List of works - Lior Pachter

A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans

scientific article published in March 2006

A Python library for probabilistic analysis of single-cell omics data

scientific article published on 07 February 2022

A closer look at RNA editing ⬇️

scientific article published on 07 March 2012

A curated database reveals trends in single-cell transcriptomics

scientific article published on 01 November 2020

A dictionary based approach for gene annotation

article

A dictionary-based approach for gene annotation

scientific article

A direct comparison of genome alignment and transcriptome pseudoalignment

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

scientific article published on 21 January 2019

A diverse epigenetic landscape at human exons with implication for expression

scientific article

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

scientific article published on 17 January 2014

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

scientific article published on 3 November 2015

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

AVID: A global alignment program

scientific article

Accurate design of translational output by a neural network model of ribosome distribution

scientific article published on 02 July 2018

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

scientific article published on April 2004

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

scientific article published on 6 July 2020

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

scientific article

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems

article

Association mapping from sequencing reads using k-mers.

scientific article published on 13 June 2018

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

scientific article

Barcode identification for single cell genomics

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates

scientific article

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

scientific article

Bioinformatics for whole-genome shotgun sequencing of microbial communities

scientific article

CGAL: computing genome assembly likelihoods

scientific article published on 29 January 2013

Combinatorics of least-squares trees

scholarly article

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

scientific article published on 18 March 2008

Comparison of pattern detection methods in microarray time series of the segmentation clock

scientific article

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

scientific article

Controlling for conservation in genome-wide DNA methylation studies

scientific article

Coverage statistics for sequence census methods

scientific article

Decrease in ACE2 mRNA expression in aged mouse lung

scientific article published on 05 April 2020

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains

scientific article published on 23 September 2011

Deterministic column subset selection for single-cell RNA-Seq

scientific article published in PLoS ONE

Development of a low bias method for characterizing viral populations using next generation sequencing technology

scientific article (publication date: 22 October 2010)

Differential analysis of RNA-seq incorporating quantification uncertainty

scientific article published on 05 June 2017

Differential analysis of gene regulation at transcript resolution with RNA-seq

scientific article (publication date: 2013)

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

scientific article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Disordered microbial communities in asthmatic airways

scientific article

Erratum: Near-optimal probabilistic RNA-seq quantification

scientific article published on 01 August 2016

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements

scientific article published on 22 November 2016

Evolution at the nucleotide level: the problem of multiple whole-genome alignment

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Exon-level microarray analyses identify alternative splicing programs in breast cancer

scientific article

Exploring the genetic basis of variation in gene predictions with a synthetic association study

scientific article (publication date: 29 July 2010)

Expression reflects population structure

scientific article published on 19 December 2018

Factor analysis for survival time prediction with informative censoring and diverse covariates

scientific article published on 04 June 2019

Fast and accurate diagnostics from highly multiplexed sequencing assays

scientific article published on 17 May 2020

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

scientific article published on 26 May 2016

Fast and scalable querying of eukaryotic linear motifs with <i>gget elm</i>

scientific article published in 2024

Fast statistical alignment

scientific article

Finding Convex Sets Among Points in the Plane

scientific article (publication date: March 1998)

Fragment assignment in the cloud with eXpress-D

scientific article

Fusion detection and quantification by pseudoalignment

article published in 2017

Gene-level differential analysis at transcript-level resolution

scientific article published on 12 April 2018

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

HMM sampling and applications to gene finding and alternative splicing

article

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins

scientific article published on 23 December 2019

Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells.

scientific article

Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and correction of systematic error in high-throughput sequence data

scientific article

Identification of evolutionary hotspots in the rodent genomes

scientific article published on April 2004

Identification of novel transcripts in annotated genomes using RNA-Seq

scientific article published on 21 June 2011

Identification of transposable elements using multiple alignments of related genomes

scientific article published on 14 December 2005

Improving RNA-Seq expression estimates by correcting for fragment bias

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

Interpretable factor models of single-cell RNA-seq via variational autoencoders

scientific article published on 16 March 2020

Interpreting the unculturable majority

scientific article published on 01 June 2007

Intraspecies sequence comparisons for annotating genomes

scientific article

Isoform cell-type specificity in the mouse primary motor cortex

scientific article published on 06 October 2021

Large multiple organism gene finding by collapsed Gibbs sampling.

