Rxivist logo

Author: Lior Pachter

Rankings

  • All-time downloads: 156,825 (rank: 655 )
  • Categories:
    • bioengineering: 4,839 (rank: 303 (tie) )
    • bioinformatics: 70,516 (rank: 17 )
    • biophysics: 2,824 (rank: 1,476 )
    • developmental biology: 430 (rank: 13,340 (tie) )
    • evolutionary biology: 473 (rank: 16,162 (tie) )
    • genomics: 45,799 (rank: 240 )
    • health informatics: 1,466 (rank: 655 (tie) )
    • health policy: 6,523 (rank: 84 (tie) )
    • infectious diseases: 5,748 (rank: 9,008 (tie) )
    • molecular biology: 1,864 (rank: 3,261 (tie) )
    • neuroscience: 14,038 (rank: 849 (tie) )
    • systems biology: 2,305 (rank: 2,022 (tie) )

Downloads per author, site-wide

Preprints

The Specious Art of Single-Cell Genomics

genomics more details view paper
  • Downloaded 13,869 times
  • Download rankings, all-time:
    • Site-wide: 682
    • In genomics: 35
  • Year to date:
    • Site-wide: 191
  • Since beginning of last month:
    • Site-wide: 57

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

genomics more details view paper
  • Downloaded 10,812 times
  • Download rankings, all-time:
    • Site-wide: 951
    • In genomics: 64
  • Year to date:
    • Site-wide: 9,619
  • Since beginning of last month:
    • Site-wide: 11,642

Differential analysis of RNA-Seq incorporating quantification uncertainty

bioinformatics more details view paper
  • Downloaded 9,356 times
  • Download rankings, all-time:
    • Site-wide: 1,144
    • In bioinformatics: 54
  • Year to date:
    • Site-wide: 10,533
  • Since beginning of last month:
    • Site-wide: 26,729

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

bioinformatics more details view paper
  • Downloaded 8,567 times
  • Download rankings, all-time:
    • Site-wide: 1,279
    • In bioinformatics: 68
  • Year to date:
    • Site-wide: 3,625
  • Since beginning of last month:
    • Site-wide: 11,134

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

bioinformatics more details view paper
  • Downloaded 7,731 times
  • Download rankings, all-time:
    • Site-wide: 1,448
    • In bioinformatics: 82
  • Year to date:
    • Site-wide: 11,533
  • Since beginning of last month:
    • Site-wide: 22,234

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

neuroscience more details view paper
  • Downloaded 6,723 times
  • Download rankings, all-time:
    • Site-wide: 1,721
    • In neuroscience: 81
  • Year to date:
    • Site-wide: 1,370
  • Since beginning of last month:
    • Site-wide: 1,912

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

health policy more details view paper
  • Downloaded 6,523 times
  • Download rankings, all-time:
    • Site-wide: 1,793
    • In health policy: 12
  • Year to date:
    • Site-wide: 5,914
  • Since beginning of last month:
    • Site-wide: 8,007

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

infectious diseases more details view paper
  • Downloaded 5,748 times
  • Download rankings, all-time:
    • Site-wide: 2,146
    • In infectious diseases: 561
  • Year to date:
    • Site-wide: 2,956
  • Since beginning of last month:
    • Site-wide: 6,952

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

genomics more details view paper
  • Downloaded 5,221 times
  • Download rankings, all-time:
    • Site-wide: 2,417
    • In genomics: 212
  • Year to date:
    • Site-wide: 69,106
  • Since beginning of last month:
    • Site-wide: 127,572

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

bioinformatics more details view paper
  • Downloaded 4,962 times
  • Download rankings, all-time:
    • Site-wide: 2,608
    • In bioinformatics: 201
  • Year to date:
    • Site-wide: 5,955
  • Since beginning of last month:
    • Site-wide: 32,667

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

neuroscience more details view paper
  • Downloaded 4,850 times
  • Download rankings, all-time:
    • Site-wide: 2,690
    • In neuroscience: 157
  • Year to date:
    • Site-wide: 1,679
  • Since beginning of last month:
    • Site-wide: 1,396

A curated database reveals trends in single-cell transcriptomics

genomics more details view paper
  • Downloaded 4,847 times
  • Download rankings, all-time:
    • Site-wide: 2,693
    • In genomics: 256
  • Year to date:
    • Site-wide: 14,008
  • Since beginning of last month:
    • Site-wide: 25,063

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

bioinformatics more details view paper
  • Downloaded 4,731 times
  • Download rankings, all-time:
    • Site-wide: 2,782
    • In bioinformatics: 217
  • Year to date:
    • Site-wide: 10,158
  • Since beginning of last month:
    • Site-wide: 13,785

A direct comparison of genome alignment and transcriptome pseudoalignment

bioinformatics more details view paper
  • Downloaded 4,323 times
  • Download rankings, all-time:
    • Site-wide: 3,162
    • In bioinformatics: 256
  • Year to date:
    • Site-wide: 4,744
  • Since beginning of last month:
    • Site-wide: 6,666

