Saturday, April 5, 2014

If you only read ONE paper this year...

...make it this paper:

Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, et al. (2014) Ten Simple Rules for Effective Computational Research. PLoS Comput Biol, 10(3): e1003506. doi:10.1371/journal.pcbi.1003506

INCLUDING the supporting information text, which is very detailed and provides a fantastic trove of resources explaining how to get started.

As someone who has moved from lab-based biology towards computational research, I can tell you that I've learned many of these lessons the hard way. I wish someone had handed me this paper four years ago when started transitioning fields during my first postdoc. For biologists, this paper provides great advice for how to a) make computational tasks less painful, b) work with computer scientists and bioinformaticians, and c) how to do better science. If you don't think you need to learn GitHub, that you can get by without it...sure, you can, but you'll probably end up there anyway. And then you'll discover how much easier and efficient your research will become:

Thursday, March 27, 2014

Lateral Gene Transfer detected in Eukaryotic rRNA genes

This paper is an example of super cool science that also makes me worry. Eukaryote are known to have lower levels of Lateral Gene Transfer (LGT), and before this paper I assumed that LGT would not impact eukaryotic rRNA genes. However, this not so according to Yabuki et al. (2014):
Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genomewalking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two proteincoding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.
Why is this paper worrisome? Well, if LGT of rRNA genes is a widespread phenomenon in microbial eukaryotes, it will conflate biodiversity estimates obtained from environmental sequencing studies. If you had a environmental rRNA Illumina dataset, your bioinformatic analysis would show taxonomic assignments for an alveolate and stremenopile (detecting 2 taxa from one genome, one true assignment, one false). The authors cite this concern in their conclusion:
These large-scale [environmental] surveys may detect transferred rRNA genes and such transferred rRNA genes may confuse our understanding of the true diversity and distribution of microbial eukaryotes, even if the frequency of lateral transfers of the rRNA gene is rare and the copy numbers of the transferred rRNA gene in environments are low. We agree that environmental rRNA gene surveys with PCR are still useful and effective to estimate the diversity/ distribution of microbial eukaryotes. However, the fact that recovered rRNA gene sequences do not always reflect the actual existence of microbial eukaryotes corresponding to these sequences should be kept in mind based on our findings. 
In other words, more research is needed to determine exactly how widespread this rRNA LGT phenomenon is in may be something else we need to take into account when designing software workflows for environmental sequence data.


Yabuki, A., Toyofuku, T., & Takishita, K. (2014). Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes, 1–4. doi:10.1038/ismej.2013.252

Wednesday, March 26, 2014

Exploring Statistics for Metagenomic Datasets

Recent lab discussions have made me think a lot about statistical tests we can use to detect and verify differences between metagenomic datasets. Since I don't have a strong background in statistics, my knowledge of this topic is still evolving - the scale and distribution of genomic datasets can be a tricky issue to deal with in a lot of statistical tests, it seems.

Some of of the most useful resources I've found so far are as follows (feel free to comment and recommend more resources):

Parks, D. H., & Beiko, R. G. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26(6), 715–721. doi:10.1093/bioinformatics/btq041 (good rundown of the different statistical techniques applied to genomic data, including their implementation in the STAMP pipeline)

Primmer, C. R., Papakostas, S., Leder, E. H., Davis, M. J., & Ragan, M. A. (2013). Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology, 22(12), 3216–3241. doi:10.1111/mec.12309 (especially Box 3 - Gene Ontology enrichment tests)

Metagenome Ordination in IMG - provides a good comparison of PCA vs. PCoA vs. NDMS, particularly in regard to how each of these statistics are calculated (and differ from one another).

