Research News

April 9, 2012. TopHat 2.0 is released! TopHat 2.0 is a major new release of the TopHat software, which aligns next-generation sequences from RNA-seq experiments to a genome with or without a reference annotation, allowing for the discovery of many novel splice sites. TopHat 2.0's improvements, developed primarily by Daehwan Kim and Geo Pertea, include compatibility with Bowtie 2 and parallelization of many steps to reduce runtime. See the TopHat website for details and downloads.

March 4, 2012. Ben Langmead and Steven Salzberg publish a paper in Nature Methods describing Bowtie 2, a new, more sensitive, very fast alignment program for next-generation sequences. Bowtie 2 handles gapped and ungapped alignments and is superior in speed and accuracy to virtually all previous methods.
Article: B. Langmead and S.L. Salzberg. Fast gapped-read alignment with Bowtie 2.
Nature Methods 9, 357-359 (2012). Publ. online 4 March.

December 6, 2011. A team of assembly experts from JHU and the University of Maryland publish the results of the GAGE competition, a detailed evaluation of the leading genome assembly programs for next generation sequencing data. Article: SL Salzberg, AM Phillippy, A Zimin, D Puiu, T Magoc, S Koren, TJ Treangen, MC Schatz, AL Delcher, M Roberts, G. Marcais, M Pop, and JA Yorke. GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Genome Research 22, 557-567 (2012). Publ. online 6 Dec 2011.

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 13, 36-46 (2012). Publ. online 29 Nov 2011.

For more news, go to: Previous Highlights

News & Events

  • The 2nd Annual Practical Genomics: From Biology to Biostatistics Workshop has been scheduled for October 1, 2, and 3rd. Mark your calendars!
  • March 2012 - Nature Methods publishes a news article discussing the ins and outs of genome assembly, including a detailed discussion of the GAGE competition led by Hopkins genomicists and colleagues at several other institutions.
  • December 2011 - The McKusick-Nathans Institute of Genetic Medicine has been named one of three Mendelian Disorders Genome Centers by the National Human Genome Research Institute and will receive $16 million over the next four years to identify causes of genetic disease.
  • Genomics seminar series beginning, Mondays at 2:30 in PCTB 517

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