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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 62,292 bioRxiv papers from 276,522 authors.

Author: Lior Pachter

  • ORCiD: http://orcid.org/0000-0002-9164-6231
  • Most recently observed institution: Division of Biology and Biological Engineering & Department of Computing and Mathematical Sciences, California Institute of Technology

Rankings

  • All-time downloads: 63,177 (rank: 187 out of 276,522)
  • Categories:
    • bioengineering: 2,984 (rank: 149 (tie) out of 6,803)
    • bioinformatics: 38,916 (rank: 46 out of 24,276)
    • genomics: 21,277 (rank: 308 out of 31,837)

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 8,314 times
  • Download rankings, all-time:
    • Site-wide: 148 out of 62,292
    • In genomics: 47 out of 4,282
  • Year to date:
    • Site-wide: 328 out of 62,292
  • Since beginning of last month:
    • Site-wide: 967 out of 62,292

Differential analysis of RNA-Seq incorporating quantification uncertainty

bioinformatics more details view paper
  • Downloaded 7,624 times
  • Download rankings, all-time:
    • Site-wide: 175 out of 62,292
    • In bioinformatics: 30 out of 6,225
  • Year to date:
    • Site-wide: 2,126 out of 62,292
  • Since beginning of last month:
    • Site-wide: 3,583 out of 62,292

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

bioinformatics more details view paper
  • Downloaded 5,974 times
  • Download rankings, all-time:
    • Site-wide: 293 out of 62,292
    • In bioinformatics: 52 out of 6,225
  • Year to date:
    • Site-wide: 864 out of 62,292
  • Since beginning of last month:
    • Site-wide: 2,503 out of 62,292

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

genomics more details view paper
  • Downloaded 4,850 times
  • Download rankings, all-time:
    • Site-wide: 414 out of 62,292
    • In genomics: 110 out of 4,282
  • Year to date:
    • Site-wide: 9,355 out of 62,292
  • Since beginning of last month:
    • Site-wide: 23,407 out of 62,292

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

bioinformatics more details view paper
  • Downloaded 4,121 times
  • Download rankings, all-time:
    • Site-wide: 586 out of 62,292
    • In bioinformatics: 117 out of 6,225
  • Year to date:
    • Site-wide: 95 out of 62,292
  • Since beginning of last month:
    • Site-wide: 42 out of 62,292

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

genomics more details view paper
  • Downloaded 3,454 times
  • Download rankings, all-time:
    • Site-wide: 820 out of 62,292
    • In genomics: 211 out of 4,282
  • Year to date:
    • Site-wide: 13,090 out of 62,292
  • Since beginning of last month:
    • Site-wide: None out of 62,292

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

bioengineering more details view paper
  • Downloaded 2,984 times
  • Download rankings, all-time:
    • Site-wide: 1,072 out of 62,292
    • In bioengineering: 15 out of 1,235
  • Year to date:
    • Site-wide: 174 out of 62,292
  • Since beginning of last month:
    • Site-wide: 1,603 out of 62,292

Association Mapping From Sequencing Reads Using K-mers

bioinformatics more details view paper
  • Downloaded 2,731 times
  • Download rankings, all-time:
    • Site-wide: 1,269 out of 62,292
    • In bioinformatics: 261 out of 6,225
  • Year to date:
    • Site-wide: 14,178 out of 62,292
  • Since beginning of last month:
    • Site-wide: 23,133 out of 62,292

Barcode identification for single cell genomics

bioinformatics more details view paper
  • Downloaded 2,203 times
  • Download rankings, all-time:
    • Site-wide: 1,842 out of 62,292
    • In bioinformatics: 379 out of 6,225
  • Year to date:
    • Site-wide: 8,624 out of 62,292
  • Since beginning of last month:
    • Site-wide: 21,913 out of 62,292

RNA velocity and protein acceleration from single-cell multiomics experiments

bioinformatics more details view paper
  • Downloaded 2,099 times
  • Download rankings, all-time:
    • Site-wide: 2,017 out of 62,292
    • In bioinformatics: 415 out of 6,225
  • Year to date:
    • Site-wide: 338 out of 62,292
  • Since beginning of last month:
    • Site-wide: 1,562 out of 62,292

Gene-level differential analysis at transcript-level resolution

bioinformatics more details view paper
  • Downloaded 2,027 times
  • Download rankings, all-time:
    • Site-wide: 2,152 out of 62,292
    • In bioinformatics: 445 out of 6,225
  • Year to date:
    • Site-wide: 17,515 out of 62,292
  • Since beginning of last month:
    • Site-wide: 25,797 out of 62,292

Fusion detection and quantification by pseudoalignment

bioinformatics more details view paper
  • Downloaded 1,958 times
  • Download rankings, all-time:
    • Site-wide: 2,294 out of 62,292
    • In bioinformatics: 476 out of 6,225
  • Year to date:
    • Site-wide: 4,084 out of 62,292
  • Since beginning of last month:
    • Site-wide: 5,876 out of 62,292

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

bioinformatics more details view paper
  • Downloaded 1,887 times
  • Download rankings, all-time:
    • Site-wide: 2,431 out of 62,292
    • In bioinformatics: 498 out of 6,225
  • Year to date:
    • Site-wide: 429 out of 62,292
  • Since beginning of last month:
    • Site-wide: 276 out of 62,292

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

genomics more details view paper
  • Downloaded 1,823 times
  • Download rankings, all-time:
    • Site-wide: 2,578 out of 62,292
    • In genomics: 528 out of 4,282
  • Year to date:
    • Site-wide: 453 out of 62,292
  • Since beginning of last month:
    • Site-wide: 12 out of 62,292

The Barcode, UMI, Set format and BUStools

bioinformatics more details view paper
  • Downloaded 1,762 times
  • Download rankings, all-time:
    • Site-wide: 2,740 out of 62,292
    • In bioinformatics: 558 out of 6,225
  • Year to date:
    • Site-wide: 1,826 out of 62,292
  • Since beginning of last month:
    • Site-wide: 6,615 out of 62,292

A direct comparison of genome alignment and transcriptome pseudoalignment

bioinformatics more details view paper
  • Downloaded 1,401 times
  • Download rankings, all-time:
    • Site-wide: 4,020 out of 62,292
    • In bioinformatics: 804 out of 6,225
  • Year to date:
    • Site-wide: 2,447 out of 62,292
  • Since beginning of last month:
    • Site-wide: 1,013 out of 62,292

Expression reflects population structure

genomics more details view paper
  • Downloaded 1,176 times
  • Download rankings, all-time:
    • Site-wide: 5,332 out of 62,292
    • In genomics: 915 out of 4,282
  • Year to date:
    • Site-wide: 35,184 out of 62,292
  • Since beginning of last month:
    • Site-wide: 46,136 out of 62,292

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways

bioinformatics more details view paper
  • Downloaded 1,115 times
  • Download rankings, all-time:
    • Site-wide: 5,827 out of 62,292
    • In bioinformatics: 1,117 out of 6,225
  • Year to date:
    • Site-wide: 48,172 out of 62,292
  • Since beginning of last month:
    • Site-wide: 40,786 out of 62,292

SWALO: scaffolding with assembly likelihood optimization

bioinformatics more details view paper
  • Downloaded 1,071 times
  • Download rankings, all-time:
    • Site-wide: 6,258 out of 62,292
    • In bioinformatics: 1,183 out of 6,225
  • Year to date:
    • Site-wide: 40,672 out of 62,292
  • Since beginning of last month:
    • Site-wide: 35,855 out of 62,292

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

bioinformatics more details view paper
  • Downloaded 1,022 times
  • Download rankings, all-time:
    • Site-wide: 6,740 out of 62,292
    • In bioinformatics: 1,242 out of 6,225
  • Year to date:
    • Site-wide: 1,342 out of 62,292
  • Since beginning of last month:
    • Site-wide: 4,543 out of 62,292

Column subset selection for single-cell RNA-Seq clustering

bioinformatics more details view paper
  • Downloaded 977 times
  • Download rankings, all-time:
    • Site-wide: 7,216 out of 62,292
    • In bioinformatics: 1,320 out of 6,225
  • Year to date:
    • Site-wide: 45,243 out of 62,292
  • Since beginning of last month:
    • Site-wide: 42,822 out of 62,292

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

bioinformatics more details view paper
  • Downloaded 944 times
  • Download rankings, all-time:
    • Site-wide: 7,614 out of 62,292
    • In bioinformatics: 1,362 out of 6,225
  • Year to date:
    • Site-wide: 54,873 out of 62,292
  • Since beginning of last month:
    • Site-wide: 43,920 out of 62,292

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

genomics more details view paper
  • Downloaded 863 times
  • Download rankings, all-time:
    • Site-wide: 8,799 out of 62,292
    • In genomics: 1,349 out of 4,282
  • Year to date:
    • Site-wide: 50,355 out of 62,292
  • Since beginning of last month:
    • Site-wide: 45,202 out of 62,292

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

genomics more details view paper
  • Downloaded 797 times
  • Download rankings, all-time:
    • Site-wide: 9,941 out of 62,292
    • In genomics: 1,466 out of 4,282
  • Year to date:
    • Site-wide: 54,249 out of 62,292
  • Since beginning of last month:
    • Site-wide: None out of 62,292

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