127 citations · 130 across the 3 of their papers we have counts for
4 papers
Pseudoalignment for metagenomic read assignment
Lorian Schaeffer, Harold Pimentel, Nicolas Bray +2
We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment i…
Near-optimal RNA-Seq quantification
Nicolas Bray, Harold Pimentel, Páll Melsted +1
We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 mil…
Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions"
Nicolas Bray, Lior Pachter
Ward and Kellis (Reports, September 5 2012) identify regulatory regions in the human genome exhibiting lineage-specific constraint and estimate the extent of purifying selection. T…
MAVID: Constrained ancestral alignment of multiple sequences
Nicolas Bray, Lior Pachter
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maxi…