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

genomics more details view paper
  • Downloaded 4,150 times
  • Download rankings, all-time:
    • Site-wide: 3,334
    • In genomics: 327
  • Year to date:
    • Site-wide: 37,080
  • Since beginning of last month:
    • Site-wide: 34,748

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

bioengineering more details view paper
  • Downloaded 3,868 times
  • Download rankings, all-time:
    • Site-wide: 3,677
    • In bioengineering: 37
  • Year to date:
    • Site-wide: 31,904
  • Since beginning of last month:
    • Site-wide: 33,405

Museum of Spatial Transcriptomics

bioinformatics more details view paper
  • Downloaded 3,764 times
  • Download rankings, all-time:
    • Site-wide: 3,817
    • In bioinformatics: 343
  • Year to date:
    • Site-wide: 773
  • Since beginning of last month:
    • Site-wide: 2,094

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

genomics more details view paper
  • Downloaded 3,633 times
  • Download rankings, all-time:
    • Site-wide: 4,012
    • In genomics: 399
  • Year to date:
    • Site-wide: 10,972
  • Since beginning of last month:
    • Site-wide: 24,474

Association Mapping From Sequencing Reads Using K-mers

bioinformatics more details view paper
  • Downloaded 2,999 times
  • Download rankings, all-time:
    • Site-wide: 5,254
    • In bioinformatics: 504
  • Year to date:
    • Site-wide: 130,614
  • Since beginning of last month:
    • Site-wide: 126,177

Fusion detection and quantification by pseudoalignment

bioinformatics more details view paper
  • Downloaded 2,975 times
  • Download rankings, all-time:
    • Site-wide: 5,316
    • In bioinformatics: 513
  • Year to date:
    • Site-wide: 24,816
  • Since beginning of last month:
    • Site-wide: 28,597

RNA velocity and protein acceleration from single-cell multiomics experiments

bioinformatics more details view paper
  • Downloaded 2,834 times
  • Download rankings, all-time:
    • Site-wide: 5,712
    • In bioinformatics: 558
  • Year to date:
    • Site-wide: 87,686
  • Since beginning of last month:
    • Site-wide: 144,570

The Barcode, UMI, Set format and BUStools

bioinformatics more details view paper
  • Downloaded 2,585 times
  • Download rankings, all-time:
    • Site-wide: 6,530
    • In bioinformatics: 679
  • Year to date:
    • Site-wide: 31,426
  • Since beginning of last month:
    • Site-wide: 48,661

Barcode identification for single cell genomics

bioinformatics more details view paper
  • Downloaded 2,541 times
  • Download rankings, all-time:
    • Site-wide: 6,699
    • In bioinformatics: 704
  • Year to date:
    • Site-wide: 113,341
  • Since beginning of last month:
    • Site-wide: 142,818

Isoform cell type specificity in the mouse primary motor cortex

neuroscience more details view paper
  • Downloaded 2,465 times
  • Download rankings, all-time:
    • Site-wide: 7,016
    • In neuroscience: 629
  • Year to date:
    • Site-wide: 7,043
  • Since beginning of last month:
    • Site-wide: 6,757

Gene-level differential analysis at transcript-level resolution

bioinformatics more details view paper
  • Downloaded 2,416 times
  • Download rankings, all-time:
    • Site-wide: 7,211
    • In bioinformatics: 778
  • Year to date:
    • Site-wide: 63,378
  • Since beginning of last month:
    • Site-wide: 133,845

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

systems biology more details view paper
  • Downloaded 2,305 times
  • Download rankings, all-time:
    • Site-wide: 7,733
    • In systems biology: 125
  • Year to date:
    • Site-wide: 1,435
  • Since beginning of last month:
    • Site-wide: 4,317

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

bioinformatics more details view paper
  • Downloaded 2,061 times
  • Download rankings, all-time:
    • Site-wide: 9,078
    • In bioinformatics: 1,014
  • Year to date:
    • Site-wide: 25,998
  • Since beginning of last month:
    • Site-wide: 54,455

Decrease in ACE2 mRNA expression in aged mouse lung

molecular biology more details view paper
  • Downloaded 1,864 times
  • Download rankings, all-time:
    • Site-wide: 10,525
    • In molecular biology: 274
  • Year to date:
    • Site-wide: 53,758
  • Since beginning of last month:
    • Site-wide: 62,779

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

bioinformatics more details view paper
  • Downloaded 1,765 times
  • Download rankings, all-time:
    • Site-wide: 11,421
    • In bioinformatics: 1,285
  • Year to date:
    • Site-wide: 2,016
  • Since beginning of last month:
    • Site-wide: 3,894

Fast and accurate diagnostics from highly multiplexed sequencing assays

health informatics more details view paper
  • Downloaded 1,466 times
  • Download rankings, all-time:
    • Site-wide: 15,097
    • In health informatics: 73
  • Year to date:
    • Site-wide: 77,170
  • Since beginning of last month:
    • Site-wide: 130,462

