Archive for the 'News' Category

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.


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.

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).

Dr Jess Vera

January 19, 2016

We congratulate:

Dr. Jess Vera whose thesis work on cryptic unstable transcripts was recently defended and completed.