Rxivist logo

Author: Carl Kingsford

Rankings

  • All-time downloads: 46,548 (rank: 739 out of 365,919)
  • Categories:
    • bioinformatics: 41,909 (rank: 60 out of 31,540)
    • genomics: 4,210 (rank: 4,301 out of 39,354)
    • microbiology: 429 (rank: 17,847 (tie) out of 40,398)

Downloads per author, site-wide

Preprints

Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

bioinformatics more details view paper
  • Downloaded 21,413 times
  • Download rankings, all-time:
    • Site-wide: 61 out of 85,056
    • In bioinformatics: 5 out of 8,141
  • Year to date:
    • Site-wide: 498 out of 85,056
  • Since beginning of last month:
    • Site-wide: 1,190 out of 85,056

Alignment and mapping methodology influence transcript abundance estimation

bioinformatics more details view paper
  • Downloaded 3,997 times
  • Download rankings, all-time:
    • Site-wide: 1,040 out of 85,056
    • In bioinformatics: 184 out of 8,141
  • Year to date:
    • Site-wide: 725 out of 85,056
  • Since beginning of last month:
    • Site-wide: 1,113 out of 85,056

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

bioinformatics more details view paper
  • Downloaded 1,891 times
  • Download rankings, all-time:
    • Site-wide: 3,770 out of 85,056
    • In bioinformatics: 692 out of 8,141
  • Year to date:
    • Site-wide: 65,874 out of 85,056
  • Since beginning of last month:
    • Site-wide: 54,785 out of 85,056

SQUID: Transcriptomic Structural Variation Detection from RNA-seq

bioinformatics more details view paper
  • Downloaded 1,736 times
  • Download rankings, all-time:
    • Site-wide: 4,352 out of 85,056
    • In bioinformatics: 821 out of 8,141
  • Year to date:
    • Site-wide: 39,813 out of 85,056
  • Since beginning of last month:
    • Site-wide: 56,619 out of 85,056

Scallop Enables Accurate Assembly Of Transcripts Through Phasing-Preserving Graph Decomposition

bioinformatics more details view paper
  • Downloaded 1,422 times
  • Download rankings, all-time:
    • Site-wide: 6,024 out of 85,056
    • In bioinformatics: 1,082 out of 8,141
  • Year to date:
    • Site-wide: 46,645 out of 85,056
  • Since beginning of last month:
    • Site-wide: 66,102 out of 85,056

Locality sensitive hashing for the edit distance

bioinformatics more details view paper
  • Downloaded 1,326 times
  • Download rankings, all-time:
    • Site-wide: 6,794 out of 85,056
    • In bioinformatics: 1,215 out of 8,141
  • Year to date:
    • Site-wide: 11,171 out of 85,056
  • Since beginning of last month:
    • Site-wide: 13,896 out of 85,056

Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

bioinformatics more details view paper
  • Downloaded 1,182 times
  • Download rankings, all-time:
    • Site-wide: 8,237 out of 85,056
    • In bioinformatics: 1,413 out of 8,141
  • Year to date:
    • Site-wide: 67,938 out of 85,056
  • Since beginning of last month:
    • Site-wide: 66,916 out of 85,056

Topological data analysis reveals principles of chromosome structure throughout cellular differentiation

genomics more details view paper
  • Downloaded 1,152 times
  • Download rankings, all-time:
    • Site-wide: 8,604 out of 85,056
    • In genomics: 1,295 out of 5,477
  • Year to date:
    • Site-wide: 8,657 out of 85,056
  • Since beginning of last month:
    • Site-wide: 9,686 out of 85,056

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

genomics more details view paper
  • Downloaded 1,103 times
  • Download rankings, all-time:
    • Site-wide: 9,221 out of 85,056
    • In genomics: 1,375 out of 5,477
  • Year to date:
    • Site-wide: 75,128 out of 85,056
  • Since beginning of last month:
    • Site-wide: 53,527 out of 85,056

Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

genomics more details view paper
  • Downloaded 936 times
  • Download rankings, all-time:
    • Site-wide: 12,009 out of 85,056
    • In genomics: 1,669 out of 5,477
  • Year to date:
    • Site-wide: 65,001 out of 85,056
  • Since beginning of last month:
    • Site-wide: 50,294 out of 85,056

