Research News

• Repetitive DNA and next-generation sequencing: computational challenges and solutions
• Temporal dynamics and genetic control of transcription in the human brain
• Bowtie 2.0 beta is released!
• TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
• Sequencing technology does not eliminate biological variability
  

November 29, 2011. JHU scientists Todd Treangen and Steven Salzberg publish a review in Nature Reviews Genetics discussing the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.
Article: Treangen TJ and Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Nature Reviews Genetics 2011 Nov 29

October 27, 2011. Faculty members Carlo Colantuoni (from the Lieber Institute), Jeff Leek, and colleagues from JHU and NIH publish a paper in Nature about their discovery of a wave of gene expression changes occurring during fetal development.
Article: Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao, Leek JT, Colantuoni E, Elkahloun AG, Herman M, Weinberger DR & Kleinman J. Temporal dynamics and genetic control of transcription in the human brain.
Nature 478, 519-523

October 16, 2011. Bowtie 2.0 beta is released! A major new version of the popular Bowtie short-read alignment program, developed by Hopkins/UMD researcher Ben Langmead, is now available from the Bowtie website and the new Bowtie2 page. Bowtie 2 supports gapped alignment with affine gap penalties, and allows any number of gaps and any gap length. For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. Other differences are described on the Bowtie page.

August 11, 2011. Ph.D. student Daehwan Kim and Prof. Steven Salzberg publish a new software algorithm, TopHat-Fusion, designed to discover transcription produced by fusion gene products. Fusion genes are a common phenomenon in cancer cells, where the breakage and re-joining of chromosomes can lead to aberrant genes that may be responsible for tumorigenesis.
Article: Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Genome Biology 2011, 12:R72.

July 11, 2011. JHU scientists Kasper Hansen, Rafael Irizarry, and Jeff Leek, together with Brown University scientist zhijin Wu, publish a report in Nature Biotechnology describing how biological variability remains a significant problem in next-generation experiments using RNA-seq methods, requiring more replicate studies than are commonly being done today.
Article: Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability.
Nature Biotechnology, 29, 572-573 (2011).

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