly (e.g., by glyphosate itself being in the food and directly affecting microbomes"
• Indirectly (by glyphosate affecting the microbiome of the food which in turn affects the microbiome of the consumer)
• If glyphosate affects any of these microbiomes above, are these significant affects (e.g., in terms of health)?

Now I am not the only person who is interested in this topic.  In fact, there have been many people looking into these and related topics for years.  Some of the things I have seen on this topic in the popular press and the scientific literature are, well, not good science.  And some of the things I have seen are fascinating and well done. 

So as a first step in looking into this, I scoured the literature for papers of interest.  And that is really why I am writing this.  I created an open collection of the papers I have found with the Zotero reference collection system.  See this link for the collection.  And if you know of any other papers truly related to this topic, please add them to the collection (learn more about Zotero here).  I do not profess to know everything about this topic.  But I think it is interesting and possibly important.  

Four simple tools to promote gender balance at conferences - guest post from Julie Pfeiffer @jkpfeiff

Guest post from Julie Pfeiffer.

Julie Pfeiffer
Associate Professor of Microbiology
University of Texas Southwestern Medical Center
https://twitter.com/jkpfeiff
http://www4.utsouthwestern.edu/pfeifferlab/Index/Home.html

---

Four simple tools to promote gender balance at conferences 

1. Know that you are biased. Identify your biases.

We all have biases and many of them are unconscious. You can discover your own biases using online social attitude tests developed by Project Implicit, a non-profit organization affiliated with Harvard University. The Gender-Science Implicit Association Test is particularly relevant here. It turns out that I have moderate bias linking science with males, as well as other biases. Knowing this fact has been extremely important. It is very difficult to alter unconscious bias, but it is easy to understand that you are biased and edit your actions accordingly. For example, if I need to make a list of potential speakers or authors quickly, the list will be of senior men from the United States. The key is to spend time EDITING the list to ensure diversity.

2. Keep track of numbers.

Most individuals in leadership positions are not seeking to exclude women or other groups from plenary talks, career opportunities, etc. Instead, they simply forget to count. They forget to keep track of gender ratio and other types of diversity. They forget to edit. When leaders/organizers have diversity in mind, diversity is relatively easy to achieve. Two examples illustrate this point:

1) Vincent Racaniello is President of the American Society for Virology and his goal was to put together an outstanding and diverse group of plenary speakers for the annual meeting in 2015. He asked for speaker suggestions via emails and Twitter (https://twitter.com/profvrr). He made a list and he edited it. The result? The best representation of female scientists at a conference I have ever seen--- 50% of the plenary speakers at ASV this year are female.



2) The Associate Editors at the Journal of Virology choose topics and authors for short reviews called “Gems”. The goal was to have high diversity in several areas including author gender, author career stage, author location, and topic. To keep ourselves on track to achieve this goal, we included several extra columns in our author/topic spreadsheet: Female? Non-USA location? Junior PI? This simple reminder in the spreadsheet has helped us select relatively diverse authors and topics: ~30% are female, ~30% are Assistant Professors, and ~20% are at institutions outside the United States.

3. Create lists and ask people for suggestions. 


Trying to come up with names of female scientists de novo can be a challenge. A few months ago, Carolyn Coyne, Erica Ollmann-Saphire, and Clodagh O’Shea made a list of as many female virologists as they could. Over wine, they devised a list of 70 names. We have circulated this list to many of our colleagues and tweeted a request to send missing names. The list is now at 349 and is publicly available (please tweet missing names to https://twitter.com/jkpfeiff). It is much easier to think of diverse options for speakers and authors by using a pre-existing list. Virologists with this list can no longer claim that they “couldn’t think of a female speaker”. Each field could benefit from a list like this, which could also include other underrepresented groups. Several of these lists exist, as has been highlighted on this and other blogs.

