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Advanced filters: Author: Francesco Strino Clear advanced filters

Gene trajectory inference for single-cell data by optimal transport metrics

Gene dynamics of concurrent biological processes are unraveled by considering gene trajectories instead of cell trajectories.

Rihao Qu
Xiuyuan Cheng
Yuval Kluger
Research05 Apr 2024
Nature Biotechnology

Volume: 43, P: 258-268
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.

Matthew Murtha
Zeynep Tokcaer-Keskin
Lisa Dailey
Research23 Mar 2014
Nature Methods

Volume: 11, P: 559-565
Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

LMD identifies genes localized in high-dimensional transcriptomic neighborhoods, detecting subpopulations missed by clustering. Per-gene analysis reveals condition-specific or shared localization patterns without requiring batch correction.

Ruiqi Li
Rihao Qu
Yuval Kluger
ResearchOpen Access16 Jul 2025
Communications Biology

Volume: 8, P: 1-15