scientific article published in July 2005

Low-cost, scalable, and automated fluid sampling for fluidics applications

scientific article published on 31 May 2021

MAVID multiple alignment server

scientific article

MAVID: constrained ancestral alignment of multiple sequences

scientific article

Mapping and identification of essential gene functions on the X chromosome of Drosophila

scientific article

MetMap enables genome-scale Methyltyping for determining methylation states in populations

scientific article

Modeling and automation of sequencing-based characterization of RNA structure

scientific article

Modeling bursty transcription and splicing with the chemical master equation

scientific article published in 2022

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

scientific article published on 01 October 2019

Multiple alignment by sequence annealing.

scientific article published in January 2007

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny

scientific article published on 26 February 2004

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

scientific article

Museum of spatial transcriptomics

scientific article

Near-optimal probabilistic RNA-seq quantification

scientific article

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

scientific article published on 23 July 2020

On the optimality of the neighbor-joining algorithm

scientific article

PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays

scientific article published on 09 May 2017

Pair hidden Markov models

Parametric alignment of Drosophila genomes

scientific article published on 10 May 2006

Parametric alignment of Drosophila genomes

scientific article

Parametric inference for biological sequence analysis

scholarly article

Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor

scientific article published on 11 May 2007

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

scientific article published on 9 September 2011

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

scientific article

Picking alignments from (Steiner) trees

scientific article published in January 2003

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

scientific article

Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis

scientific article published on 18 December 2015

Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study

scientific article

Principles of open source bioinstrumentation applied to the poseidon syringe pump system

scientific article published on 27 August 2019

Protein velocity and acceleration from single-cell multiomics experiments

scientific article published on 18 February 2020

Quantifying uniformity of mapped reads

scientific article

RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq

scientific article published on 01 October 2018

RNA-Seq and find: entering the RNA deep field

scientific article published on 22 November 2011

Rational experiment design for sequencing-based RNA structure mapping

scientific article

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

scientific article published on 02 June 2020

Reference based annotation with GeneMapper

scientific article (publication date: 2006)

Reliable and accurate diagnostics from highly multiplexed sequencing assays

scientific article published on 10 December 2020

SHAPE–Seq: High‐Throughput RNA Structure Analysis ⬇️

scientific article published on December 1, 2012

SLAM web server for comparative gene finding and alignment

scientific article

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model

scientific article published on March 2003

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Shape-based peak identification for ChIP-Seq

scientific article

Single-cell analysis at the threshold

scientific article

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

scientific article

Special function methods for bursty models of transcription

scientific article published on 01 August 2020

Specific alignment of structured RNA: stochastic grammars and sequence annealing

scientific article published on 16 September 2008

Strategies and tools for whole-genome alignments

scientific article

Streaming fragment assignment for real-time analysis of sequencing experiments

scientific article published on 18 November 2012

Structural variation among wild and industrial strains of Penicillium chrysogenum

scientific article

Subtree power analysis and species selection for comparative genomics

scientific article

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

scientific article published on 03 September 2020

The BUS Format for Single-Cell RNA-Seq Processing and Analysis

The Barcode, UMI, Set format and BUStools

The Lair: a resource for exploratory analysis of published RNA-Seq data

scientific article

The NIH BD2K center for big data in translational genomics

scientific article

The barcode, UMI, set format and BUStools

scientific article published on 01 November 2019

The computational challenges of applying comparative-based computational methods to whole genomes

scientific article

The cyclohedron test for finding periodic genes in time course expression studies

scientific article

TopHat: discovering splice junctions with RNA-Seq

scientific article

Toward the human genotope

scientific article published on 15 September 2007

Tracing the most parsimonious indel history

scientific article published on 5 July 2011

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

scientific article

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity

scientific article published on 10 September 2016

Tropical geometry of statistical models

scholarly article

Updating RNA-Seq analyses after re-annotation

scientific article published on 14 May 2013

VISTA: computational tools for comparative genomics

scientific article (publication date: July 2004)

