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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 65,353 bioRxiv papers from 289,502 authors.

Author: Anshul Kundaje

Rankings

  • All-time downloads: 101,168 (rank: 67 out of 289,502)
  • Categories:
    • bioinformatics: 68,835 (rank: 5 out of 25,220)
    • genetics: 4,083 (rank: 3,214 out of 28,745)
    • genomics: 28,015 (rank: 201 out of 32,929)
    • molecular biology: 235 (rank: 8,845 (tie) out of 13,667)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 51,122 times
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    • Site-wide: 7 out of 65,353
    • In bioinformatics: 1 out of 6,477
  • Year to date:
    • Site-wide: 105 out of 65,353
  • Since beginning of last month:
    • Site-wide: 516 out of 65,353

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

genomics more details view paper
  • Downloaded 3,782 times
  • Download rankings, all-time:
    • Site-wide: 737 out of 65,353
    • In genomics: 189 out of 4,462
  • Year to date:
    • Site-wide: 4,063 out of 65,353
  • Since beginning of last month:
    • Site-wide: 14,063 out of 65,353

Transcriptome-wide association studies: opportunities and challenges

genetics more details view paper
  • Downloaded 3,568 times
  • Download rankings, all-time:
    • Site-wide: 822 out of 65,353
    • In genetics: 78 out of 3,698
  • Year to date:
    • Site-wide: 1,221 out of 65,353
  • Since beginning of last month:
    • Site-wide: 3,746 out of 65,353

Denoising genome-wide histone ChIP-seq with convolutional neural networks

bioinformatics more details view paper
  • Downloaded 3,141 times
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    • Site-wide: 1,038 out of 65,353
    • In bioinformatics: 212 out of 6,477
  • Year to date:
    • Site-wide: 16,174 out of 65,353
  • Since beginning of last month:
    • Site-wide: 19,279 out of 65,353

Reverse-complement parameter sharing improves deep learning models for genomics

bioinformatics more details view paper
  • Downloaded 2,929 times
  • Download rankings, all-time:
    • Site-wide: 1,207 out of 65,353
    • In bioinformatics: 242 out of 6,477
  • Year to date:
    • Site-wide: 3,718 out of 65,353
  • Since beginning of last month:
    • Site-wide: 5,147 out of 65,353

Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

genomics more details view paper
  • Downloaded 2,869 times
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    • Site-wide: 1,245 out of 65,353
    • In genomics: 288 out of 4,462
  • Year to date:
    • Site-wide: 19,363 out of 65,353
  • Since beginning of last month:
    • Site-wide: 24,114 out of 65,353

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

bioinformatics more details view paper
  • Downloaded 2,818 times
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    • Site-wide: 1,282 out of 65,353
    • In bioinformatics: 261 out of 6,477
  • Year to date:
    • Site-wide: 751 out of 65,353
  • Since beginning of last month:
    • Site-wide: 1,855 out of 65,353

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

bioinformatics more details view paper
  • Downloaded 2,797 times
  • Download rankings, all-time:
    • Site-wide: 1,296 out of 65,353
    • In bioinformatics: 264 out of 6,477
  • Year to date:
    • Site-wide: 13,370 out of 65,353
  • Since beginning of last month:
    • Site-wide: 26,951 out of 65,353

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

genomics more details view paper
  • Downloaded 2,689 times
  • Download rankings, all-time:
    • Site-wide: 1,384 out of 65,353
    • In genomics: 318 out of 4,462
  • Year to date:
    • Site-wide: 11,841 out of 65,353
  • Since beginning of last month:
    • Site-wide: 26,583 out of 65,353

Measuring the reproducibility and quality of Hi-C data

genomics more details view paper
  • Downloaded 2,490 times
  • Download rankings, all-time:
    • Site-wide: 1,590 out of 65,353
    • In genomics: 356 out of 4,462
  • Year to date:
    • Site-wide: 4,580 out of 65,353
  • Since beginning of last month:
    • Site-wide: 15,235 out of 65,353

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

genomics more details view paper
  • Downloaded 2,332 times
  • Download rankings, all-time:
    • Site-wide: 1,784 out of 65,353
    • In genomics: 393 out of 4,462
  • Year to date:
    • Site-wide: 700 out of 65,353
  • Since beginning of last month:
    • Site-wide: 3,790 out of 65,353

Deep learning at base-resolution reveals motif syntax of the cis-regulatory code

genomics more details view paper
  • Downloaded 2,154 times
  • Download rankings, all-time:
    • Site-wide: 2,081 out of 65,353
    • In genomics: 449 out of 4,462
  • Year to date:
    • Site-wide: 426 out of 65,353
  • Since beginning of last month:
    • Site-wide: 314 out of 65,353

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

genomics more details view paper
  • Downloaded 1,834 times
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    • Site-wide: 2,712 out of 65,353
    • In genomics: 545 out of 4,462
  • Year to date:
    • Site-wide: 2,885 out of 65,353
  • Since beginning of last month:
    • Site-wide: 14,572 out of 65,353

Semi-automated genome annotation using epigenomic data and Segway

bioinformatics more details view paper
  • Downloaded 1,775 times
  • Download rankings, all-time:
    • Site-wide: 2,883 out of 65,353
    • In bioinformatics: 581 out of 6,477
  • Year to date:
    • Site-wide: 15,202 out of 65,353
  • Since beginning of last month:
    • Site-wide: 16,912 out of 65,353

Impact of regulatory variation across human iPSCs and differentiated cells

genomics more details view paper
  • Downloaded 1,647 times
  • Download rankings, all-time:
    • Site-wide: 3,268 out of 65,353
    • In genomics: 630 out of 4,462
  • Year to date:
    • Site-wide: 33,997 out of 65,353
  • Since beginning of last month:
    • Site-wide: 31,042 out of 65,353