4. Speak up and enlist the help of supportive senior faculty.

Expressing concern to conference organizers about low speaker diversity can go a long way. While it may be difficult to change the speaker list close to the conference date, mentioning the lack of diversity could change the future landscape of the conference. I have an example from my own experience: I created an international shitstorm that had a great outcome. In year three of my faculty position I was considering whether to attend a major conference, so I checked the speaker list to help make my decision. Zero of 18 plenary speakers were female. I decided not to attend. Instead, I emailed the conference organizer to express my disappointment with the complete lack of female plenary speakers. His response, over several emails, was less than supportive:

“…. Finally, the gender, race, religion has never been, to my opinion, valuable ways to select presenters of scientific works. The selection of the Plenary Lectures has been made by the Organizing Committee, that comprises a woman, based on the topic, then the best possible speaker on the topic…. I am aware of the current debate in our societies about "minimum numbers". I do not think they would help the cause of women in science.”

While this organizer was not supportive or responsive to my speaker suggestions, five senior (famous) faculty members in the field were hyper-supportive. Upon hearing this story, they each contacted the organizer and expressed their concern about the lack of diversity. It was too late to change the program for the conference that year. However, in every subsequent year, the plenary speakers at this conference have included women and other underrepresented groups. So, it’s possible that a simple email from a young scientist can make a difference, particularly with the help of senior faculty.

Painful, kind of hilarious, typesetting error in a #PLOSOne paper from my lab - should I try to get it fixed?

Saw this tweet:

@phylogenomics Funny/interesting typesetting trainwreck in equation 4 of PLOS PhyEco paper. English letters were replaced by Greek!
— Michael Hall (@mikehall_dal) March 30, 2015

So I went and found the paper.

Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

And discovered what he was pointing to

Then I looked at the Pubmed Central version of the paper and it was the same.  So I wnet and found the arXiv version of the paper and it looked correct.

So apparently, PLOS One somehow replaced "nonmember" with

Brutal.  And even worse, this may have been there all along and I missed it.  So I responded:

@mikehall_dal OMG OMG OMG how could I not notice that? (maybe this changed somehow) OMG
— Jonathan Eisen (@phylogenomics) March 30, 2015

And then Michael Hall pointed out another mistake.

@phylogenomics And while I'm on the topic, is the base for equation 3 supposed to be e and not epsilon?
— Michael Hall (@mikehall_dal) March 30, 2015

@mikehall_dal oh #FFS - yes - I have no idea what happened there - thanks for finding this
— Jonathan Eisen (@phylogenomics) March 30, 2015

@mikehall_dal note - note in the arxiv version http://t.co/Q8gnIrgU4X
— Jonathan Eisen (@phylogenomics) March 30, 2015

@phylogenomics Ahh, that's much better. Looks like every equation has a wee bit of Greek-ification (n to nu in 1 and 2). Fun! :)
— Michael Hall (@mikehall_dal) March 30, 2015

Aaargh.  And funny too.  So now the question I guess is - should I fix it? And if so, how do I do that?

Calling attention to meetings with skewed speaker gender ratios, even when it hurts, part 2

A few weeks ago I gave a talk at the Future of Genomic Medicine 2015 (aka #FOGM15) meeting.  The talk seemed to go over well.  I talked right after Martin Blaser in a session on "The Microbiome".  I posted my slides and then a video of my talk as well as notes from the meeting: see My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute.  And I met some really interesting people at the meeting and enjoyed most of the talks I went to.

But alas, one thing stuck in my head from this meeting.  One single Tweet from someone out there threw me for a loop:

Hey @phylogenomics, 77% of talks at #FOGM15 given by male speakers #justsayin
— Mick Watson (@BioMickWatson) March 6, 2015

And this let to a bit of soul searching on my part.  Some of the conversations on Twitter are captured in this Storify:

Which I guess culminated in a post to the organizers of the meeting

Dear #FOGM15 organizers - next time - you can (and really MUST) do MUCH better with the gender ratio of speakers
— Jonathan Eisen (@phylogenomics) March 6, 2015

Then, when I left the meeting I went to say goodbye to the organizers.  And, well, one of them did not take too kindly to the critique of the meeting, saying that they were doing a better job than other healthcare meetings.  I disagreed and said I thought they could do much better, but I had no numbers to cite at the time and the conversation ended there.

So on the way to the airport I started digging around for some numbers and I found some great resources - especially this from Rock Health.

Reading - The XX Speaker Project — XX in Health re #fogm15 http://t.co/Z5ir26g3qd
— Jonathan Eisen (@phylogenomics) March 7, 2015

And for the last few weeks I have continued to fester wondering - well - should I post more about this?  Should I dig into the gender ratio of the FOGM meetings in more detail?  Well, why do it?  Because I think it is important to know how meetings perform in terms of diversity.  Why not do it?  Well, I like Eric Topol and the other organizers.  And the meeting has many strong points.  But, as I wrote a few days ago - sometimes one needs to call attention to meeting gender ratio issues, even when it hurts.  

So then I decided to dig a little deeper and look at past versions of the "Future of Genomic Medicine".  And, well, when I did this, things just do not look so good (detailed analysis is at the end of the post). (Note - for the numbers i counted all presenting slots - session chairs, keynotes, welcomes, etc.  The numbers are not much different if one counts just "talks").

If one compares these meetings to the ones catalogued by Rock Health, the FOGM meetings are at the low end.  Not the worst certainly.  But definitely not something to be proud of.  And certainly something that could be improved upon enormously.  So I repeat the Tweet I posted during the meeting, and I stand by it, even if it means I am unlikely to be invited back and even if it means pissing off some big shots in the world of genomics ...

Dear #FOGM15 organizers - next time - you can (and really MUST) do MUCH better with the gender ratio of speakers
— Jonathan Eisen (@phylogenomics) March 6, 2015

If you are running a meeting, please consider the ways in which bias may creep into the speaker and session chair slots.  If speakers come from invitations, perhaps the invitation list is biased.  Perhaps certain types of people are more likely to say no to invitations.  Perhaps the timing of the meeting (e.g., on weekend) may lead certain types of people to not be able to participate.  Perhaps the meeting does not provide enough travel funds or child care or the right kind of schedule.  There are so many things that can lead to bias - from explicit bias against certain groups to very subtle implicit biases.  Consider inviting people from diverse career stages, which can open up speaking slots to more women and underrepresented minorities.  Consider providing child care.  Consider asking people why they say no to invitations to try and understand what is going on if many people say no.  Consider asking for help in finding speakers covering the diversity in the field.

If you do all these things, and the meeting still does not have diverse speakers, well, try some other things.  Keep trying to figure it out.  There are resources out there that can help.  Read things like Some suggestions for having diverse speakers at meetings (by me) and Ten Simple Rules to Achieve Conference Speaker Gender Balance (by Jenny Martin) and Increasing Diversity at Your Conference by Ashe Dryden (which is just completely awesome) and How To Create A More Diverse Tech Conference ... and Would I attend my own conference? - O'Reilly Radar by Sarah Milstein.

Why is this important?  Well, speaking at a meeting is important for people's careers.  It helps in merit and promotion and tenure cases.  It helps get their work recognized and known.  Speaking at a meeting is also good practice for speaking at other meetings.  Having diverse speakers also is important in terms of providing role models to attendees.  And having diverse speakers helps a meeting not just be about the same old, white, men talking about their ideas.  Or, in other words, it makes a meeting more, well, diverse.  And almost certainly more interesting.  And so on.  Diversity of speakers at meetings is important for 100s of reasons.  And don't just focus on one aspect of diversity.  I post a lot about women speakers because, well, it is easy to make a reasonable guess as to whether a person is male or female.  But there are MANY other aspects of diversity to consider (see Increasing Diversity at Your Conference by Ashe Dryden (which I referenced above and which really is awesome).

Anyway - if you are organizing a meeting, make sure to think about these issues.  And do something about them.  And if you are invited to a meeting, look at the speaker list (if it is available) and consider saying no to speaking if the meeting has diversity issues (see a post of mine about doing this here: Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM).

And if you are considering attending a meeting, consider diversity of speakers when deciding whether or not to attend.  Meetings with high diversity of speakers should be supported.  Meetings with poor diversity relative to possible candidate speakers (e.g., who is in the field) should be avoided, shunned, and called out.  We need to force change upon some fields and the only way will be to call out the bad apples.  Mind you, it is not possible to know WHY a meeting has a skew in terms of diversity of speakers.  Thus one additional thing to consider is whether something is a consistent pattern.  For example see my post about meetings from the National Academy of Sciences Sackler Colloquia - Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM. Sadly it seems to me that the FOGM meetings have a consistent pattern of poor representation of women among the presenters.  Unless the organizers commit to changing this, I think people should not attend this meeting in the future.

---

Detailed analyses of these meetings are below.

People I have identified as males are labelled in yellow.  People I have identified as females are in green.  I realize that this is an imperfect thing to do.  I may make mistakes in my inferences.  And dividing people into two categories is not representative of the true diversity in the human population.  But I still think this is a useful, informative thing to try to do.

---

2015 FOGM (schedule is from the one sent around to participants on 3/4/15)

• Welcome
• Eric Topol
• Pateint #1 - Eunice Lee and Nilesh Dharajiya
• Francis Collins
• Session 1
• Moderator Ali Torkamani
• Diana Bianchi
• Evan Muse
• Stephen Quake
• David Hoon
• Session 2
• Moderator Ali Torkamani
• Mark McCarthy
• Christopher Austin
• George Yancopoulos
• Session 3
• Moderators Nathan Wineinger and Andrew Su
• Atul Butte
• Eric Schadt
• Andrew Su
• Joe Pickrell
• Welcome Day 2
• Patient #2
• Eric Topol
• Session 4: 
• Moderator Ali Torkamani
• Cristian Tomasetti
• Nazneen Rahman
• Roni Ziegler
• Session 5
• Moderators Kristin Baldwin and Fyodor Urnov
• J. Keith Joung
• Fyodor Urnov
• TBD
• Kristin Baldwin
• Session 5
• Moderator Kristian Andersen
• Martin Blaser
• Jonathan Eisen
• Stephen Steinhubl
• Session 6
• Moderator David Goldstein  (he did not show up)
• Elizabeth Worthey
• Ali Torkamani
• Seth Mnookin
• Virginia Hughes

All speaker and session chair slots

• Male: 30 (81%)
• Female: 7 (19%)

Just speakers

• Male: 23
• Female: 6

---

2014 - Future of Genomic Medicine VII -  schedule from here

• Welcome
• Chris Van Gorder, FACHE
• Eric J. Topol, MD
• Patient / Family #1
• Session 1
• Frank McCormick
• Bert Vogelstein
• Elaine Mardis
• Robert Nussbaum
• Sarah Jane Dawson
• Michael Pellini
• Session 2
• J. Craig Venter
• Eric Topol 
• Al Gore
• Heidi Rehm
• Muin Khoury
• Session 3
• Moderator Katrina Kelner
• Leonid Kruglyak
• Carl Zimmer
• Magdalena Skipper
• Chris Gunter
• Session 4
• Patient / Family #2
• Athur Beaudet
• Jay Shendure
• Howard Jacob
• Hakon Hakonarson
• David Epstein
• Nir Birzalai
• Ali Torkamani
• Jeffrey Hammerbacher
• Session 5
• Michael Specter
• Jessica Richman
• Andrew Feinberg
• Russ Altman
• Anne Wojcicki
• Harry Greenspun
• Zubin Damania

Speakers

• Male: 25 (76%)
• Female: 8 (24%)

