Pachter, Lior

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

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 15,556

Near-optimal probabilistic RNA-seq quantification

Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 9,723

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

Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 3,492

Improving RNA-Seq expression estimates by correcting for fragment bias

Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 1,725

Differential analysis of RNA-seq incorporating quantification uncertainty

Pimentel, H., Bray, N. L., Puente, S., Melsted, P., & Pachter, L. (2017) · Nature Methods

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 1,534

Museum of spatial transcriptomics

Moses, L., & Pachter, L. (2022) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,255

Museum of Spatial Transcriptomics

Moses, L., & Pachter, L. (2021) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,255

Streaming fragment assignment for real-time analysis of sequencing experiments

Roberts, A., & Pachter, L. (2013) · Nature Methods

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 1,063

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

Gayoso, A., Lopez, R., Xing, G., Boyeau, P., Valiollah Pour Amiri, V., Hong, J., Wu, K., Jayasuriya, M., Mehlman, E., Langevin, M., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 789

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

BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 522

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, I., Pachter, L., & Rubin, E. M. (2003) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 516

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

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

The Specious Art of Single-Cell Genomics

Chari, T., & Pachter, L. (2021) · PLoS Computational Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 379

Multimodal analysis of cell types in a hypothalamic node controlling social behavior

Kim, D.-W., Yao, Z., Graybuck, L. T., Kim, T. K., Nguyen, T. N., Smith, K. A., Fong, O., Yi, L., Koulena, N., Pierson, N., et al. (2019) · Cell

Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research

Cited by 259

Strategies and tools for whole-genome alignments

Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., & Dubchak, I. (2003) · Genome Research

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 224

A curated database reveals trends in single-cell transcriptomics

Svensson, V., da Veiga Beltrame, E., & Pachter, L. (2020) · Database

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 223

RNA velocity unraveled

Gorin, G., Fang, M., Chari, T., & Pachter, L. (2022) · PLOS Computational Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 186

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

Gehring, J., Hwee Park, J., Chen, S., Thomson, M., & Pachter, L. (2020) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 122

Normalization for sampled count data

Booeshaghi, A. S., Hallgrímsdóttir, I. B., Gálvez-Merchán, Á., & Pachter, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 39

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

Li, B., Tambe, A., Aviran, S., & Pachter, L. (2017) · Cell Systems

RNA modifications and cancerGenomics and Phylogenetic Studies

Cited by 15

Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays

Li, B., Tambe, A., Aviran, S., & Pachter, L. (2016) · Cell Systems

RNA modifications and cancerGenomics and Phylogenetic Studies

Cited by 15

Science should be machine-readable

Booeshaghi, A. S., Luebbert, L., & Pachter, L. (2026) · bioRxiv (Cold Spring Harbor Laboratory)

Academic Publishing and Open AccessAdvanced Text Analysis Techniques

Cited by 3

Fast and scalable querying of eukaryotic linear motifs with gget elm

Luebbert, L., Hoang, C., Kumar, M., & Pachter, L. (2023) · Bioinformatics

Bioinformatics and Genomic NetworksMachine Learning in Bioinformatics

Cited by 1