Viral population estimation using pyrosequencing

scientific article

Visualization of multiple genome annotations and alignments with the K-BROWSER.

scientific article published on April 2004

Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across <i>Clytia</i> medusa cell types

scientific article published on 26 November 2021

Why Neighbor-Joining Works

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

scientific article

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

scientific article (publication date: 27 April 2017)

log(x+1)* and log(1+x)*

scientific article published on 20 May 2020

rVista for comparative sequence-based discovery of functional transcription factor binding sites

scientific article published on May 2002

List of works by Lior Pachter

A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans

A Python library for probabilistic analysis of single-cell omics data

A closer look at RNA editing ⬇️

A curated database reveals trends in single-cell transcriptomics

A dictionary based approach for gene annotation

A dictionary-based approach for gene annotation

A direct comparison of genome alignment and transcriptome pseudoalignment

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

A diverse epigenetic landscape at human exons with implication for expression

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

A multimodal cell census and atlas of the mammalian primary motor cortex

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

AVID: A global alignment program

Accurate design of translational output by a neural network model of ribosome distribution

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems

Association mapping from sequencing reads using k-mers.

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Barcode identification for single cell genomics

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

Bioinformatics for whole-genome shotgun sequencing of microbial communities

CGAL: computing genome assembly likelihoods

Combinatorics of least-squares trees

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

Comparison of pattern detection methods in microarray time series of the segmentation clock

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

Controlling for conservation in genome-wide DNA methylation studies

Coverage statistics for sequence census methods

Decrease in ACE2 mRNA expression in aged mouse lung

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains

Deterministic column subset selection for single-cell RNA-Seq

Development of a low bias method for characterizing viral populations using next generation sequencing technology

Differential analysis of RNA-seq incorporating quantification uncertainty

Differential analysis of gene regulation at transcript resolution with RNA-seq

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Disordered microbial communities in asthmatic airways

Erratum: Near-optimal probabilistic RNA-seq quantification

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements

Evolution at the nucleotide level: the problem of multiple whole-genome alignment

Evolution of genes and genomes on the Drosophila phylogeny

Exon-level microarray analyses identify alternative splicing programs in breast cancer

Exploring the genetic basis of variation in gene predictions with a synthetic association study

Expression reflects population structure

Factor analysis for survival time prediction with informative censoring and diverse covariates

Fast and accurate diagnostics from highly multiplexed sequencing assays

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

Fast and scalable querying of eukaryotic linear motifs with <i>gget elm</i>

Fast statistical alignment

Finding Convex Sets Among Points in the Plane

Fragment assignment in the cloud with eXpress-D

Fusion detection and quantification by pseudoalignment

Gene-level differential analysis at transcript-level resolution

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

HMM sampling and applications to gene finding and alternative splicing

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins

Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells.

Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification and correction of systematic error in high-throughput sequence data

Identification of evolutionary hotspots in the rodent genomes

Identification of novel transcripts in annotated genomes using RNA-Seq

Identification of transposable elements using multiple alignments of related genomes

Improving RNA-Seq expression estimates by correcting for fragment bias

Initial sequencing and comparative analysis of the mouse genome

Interpretable factor models of single-cell RNA-seq via variational autoencoders

Interpreting the unculturable majority

Intraspecies sequence comparisons for annotating genomes

Isoform cell-type specificity in the mouse primary motor cortex

Large multiple organism gene finding by collapsed Gibbs sampling.

Low-cost, scalable, and automated fluid sampling for fluidics applications

MAVID multiple alignment server

MAVID: constrained ancestral alignment of multiple sequences