---

2013 - Future of Genomic Medicine VI - schedule from here

• Welcome: Eric Topol
• Patient / Family #1
• Session 1:
• Michael Snyder
• William Gahl
• Howard Jacob
• Ali Torkamani
• Gholson Lyon
• Cinnamon Bloss
• Misha Angrist
• Session 2
• Evan Eichler
• Eric Schadt
• Katrina Armstrong
• George Weinstock
• Session 3
• Joe Ecker
• Stephen Kingsmore
• Stephen Quake
• Session 4
• Patient / Family #2
• Siddhartha Mukherjee
• Elaine Mardis
• Daniel D. Von Hoff
• Randy Scott
• Susan Desmond Hellman
• Elias Zerhouni
• Janet Woodcock
• Session 5
• Peter Vesscher
• David Goldstein
• George Church
• Jonathan Eisen
• Atul Butte
• AJ Jacobs
• Neil Risch
• Lonny Reisman
• Daniel MacArthur

Speakers

• Male: 26 (84%)
• Female: 5 (16%)

---

2012 Future of Genomic Medicine V - schedule from here

• Welcome
• Chris Van Gorder, FACHE
• Eric J. Topol, MD
• Joseph Beery and Family
• Moderators: Samuel Levy, PhD and Eric J. Topol, MD
• Samuel Levy, PhD
• Matthew J. Price, MD
• Julie Johnson, PharmD
• Michael R. Hayden MB, ChB, PhD
• William E. Evans, PharmD
• Moderators: Evan Eichler, PhD and Sarah Murray,
• Evan Eichler, PhD
• Christofer Toumazou, PhD
• Siddharta Mukherjee, MD, PhD
• Sarah Murray, PhD
• Moderators Nicholas Schork, PhD and Bradley Patay, MD
• Hakon Hakonarson, MD, PhD
• Isaac Kohane , MD, PhD
• John A. Todd, FRS, PhD
• Moderators Eric J. Topol, MD and Nicholas Schork, PhD
• Howard J. Jacob, PhD
• Joseph G. Gleeson, MD
• Stanley F. Nelson, MD
• Lynn Jorde, PhD (note - originalled labelled as female - corrected thanks to comment from Bruce Rannala)
• Eric J. Topol, MD
• Moderators: Aravinda Chakravarti, PhD and Richard Klausner, 
• Aravinda Chakravarti, PhD
• Joseph Nadeau, PhD
• Nicholas Schork, PhD
• Hakon Hakonarson MD, PhD
• Moderator Eric Topol
• Matthew Herper
• Daniel B. Vorhaus, JD, MA
• Issam Zineh, PharmD, MPH
• Moderators: Elaine Mardis, PhD and Jeffrey Trent, PhD
• Richard D. Klausner, MD
• Thomas J. Hudson, MD
• Jeffrey M. Trent, PhD
• Daniel D. Von Hoff, MD
• Elaine R. Mardis, PhD
• Moderators: Samuel Levy, PhD and Fred Gage, PhD
• Fred H. Gage, PhD
• Bruce D. Gelb, MD
• Joseph C. Wu, MD, PhD

All speaker and session chair slots

• Male: 44 (88%)  45 (90 %)
• Female: 6 (12%) 5 (10 %)

Just speakers

• Male: 31 32 (91.4%)
• Female: 4  3 (8.6%)

---

2011 Future of Genomic Medicine IV - schedule from here

• Session 1: Moderators: Sarah S. Murray, PhD and Eric J. Topol, MD
• Hannah A. Valantine, MD
• Geoff Ginsburg, MD, PhD
• Steve Shak, MD
• Cinnamon S. Bloss, PhD
• Matthew J. Price, MD
• Session 2: Moderators: Bradley Patay, MD and Nicholas J. Schork, PhD
• Kevin Davies, PhD
• Thomas Goetz, MPh
• Melanie Swan, MBA
• Session 3: Moderators: Samuel Levy, PhD and Nicholas J. Schork, PhD
• Kári Stefánsson, MD
• Aravinda Chakravarti, PhD
• Howard J. Jacob, PhD
• Sarah S. Murray, PhD
• James R. Lupski, MD, PhD
• Nicholas J. Schork, PhD
• Stephen L. Hauser, MD
• David R. Bentley, D.Phil, F.Med.Sci.
• Keynote: Juan Enriquez, BA, MBA
• Session 4: Moderators: Robert L. Strausberg, PhD and Samuel Levy, PhD
• Robert L. Strausberg, PhD
• Elaine R. Mardis, PhD
• Thomas J. Kipps, MD, PhD
• Samuel Levy, PhD
• Daniel D. Von Hoff, MD
• Dennis A. Carson, MD
• Session 5: Moderators: Eric J. Topol, MD and Bradley Patay, MD
• Eric J. Topol, MD
• Amy Harmon
• Misha Angrist, PhD
• Session 6: Moderators: Sarah S. Murray, PhD and Samuel Levy, PhD
• Hakon Hakonarson, MD, PhD
• Mark McCarthy, MD, F.Med.Sci.
• Karen Mohlke, PhD
• Stephen S. Rich, PhD
• Philippe Froguel, MD, PhD
• Muredach P. Reilly, MB, MS