Dinsdale, E. A., Edwards, R. A., Bailey, B. A., Tuba, I., Akhter, S., McNair, K., et al. (2013). Multivariate analysis of functional metagenomes. Frontiers in Genetics, 4, 41. doi:10.3389/fgene.2013.00041 (added to list 5/10/14 - comprehensive and thought-provoking overview of metagenomic data analysis)

Monday, February 10, 2014

Meeting Announcement: Evolutionary Biology of Caenorhabditis & Other Nematodes

Since I'm on the organizing committee for this upcoming meeting, it's time to start advertising! Abstract submissions are now open (click here for meeting website):

Evolutionary Biology of Caenorhabditis and other Nematodes 

June 14-17, 2014, Hinxton, UK

This conference will bring together scientists studying evolutionary processes in diverse nematode groups. In addition to attracting many researchers studying evolution in Caenorhabditis elegans as model organism (and its closer relatives such as C. briggsae and C. remanei), the meeting will also welcome scientists investigating other free-living groups and the numerous animal- and plant-parasitic nematode species that threaten human health and the global economy. There will be a strong emphasis on genomic approaches and perspectives. The topics highlighted will include experimental evolution, fundamental evolutionary forces, genotype-phenotype relationships, metagenomic analyses, and processes of parasitism. The programme plays a critical role in promoting interaction and collaboration between evolutionary scientists training in the C. elegans tradition and those focused on other nematode groups.

A limited number of registration bursaries are available for PhD students and junior post-docs to attend this conference (up to 50% of the registration fee).

Abstract and bursary deadline: May 2, 2014
Registration deadline: May 16, 2014

Monday, January 6, 2014

NRC survey: Research Priorities for Marine Science

I received an e-mail from the INDEEP mailing list, asking me to participate in a Virtual Town Hall on marine science research priorities, currently being run by the NRC. Here's the rundown from their website:
The National Research Council, at the request of the National Science Foundation, is seeking guidance from the ocean sciences community on the prioritization of research and facilities for the coming decade. The Decadal Survey of Ocean Sciences (DSOS) committee has been assembled for this task. To fulfill its charge, the DSOS committee is asking for community input via this Virtual Town Hall. To submit your input, please fill out the following identifying information, since anonymous comments will not be collected or posted. The deadline to submit your comments is March 15, 2014.
I figured I'd post my survey answers here (it would be great to generate some discussion about how we can promote greater emphasis on genomic tools and high-throughput sequencing in marine ecosystems - in particular the deep sea):

Across all ocean science disciplines, please list 3 important scientific questions that you believe will drive ocean research over the decade.

1) What is the role of microbial processes in ecosystem function?

2) How do microbes respond to (and impact) climate change?

3) How do we integrate knowledge from different fields (e.g. physical oceanography, biogeochemistry, taxonomy, marine biology) to gain a more comprehensive view of the marine environment?

Within your own discipline, please list 3 important scientific questions that you believe will drive ocean research over the next decade.

1) Characterizing phylogeographic patterns in microbial eukaryotes using genomic data. What is the proportion of comopolitan vs. regionally restricted species in different marine habitats?

2) Linking genomic data (DNA, RNA, genome sequences) to the existing body of morphological, ecological and taxonomic data. Particularly important for microbial species where each of these data types exists in discipline-specific silos. How can such linked data further our understanding of marine ecosystems?

3) How do we build accurate models (e.g. using robust algorithms and existing data as training sets) to predict species distributions and the potential impacts of climate change?

Please list 3 ideas for programs, technology, infrastructure, or facilities that you believe will play a major role in addressing the above questions over the next decade. Please consider both existing and new technology/facilities/infrastructure/programs that could be deployed in this timeframe. What mechanisms might be identified to best leverage these investments (interagency collaborations, international partnerships, etc.)?

1) In order to address ecosystem-scale questions, and use cutting-edge methods to do so, the marine science community (particularly ecologists and taxonomists) need to forge links with researchers in genomics and computational biology. DNA sequencing is largely under utilized in marine environments (notably lacking in the deep-sea), yet it offers a deep, cost-effective view of species, populations, and communities. Yet, computational expertise is needed to effectively apply genomic tools to marine systems, and that expertise must come from researchers who are knowledgeable about current software and algorithms (workflows optimized for "big data").