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

genomics more details view paper
  • Downloaded 1,641 times
  • Download rankings, all-time:
    • Site-wide: 3,280 out of 65,353
    • In genomics: 632 out of 4,462
  • Year to date:
    • Site-wide: 3,028 out of 65,353
  • Since beginning of last month:
    • Site-wide: 9,238 out of 65,353

Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements

genomics more details view paper
  • Downloaded 1,590 times
  • Download rankings, all-time:
    • Site-wide: 3,456 out of 65,353
    • In genomics: 657 out of 4,462
  • Year to date:
    • Site-wide: 750 out of 65,353
  • Since beginning of last month:
    • Site-wide: 10,652 out of 65,353

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences

bioinformatics more details view paper
  • Downloaded 1,564 times
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    • Site-wide: 3,551 out of 65,353
    • In bioinformatics: 713 out of 6,477
  • Year to date:
    • Site-wide: 14,400 out of 65,353
  • Since beginning of last month:
    • Site-wide: 24,023 out of 65,353

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

genomics more details view paper
  • Downloaded 1,506 times
  • Download rankings, all-time:
    • Site-wide: 3,787 out of 65,353
    • In genomics: 699 out of 4,462
  • Year to date:
    • Site-wide: 820 out of 65,353
  • Since beginning of last month:
    • Site-wide: 6,835 out of 65,353

Umap and Bismap: quantifying genome and methylome mappability

genomics more details view paper
  • Downloaded 1,086 times
  • Download rankings, all-time:
    • Site-wide: 6,565 out of 65,353
    • In genomics: 1,075 out of 4,462
  • Year to date:
    • Site-wide: 38,451 out of 65,353
  • Since beginning of last month:
    • Site-wide: 32,567 out of 65,353

Impact of the X chromosome and sex on regulatory variation

genomics more details view paper
  • Downloaded 1,026 times
  • Download rankings, all-time:
    • Site-wide: 7,180 out of 65,353
    • In genomics: 1,161 out of 4,462
  • Year to date:
    • Site-wide: 58,209 out of 65,353
  • Since beginning of last month:
    • Site-wide: 60,769 out of 65,353

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

bioinformatics more details view paper
  • Downloaded 1,013 times
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    • Site-wide: 7,315 out of 65,353
    • In bioinformatics: 1,307 out of 6,477
  • Year to date:
    • Site-wide: 34,009 out of 65,353
  • Since beginning of last month:
    • Site-wide: 29,817 out of 65,353

Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines Using Integrated Gradients

bioinformatics more details view paper
  • Downloaded 657 times
  • Download rankings, all-time:
    • Site-wide: 14,093 out of 65,353
    • In bioinformatics: 2,259 out of 6,477
  • Year to date:
    • Site-wide: 10,649 out of 65,353
  • Since beginning of last month:
    • Site-wide: 23,494 out of 65,353

A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization

genomics more details view paper
  • Downloaded 612 times
  • Download rankings, all-time:
    • Site-wide: 15,597 out of 65,353
    • In genomics: 1,993 out of 4,462
  • Year to date:
    • Site-wide: 45,105 out of 65,353
  • Since beginning of last month:
    • Site-wide: 31,297 out of 65,353

Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

genomics more details view paper
  • Downloaded 558 times
  • Download rankings, all-time:
    • Site-wide: 17,716 out of 65,353
    • In genomics: 2,159 out of 4,462
  • Year to date:
    • Site-wide: 56,007 out of 65,353
  • Since beginning of last month:
    • Site-wide: 61,402 out of 65,353

PyBoost: A parallelized Python implementation of 2D boosting with hierarchies

bioinformatics more details view paper
  • Downloaded 535 times
  • Download rankings, all-time:
    • Site-wide: 18,633 out of 65,353
    • In bioinformatics: 2,783 out of 6,477
  • Year to date:
    • Site-wide: 49,688 out of 65,353
  • Since beginning of last month:
    • Site-wide: 61,090 out of 65,353

Cell cycle dynamics of human pluripotent stem cells primed for differentiation

genetics more details view paper
  • Downloaded 515 times
  • Download rankings, all-time:
    • Site-wide: 19,639 out of 65,353
    • In genetics: 1,313 out of 3,698
  • Year to date:
    • Site-wide: 5,533 out of 65,353
  • Since beginning of last month:
    • Site-wide: 29,354 out of 65,353

Targeted optimization of regulatory DNA sequences with neural editing architectures

bioinformatics more details view paper
  • Downloaded 484 times
  • Download rankings, all-time:
    • Site-wide: 21,160 out of 65,353
    • In bioinformatics: 3,064 out of 6,477
  • Year to date:
    • Site-wide: 6,148 out of 65,353
  • Since beginning of last month:
    • Site-wide: 13,702 out of 65,353

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

molecular biology more details view paper
  • Downloaded 235 times
  • Download rankings, all-time:
    • Site-wide: 42,096 out of 65,353
    • In molecular biology: 1,249 out of 2,070
  • Year to date:
    • Site-wide: 18,824 out of 65,353
  • Since beginning of last month:
    • Site-wide: 1,028 out of 65,353

A genome-wide almanac of co-essential modules assigns function to uncharacterized genes

genomics more details view paper
  • Downloaded 199 times
  • Download rankings, all-time:
    • Site-wide: 46,691 out of 65,353
    • In genomics: 3,803 out of 4,462
  • Year to date:
    • Site-wide: 23,274 out of 65,353
  • Since beginning of last month:
    • Site-wide: 1,378 out of 65,353

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