Expression reflects population structure

genomics more details view paper
  • Downloaded 1,338 times
  • Download rankings, all-time:
    • Site-wide: 17,339
    • In genomics: 1,685
  • Year to date:
    • Site-wide: 155,210
  • Since beginning of last month:
    • Site-wide: 153,898

SWALO: scaffolding with assembly likelihood optimization

bioinformatics more details view paper
  • Downloaded 1,323 times
  • Download rankings, all-time:
    • Site-wide: 17,631
    • In bioinformatics: 2,002
  • Year to date:
    • Site-wide: 103,107
  • Since beginning of last month:
    • Site-wide: 117,126

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

bioinformatics more details view paper
  • Downloaded 1,291 times
  • Download rankings, all-time:
    • Site-wide: 18,276
    • In bioinformatics: 2,065
  • Year to date:
    • Site-wide: 123,624
  • Since beginning of last month:
    • Site-wide: 156,139

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

bioinformatics more details view paper
  • Downloaded 1,234 times
  • Download rankings, all-time:
    • Site-wide: 19,547
    • In bioinformatics: 2,211
  • Year to date:
    • Site-wide: 3,320
  • Since beginning of last month:
    • Site-wide: 30,436

Column subset selection for single-cell RNA-Seq clustering

bioinformatics more details view paper
  • Downloaded 1,208 times
  • Download rankings, all-time:
    • Site-wide: 20,172
    • In bioinformatics: 2,300
  • Year to date:
    • Site-wide: 116,199
  • Since beginning of last month:
    • Site-wide: 126,201

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

bioinformatics more details view paper
  • Downloaded 1,083 times
  • Download rankings, all-time:
    • Site-wide: 23,688
    • In bioinformatics: 2,688
  • Year to date:
    • Site-wide: 157,757
  • Since beginning of last month:
    • Site-wide: 158,059

Length Biases in Single-Cell RNA Sequencing of pre-mRNA

biophysics more details view paper
  • Downloaded 1,055 times
  • Download rankings, all-time:
    • Site-wide: 24,685
    • In biophysics: 661
  • Year to date:
    • Site-wide: 4,139
  • Since beginning of last month:
    • Site-wide: 8,535

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

genomics more details view paper
  • Downloaded 1,035 times
  • Download rankings, all-time:
    • Site-wide: 25,401
    • In genomics: 2,335
  • Year to date:
    • Site-wide: 133,410
  • Since beginning of last month:
    • Site-wide: 157,791

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

bioengineering more details view paper
  • Downloaded 971 times
  • Download rankings, all-time:
    • Site-wide: 27,923
    • In bioengineering: 486
  • Year to date:
    • Site-wide: 4,706
  • Since beginning of last month:
    • Site-wide: 18,883

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

genomics more details view paper
  • Downloaded 894 times
  • Download rankings, all-time:
    • Site-wide: 31,376
    • In genomics: 2,706
  • Year to date:
    • Site-wide: 159,268
  • Since beginning of last month:
    • Site-wide: 151,704

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

bioinformatics more details view paper
  • Downloaded 767 times
  • Download rankings, all-time:
    • Site-wide: 38,998
    • In bioinformatics: 4,173
  • Year to date:
    • Site-wide: 69,942
  • Since beginning of last month:
    • Site-wide: 104,740

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

biophysics more details view paper
  • Downloaded 710 times
  • Download rankings, all-time:
    • Site-wide: 43,429
    • In biophysics: 1,403
  • Year to date:
    • Site-wide: 7,544
  • Since beginning of last month:
    • Site-wide: 17,530

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 473 times
  • Download rankings, all-time:
    • Site-wide: 71,670
    • In evolutionary biology: 3,613
  • Year to date:
    • Site-wide: 13,821
  • Since beginning of last month:
    • Site-wide: 37,469

Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments

biophysics more details view paper
  • Downloaded 432 times
  • Download rankings, all-time:
    • Site-wide: 78,704
    • In biophysics: 2,880
  • Year to date:
    • Site-wide: 15,888
  • Since beginning of last month:
    • Site-wide: 1,146

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 430 times
  • Download rankings, all-time:
    • Site-wide: 79,036
    • In developmental biology: 2,040
  • Year to date:
    • Site-wide: 130,733
  • Since beginning of last month:
    • Site-wide: 120,736

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

biophysics more details view paper
  • Downloaded 372 times
  • Download rankings, all-time:
    • Site-wide: 90,674
    • In biophysics: 3,375
  • Year to date:
    • Site-wide: 87,247
  • Since beginning of last month:
    • Site-wide: 88,082

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

biophysics more details view paper
  • Downloaded 255 times
  • Download rankings, all-time:
    • Site-wide: 119,213
    • In biophysics: 4,580
  • Year to date:
    • Site-wide: 33,477
  • Since beginning of last month:
    • Site-wide: 42,754

PanLingua

News