2) Funding initiatives or programs emphasizing microbial eukaryotes are needed to complement the (currently much greater) emphasis on bacteria/archaea, macro fauna and megafauna. Meiofauna and protists underpin many key ecosystem processes (e.g. nutrient cycling), but their role in marine habitats is perpetually understudied. We lack even a basic understanding of global biodiversity and species distributions for the majority of microbial metazoan phyla.

3) Marine sampling protocols MUST adopt forward-looking approaches. Ship time is expensive, and samples from habitats such as the deep-sea are precious and difficult to obtain (particularly for researchers in the genomics or computational biology communities, who may not have the professional connections needed to obtain biological samples). Many sample preservation methods do not consider the potential long-term use of a sample; for example, using formalin to preserve sediment immediately destroys the possibility of using that sample for DNA sequencing. There are many alternate sample preservation methods that preserve both DNA and morphological features (e.g. DESS is effective for sampling microbial metazoa). Giving deeper thought to sample collection, and prioritizing DNA preservation from diverse marine environments, is CRITICAL for furthering our understanding of marine biodiversity, biogeography, and ecology.

To give your own input, fill out the survey at this link:

Sunday, December 29, 2013

PFTF Discussion: Job talks, chalk talks, and teaching demonstrations

Last month we finished off winter quarter with another talk about the academic job search, where UC Davis faculty Siobhan Brady (Plant Sciences) and Sarah Perrault (University Writing Program) gave us the rundown on job talks, chalk talks, and teaching demonstrations.

Firstly, we discussed how these three presentations differ:
  • Job talk (research talk, about 50 minutes long) - what you did in the past
  • Chalk talk (research plans, can be 20-90 minutes long) - what you're going to do in the future
  • Teaching demonstration (can be 25-60 minutes) - mock classroom or course instruction

Then we broached the finer details.:

Chalk talks usually put forth the aims listed in your research statement (e.g. they can be the exact points you outlined in your original job application packet). Few institutions will allow any type of presentation aids for chalk talks (and if powerpoint is allowed, you'll usually be limited to just a few slides). The focus of this talk should be on your research goals (both short-term and long-term) as well as your long-term research questions. Some tips for chalk talks:
  • Speak quickly on your feet and show mastery of your field
  • Introduce your long-term research questions during your job talk
  • Being conservative here can help - people will see you as practical and thus able to get funding (and show preliminary data, if possible)
  • Gear your chalk talk towards faculty; talk about methods but don't be too technical: talk about what equipment and personnel you will need
  • People will interrupt you nonstop (in this sense, a chalk talk is similar to a PhD qualifying exam). Your responses will indicate how much (and how deeply) you have thought about the future.
  • People often fall apart because of a) nervousness and/or b) falling prey to the potential pitfalls of your subject matter
  • Most importantly: practice! Practice your chalk talk a lot before your interview, using diverse audiences (faculty, postdocs, etc.) Be critical as you strive to perfect this talk.

Job Talks
 are perhaps the most familiar, but we hit on some critical points that will ensure a successful presentation:

  • Keep your slides simple, use black text on a white background. Use 40pt font to make your slides readable in a large room
  • Use sentences for slide headings - these are more memorable than topical phrases (studies have shown this is true)
  • Use clean, simple graphics. Watch some TED talks to get an idea of how to use good visuals.
  • Beware of humor in a job talk: it can backfire
  • During questions, if you need to buy time to think you can ask "Can you repeat/rephrase the question?"
  • Be sure to remain poised and composed if you're battered with questions that seem to come out of left field (composure is what people are looking for). Sometimes these difficult questions are a result of faculty performing out of ego, or for the sake of their peers.

Teaching seminars come in different formats, and we discussed two different scenarios that our speakers had experienced.

