Brian Haas

Summary

Publications

  1. ncbi Illumina identification of RsrA, a conserved C2H2 transcription factor coordinating the NapA mediated oxidative stress signaling pathway in Aspergillus
    Jin Woo Bok
    Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, WI, USA
    BMC Genomics 15:1011. 2014
  2. pmc A universal genomic coordinate translator for comparative genomics
    Neda Zamani
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 15:227. 2014
  3. pmc De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
    Brian J Haas
    Broad Institute of Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
    Nat Protoc 8:1494-512. 2013
  4. pmc Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
    Georgia Giannoukos
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 13:R23. 2012
  5. pmc How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:734. 2012
  6. pmc De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
    Musa A Hassan
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    BMC Genomics 13:696. 2012

Collaborators

  • Jonathan Livny
  • Bo Li
  • Alexie Papanicolaou
  • Nir Friedman
  • Nathalie Pochet
  • Neda Zamani
  • Jin Woo Bok
  • Musa A Hassan
  • Georgia Giannoukos
  • Fang Yun Lim
  • Jennifer R S Meadows
  • Manfred G Grabherr
  • Jennifer Wortman
  • Gorel Sundstrom
  • Nancy P Keller
  • Graeme S Garvey
  • Jacques Dainat
  • Philipp Wiemann
  • Marc P Höppner
  • Henrik Lantz
  • Doyle V Ward
  • Kirk D C Jensen
  • Jacques Izard
  • Joshua Z Levin
  • Jeroen P J Saeij
  • Dirk Gevers
  • Bruce W Birren
  • Chad Nusbaum
  • Mariane B Melo
  • Ashlee M Earl
  • Dawn M Ciulla
  • Andreas Gnirke
  • Katherine Huang

Detail Information

Publications6

  1. ncbi Illumina identification of RsrA, a conserved C2H2 transcription factor coordinating the NapA mediated oxidative stress signaling pathway in Aspergillus
    Jin Woo Bok
    Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, WI, USA
    BMC Genomics 15:1011. 2014
    ..Identifying the mutation from such screens, however, often fails when using methodologies involving transformation of the mutant to wild type phenotype with DNA libraries...
  2. pmc A universal genomic coordinate translator for comparative genomics
    Neda Zamani
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 15:227. 2014
    ..However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N...
  3. pmc De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
    Brian J Haas
    Broad Institute of Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
    Nat Protoc 8:1494-512. 2013
    ..sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h. ..
  4. pmc Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
    Georgia Giannoukos
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 13:R23. 2012
    ..The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA...
  5. pmc How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:734. 2012
    ..A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance...
  6. pmc De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
    Musa A Hassan
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    BMC Genomics 13:696. 2012
    ..In this study, we used de novo transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in Toxoplasma and to improve the current Toxoplasma gene annotations...