List of works - Rob Patro

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

scientific article published on 01 July 2020

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

scientific article

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

scientific article published on 17 January 2019

A space and time-efficient index for the compacted colored de Bruijn graph.

scientific article published in July 2018

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

scientific article published on 31 January 2022

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

scientific article published on 27 March 2019

Alignment and mapping methodology influence transcript abundance estimation

scientific article published on 07 September 2020

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search

scientific article published on 16 March 2020

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

scientific article published on 25 June 2015

Data-dependent bucketing improves reference-free compression of sequencing reads

scientific article

Global network alignment using multiscale spectral signatures ⬇️

scientific article published on October 9, 2012

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis

scientific article published on 01 October 2018

Identification of alternative topological domains in chromatin

scientific article

Improved data-driven likelihood factorizations for transcript abundance estimation

scientific article published on July 2017

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

scientific article published on 20 June 2018

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

scientific article published on 01 July 2019

Nonparametric expression analysis using inferential replicate counts

scientific article published on 01 October 2019

Parsimonious reconstruction of network evolution ⬇️

scientific article published on September 19, 2012

Predicting protein interactions via parsimonious network history inference

scientific article published on July 2013

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

scientific article published on 11 January 2021

Quark enables semi-reference-based compression of RNA-seq data

scientific article published on November 2017

RNA sequencing data: hitchhiker's guide to expression analysis

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

scientific article published on June 2016

Reference-based compression of short-read sequences using path encoding

scientific article

Resolving spatial inconsistencies in chromosome conformation measurements ⬇️

scientific article published on March 9, 2013

Rich Chromatin Structure Prediction from Hi-C Data

scientific article published on 28 June 2018

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

scientific article

Salmon provides fast and bias-aware quantification of transcript expression

scientific article published on 6 March 2017

Squeakr: an exact and approximate k-mer counting system

scientific article published in February 2018

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

article by Michael I Love et al published 1 October 2018 in F1000Research

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

article by Michael I Love et al published 27 June 2018 in F1000Research

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

scientific article published on 01 July 2020

TransRate: reference free quality assessment of de-novo transcriptome assemblies

TransRate: reference-free quality assessment of de novo transcriptome assemblies

scientific article

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

scientific article published on 25 February 2020

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

scientific article published on July 2017

List of works by Rob Patro

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

A space and time-efficient index for the compacted colored de Bruijn graph.

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Alignment and mapping methodology influence transcript abundance estimation

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

Data-dependent bucketing improves reference-free compression of sequencing reads

Global network alignment using multiscale spectral signatures ⬇️

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis

Identification of alternative topological domains in chromatin

Improved data-driven likelihood factorizations for transcript abundance estimation

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

Nonparametric expression analysis using inferential replicate counts

Parsimonious reconstruction of network evolution ⬇️

Predicting protein interactions via parsimonious network history inference

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Quark enables semi-reference-based compression of RNA-seq data

RNA sequencing data: hitchhiker's guide to expression analysis

RNA sequencing data: hitchhiker's guide to expression analysis

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Reference-based compression of short-read sequences using path encoding

Resolving spatial inconsistencies in chromosome conformation measurements ⬇️

Rich Chromatin Structure Prediction from Hi-C Data

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

Salmon provides fast and bias-aware quantification of transcript expression

Squeakr: an exact and approximate k-mer counting system

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

TransRate: reference free quality assessment of de-novo transcriptome assemblies

TransRate: reference-free quality assessment of de novo transcriptome assemblies

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph