Bioinformatics Post-doc position in Hawaii

A friend of mine asked me to distribute this.  It’s been a while since I’ve posted anything bioinformatics related, but if you’re looking for a bioinformatics post doc position in a beautiful location, this one sounds pretty good.  Yes, I used my danish keyboard to obfuscate the email address… shouldn’t be too hard to figure out, for those who aspire to be post docs. (-;

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Garmire Group (starting 09/01/2012 or later)

University of Hawaii Cancer Research Center

Job description: Located on the beautiful sea shore of Honolulu, Hawaii, overlooking the Pacific Ocean, the University of Hawaii Cancer Center (UHCC) is one of only 66 research organizations in the country designated by the National Cancer Institute. Its mission is to focus on key cancers that impact the multi-ethic population of Hawaii, as well as worldwide. Home to some of the nation’s leading cancer experts, UHCC is ambitiously recruiting more new talents to work collaboratively towards international excellence: developing new strategies for discovery, driving findings into clinical practice and delivering the optimal outcome when a patient is faced with the prospect of treatment and recovery.

Projects available in the bioinformatics/genomics group, include but are not limited to (1) Integrative analysis with next-generation sequence etc. to decipher the regulatory role of microRNAs genome-wide. (2) microRNA biomarker discovery in various cancers using next-generation sequence data, microarray data, and survival data etc. (3) GWAS study of DNA methylation given different nutritional statuses. (4) Characterization and comparative genomics of long-intergenic non-coding RNAs with next-generation sequencing data etc. (5) developing sensitive structural variation detection algorithm(s) in targeted deep sequencing technology applied to cancer samples.

Requirements:

  • PhD degree in bioinformatics, bioengineering, biostatistics, (bio)physics, electrical engineering, or computer science.
  • Strong independent research capabilities with high profile, first-author publications
  • Experience with high-throughput data processing using next generation sequencing, microarray etc.
  • Proficient with Linux/Unix environment
  • Advanced experience in two or more programming languages: perl, R, matlab, C, C++, Java
  • Familiar with machine learning and data mining methods
  • Experience with collaborations with experimental biologists
  • Experience with high-performance computing is a plus

Salaries are competitive depending on qualification and experience. If interested, please send your CV and contact information of three references to lgarmire åt gmail døt com

Preparing for “the After”

I’ve been thinking quite a bit about “the after”. That is, the post-PhD period. Personally, I’ve got a job lined up and the details are generally falling into place. While I’ll save the talk about moving for later, I thought it would still be a good opportunity for reflection, as things could have turned out quite differently.  I searched for other posts on the topic, but mostly found advice on how to become an academic, or how to find industry jobs – not quite the same thing as how to gracefully exit a PhD.  (Of course, it could be argued that I’m not exactly exiting gracefully and shouldn’t be giving advice, but that’s a matter of opinion.)

Several things stood out for me in the process. Right from the start, I probably shouldn’t have started thinking about “the after” until closer to my defense. This was a major mistake on my part.  Without a defense date in hand, I was simply operating on someone else’s assurances that I’d be done at a given time. Regardless of who it was that said it was possible, dates WILL slip until a defense date has been filed with the university.  As a grad student, you are dependent on other people setting aside time to edit, comment and process your thesis.  Your tuition does not pay their salaries.  Well, actually, it does, but they’re still not a service industry.  (ie, if your university gives someone 6 weeks to respond to your thesis, they’ll take 5.999999 weeks, if not 7 weeks.)

Anyhow, given that I messed that part up, there were other valuable lessons that I learned.

First, take the time to work out what you want to be doing “after”.  There’s no point in hunting for your dream job, if you don’t know what that dream job is.  Easier said than done, but an important first step – and gets my longest rant.  (feel free to skip down, if you want the tl;dr version)

Personally, I had spent a lot of time on this one issue, but even so, I wasn’t really sure what I wanted. One of my committee members took the time to promote the academic career to me about a year ago, and it left an impression on me.  I had to re-evaluate if that was something that would fit – and for nearly a year I seriously contemplated an academic track. A more ruthless consideration of whether I was happy with the actual job would probably have helped.  (Readers of my blog might remember a few posts when I was seriously debating the two possible courses.  In the end, I came to the conclusion that i just can’t see myself pursuing grants… but I would be happy to talk with investors again.)

In fact, I even went so far as to visit a highly respected academic institution who’s researchers work in the field in which I was most interested only to discover that I just didn’t fit there.  It wasn’t something I knew before going, but it became incredibly apparent after visiting.  While there, I gathered a lot of information that I needed in order to do some serious soul searching to figure it out. To have saved everyone the time and effort, I should have spoken to more people before – and filtered some of that advice much more rigorously.