Graph-Guided Assembly For Novel HLA Allele Discovery

bioinformatics more details view paper
  • Downloaded 863 times
  • Download rankings, all-time:
    • Site-wide: 13,628 out of 85,056
    • In bioinformatics: 2,160 out of 8,141
  • Year to date:
    • Site-wide: 54,734 out of 85,056
  • Since beginning of last month:
    • Site-wide: 45,089 out of 85,056

More accurate transcript assembly via parameter advising

bioinformatics more details view paper
  • Downloaded 796 times
  • Download rankings, all-time:
    • Site-wide: 15,406 out of 85,056
    • In bioinformatics: 2,384 out of 8,141
  • Year to date:
    • Site-wide: 24,516 out of 85,056
  • Since beginning of last month:
    • Site-wide: 28,391 out of 85,056

Analysis of the structural variability of topologically associated domains as revealed by Hi-C

genomics more details view paper
  • Downloaded 737 times
  • Download rankings, all-time:
    • Site-wide: 17,345 out of 85,056
    • In genomics: 2,150 out of 5,477
  • Year to date:
    • Site-wide: 45,354 out of 85,056
  • Since beginning of last month:
    • Site-wide: 48,052 out of 85,056

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines

bioinformatics more details view paper
  • Downloaded 720 times
  • Download rankings, all-time:
    • Site-wide: 17,966 out of 85,056
    • In bioinformatics: 2,706 out of 8,141
  • Year to date:
    • Site-wide: 80,468 out of 85,056
  • Since beginning of last month:
    • Site-wide: 74,940 out of 85,056

Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths

bioinformatics more details view paper
  • Downloaded 697 times
  • Download rankings, all-time:
    • Site-wide: 18,840 out of 85,056
    • In bioinformatics: 2,798 out of 8,141
  • Year to date:
    • Site-wide: 72,598 out of 85,056
  • Since beginning of last month:
    • Site-wide: 46,204 out of 85,056

Compression of short-read sequences using path encoding

bioinformatics more details view paper
  • Downloaded 675 times
  • Download rankings, all-time:
    • Site-wide: 19,712 out of 85,056
    • In bioinformatics: 2,907 out of 8,141
  • Year to date:
    • Site-wide: 80,147 out of 85,056
  • Since beginning of last month:
    • Site-wide: 81,893 out of 85,056

Improving the performance of minimizers and winnowing schemes

bioinformatics more details view paper
  • Downloaded 606 times
  • Download rankings, all-time:
    • Site-wide: 23,077 out of 85,056
    • In bioinformatics: 3,267 out of 8,141
  • Year to date:
    • Site-wide: 81,825 out of 85,056
  • Since beginning of last month:
    • Site-wide: 65,197 out of 85,056

Detecting anomalies in RNA-seq quantification

bioinformatics more details view paper
  • Downloaded 597 times
  • Download rankings, all-time:
    • Site-wide: 23,528 out of 85,056
    • In bioinformatics: 3,320 out of 8,141
  • Year to date:
    • Site-wide: 28,050 out of 85,056
  • Since beginning of last month:
    • Site-wide: 38,468 out of 85,056

Practical universal k-mer sets for minimizer schemes

bioinformatics more details view paper
  • Downloaded 592 times
  • Download rankings, all-time:
    • Site-wide: 23,842 out of 85,056
    • In bioinformatics: 3,342 out of 8,141
  • Year to date:
    • Site-wide: 20,508 out of 85,056
  • Since beginning of last month:
    • Site-wide: 19,934 out of 85,056

VariantStore: A Large-Scale Genomic Variant Search Index

bioinformatics more details view paper
  • Downloaded 542 times
  • Download rankings, all-time:
    • Site-wide: 26,736 out of 85,056
    • In bioinformatics: 3,637 out of 8,141
  • Year to date:
    • Site-wide: 7,716 out of 85,056
  • Since beginning of last month:
    • Site-wide: 6,124 out of 85,056