  • The first scenario is more common in teaching universities: a candidate was asked to teach an intro course that was completely different from their own disciplinary subject area. The candidate was given good guidelines and plenty of preparation time (in this case, they were given a course textbook and told to teach the first chapter). At the interview, the audience for this teaching demo was comprised of the search committee and undergraduates. 
  • The second scenario was much less structured, with only one instruction: no powerpoint allowed. The candidate was asked to teach a class as if it were an upper-level course, using only the blackboard. The demo only lasted 25 minutes, and the audience was the search committee. In this scenario, a good interview strategy would be to show expertise in a class not currently offered by the university (e.g. to show your potential fit in the Department). For the sake of the audience, it's also prudent to state your learning goals as well as a textbook, chapter, and figures that complement your teaching demo.

We also had an interesting discussion about "illegal questions" - the inevitable queries about your personal life that interviewers aren't supposed to ask (Are you married? Do you have kids? Do you want kids?). Someone suggested that you should be honest - after all, you don't want to insult your possible future colleagues. Another person suggested ways to deflect the question (and address the underlying concern that prompted the question), without answering or insulting: for example, saying something like "If this is about my productivity, I can assure you that I'm first and foremost passionate about my research..." It was interesting to hear different thoughts on this tricky subject.

Overall, our discussion provided a very eye-opening look into the interview process, and I learned a lot. We ended with some final tips and general guidance:
  • Keep your presentations backed up on a thumb drive during all interviews (just in case!)
  • At some institutions (UC Davis is one), admin staff will give their input during the faculty hiring process. So when you interview, keep in mind that every single person you encounter is your "audience" during a campus visit. 
  • Keep a supply of water and energy snacks in your bag - interviews are exhausting, and you will need them.
  • Make a cheat sheet of people based on your interview schedule - note their recent publications, research interests, and other professional activities.
  • Never bluff answers. It's better to just say "I don't know". Or better yet, "I'd be happy to get back to you" - and then take their name and follow-up later with the answer.
  • For phone or Skype interviews, it's a good idea to dress in interview clothes and book a conference room to make sure you feel professional.
  • Make a mental note of people throwing their weight around - if other faculty don't shut them down, it might be an indicator of departmental culture (or indicate people that might have power over your career).

Friday, October 25, 2013

PFTF discussion: The Academic Interview Process

The topic at last week's Professors for the Future meeting was the academic interview process! UCD faculty members Julia Simon and Warren Pickett led a great discussion, answering all of our eager questions (and there were indeed many questions).Here are my notes from the meeting, representing a mix of the speakers' slides and other discussion points I jotted down:

Presenting Yourself

Your apparel:
  • Don't stand out because of what you wear - the search committee is not looking for a mannequin
  • You should be comfortable in what you wear, and other people should not be made to feel uncomfortable because of what you wear.
  • The best scenario: your host should not be able to remember.
  • Its about what you know and do, not about what you wear.
  • Practices might be different in law school, business, vet school, etc. - Know your discipline and its general practices.
Note: I disagree with some of the above advice. Dressing yourself for an interview is both a skill and an art (and should be highly personalized). A memorable piece of clothing (shoes, scarf, printed skirt) can be a conversation point, so don't feel you need that you have to dress boring to be taken seriously. This topic deserves its own post, but I reccommend you check you this article at Inside HigherEd.

Don't be someone else - be yourself, but be on your "best behavior"
  • Be positive, and express enthusiasm about the future and the institution
  • Be prepared to ask questions - to learn about the new environment
  • Know your viewpoints on the questions of the day (in your discipline)
  • Keep a lid on your politics - it will not help, and it might hurt. Don't play stupid, but just put on a tolerant front.

