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Author: Lior Pachter

Rankings

  • All-time downloads: 91,710 (rank: 413 out of 404,161)
  • Categories:
    • bioengineering: 3,453 (rank: 268 (tie) out of 12,052)
    • bioinformatics: 53,315 (rank: 52 out of 34,272)
    • developmental biology: 355 (rank: 9,258 (tie) out of 15,768)
    • genomics: 28,459 (rank: 270 out of 42,763)
    • molecular biology: 1,541 (rank: 2,249 (tie) out of 21,566)
    • neuroscience: 4,587 (rank: 2,822 (tie) out of 67,824)

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Preprints

Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces

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Differential analysis of RNA-Seq incorporating quantification uncertainty

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Identification of transcriptional signatures for cell types from single-cell RNA-Seq

bioinformatics more details view paper
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Modular and efficient pre-processing of single-cell RNA-seq

bioinformatics more details view paper
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Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts

genomics more details view paper
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A curated database reveals trends in single-cell transcriptomics

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Shannon: An Information-Optimal de Novo RNA-Seq Assembler

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

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Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example

bioengineering more details view paper
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log(x+1)* and log(1+x)*

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

neuroscience more details view paper
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Association Mapping From Sequencing Reads Using K-mers

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A direct comparison of genome alignment and transcriptome pseudoalignment

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Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq

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RNA velocity and protein acceleration from single-cell multiomics experiments

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Fusion detection and quantification by pseudoalignment

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Barcode identification for single cell genomics

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Gene-level differential analysis at transcript-level resolution

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The Barcode, UMI, Set format and BUStools

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Decrease in ACE2 mRNA expression in aged mouse lung

molecular biology more details view paper
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Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data

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Isoform cell type specificity in the mouse primary motor cortex

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Expression reflects population structure

genomics more details view paper
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Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

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SWALO: scaffolding with assembly likelihood optimization

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Column subset selection for single-cell RNA-Seq clustering

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

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

genomics more details view paper
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Accurate design of translational output by a neural network model of ribosome distribution

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

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Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos

developmental biology more details view paper
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