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BMCBI
2010
137views more  BMCBI 2010»
15 years 4 months ago
BS Seeker: precise mapping for bisulfite sequencing
Background: Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not ...
Pao-Yang Chen, Shawn Cokus, Matteo Pellegrini
99
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BMCBI
2010
86views more  BMCBI 2010»
15 years 4 months ago
ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite
Background: Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents...
Evgeniy V. Petrotchenko, Christoph H. Borchers
130
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BMCBI
2010
95views more  BMCBI 2010»
15 years 4 months ago
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Background: ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of prot...
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson...
BMCBI
2010
107views more  BMCBI 2010»
15 years 4 months ago
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
Background: Sequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences from the datasets. The sequenced reads ca...
Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robe...
BMCBI
2010
156views more  BMCBI 2010»
15 years 4 months ago
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
Background: High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical question...
James H. Bullard, Elizabeth Purdom, Kasper D. Hans...
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