Asymptotically optimal minimizers schemes

bioinformatics more details view paper
  • Downloaded 488 times
  • Download rankings, all-time:
    • Site-wide: 30,437 out of 85,056
    • In bioinformatics: 3,977 out of 8,141
  • Year to date:
    • Site-wide: 73,713 out of 85,056
  • Since beginning of last month:
    • Site-wide: 78,424 out of 85,056

Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads

bioinformatics more details view paper
  • Downloaded 471 times
  • Download rankings, all-time:
    • Site-wide: 31,828 out of 85,056
    • In bioinformatics: 4,115 out of 8,141
  • Year to date:
    • Site-wide: 39,428 out of 85,056
  • Since beginning of last month:
    • Site-wide: 62,727 out of 85,056

Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head

microbiology more details view paper
  • Downloaded 429 times
  • Download rankings, all-time:
    • Site-wide: 35,542 out of 85,056
    • In microbiology: 2,368 out of 7,229
  • Year to date:
    • Site-wide: 36,386 out of 85,056
  • Since beginning of last month:
    • Site-wide: 34,708 out of 85,056

Improved design and analysis of practical minimizers

bioinformatics more details view paper
  • Downloaded 374 times
  • Download rankings, all-time:
    • Site-wide: 41,047 out of 85,056
    • In bioinformatics: 4,962 out of 8,141
  • Year to date:
    • Site-wide: 4,593 out of 85,056
  • Since beginning of last month:
    • Site-wide: 9,631 out of 85,056

Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming

bioinformatics more details view paper
  • Downloaded 352 times
  • Download rankings, all-time:
    • Site-wide: 43,599 out of 85,056
    • In bioinformatics: 5,173 out of 8,141
  • Year to date:
    • Site-wide: 36,421 out of 85,056
  • Since beginning of last month:
    • Site-wide: 47,540 out of 85,056

Context-Aware Seeds for Read Mapping

bioinformatics more details view paper
  • Downloaded 299 times
  • Download rankings, all-time:
    • Site-wide: 50,513 out of 85,056
    • In bioinformatics: 5,708 out of 8,141
  • Year to date:
    • Site-wide: 69,532 out of 85,056
  • Since beginning of last month:
    • Site-wide: 52,437 out of 85,056

A statistical nonparametric method for identifying consistently important features across samples

genomics more details view paper
  • Downloaded 282 times
  • Download rankings, all-time:
    • Site-wide: 53,025 out of 85,056
    • In genomics: 4,330 out of 5,477
  • Year to date:
    • Site-wide: 22,785 out of 85,056
  • Since beginning of last month:
    • Site-wide: 47,986 out of 85,056

Finding ranges of optimal transcript expression quantification in cases of non-identifiability

bioinformatics more details view paper
  • Downloaded 252 times
  • Download rankings, all-time:
    • Site-wide: 57,410 out of 85,056
    • In bioinformatics: 6,209 out of 8,141
  • Year to date:
    • Site-wide: 22,819 out of 85,056
  • Since beginning of last month:
    • Site-wide: 46,730 out of 85,056

Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem

bioinformatics more details view paper
  • Downloaded 228 times
  • Download rankings, all-time:
    • Site-wide: 61,211 out of 85,056
    • In bioinformatics: 6,466 out of 8,141
  • Year to date:
    • Site-wide: 60,045 out of 85,056
  • Since beginning of last month:
    • Site-wide: 33,806 out of 85,056

Estimating mutual information under measurement error

bioinformatics more details view paper
  • Downloaded 218 times
  • Download rankings, all-time:
    • Site-wide: 63,015 out of 85,056
    • In bioinformatics: 6,598 out of 8,141
  • Year to date:
    • Site-wide: 34,312 out of 85,056
  • Since beginning of last month:
    • Site-wide: 37,933 out of 85,056

HARVESTMAN: A framework for hierarchical feature learning and selection from whole genome sequencing data

bioinformatics more details view paper
  • Downloaded 172 times
  • Download rankings, all-time:
    • Site-wide: 70,529 out of 85,056
    • In bioinformatics: 7,140 out of 8,141
  • Year to date:
    • Site-wide: 15,088 out of 85,056
  • Since beginning of last month:
    • Site-wide: 19,537 out of 85,056

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News