Structure of the Interview Schedule

  • Typically, interviews are a two day campus visit where you meet with the department chair, the dean, and many other people (e.g. half-hour meeting with prospective colleagues).
  • Do some homework (IMPORTANT!):
    • Learn about your schedule and presentations (even though you might only get it 2 days beforehand)
    • Know something about the department and institution
    • Know something about several faculty members
    • Ask people about their interests, as well as talking about yours.
  • Generally be an interesting person to converse with
  • Often the search committee is invisible - but they will be paying much more attention than the typical faculty member.
  • The most important people you'll meet during your interview are: 
    • The faculty in your area of research
    • The rest of the faculty 
    • The chair (whose job it is to work with you)
    • The dean (who improves the faculty, while balancing the budget). Although the faculty vote on who to hire, the dean has to sign off on this decision: so be sure not to rub them the wrong way!
  • Be prepared! Understand the needs of the group (e.g. the department) and the reason for the search. Is the search specific, to fill a particular need? Or is it more general: to shore up the group and its teaching needs, to find the "best person at this time?"
    • This aspect becomes more important at higher levels of hiring - what is your "vision" (for the group, department, division, college)? What are the existing strengths and imminent challenges?
  • Things that you can (should) ask the dean/chair: 
    • What is the tenure review process? What is the typical teaching load (and is there a policy for new faculty to have a one-semester reprieve while they adjust to the new job)?
    • What is the sabbatical policy? What is the family/childcare policy? - but perhaps consider the kind of institution you're interviewing at before asking these two questions

Research Presentations

  • You will be expected to give one or two talks (and be sure to understand the purpose and audience): 
    • one for a "general" audience, colloquium style for all in the department/group
    • one or more related to your research specialty - still, do not be specific for these talks. Introduce the field, discuss various viewpoints, finally get to the point(s) you want to convey to the audience. But avoid too many details; let them read your papers.
  • Your presentation gives the exceedingly important impression of how well you can get your ideas across - essential for both education and for research, and more generally in interactions with colleagues 
  • Caveat: being a good speaker is important; but you don't have to be the best 
  • Most important: know your audience and keep them interested

Your Self-Presentation

  • Important: know what your plans and hopes are, and be able to articulate them well and field questions
    • Have a well thought-out research plan
    • What is the intellectual "hook" that makes you so excited?
    • Where will the funding support come from? Do you have experience?
    • What broader requirements do you have? Collaborators, travel, seasonal restrictions?
    • To what degree are you already connected in the field?
  • Education: readiness and aspirations
    • What style of teaching is effective in your field and why?
    • What new approaches do you find intriguing, exciting?
    • You can suggest what courses you'd like to teach, but be careful in case a course is someone's "pet". 
    • Good to ask "what are your undergraduates like?" - this is something you'll want to know, but also show that you did your homework.
Examples of what NOT do do or say:
  • "I'm enthusiastic about research now. I may go into administration when I get tired of research" (said to a dean)
  • Don't paint yourself into a corner by demanding/requesting a larger start-up package than is reasonable. Find out what is customary, perhaps get some input on limitations.
  • Don't give the impression you need/deserve special considerations (the process needs to be fair to all)
  • Don't be derogatory about planned social events - complaining about restaurants, food, etc.

Other things to consider

What usually seals the deal: 
  • Research Area Fit (you can't control this - this is a search committee decision)
  • Whether or not you connect with everyone and can have intellectual discussions during your interview (you can practice and prepare for this)
If you have a phone interview, try to use Skype if at all possible (and remember to look at the camera, and be sure the background is appropriate). Its generally hard to be engaging and sell yourself over a speakerphone.

Be concise in answering questions - aim for a 3 minute answer, then watch for body language and engagement with the person. Your eye contact and body language are also very important - don't look too rigid or too relaxed (no lazing on a sofa).

You'll have to be adaptable for questions about "service" - you can't be sure what they'll ask, and you will have to think on your feet.

Be prepared to defend yourself - search committees may want to challenge candidates. Politely, calmly stand your ground and give good arguments.

The Bottom Line

The search committee and faculty are a group of individuals, with different opinions and means of evaluation. What works for some may not work for others. Search committee members negotiate with one another and present a recommendation to the faculty, who then vote. 

The above guidelines may be helpful. But the bottom line is, there is no bottom line.