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Author: Lior Pachter

Rankings

  • All-time downloads: 135,284 (rank: 706 )
  • Categories:
    • bioengineering: 4,672 (rank: 258 (tie) )
    • bioinformatics: 67,774 (rank: 17 )
    • biophysics: 1,141 (rank: 4,589 (tie) )
    • developmental biology: 399 (rank: 12,465 (tie) )
    • evolutionary biology: 410 (rank: 16,604 (tie) )
    • genomics: 31,367 (rank: 385 )
    • health informatics: 1,434 (rank: 595 (tie) )
    • health policy: 6,298 (rank: 84 (tie) )
    • infectious diseases: 5,491 (rank: 8,115 (tie) )
    • molecular biology: 1,818 (rank: 3,008 (tie) )
    • neuroscience: 12,475 (rank: 999 (tie) )
    • systems biology: 2,005 (rank: 2,199 (tie) )

Downloads per author, site-wide

Preprints

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

genomics more details view paper
  • Downloaded 10,668 times
  • Download rankings, all-time:
    • Site-wide: 858
    • In genomics: 62
  • Year to date:
    • Site-wide: 8,804
  • Since beginning of last month:
    • Site-wide: 14,025

Differential analysis of RNA-Seq incorporating quantification uncertainty

bioinformatics more details view paper
  • Downloaded 9,169 times
  • Download rankings, all-time:
    • Site-wide: 1,036
    • In bioinformatics: 53
  • Year to date:
    • Site-wide: 11,501
  • Since beginning of last month:
    • Site-wide: 17,229

Modular and efficient pre-processing of single-cell RNA-seq

bioinformatics more details view paper
  • Downloaded 8,363 times
  • Download rankings, all-time:
    • Site-wide: 1,170
    • In bioinformatics: 68
  • Year to date:
    • Site-wide: 3,080
  • Since beginning of last month:
    • Site-wide: 4,804

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

bioinformatics more details view paper
  • Downloaded 7,609 times
  • Download rankings, all-time:
    • Site-wide: 1,314
    • In bioinformatics: 79
  • Year to date:
    • Site-wide: 10,273
  • Since beginning of last month:
    • Site-wide: 11,291

Markedly heterogeneous COVID-19 testing plans among US colleges and universities

health policy more details view paper
  • Downloaded 6,298 times
  • Download rankings, all-time:
    • Site-wide: 1,677
    • In health policy: 12
  • Year to date:
    • Site-wide: 5,832
  • Since beginning of last month:
    • Site-wide: 6,126

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

neuroscience more details view paper
  • Downloaded 6,086 times
  • Download rankings, all-time:
    • Site-wide: 1,770
    • In neuroscience: 87
  • Year to date:
    • Site-wide: 1,336
  • Since beginning of last month:
    • Site-wide: 1,776

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

infectious diseases more details view paper
  • Downloaded 5,491 times
  • Download rankings, all-time:
    • Site-wide: 2,027
    • In infectious diseases: 504
  • Year to date:
    • Site-wide: 2,534
  • Since beginning of last month:
    • Site-wide: 3,572

Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts

genomics more details view paper
  • Downloaded 5,202 times
  • Download rankings, all-time:
    • Site-wide: 2,173
    • In genomics: 198
  • Year to date:
    • Site-wide: 51,265
  • Since beginning of last month:
    • Site-wide: 74,354

Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*

bioinformatics more details view paper
  • Downloaded 4,858 times
  • Download rankings, all-time:
    • Site-wide: 2,414
    • In bioinformatics: 196
  • Year to date:
    • Site-wide: 4,521
  • Since beginning of last month:
    • Site-wide: 9,017

A curated database reveals trends in single-cell transcriptomics

genomics more details view paper
  • Downloaded 4,739 times
  • Download rankings, all-time:
    • Site-wide: 2,482
    • In genomics: 250
  • Year to date:
    • Site-wide: 12,441
  • Since beginning of last month:
    • Site-wide: 22,325

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

bioinformatics more details view paper
  • Downloaded 4,548 times
  • Download rankings, all-time:
    • Site-wide: 2,629
    • In bioinformatics: 218
  • Year to date:
    • Site-wide: 10,835
  • Since beginning of last month:
    • Site-wide: 22,350

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

neuroscience more details view paper
  • Downloaded 4,194 times
  • Download rankings, all-time:
    • Site-wide: 2,962
    • In neuroscience: 196
  • Year to date:
    • Site-wide: 1,811
  • Since beginning of last month:
    • Site-wide: 2,293

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

genomics more details view paper
  • Downloaded 4,087 times
  • Download rankings, all-time:
    • Site-wide: 3,067
    • In genomics: 320
  • Year to date:
    • Site-wide: 33,280
  • Since beginning of last month:
    • Site-wide: 32,849

