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» Inference of Isoforms from Short Sequence Reads
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BMCBI
2010
129views more  BMCBI 2010»
13 years 10 months ago
Geoseq: a tool for dissecting deep-sequencing datasets
Background: Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SR...
James Gurtowski, Anthony Cancio, Hardik Shah, Chay...
BIBM
2009
IEEE
155views Bioinformatics» more  BIBM 2009»
14 years 4 months ago
Towards Reliable Isoform Quantification Using RNA-Seq Data
Background: In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address...
Brian E. Howard, Steffen Heber
ICCABS
2011
13 years 1 months ago
CloG: A pipeline for closing gaps in a draft assembly using short reads
— Closing of gaps in draft assemblies using Next Generation Sequencing (NGS) data is becoming increasingly important. In this paper we present CloG, a software pipeline that uses...
Xing Yang, Daniel Medvin, Giri Narasimhan, Deborah...
ECCB
2008
IEEE
13 years 11 months ago
Optimal spliced alignments of short sequence reads
ent> <title> <p>Highlights from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium</p> </title> <editor>Lu...
Fabio De Bona, Stephan Ossowski, Korbinian Schneeb...
BMCBI
2010
120views more  BMCBI 2010»
13 years 10 months ago
Short clones or long clones? A simulation study on the use of paired reads in metagenomics
Background: Metagenomics is the study of environmental samples using sequencing. Rapid advances in sequencing technology are fueling a vast increase in the number and scope of met...
Suparna Mitra, Max Schubach, Daniel H. Huson