I also had an opportunity to do something that would have given me a lot of responsibility, to work with a great team (ok, it was really an exceptional team) and to stay in Vancouver – and in the end, I had to turn it down for the simple reason that I really wanted to stay “hands on” in bioinformatics a little longer.  Once I figured out what it was I wanted to be doing, the choice became clear – even though the decision was still hard to make.  (I might kick myself for it later, but that remains to be seen.)

Second, while I don’t think you should be working on your “after” plans from the start of your graduate degree, remember that networking starts long before you’re ready to graduate.  As it turns out, I met the contact that led to my position several years ago, well before I was even close to finishing.

Actually, that itself is probably worthy of it’s own post.  However, the short version of how I found my “after” plan involves meeting and talking with someone over several years at AGBT, where I would spend 12 hours a day taking notes, 6 hours trying to network at parties, and maybe 5 hours sleeping, all while jetlagged.  The last time I met him in person I was working through a 9 hour jetlag.  The fact that I was able to hold coherent conversations at all, and that the people I met didn’t write me off because of it should be considered a miracle! You never know who will lead to a great position – or who might point you in the right direction – and there’s no reason to think that only contacts you meet at the end will be the ones that can help you find your dream job.

There are two minor points that should be apparent from my example: 1. even when you’re not at your best, try to be at your best!  You never know who will lead you to a job, a contact or a collaboration.  Networking is important, and I can’t stress that enough – even for a nerd like myself – even when you don’t think you’re networking.  2) Keep an open mind – but don’t waste other people’s time. I’ve interviewed people for positions before who had no real interest in taking it, once it was offered.  It doesn’t help anyone out, and doesn’t reflect well on you either.

Third, set a time line.  This may be the one thing I did right – Once I had an offer, I set a time limit on when I wanted to make a final decision. This had several effects:  It made me invest the time that went into the search up front, it also forced me to stop looking at some point and, of course, it leveled the playing field, so to speak – everyone I spoke to knew when I expected to have a decision so that the process wouldn’t be dragged out.  Admittedly, it felt dragged out, but that’s probably the time dilation that comes from working on a thesis.

A few things could have gone more smoothly, however: I should have had a time line that matched up with my defense date, rather than with my anticipated time of completion.  However badly off the time line was, it forced the process to be relatively transparent both for my self and for the people I spoke with.  I certainly didn’t want to leave anyone waiting for an answer.

The time line also had the effect of clearing off my desk.  Once the process was done, at least I could focus back on the task at hand: finishing my thesis.

Fourth, use your time wisely.  That might sound like a silly warning, but I could have done better.  There will come a time during your thesis writing when you realize you have nothing to do. You’ll be waiting on people to get back to you, or waiting on revisions, or something of the sort.  It is a great time to start your job search.

Having jumped the gun on this one, I’m instead using the time to plan an inter-continental move, so I guess I’m not doing too badly.  Yet, it did make the writing period a bit more stressful as I was setting aside time to meet/phone people while trying to hash out the drafts and chapters.  Deciding your career path does have a strange tendency to distract you from writing about your work.

Also, and as a complete aside, airplanes and laptops are a great combination.  You can write an awful lot without any distractions when you have a total of ~1.5 cubic meters of space – and no where to go.

Finally, talk to everyone you can.  If you’re not dead set on one specific job, it can really help to have sounding boards with whom you can discuss your options.  The more you know about things, the better.  Of course, that’s not to say that you should let people convince you not to do something you’d like to – but the more you know, the better prepared you will be for deciding where you want your life to do.

And, the corollary is, naturally, to listen to what they have to say.

So – recap time:

  • Work out your schedule so you know when you’ll be available to start the “after” part of your life.
  • Try to figure out what it is you want to be doing and get a clear picture of what you want and need.
  • Talk to people about what’s available that matches your dream job – or find out if your mental picture is real.
  • Build a realistic time line that includes deadlines for when you’ll have decisions.
  • Manage your time wisely
  • Talk with your friends to find out what they know – and to work through the tough choices.

If you manage to do all of that, you should be in good shape.

The next question, however, is: did I miss anything? What other advice should you give for planning your exit from your grad school degree?

Letting the Cat out of the Bag.

