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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 60,239 bioRxiv papers from 267,831 authors.

Author: Anshul Kundaje

Rankings

  • All-time downloads: 98,070 (rank: 67 out of 267,831)
  • Categories:
    • bioinformatics: 67,746 (rank: 5 out of 23,908)
    • genetics: 3,921 (rank: 3,175 out of 27,094)
    • genomics: 26,403 (rank: 205 out of 31,259)

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 50,610 times
  • Download rankings, all-time:
    • Site-wide: 7 out of 60,239
    • In bioinformatics: 1 out of 6,078
  • Year to date:
    • Site-wide: 91 out of 60,239
  • Since beginning of last month:
    • Site-wide: 506 out of 60,239

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

genomics more details view paper
  • Downloaded 3,708 times
  • Download rankings, all-time:
    • Site-wide: 704 out of 60,239
    • In genomics: 183 out of 4,181
  • Year to date:
    • Site-wide: 3,777 out of 60,239
  • Since beginning of last month:
    • Site-wide: 5,337 out of 60,239

Transcriptome-wide association studies: opportunities and challenges

genetics more details view paper
  • Downloaded 3,435 times
  • Download rankings, all-time:
    • Site-wide: 815 out of 60,239
    • In genetics: 80 out of 3,435
  • Year to date:
    • Site-wide: 1,111 out of 60,239
  • Since beginning of last month:
    • Site-wide: 3,823 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 3,096 times
  • Download rankings, all-time:
    • Site-wide: 980 out of 60,239
    • In bioinformatics: 200 out of 6,078
  • Year to date:
    • Site-wide: 16,146 out of 60,239
  • Since beginning of last month:
    • Site-wide: 20,173 out of 60,239

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

genomics more details view paper
  • Downloaded 2,837 times
  • Download rankings, all-time:
    • Site-wide: 1,158 out of 60,239
    • In genomics: 273 out of 4,181
  • Year to date:
    • Site-wide: 18,102 out of 60,239
  • Since beginning of last month:
    • Site-wide: 25,026 out of 60,239

Reverse-complement parameter sharing improves deep learning models for genomics

bioinformatics more details view paper
  • Downloaded 2,825 times
  • Download rankings, all-time:
    • Site-wide: 1,172 out of 60,239
    • In bioinformatics: 243 out of 6,078
  • Year to date:
    • Site-wide: 3,733 out of 60,239
  • Since beginning of last month:
    • Site-wide: 5,649 out of 60,239

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

bioinformatics more details view paper
  • Downloaded 2,768 times
  • Download rankings, all-time:
    • Site-wide: 1,223 out of 60,239
    • In bioinformatics: 252 out of 6,078
  • Year to date:
    • Site-wide: 11,778 out of 60,239
  • Since beginning of last month:
    • Site-wide: 19,880 out of 60,239

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

genomics more details view paper
  • Downloaded 2,658 times
  • Download rankings, all-time:
    • Site-wide: 1,295 out of 60,239
    • In genomics: 301 out of 4,181
  • Year to date:
    • Site-wide: 10,400 out of 60,239
  • Since beginning of last month:
    • Site-wide: 30,178 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 2,626 times
  • Download rankings, all-time:
    • Site-wide: 1,321 out of 60,239
    • In bioinformatics: 267 out of 6,078
  • Year to date:
    • Site-wide: 692 out of 60,239
  • Since beginning of last month:
    • Site-wide: 1,203 out of 60,239

Measuring the reproducibility and quality of Hi-C data

genomics more details view paper
  • Downloaded 2,443 times
  • Download rankings, all-time:
    • Site-wide: 1,508 out of 60,239
    • In genomics: 344 out of 4,181
  • Year to date:
    • Site-wide: 3,933 out of 60,239
  • Since beginning of last month:
    • Site-wide: 14,206 out of 60,239

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

genomics more details view paper
  • Downloaded 2,136 times
  • Download rankings, all-time:
    • Site-wide: 1,914 out of 60,239
    • In genomics: 423 out of 4,181
  • Year to date:
    • Site-wide: 645 out of 60,239
  • Since beginning of last month:
    • Site-wide: 4,236 out of 60,239

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

genomics more details view paper
  • Downloaded 1,788 times
  • Download rankings, all-time:
    • Site-wide: 2,610 out of 60,239
    • In genomics: 535 out of 4,181
  • Year to date:
    • Site-wide: 2,388 out of 60,239
  • Since beginning of last month:
    • Site-wide: 10,118 out of 60,239

Semi-automated genome annotation using epigenomic data and Segway

bioinformatics more details view paper
  • Downloaded 1,726 times
  • Download rankings, all-time:
    • Site-wide: 2,781 out of 60,239
    • In bioinformatics: 562 out of 6,078
  • Year to date:
    • Site-wide: 15,404 out of 60,239
  • Since beginning of last month:
    • Site-wide: 13,434 out of 60,239

