Lior Pachter
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Explore the profile of Lior Pachter including associated specialties, affiliations and a list of published articles.
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177
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49975
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Recent Articles
1.
Moses L, Huseynov A, Rich J, Pachter L
bioRxiv
. 2025 Mar;
PMID: 40060564
SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for...
2.
Felce C, Gorin G, Pachter L
Phys Rev E
. 2025 Feb;
110(6-1):064405.
PMID: 39916216
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) can be used to identify open chromatin regions, providing complementary information to RNA-seq which measures gene expression by sequencing. Single-cell multiome methods...
3.
Fang M, Gorin G, Pachter L
PLoS Comput Biol
. 2025 Jan;
21(1):e1012752.
PMID: 39836699
Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. These snapshots have been used to infer trajectories and dynamic information even without intensive, time-series data...
4.
Sullivan D, Hjorleifsson K, Swarna N, Oakes C, Holley G, Melsted P, et al.
Nucleic Acids Res
. 2024 Dec;
53(1.
PMID: 39657125
In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in accurate read mapping and the interpretation of count matrices....
5.
Sullivan D, Min K, Hjorleifsson K, Luebbert L, Holley G, Moses L, et al.
Nat Protoc
. 2024 Oct;
20(3):587-607.
PMID: 39390263
The term 'RNA-seq' refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto, bustools and...
6.
Chari T, Gorin G, Pachter L
Nat Comput Sci
. 2024 Sep;
4(9):677-689.
PMID: 39317762
Multimodal, single-cell genomics technologies enable simultaneous measurement of multiple facets of DNA and RNA processing in the cell. This creates opportunities for transcriptome-wide, mechanistic studies of cellular processing in heterogeneous...
7.
Loving R, Sullivan D, Booeshagi A, Reese F, Rebboah E, Sakr J, et al.
bioRxiv
. 2024 Jul;
PMID: 39071335
RNA abundance quantification has become routine and affordable thanks to high-throughput "short-read" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length,...
8.
Jackson K, Booeshaghi A, Galvez-Merchan A, Moses L, Chari T, Kim A, et al.
bioRxiv
. 2024 Jul;
PMID: 39071320
Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate...
9.
Carilli M, Gorin G, Choi Y, Chari T, Pachter L
Nat Methods
. 2024 Jul;
21(8):1466-1469.
PMID: 39054391
Here we present biVI, which combines the variational autoencoder framework of scVI with biophysical models describing the transcription and splicing kinetics of RNA molecules. We demonstrate on simulated and experimental...
10.
Chari T, Gorin G, Pachter L
bioRxiv
. 2024 Jul;
PMID: 39005347
Recent advances in high-throughput, multi-condition experiments allow for genome-wide investigation of how perturbations affect transcription and translation in the cell across multiple biological entities or modalities, from chromatin and mRNA...