- Statistical methods for identifying differentially expressed genes in RNA-Seq experimentsZhide Fang
Biostatistics Program, School of Public Health, LSU Health Sciences Center, 2020 Gravier Street, 3rd Floor, New Orleans, LA, 70112, USA
Cell Biosci 2:26. 2012..This review attempts to give an in-depth review of these statistical methods, with the goal of providing a comprehensive guide when choosing appropriate metrics for RNA-Seq statistical analyses...
- Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq readsJeffrey Martin
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
BMC Genomics 11:663. 2010....
- Bacillus anthracis genome organization in light of whole transcriptome sequencingJeffrey Martin
DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
BMC Bioinformatics 11:S10. 2010..Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity...
- Next-generation transcriptome assemblyJeffrey A Martin
Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA
Nat Rev Genet 12:671-82. 2011..This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future...