All speaker and session chair slots

• Male: 35 (80%)
• Female: 9 (20%)

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting

• Planetary Protection Workshop (Forward Contamination)
• Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro)

My posts:

• Is the MinION thumb drive sequencer taking off? Seems so …
• Interesting analysis of data sharing in paleogenetics #OpenScience
• Great “Hidden Life” (of homes and people) Learning Activity from the NY Times #microbiology
• Important read from Aaron Darling: Not so fast, FastTree
• Fascinating and distressing look at cruise ship turnaround
• Resistance (The Film) coming to UC Davis April 9
• Great #openaccess collection of papers on RNA
• Today in germophobia and antimicrobiomism: grandparents who hate microbes
• I love that @eLIFE is publishing draft papers now (brewery microbiome)
• Evolution of DNA Sequencing 2015 Version
• Methylisothiazolinone in household items – a growing (or well, killing) problem #germophobia
• Cool: James Clemens High School-Hudson Alpha Classroom Microbiome Project
• Well, I guess this means microbiome engineering has arrived (sort of)
• Today in “where’s the pathogen?” Can you find Burkholderia on 500 acres with 50 samples?
• Yes Virginia, there is a paper on microbial transfer during beer pong
• Healthy Buildings 2015 meeting promo / preview

Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

• CAMI Challenge is Now Open for Participation

Elisabeth Bik from Stanford roundups from Microbiome Digest

• Best of MicrobiomeDigest: Fisherman’s Friends
• MicrobiomeDigest – your daily fix of microbiome literature

Greg Caporaso from Northern Arizona University on SciPy

• SciPy 2015 Computational Life and Medical Sciences Mini-Symposium: Call for Abstracts

David Coil (a staff scientist at UC Davis in my lab)

• Official release of Gut Check: The Microbiome Game “print-at-home” edition
• Nostra culpa: Revised results for the microbial playoffs in space
• Gizmodo article regarding discussing data uncertainty in microbiome studies

Bill Van Bonn (of the Shedd Aquairum)  on the Aquarium Microbiome Project

• The Built Aquatic Environment

Linsey Marr of Virginia Tech

• What sequencing core do you recommend for environmental samples with low concentrations?

Alex Alexiev - undergraduate in my lab

• Microbes Corroding Concrete
• Using Sewage to Estimate a City’s Gut Health?

Maria Nunez of Mycoteam

• Microbial sampling in building surveys: what and why are we sampling?

Amanda Makowiecki at UC Boulder

• Acquired Resistance to Ultraviolet Germicidal Irradiation

Rachel Adams - post doc at UC Berkeley

• Fungal amplicons

Ben Kirkup of the  Naval Research Laboratory

• Bad-omics

Embryete Hyde from UCSD

• Rob Knight’s lab moves to UCSD
• Rob Knight’s TED Talk Released!

Brent Stephens of the Illinois Institute of Technology

• Building science measurements in the Hospital Microbiome Project: Part 2

Bubba Brooks from UC Berkeley

• New paper on diseased vs healthy infants in a NICU, possible impacts for future hospital microbiome work

Kyle Bibby of the University of Pittsburg

• The Pittsburgh Water Microbiome Project