Lukas Habegger

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    Lukas Habegger
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Bioinformatics 27:281-3. 2011
  2. ncbi VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
  3. ncbi IQSeq: integrated isoform quantification analysis based on next-generation sequencing
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 7:e29175. 2012
  4. ncbi Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    Ashish Agarwal
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 11:383. 2010
  5. ncbi FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
  6. ncbi The GENCODE pseudogene resource
    Baikang Pei
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R51. 2012
  7. ncbi Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
  8. ncbi Gene inactivation and its implications for annotation in the era of personal genomics
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 25:1-10. 2011

Detail Information

Publications8

  1. ncbi RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
    Lukas Habegger
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Bioinformatics 27:281-3. 2011
    ..Availability and implementation: RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/...
  2. ncbi VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
    Lukas Habegger
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 28:2267-9. 2012
    ..AVAILABILITY AND IMPLEMENTATION: VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org...
  3. ncbi IQSeq: integrated isoform quantification analysis based on next-generation sequencing
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 7:e29175. 2012
    ..This allows one to have a modular, "plugin-able" read-generation function to support the particularities of the many evolving sequencing technologies...
  4. ncbi Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    Ashish Agarwal
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    BMC Genomics 11:383. 2010
    ..Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs...
  5. ncbi FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    Andrea Sboner
    Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA
    Genome Biol 11:R104. 2010
    ..It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements...
  6. ncbi The GENCODE pseudogene resource
    Baikang Pei
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R51. 2012
    ..However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data...
  7. ncbi Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome...
  8. ncbi Gene inactivation and its implications for annotation in the era of personal genomics
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 25:1-10. 2011
    ..In addition, we call for the development of an expanded gene set to include human-specific genes that have arisen recently and are absent from the ancestral set...