World's Best Scientists 2026 revealed!

D-Index & Metrics

Genetics

D-Index
84
Citations
119115
World Ranking
1328
National Ranking
629

Research.com Recognitions

  • 2003 - Fellow of Alfred P. Sloan Foundation

Overview

Lior Pachter is affiliated with the California Institute of Technology in the United States. Their work primarily spans the fields of Biochemistry, Genetics and Molecular Biology, with a focus on Molecular Biology, Genetics, Biophysics, Cancer Research, and Biomedical Engineering.

The scientist's research topics cover a range of areas including Single-cell and spatial transcriptomics, Gene Regulatory Network Analysis, RNA Research and Splicing, Gene expression and cancer classification, Cell Image Analysis Techniques, Genomics and Phylogenetic Studies, and Extracellular vesicles in disease.

Prominent recent publications by Lior Pachter include:

  • "Museum of spatial transcriptomics" (2022, Nature Methods)
  • "A Python library for probabilistic analysis of single-cell omics data" (2022, Nature Biotechnology)
  • "A multimodal cell census and atlas of the mammalian primary motor cortex" (2021, Nature)
  • "Modular, efficient and constant-memory single-cell RNA-seq preprocessing" (2021, Nature Biotechnology)
  • "A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex" (2021, Nature)

Frequent co-authors include:

  • Gennady Gorin (41 joint papers)
  • A. Sina Booeshaghi (38 joint papers)
  • Tara Chari (19 joint papers)
  • Laura Luebbert (19 joint papers)
  • Delaney K. Sullivan (16 joint papers)

The scientist has published extensively in venues such as bioRxiv (Cold Spring Harbor Laboratory), with 67 publications, Zenodo (CERN European Organization for Nuclear Research) with 8 publications, Bioinformatics with 7 publications, arXiv (Cornell University) with 6 publications, and Nature with 5 publications.

Lior Pachter received the Fellow of Alfred P. Sloan Foundation award in 2003.

Best Publications

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

    Cole Trapnell;Cole Trapnell;Brian A Williams;Geo Pertea;Ali Mortazavi

  • TopHat: discovering splice junctions with RNA-Seq

    Cole Trapnell;Lior Pachter;Steven L. Salzberg

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

    Cole Trapnell;Adam Roberts;Loyal Goff;Loyal Goff;Loyal Goff;Geo Pertea

  • Initial sequencing and comparative analysis of the mouse genome.

    Robert H. Waterston;Kerstin Lindblad-Toh;Ewan Birney;Jane Rogers

  • Near-optimal probabilistic RNA-seq quantification

    Nicolas L Bray;Harold Pimentel;Páll Melsted;Lior Pachter

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

    Ewan Birney;John A. Stamatoyannopoulos;Anindya Dutta;Roderic Guigó

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

    Cole Trapnell;David G Hendrickson;David G Hendrickson;Martin Sauvageau;Martin Sauvageau;Loyal Goff;Loyal Goff

  • The ENCODE (ENCyclopedia of DNA elements) Project

    E. A. Feingold;P. J. Good;M. S. Guyer;S. Kamholz

  • Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

    Daniel J. Brat;Roel G.W. Verhaak;Kenneth D. Aldape;W. K.Alfred Yung

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

    Ladeana W. Hillier;Webb Miller;Ewan Birney;Wesley Warren

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

    Richard A. Gibbs;George M. Weinstock;Michael L. Metzker;Donna M. Muzny

  • VISTA: computational tools for comparative genomics

    Kelly A. Frazer;Lior Pachter;Alexander Poliakov;Edward M. Rubin

  • Evolution of genes and genomes on the Drosophila phylogeny.

    Andrew G. Clark;Michael B. Eisen;Michael B. Eisen;Douglas R. Smith;Casey M. Bergman

  • Improving RNA-Seq expression estimates by correcting for fragment bias

    Adam B Roberts;Cole Trapnell;Cole Trapnell;Julie Donaghey;John L Rinn;John L Rinn

  • Differential analysis of RNA-seq incorporating quantification uncertainty.

    Harold Pimentel;Nicolas L Bray;Suzette Puente;Páll Melsted

  • VISTA : visualizing global DNA sequence alignments of arbitrary length.

    Chris Mayor;Michael Brudno;Jody R. Schwartz;Alexander Poliakov

  • Identification of novel transcripts in annotated genomes using RNA-Seq

    Adam Roberts;Harold Pimentel;Cole Trapnell;Lior Pachter

  • Streaming fragment assignment for real-time analysis of sequencing experiments

    Adam Roberts;Lior Pachter

  • Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

    David J. Begun;Alisha K. Holloway;Kristian Stevens;La Deana W. Hillier

  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

    Alexander Stark;Michael F Lin;Pouya Kheradpour;Jakob Skou Pedersen;Jakob Skou Pedersen

Frequent Co-Authors

Bernd Sturmfels
Bernd Sturmfels Max Planck Institute for Mathematics in the Sciences
Cole Trapnell
Cole Trapnell University of Washington
Edward M. Rubin
Edward M. Rubin Joint Genome Institute
Inna Dubchak
Inna Dubchak Lawrence Berkeley National Laboratory
Eric S. Lander
Eric S. Lander Broad Institute
Serafim Batzoglou
Serafim Batzoglou Stanford University
David Haussler
David Haussler University of California, Santa Cruz
Roderic Guigó
Roderic Guigó Pompeu Fabra University
John L. Rinn
John L. Rinn University of Colorado Boulder
Michael B. Eisen
Michael B. Eisen University of California, Berkeley

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