Research Topics
| Andrea SbonerSummaryAffiliation: Yale University Country: USA Publications
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Detail Information
Publications
Molecular sampling of prostate cancer: a dilemma for predicting disease progressionAndrea Sboner
Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
BMC Med Genomics 3:8. 2010..Hence, we sought to develop a molecular panel for prostate cancer progression by reasoning that molecular profiles might further improve current clinical models...- FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing dataAndrea 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... - RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summariesLukas 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/... - IQSeq: integrated isoform quantification analysis based on next-generation sequencingJiang 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... - VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environmentLukas 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... - Genomics and privacy: implications of the new reality of closed data for the fieldDov Greenbaum
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
PLoS Comput Biol 7:e1002278. 2011..However, teaching personal genomics with identifiable subjects in the university setting will, in turn, create additional privacy issues and social conundrums... - The real cost of sequencing: higher than you think!Andrea Sboner
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
Genome Biol 12:125. 2011..Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'?.. - Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectMark 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... - Comparison and calibration of transcriptome data from RNA-Seq and tiling arraysAshish 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...