Papers accepted!

August 23, 2016

A number of papers have recently recently been accepted:

  1. Identification of Mediator kinase substrates in human cells using cortistatin A and quantitative phosphoproteomics.

    Z.C. Poss, C.C. Ebmeier, A. Odell, A. Tangpeerachaikul, T. Lee, H. E. Pelish, M.D. Shair, R.D. Dowell, W. Old, D.J. Taatjes. Cell Reports Apr 12;15(2):436-50

  2. RNA Pol II transcription model and interpretation of GRO-seq data

    M.E. Lladser, J.G. Azofeifa, M.A. Allen, R.D. Dowell. Journal of Mathematical Biology First online: 03 May 2016

  3. Evidence for Association Between Low Frequency Variants in CHRNA6/CHRNB3 and Antisocial Drug Dependence

    H.M. Kamens, R.P. Corley, P.A. Richmond, T.M. Darlington, R.Dowell, C.J. Hopfer, M.C. Stallings, J.K. Hewitt, S.A. Brown, Marissa A. Ehringer. Behavior Genetics Sep;46(5):693-704

  4. Survey of cryptic unstable transcripts in yeast

    J. Vera and R.D. Dowell. BMC Genomics 17:305

  5. Genome Characterization of the Selected Long and Short Sleep Mouse Lines

    R.D. Dowell, A. Odell, P. Richmond, D. Malmer, E. Halper-Stromberg, B. Bennett, C. Larson, S. Leach, R.A. Radcliffe. Mammalian Genome to appear

Some of these papers were reviewed and published quickly, whereas others have been a long time coming.  Funny how they all passed the threshold around the same time!


Keystone Enhancers in Cancer Meeting

February 27, 2016

The Keystone Enhancers in Cancer meeting was held jointly with the Noncoding RNA in disease meeting in beautiful Santa Fe New Mexico.

Briefly (and grossly over-summarized), the major themes of the meeting were:

  1. Enhancer Assembly — what is the ordering of marks, positioning, TF binding, transcription?
  2. Enhancer Activity and Function … what do eRNAs do (if anything)?
  3. Cellular looping/structure (cohesion, topological domains, orientation, distances)
  4. Impact of mutants on function/activity of enhancers.
    1. mutate the TF, what changes?
    2. mutate the enhancers, what changes?
    3. sample sequences, can they act as promoters and/or enhancers?

Li’s paper is published!

February 6, 2016

Foxc1 reinforces quiescence in self-renewing hair follicle stem cells.

L. Wang, J.A. Siegenthaler, R.D. Dowell, R. Yi. Science 351(6273): 613-617 (2016)

Joey’s FStitch paper published!

January 26, 2016

An annotation agnostic algorithm for detecting nascent RNA transcripts in GRO-seq

J. Azofeifa, M.A. Allen, M.Lladser, and R.D. Dowell. IEEE/ACM Transactions on Computational Biology and Bioinformatics (to appear; accepted Jan 2016)

Dr Jess Vera

January 19, 2016

We congratulate:

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