Impact of regulatory variation across human iPSCs and differentiated cells

genomics more details view paper
  • Downloaded 1,626 times
  • Download rankings, all-time:
    • Site-wide: 3,061 out of 60,239
    • In genomics: 598 out of 4,181
  • Year to date:
    • Site-wide: 31,501 out of 60,239
  • Since beginning of last month:
    • Site-wide: 23,069 out of 60,239

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

genomics more details view paper
  • Downloaded 1,573 times
  • Download rankings, all-time:
    • Site-wide: 3,228 out of 60,239
    • In genomics: 627 out of 4,181
  • Year to date:
    • Site-wide: 2,673 out of 60,239
  • Since beginning of last month:
    • Site-wide: 10,987 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 1,536 times
  • Download rankings, all-time:
    • Site-wide: 3,364 out of 60,239
    • In bioinformatics: 679 out of 6,078
  • Year to date:
    • Site-wide: 12,745 out of 60,239
  • Since beginning of last month:
    • Site-wide: 12,354 out of 60,239

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

genomics more details view paper
  • Downloaded 1,523 times
  • Download rankings, all-time:
    • Site-wide: 3,417 out of 60,239
    • In genomics: 655 out of 4,181
  • Year to date:
    • Site-wide: 585 out of 60,239
  • Since beginning of last month:
    • Site-wide: 35 out of 60,239

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

genomics more details view paper
  • Downloaded 1,470 times
  • Download rankings, all-time:
    • Site-wide: 3,634 out of 60,239
    • In genomics: 684 out of 4,181
  • Year to date:
    • Site-wide: 633 out of 60,239
  • Since beginning of last month:
    • Site-wide: 3,667 out of 60,239

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

genomics more details view paper
  • Downloaded 1,422 times
  • Download rankings, all-time:
    • Site-wide: 3,828 out of 60,239
    • In genomics: 715 out of 4,181
  • Year to date:
    • Site-wide: 673 out of 60,239
  • Since beginning of last month:
    • Site-wide: 4,561 out of 60,239

Umap and Bismap: quantifying genome and methylome mappability

genomics more details view paper
  • Downloaded 1,065 times
  • Download rankings, all-time:
    • Site-wide: 6,194 out of 60,239
    • In genomics: 1,036 out of 4,181
  • Year to date:
    • Site-wide: 36,293 out of 60,239
  • Since beginning of last month:
    • Site-wide: 47,535 out of 60,239

Impact of the X chromosome and sex on regulatory variation

genomics more details view paper
  • Downloaded 1,018 times
  • Download rankings, all-time:
    • Site-wide: 6,661 out of 60,239
    • In genomics: 1,103 out of 4,181
  • Year to date:
    • Site-wide: 52,416 out of 60,239
  • Since beginning of last month:
    • Site-wide: 40,184 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 986 times
  • Download rankings, all-time:
    • Site-wide: 6,983 out of 60,239
    • In bioinformatics: 1,274 out of 6,078
  • Year to date:
    • Site-wide: 33,021 out of 60,239
  • Since beginning of last month:
    • Site-wide: 48,752 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 625 times
  • Download rankings, all-time:
    • Site-wide: 13,774 out of 60,239
    • In bioinformatics: 2,217 out of 6,078
  • Year to date:
    • Site-wide: 9,304 out of 60,239
  • Since beginning of last month:
    • Site-wide: 30,718 out of 60,239

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

genomics more details view paper
  • Downloaded 586 times
  • Download rankings, all-time:
    • Site-wide: 15,075 out of 60,239
    • In genomics: 1,938 out of 4,181
  • Year to date:
    • Site-wide: 45,160 out of 60,239
  • Since beginning of last month:
    • Site-wide: 46,295 out of 60,239

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

genomics more details view paper
  • Downloaded 550 times
  • Download rankings, all-time:
    • Site-wide: 16,366 out of 60,239
    • In genomics: 2,059 out of 4,181
  • Year to date:
    • Site-wide: 49,972 out of 60,239
  • Since beginning of last month:
    • Site-wide: 43,757 out of 60,239

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

bioinformatics more details view paper
  • Downloaded 527 times
  • Download rankings, all-time:
    • Site-wide: 17,278 out of 60,239
    • In bioinformatics: 2,640 out of 6,078
  • Year to date:
    • Site-wide: 43,485 out of 60,239
  • Since beginning of last month:
    • Site-wide: 50,274 out of 60,239

Cell cycle dynamics of human pluripotent stem cells primed for differentiation

genetics more details view paper
  • Downloaded 486 times
  • Download rankings, all-time:
    • Site-wide: 19,122 out of 60,239
    • In genetics: 1,297 out of 3,435
  • Year to date:
    • Site-wide: 4,534 out of 60,239
  • Since beginning of last month:
    • Site-wide: 21,397 out of 60,239

Targeted optimization of regulatory DNA sequences with neural editing architectures

bioinformatics more details view paper
  • Downloaded 421 times
  • Download rankings, all-time:
    • Site-wide: 22,575 out of 60,239
    • In bioinformatics: 3,212 out of 6,078
  • Year to date:
    • Site-wide: 5,772 out of 60,239
  • Since beginning of last month:
    • Site-wide: 1,849 out of 60,239

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