Annual Short Read Workshop!

June 16, 2017

For several years we have run an annual short read analysis workshop.  This year the Workshop runs July 10-July 21.  Please register now if interested in attending!

The goal of this workshop is to teach the fundamental computational skills necessary for many short read sequencing analyses. In the first five days of this course participants will learn basic Unix/Linux, how to use large compute servers, sequencing read quality control, and read mapping. In the second week we will cover the basic fundamentals of commonly used genomic short read sequencing approaches including basic pipelines for genome re-sequencing, ChIP-Seq and differential expression for RNA-Seq. Our goal is to provide the basic skills necessary for participants to be enabled to learn how to analyze their own data after the course (though some self-study after the course will be necessary).

The format of this course is reverse classroom. Attendees will be asked to watch video lectures outside of class. During classroom time (9am to noon daily) attendees will be working through example analysis. In addition, each day we will provide attendees with homework activities that they will need to complete before the next day’s classroom time. Help sessions will be available each afternoon.

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May 2017 Graduates

May 25, 2017

We congratulate Dr. Joey Azofeifa (CS) and Dr. Amber Scott (MCDB), who both successfully defended their theses this spring.    For Dr Azofeifa’s thesis, he developed a number of algorithms for GRO-seq analysis.   Dr. Scott was focused on the impact of polyploidy on adaptation.

We also want to acknowledge another doctoral graduate, Dr. Shweta Bhandare, whose thesis project focused on unsupervised learning approaches to RNA binding proteins.


Time to Publication

May 1, 2017

One of the truly frustrating aspects of publishing is the high variability in publication times.  Specifically I’m in reference to the time between the paper acceptance and when it shows up in print (and thereby has an official citation).   Pre-publications online have at least made papers accessible far in advance of the official publication, which is good.  But once the official (on paper) versions arrive, one is faced with the problem of updating websites, CVs, and other sources on the paper.

When these lag times are highly variable between journals (and culturally the lag times that are deemed “acceptable” are highly variable between fields), it gives rise to this unfortunately phenomena of papers being published out of sync with the temporal order of the work.  In other words, a paper on earlier work comes out AFTER a paper on more recent work.   This makes it hard to convey to people the progress of a project, to have new students follow the progression of a project, and to explain what the current status of some ongoing project *really* is.

Take for example our work on nascent transcription analysis.    Temporally we published FStitich at the BCB conference in (Sept) 2014 .   As is not uncommon with some bioinformatics conferences, our submission was selected to be included into an accompanying journal article — with the condition that the journal article include 20% more material.  We submitted this extended version in Dec. 2014.   It was a slow review process as despite only minor revision, it wasn’t accepted for publication until Jan 2016.  It has yet to appear in the print version, so will likely have a 2017 (or heaven forbid, 2018) publication date.

Meanwhile we have been working in the background on a separate, more mathematical representation of nascent transcription.  The first paper on this work was drafted in 2014, but took a while to finish (our own fault), spent some time in review (again with comparably few revisions necessary), was accepted for publication in May 2016 (Lladser et. al.) but didn’t appear in print until Jan 2017.  During this process, we developed a separate (but related) model with a number of advantages (particular for human/mouse data) over our J. Math Bio model (which is, however, better for Drosophila data).   We submitted this paper to Bioinformatics in May 2016 — the same month the Lladser paper was accepted.   Bioinformatics is a comparably very fast journal.  The paper was accepted by August and appeared in print in Jan 2017, effectively making the two papers contemporaneous.   Even though the work is very much sequential.


More publications this year!

April 20, 2017

Two more papers out in the last month!

  1. Work on RNA binding protein discrimination: S. Bhandare, D.S. Goldberg, and R.D. Dowell. PLoS ONE 12(3):e0174052 (2017).
  2. A kinase independent role for CDK19: K. Audrey Audetat, Matthew D. Galbraith, Aaron T. Odell, Thomas Lee, Ahwan Pandey, Joaquin M. Espinosa, Robin D. Dowell and Dylan J. Taatjes. Molecular and Cellular Biology early release: doi:10.1128/MCB.00626-16

Starting the new year off right …

March 6, 2017

Well, we’re happy to announce:

  1. The Lladser paper is now in print:  M.E. Lladser, J.G. Azofeifa, M.A. Allen, R.D. Dowell. Journal of Mathematical Biology 74:77 (2017).
  2. The Tfit paper — describing our mixture model for nascent transcription data is now in print: J.G. Azofeifa and R.D. Dowell. Bioinformatics 33(2):227-234 (2017).
  3. A recently accepted paper on calculating heritability from high throughput sequencing data is now out:  P. Rudra, W. J. Shi, B. Vestal, P.H. Russell, A. Odell, R.D. Dowell, R.A. Radcliffe, L.M. Saba and K. Kechris. BMC Bioinformatics 18:143 (2017).