A direct comparison of genome alignment and transcriptome pseudoalignment

bioinformatics more details view paper
  • Downloaded 4,081 times
  • Download rankings, all-time:
    • Site-wide: 3,074
    • In bioinformatics: 266
  • Year to date:
    • Site-wide: 4,535
  • Since beginning of last month:
    • Site-wide: 4,979

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

bioengineering more details view paper
  • Downloaded 3,798 times
  • Download rankings, all-time:
    • Site-wide: 3,416
    • In bioengineering: 35
  • Year to date:
    • Site-wide: 28,693
  • Since beginning of last month:
    • Site-wide: 39,354

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

genomics more details view paper
  • Downloaded 3,442 times
  • Download rankings, all-time:
    • Site-wide: 3,903
    • In genomics: 407
  • Year to date:
    • Site-wide: 12,326
  • Since beginning of last month:
    • Site-wide: 31,945

Museum of Spatial Transcriptomics

bioinformatics more details view paper
  • Downloaded 3,019 times
  • Download rankings, all-time:
    • Site-wide: 4,701
    • In bioinformatics: 463
  • Year to date:
    • Site-wide: 660
  • Since beginning of last month:
    • Site-wide: 559

Association Mapping From Sequencing Reads Using K-mers

bioinformatics more details view paper
  • Downloaded 2,982 times
  • Download rankings, all-time:
    • Site-wide: 4,776
    • In bioinformatics: 473
  • Year to date:
    • Site-wide: 114,163
  • Since beginning of last month:
    • Site-wide: 101,171

Fusion detection and quantification by pseudoalignment

bioinformatics more details view paper
  • Downloaded 2,864 times
  • Download rankings, all-time:
    • Site-wide: 5,066
    • In bioinformatics: 512
  • Year to date:
    • Site-wide: 26,493
  • Since beginning of last month:
    • Site-wide: 32,725

RNA velocity and protein acceleration from single-cell multiomics experiments

bioinformatics more details view paper
  • Downloaded 2,811 times
  • Download rankings, all-time:
    • Site-wide: 5,207
    • In bioinformatics: 529
  • Year to date:
    • Site-wide: 71,532
  • Since beginning of last month:
    • Site-wide: 65,525

Barcode identification for single cell genomics

bioinformatics more details view paper
  • Downloaded 2,525 times
  • Download rankings, all-time:
    • Site-wide: 6,102
    • In bioinformatics: 651
  • Year to date:
    • Site-wide: 92,084
  • Since beginning of last month:
    • Site-wide: 92,197

The Barcode, UMI, Set format and BUStools

bioinformatics more details view paper
  • Downloaded 2,506 times
  • Download rankings, all-time:
    • Site-wide: 6,163
    • In bioinformatics: 659
  • Year to date:
    • Site-wide: 29,561
  • Since beginning of last month:
    • Site-wide: 28,234

Gene-level differential analysis at transcript-level resolution

bioinformatics more details view paper
  • Downloaded 2,391 times
  • Download rankings, all-time:
    • Site-wide: 6,612
    • In bioinformatics: 726
  • Year to date:
    • Site-wide: 48,695
  • Since beginning of last month:
    • Site-wide: 70,531

Isoform cell type specificity in the mouse primary motor cortex

neuroscience more details view paper
  • Downloaded 2,195 times
  • Download rankings, all-time:
    • Site-wide: 7,477
    • In neuroscience: 717
  • Year to date:
    • Site-wide: 8,424
  • Since beginning of last month:
    • Site-wide: 4,428

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

systems biology more details view paper
  • Downloaded 2,005 times
  • Download rankings, all-time:
    • Site-wide: 8,542
    • In systems biology: 145
  • Year to date:
    • Site-wide: 1,111
  • Since beginning of last month:
    • Site-wide: 3,153

Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data

bioinformatics more details view paper
  • Downloaded 2,004 times
  • Download rankings, all-time:
    • Site-wide: 8,551
    • In bioinformatics: 983
  • Year to date:
    • Site-wide: 20,645
  • Since beginning of last month:
    • Site-wide: 16,343

Decrease in ACE2 mRNA expression in aged mouse lung

molecular biology more details view paper
  • Downloaded 1,818 times
  • Download rankings, all-time:
    • Site-wide: 9,877
    • In molecular biology: 252
  • Year to date:
    • Site-wide: 47,201
  • Since beginning of last month:
    • Site-wide: 83,914

Fast and accurate diagnostics from highly multiplexed sequencing assays

health informatics more details view paper
  • Downloaded 1,434 times
  • Download rankings, all-time:
    • Site-wide: 14,047
    • In health informatics: 66
  • Year to date:
    • Site-wide: 65,876
  • Since beginning of last month:
    • Site-wide: 45,966

