221 citations · 932 across the 42 of their papers we have counts for
12 papers · 1 filter
Keep Me Around: Intron Retention Detection and Analysis
Harold Pimentel, John G. Conboy, Lior Pachter
We present a tool, keep me around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to red…
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…
Quantifying uniformity of mapped reads
Valerie Hower, Richard Starfield, Adam Roberts +1
Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read po…
Models for transcript quantification from RNA-Seq
Lior Pachter
RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accur…
Shape-based peak identification for ChIP-Seq
Valerie Hower, Steven N. Evans, Lior Pachter
We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspi…
Coverage statistics for sequence census methods
Steven N. Evans, Valerie Hower, Lior Pachter
Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect…
An introduction to reconstructing ancestral genomes
Lior Pachter
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for imp…
Parametric Alignment of Drosophila Genomes
Colin Dewey, Peter Huggins, Kevin Woods +2
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large g…
Subtree power analysis finds optimal species for comparative genomics
Jon D. McAuliffe, Michael I. Jordan, Lior Pachter
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. T…
Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models
Roderic Guigo, Ewan Birney, Michael Brent +5
With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November 21st and 22nd, to analyze the reasons why, after the completion of the human genome sequence, the identi…
Parametric Inference for Biological Sequence Analysis
Lior Pachter, Bernd Sturmfels
One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biologi…
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…