It is finally official – I’ll be leaving Canada and going to Europe (Denmark) in December – joining the team at CLC bio in just over a month. You’ll have to excuse my holding off on letting everyone know.  Of course, things have been in the works for some time yet, but the last few pieces have only clicked into place this week.  And, of course, one doesn’t want to jump the gun by announcing these things before everything is in place.

Of course, this doesn’t mean I’ve finished my PhD yet.  There are a still a few more hurdles – my thesis has to go through my committee and the external examiner, and I still need to officially defend it – but it was looking like the soonest that could happen would be February, and with everything going on, my wife and I decided it would be better to just start the process of settling in to Denmark as soon as possible.

So, consequently, if you read my blog, you’ll probably hear a little bit more about some topics that are currently on my mind: learning Danish (lære Dansk), traveling, maybe some cultural collisions (Danish people don’t have closets?)  and possibly some photography, depending on how busy I am.  (Yes, now that I’m not actively writing my thesis for 6-8 hours a day, I seem to have more time.)

But don’t worry – in the next month, I still have a few things I want to blog about, and likely a few papers to review.  Even though I’m leaving Grad School, I’m not leaving science behind.

To be candid, I’m looking forward to starting up at CLC partly because of the job, which already sounds pretty awesome, and because of the people.  I’ve met some of the people I’ll be working with – albeit briefly – and I’m excited to have the chance to work with them.  I can honestly say that they one one of the nicest groups of people I’ve ever met.  Must be something in the water. (-;

Anyhow, to complete the circular nature of this post (like all good fugues, which is the way to write a good post, particularly if you’ve read Gödel, Escher Bach, if that’s not getting way to involved) I have one last point to clarify. As foreshadowed lightly by the title of this post, yes, my pets will be coming with me – and undoubtedly my cat will be thrilled to be let out of the bag once we’ve arrived in Denmark… so the moving process will be bookended, effectively, by letting cats (figurative and literal) out of their respective bags.

Ollie - My wife says we have the same nose.

Why should one become an academic?

You know what?  No one ever bothers to sell the academic path.  In all the time I’ve been in school, and even during my time in industry, no one has ever tried to tell me why I should want to become an academic.

There are a hell of a lot of blogs saying why one should abandon the path to academia, but not a single one that I could find saying “hey everyone, this is why I think academia is great”.  It’s as though everyone is born wanting to be an academic, and you only have to hear the other side to be convinced away from the natural academic leanings.

Of course, there’s a huge amount of competition for academic positions, so it isn’t exactly like people want to encourage incoming students to go down that path.  All that I see in searching the web is the balanced approach about weighing the two options – and that even assumes that all academia is the same, and all industry is the same.  (A blatant lie, if I ever heard one!)

Anyhow, the best I could do in putting together my list of why one should go into academia is in the following set of links.

If there are any academics out there who want to sell the academic path, this would be a great topic for future posts.  I’d love to read it.

As best as I can glean, the only reasons for it are “better working hours, once you become tenured” and “you can be your own boss”.   Seriously, there must be more to it than that!  Anyone?

Looking for advice on moving to Europe

My wife and I have seriously been contemplating the future.  With the figurative grad school light at the end of the tunnel being visible, if not quite in focus yet, we’ve been seriously considering an opportunity to move to northern Europe.  (Yes, I’m being as generic as possible.)  However, neither one of us have lived outside of North America –  and have only visited Europe a couple of times on vacation.  That makes it pretty hard for us to critically evaluate the opportunity.

Thus, crowd-sourcing!   I was wondering if anyone had any advice they might be able to share with us on what we can do to make that move successfully – both things we should or shouldn’t do.  Or, if people think it’s a great idea, or a bad idea.  Really, we’re trying to cast the net as wide as possible on whatever advice people can give us because it’s really hard to make a decision like that without talking with people who have done it.

Some of the outstanding questions we have:

  • How did you find the language learning curve when moving to a non-English country?
  • How much of your stuff did you take with you?  What did you do with the stuff you left behind?
  • How did you find solutions to the “2-body” problem?
  • How long does the culture shock last?
  • Was it a hassle bringing pets?
  • What are the big “gottchas” that you didn’t see coming?
  • How long did it take to organize your move?  How hard was it?
  • Would you suggest that other people do it?
  • How long did you stay? (yes, not leaving ever is also an acceptable answer.)

And, of course, are we even asking the right questions?

Any advice you can give would be helpful for us, and of course, for other people who are faced with this decision in the future.

Thanks!

CPHx: Roald Forsberg, Sponsored by CLC bio.

CLC Genomics Gateway

Roald Forsberg

CLC’s take on next generation of genome informatics tools.

At the 10th aniversary of the human genome project.  We now have a common and comprehensible coordinate system.. That’s a real tangible effect of the project.  So much of the work we now do is based upon this first human genome coordinate set.    HUGE list of things we can do, because of it.

However, if you look at pre-NGS work, all of the efforts were focussed on making sense of the data and annotating it – and sometimes looking at it.  It was all centralized, curated, etc.

In the post-NGS, sequencing has now been democratized.  We have access to big dataset, changing our focus to analysis, mapping, modeling. Our data resources are now many, varied, decentralized and non-curated.  A complete paradigm shift in bioinformatics focus. [my words.]

CLC has built a platform for doing this type of work.  Server based, client based, scalability, etc..  It supports the majority of genomics workflows (de novo, reseq, chip-seq, rna-seq, smrna-seq, tag-seq.)  We lack the tools for pushing further down into integrative biology.  Pathways, diagnosis, systems biology…. but there ARE no tools for doing this.

Genome browsing is no longer enough. [Thank you, I’ve been waiting for someone to say this!]

Perl IS NOT A FRAMEWORK.  [Halelujah!]

You will not get the medical community to use this technology with perl and spreadsheets.

It is time to move downstream: CLC genomics gateway.

  • an integrated framework to visualize, analyze and combine data from the same reference genome
  • seamlessly add own expreiments in an integrated manner
  • foundation for systems biology, functional genomics, etc.

Technical details

  • One data object to store and /or point to data sources
  • lazy fetching’
  • federation of data sources
  • a graphical user interface
  • completely integrated with other bioinformatics tools
  • part of the clc systems developer kit, so developers can add components and reuse existing ones without having to maintain the gui.

Enables a wide variety of tools and integrates so you can work with other tools like blast, primer design, etc.

Visualization tools:  Bring in all of your tools into one place.  [looks clean, actually.  nice.]

Federation of data: can bring in together sources like UCSC, ENsembl, your own data, flat files, etc.

Analysis types beta. Some tools for SNP comparison and annotation, Filtering snps from federated data… basically, it brings together annotations from a variety of sources and puts it all together in one place.

More analysis types to be added, including cancer biology, further advanced features.

Beta tool is out now, with new versions coming out soon.

Also, they’re hiring bioinformaticians.

 

 

Working with Jackie Chan.

Since I’ve been posting jobs, I figured I may as well point people to another set of open positions.  Of course, again, I have no relationship with the people posting it… however, I just couldn’t not say anything about this set.

Apparently, if you work in the Pallen Group, you get to work on next gen sequencing pipelines in the lab with Jackie Chan. (Research Fellow in Microbial Bioinformatics)

How cool is that?Jackie Chan

Anyhow, The other position (Research Technician in Bioinformatics), doesn’t (apparently) involve martial arts.

Some open positions at Complete Genomics

In case anyone is looking for a bioinformatics position, Complete Genomics is currently looking to fill at least three positions:

Senior Computational Biologist, Assembly

Complete Genomics is seeking a senior Computational Biologist to develop methods and tools for its sequence assembly pipeline and genomics analysis toolset. The role will require conceiving of analysis approaches to solve key problems in a next-generation DNA sequencing pipeline, then designing, developing, testing, and deploying pragmatic solutions. The new hire will work on a pipeline that each day transforms trillions of sequenced bases into high quality human genome analyses.

Senior Software Engineer, Assembly

Senior Bioinformatician, Pipeline Validation

The assembly pipeline team is an amalgam of exceptional bioinformaticians and software engineers of diverse backgrounds, with an active and lively cross-pollination of ideas and approaches. The team is actively investigating improvements to aid in a wide variety of genomics research applications including cancer, Mendelian diseases, and large scale association studies.

They have also provided the following note:

We are especially interested in seeking out individuals who have had experience in one or more of the following:

  • Developing or modifying algorithms for the analysis of next-generation sequence read data (on the lines of GATK, Firehose, or similar)
  • Developing sets of relevant functional annotations to associate with DNA sequence variations, and analyses of annotated data for the detection of disease-associated variants in pedigrees, tumor-normal pairs, or unrelated genome sets.
  • Analyses of sequenced genomes against standard data (internal and external) to estimate errors, calibrate scores, identify signals of interest, etc…
  • We’re open to people who have spent time in academic or research settings.

If you’d like more information, the have more details at the complete genomics careers page.

Disclosure: I am not in any way affiliated with Complete Genomics – I just happen to think they’re a really interesting company and am always impressed with how accepting they are of social media.