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

bioinformatics more details view paper
  • Downloaded 1,346 times
  • Download rankings, all-time:
    • Site-wide: 15,467
    • In bioinformatics: 1,809
  • Year to date:
    • Site-wide: 1,884
  • Since beginning of last month:
    • Site-wide: 1,733

Expression reflects population structure

genomics more details view paper
  • Downloaded 1,329 times
  • Download rankings, all-time:
    • Site-wide: 15,736
    • In genomics: 1,584
  • Year to date:
    • Site-wide: 138,375
  • Since beginning of last month:
    • Site-wide: 145,861

SWALO: scaffolding with assembly likelihood optimization

bioinformatics more details view paper
  • Downloaded 1,284 times
  • Download rankings, all-time:
    • Site-wide: 16,612
    • In bioinformatics: 1,945
  • Year to date:
    • Site-wide: 106,436
  • Since beginning of last month:
    • Site-wide: 143,515

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

bioinformatics more details view paper
  • Downloaded 1,282 times
  • Download rankings, all-time:
    • Site-wide: 16,642
    • In bioinformatics: 1,951
  • Year to date:
    • Site-wide: 95,161
  • Since beginning of last month:
    • Site-wide: 130,497

Column subset selection for single-cell RNA-Seq clustering

bioinformatics more details view paper
  • Downloaded 1,193 times
  • Download rankings, all-time:
    • Site-wide: 18,485
    • In bioinformatics: 2,137
  • Year to date:
    • Site-wide: 94,185
  • Since beginning of last month:
    • Site-wide: 128,287

Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing

bioinformatics more details view paper
  • Downloaded 1,119 times
  • Download rankings, all-time:
    • Site-wide: 20,328
    • In bioinformatics: 2,353
  • Year to date:
    • Site-wide: 2,426
  • Since beginning of last month:
    • Site-wide: 13,697

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

bioinformatics more details view paper
  • Downloaded 1,075 times
  • Download rankings, all-time:
    • Site-wide: 21,561
    • In bioinformatics: 2,479
  • Year to date:
    • Site-wide: 142,384
  • Since beginning of last month:
    • Site-wide: 143,473

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

genomics more details view paper
  • Downloaded 1,017 times
  • Download rankings, all-time:
    • Site-wide: 23,373
    • In genomics: 2,221
  • Year to date:
    • Site-wide: 119,787
  • Since beginning of last month:
    • Site-wide: 137,732

Accurate design of translational output by a neural network model of ribosome distribution

genomics more details view paper
  • Downloaded 883 times
  • Download rankings, all-time:
    • Site-wide: 28,647
    • In genomics: 2,573
  • Year to date:
    • Site-wide: 148,179
  • Since beginning of last month:
    • Site-wide: 145,186

Low-cost, scalable, and automated fluid sampling for fluidics applications

bioengineering more details view paper
  • Downloaded 874 times
  • Download rankings, all-time:
    • Site-wide: 29,072
    • In bioengineering: 499
  • Year to date:
    • Site-wide: 3,455
  • Since beginning of last month:
    • Site-wide: 20,759

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

bioinformatics more details view paper
  • Downloaded 745 times
  • Download rankings, all-time:
    • Site-wide: 36,340
    • In bioinformatics: 3,965
  • Year to date:
    • Site-wide: 53,412
  • Since beginning of last month:
    • Site-wide: 66,113

Direct simulation of a stochastically driven multi-step birth-death process

biophysics more details view paper
  • Downloaded 605 times
  • Download rankings, all-time:
    • Site-wide: 47,599
    • In biophysics: 1,567
  • Year to date:
    • Site-wide: 5,881
  • Since beginning of last month:
    • Site-wide: 73,284

A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration

evolutionary biology more details view paper
  • Downloaded 410 times
  • Download rankings, all-time:
    • Site-wide: 73,742
    • In evolutionary biology: 3,875
  • Year to date:
    • Site-wide: 10,433
  • Since beginning of last month:
    • Site-wide: 33,518

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
  • Downloaded 399 times
  • Download rankings, all-time:
    • Site-wide: 75,838
    • In developmental biology: 1,920
  • Year to date:
    • Site-wide: 134,702
  • Since beginning of last month:
    • Site-wide: 138,713

Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production

biophysics more details view paper
  • Downloaded 348 times
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    • Site-wide: 85,473
    • In biophysics: 3,199
  • Year to date:
    • Site-wide: 71,155
  • Since beginning of last month:
    • Site-wide: 114,321

Analytical solutions of the chemical master equation with bursty production and isomerization reactions

biophysics more details view paper
  • Downloaded 188 times
  • Download rankings, all-time:
    • Site-wide: 122,932
    • In biophysics: 4,713
  • Year to date:
    • Site-wide: 29,806
  • Since beginning of last month:
    • Site-wide: 38,669

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