221 citations · 932 across the 42 of their papers we have counts for
9 papers · 1 filter
Estimating intrinsic and extrinsic noise from single-cell gene expression measurements
Audrey Fu, Lior Pachter
Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic)…
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…
Identifying RNA contacts from SHAPE-MaP by partial correlation analysis
Akshay Tambe, Jennifer Doudna, Lior Pachter
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides inf…
RNA structure characterization from chemical mapping experiments
Sharon Aviran, Julius B. Lucks, Lior Pachter
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental appr…
On the optimality of the neighbor-joining algorithm
Kord Eickmeyer, Peter Huggins, Lior Pachter +1
The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. Fro…
Alignment Metric Accuracy
Ariel S. Schwartz, Eugene W. Myers, Lior Pachter
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference a…
Neighbor joining with phylogenetic diversity estimates
Dan Levy, Ruriko Yoshida, Lior Pachter
The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization…
Tropical Geometry of Statistical Models
Lior Pachter, Bernd Sturmfels
This paper presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometr…