- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experimentsJames H Bullard
Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA
BMC Bioinformatics 11:94. 2010..We provide a detailed evaluation of statistical methods for normalization and differential expression (DE) analysis of Illumina transcriptome sequencing (mRNA-Seq) data...
- Biases in Illumina transcriptome sequencing caused by random hexamer primingKasper D Hansen
Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720 7358, USA
Nucleic Acids Res 38:e131. 2010..We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias...
- Conservation of an RNA regulatory map between Drosophila and mammalsAngela N Brooks
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
Genome Res 21:193-202. 2011..This observation suggests that the regulatory codes of individual RNA binding proteins may be nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable...