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Author: Lior Pachter

Rankings

  • All-time downloads: 120,190 (rank: 736 )
  • Categories:
    • bioengineering: 4,289 (rank: 233 (tie) )
    • bioinformatics: 59,510 (rank: 28 )
    • biophysics: 728 (rank: 6,499 (tie) )
    • developmental biology: 380 (rank: 11,080 (tie) )
    • genomics: 30,400 (rank: 287 )
    • health informatics: 1,365 (rank: 459 (tie) )
    • health policy: 5,898 (rank: 45 (tie) )
    • infectious diseases: 4,784 (rank: 7,176 (tie) )
    • molecular biology: 1,728 (rank: 2,588 (tie) )
    • neuroscience: 9,870 (rank: 1,168 (tie) )
    • systems biology: 1,238 (rank: 3,187 (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 10,377 times
  • Download rankings, all-time:
    • Site-wide: 718
    • In genomics: 57
  • Year to date:
    • Site-wide: 5,917
  • Since beginning of last month:
    • Site-wide: 4,869

Differential analysis of RNA-Seq incorporating quantification uncertainty

bioinformatics more details view paper
  • Downloaded 8,930 times
  • Download rankings, all-time:
    • Site-wide: 870
    • In bioinformatics: 46
  • Year to date:
    • Site-wide: 7,455
  • Since beginning of last month:
    • Site-wide: 5,771

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

bioinformatics more details view paper
  • Downloaded 7,670 times
  • Download rankings, all-time:
    • Site-wide: 1,058
    • In bioinformatics: 65
  • Year to date:
    • Site-wide: 3,227
  • Since beginning of last month:
    • Site-wide: 3,469

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

bioinformatics more details view paper
  • Downloaded 7,320 times
  • Download rankings, all-time:
    • Site-wide: 1,119
    • In bioinformatics: 70
  • Year to date:
    • Site-wide: 8,791
  • Since beginning of last month:
    • Site-wide: 15,276

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

health policy more details view paper
  • Downloaded 5,898 times
  • Download rankings, all-time:
    • Site-wide: 1,478
    • In health policy: 7
  • Year to date:
    • Site-wide: 4,438
  • Since beginning of last month:
    • Site-wide: 5,934

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

genomics more details view paper
  • Downloaded 5,131 times
  • Download rankings, all-time:
    • Site-wide: 1,794
    • In genomics: 182
  • Year to date:
    • Site-wide: 29,824
  • Since beginning of last month:
    • Site-wide: 26,142

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

neuroscience more details view paper
  • Downloaded 4,808 times
  • Download rankings, all-time:
    • Site-wide: 1,963
    • In neuroscience: 114
  • Year to date:
    • Site-wide: 1,397
  • Since beginning of last month:
    • Site-wide: 1,743

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

infectious diseases more details view paper
  • Downloaded 4,784 times
  • Download rankings, all-time:
    • Site-wide: 1,977
    • In infectious diseases: 446
  • Year to date:
    • Site-wide: 1,881
  • Since beginning of last month:
    • Site-wide: 2,625

A curated database reveals trends in single-cell transcriptomics

genomics more details view paper
  • Downloaded 4,516 times
  • Download rankings, all-time:
    • Site-wide: 2,150
    • In genomics: 237
  • Year to date:
    • Site-wide: 7,807
  • Since beginning of last month:
    • Site-wide: 7,804

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

bioinformatics more details view paper
  • Downloaded 4,373 times
  • Download rankings, all-time:
    • Site-wide: 2,249
    • In bioinformatics: 204
  • Year to date:
    • Site-wide: 3,608
  • Since beginning of last month:
    • Site-wide: 2,328

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

bioinformatics more details view paper
  • Downloaded 4,286 times
  • Download rankings, all-time:
    • Site-wide: 2,310
    • In bioinformatics: 207
  • Year to date:
    • Site-wide: 7,802
  • Since beginning of last month:
    • Site-wide: 6,799

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

genomics more details view paper
  • Downloaded 3,985 times
  • Download rankings, all-time:
    • Site-wide: 2,556
    • In genomics: 297
  • Year to date:
    • Site-wide: 17,937
  • Since beginning of last month:
    • Site-wide: 17,974

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

bioengineering more details view paper
  • Downloaded 3,663 times
  • Download rankings, all-time:
    • Site-wide: 2,908
    • In bioengineering: 27
  • Year to date:
    • Site-wide: 21,926
  • Since beginning of last month:
    • Site-wide: 15,269

A direct comparison of genome alignment and transcriptome pseudoalignment

bioinformatics more details view paper
  • Downloaded 3,357 times
  • Download rankings, all-time:
    • Site-wide: 3,300
    • In bioinformatics: 342
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

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

neuroscience more details view paper
  • Downloaded 3,265 times
  • Download rankings, all-time:
    • Site-wide: 3,442
    • In neuroscience: 280
  • Year to date:
    • Site-wide: 1,475
  • Since beginning of last month:
    • Site-wide: 1,840

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

genomics more details view paper
  • Downloaded 3,217 times
  • Download rankings, all-time:
    • Site-wide: 3,510
    • In genomics: 399
  • Year to date:
    • Site-wide: 7,804
  • Since beginning of last month:
    • Site-wide: 7,769

Association Mapping From Sequencing Reads Using K-mers

bioinformatics more details view paper
  • Downloaded 2,960 times
  • Download rankings, all-time:
    • Site-wide: 3,923
    • In bioinformatics: 416
  • Year to date:
    • Site-wide: 72,108
  • Since beginning of last month:
    • Site-wide: 66,469

RNA velocity and protein acceleration from single-cell multiomics experiments

bioinformatics more details view paper
  • Downloaded 2,768 times
  • Download rankings, all-time:
    • Site-wide: 4,307
    • In bioinformatics: 471
  • Year to date:
    • Site-wide: 36,360
  • Since beginning of last month:
    • Site-wide: 56,149

Fusion detection and quantification by pseudoalignment

bioinformatics more details view paper
  • Downloaded 2,712 times
  • Download rankings, all-time:
    • Site-wide: 4,449
    • In bioinformatics: 489
  • Year to date:
    • Site-wide: 23,320
  • Since beginning of last month:
    • Site-wide: 26,057

Barcode identification for single cell genomics

bioinformatics more details view paper
  • Downloaded 2,489 times
  • Download rankings, all-time:
    • Site-wide: 5,073
    • In bioinformatics: 566
  • Year to date:
    • Site-wide: 62,548
  • Since beginning of last month:
    • Site-wide: 83,521

The Barcode, UMI, Set format and BUStools

bioinformatics more details view paper
  • Downloaded 2,365 times
  • Download rankings, all-time:
    • Site-wide: 5,468
    • In bioinformatics: 632
  • Year to date:
    • Site-wide: 27,270
  • Since beginning of last month:
    • Site-wide: 33,725

Gene-level differential analysis at transcript-level resolution

bioinformatics more details view paper
  • Downloaded 2,317 times
  • Download rankings, all-time:
    • Site-wide: 5,637
    • In bioinformatics: 656
  • Year to date:
    • Site-wide: 27,856
  • Since beginning of last month:
    • Site-wide: 19,205

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

bioinformatics more details view paper
  • Downloaded 1,827 times
  • Download rankings, all-time:
    • Site-wide: 7,964
    • In bioinformatics: 980
  • Year to date:
    • Site-wide: 17,018
  • Since beginning of last month:
    • Site-wide: 12,667

Isoform cell type specificity in the mouse primary motor cortex

neuroscience more details view paper
  • Downloaded 1,797 times
  • Download rankings, all-time:
    • Site-wide: 8,178
    • In neuroscience: 861
  • Year to date:
    • Site-wide: 16,447
  • Since beginning of last month:
    • Site-wide: 30,419

Decrease in ACE2 mRNA expression in aged mouse lung

molecular biology more details view paper
  • Downloaded 1,728 times
  • Download rankings, all-time:
    • Site-wide: 8,697
    • In molecular biology: 226
  • Year to date:
    • Site-wide: 36,886
  • Since beginning of last month:
    • Site-wide: 24,699

Fast and accurate diagnostics from highly multiplexed sequencing assays

health informatics more details view paper
  • Downloaded 1,365 times
  • Download rankings, all-time:
    • Site-wide: 12,332
    • In health informatics: 55
  • Year to date:
    • Site-wide: 66,926
  • Since beginning of last month:
    • Site-wide: 75,660

Expression reflects population structure

genomics more details view paper
  • Downloaded 1,311 times
  • Download rankings, all-time:
    • Site-wide: 13,114
    • In genomics: 1,432
  • Year to date:
    • Site-wide: 120,054
  • Since beginning of last month:
    • Site-wide: None

SWALO: scaffolding with assembly likelihood optimization

bioinformatics more details view paper
  • Downloaded 1,261 times
  • Download rankings, all-time:
    • Site-wide: 13,905
    • In bioinformatics: 1,717
  • Year to date:
    • Site-wide: 60,745
  • Since beginning of last month:
    • Site-wide: 106,044

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

bioinformatics more details view paper
  • Downloaded 1,245 times
  • Download rankings, all-time:
    • Site-wide: 14,168
    • In bioinformatics: 1,746
  • Year to date:
    • Site-wide: 73,213
  • Since beginning of last month:
    • Site-wide: 46,557

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

systems biology more details view paper
  • Downloaded 1,238 times
  • Download rankings, all-time:
    • Site-wide: 14,309
    • In systems biology: 289
  • Year to date:
    • Site-wide: 411
  • Since beginning of last month:
    • Site-wide: 718

Column subset selection for single-cell RNA-Seq clustering

bioinformatics more details view paper
  • Downloaded 1,162 times
  • Download rankings, all-time:
    • Site-wide: 15,749
    • In bioinformatics: 1,928
  • Year to date:
    • Site-wide: 55,506
  • Since beginning of last month:
    • Site-wide: 83,564

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

bioinformatics more details view paper
  • Downloaded 1,062 times
  • Download rankings, all-time:
    • Site-wide: 18,011
    • In bioinformatics: 2,179
  • Year to date:
    • Site-wide: 112,953
  • Since beginning of last month:
    • Site-wide: 83,321

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

genomics more details view paper
  • Downloaded 988 times
  • Download rankings, all-time:
    • Site-wide: 20,033
    • In genomics: 2,030
  • Year to date:
    • Site-wide: 117,193
  • Since beginning of last month:
    • Site-wide: None

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

genomics more details view paper
  • Downloaded 875 times
  • Download rankings, all-time:
    • Site-wide: 23,880
    • In genomics: 2,321
  • Year to date:
    • Site-wide: 121,491
  • Since beginning of last month:
    • Site-wide: 104,619

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

bioinformatics more details view paper
  • Downloaded 725 times
  • Download rankings, all-time:
    • Site-wide: 31,026
    • In bioinformatics: 3,517
  • Year to date:
    • Site-wide: 759
  • Since beginning of last month:
    • Site-wide: 1,957

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

bioinformatics more details view paper
  • Downloaded 681 times
  • Download rankings, all-time:
    • Site-wide: 33,756
    • In bioinformatics: 3,817
  • Year to date:
    • Site-wide: 28,570
  • Since beginning of last month:
    • Site-wide: 25,119

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

bioengineering more details view paper
  • Downloaded 626 times
  • Download rankings, all-time:
    • Site-wide: 37,775
    • In bioengineering: 671
  • Year to date:
    • Site-wide: 933
  • Since beginning of last month:
    • Site-wide: 1,677

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

biophysics more details view paper
  • Downloaded 432 times
  • Download rankings, all-time:
    • Site-wide: 58,258
    • In biophysics: 2,062
  • Year to date:
    • Site-wide: 1,587
  • Since beginning of last month:
    • Site-wide: 3,606

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 380 times
  • Download rankings, all-time:
    • Site-wide: 66,317
    • In developmental biology: 1,707
  • Year to date:
    • Site-wide: 114,774
  • Since beginning of last month:
    • Site-wide: 95,991

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

biophysics more details view paper
  • Downloaded 296 times
  • Download rankings, all-time:
    • Site-wide: 81,389
    • In biophysics: 3,111
  • Year to date:
    • Site-wide: 46,966
  • Since beginning of last month:
    • Site-wide: 30,184

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