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Author: Anshul Kundaje

Rankings

  • All-time downloads: 139,240 (rank: 498 )
  • Categories:
    • bioinformatics: 79,507 (rank: 8 )
    • cell biology: 544 (rank: 15,014 (tie) )
    • genetic and genomic medicine: 207 (rank: 5,712 (tie) )
    • genetics: 9,350 (rank: 1,777 )
    • genomics: 47,952 (rank: 154 )
    • molecular biology: 925 (rank: 5,439 (tie) )
    • neuroscience: 755 (rank: 27,548 (tie) )

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 54,532 times
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    • Site-wide: 93
    • In bioinformatics: 3
  • Year to date:
    • Site-wide: 994
  • Since beginning of last month:
    • Site-wide: 3,034

Base-resolution models of transcription factor binding reveal soft motif syntax

genomics more details view paper
  • Downloaded 8,733 times
  • Download rankings, all-time:
    • Site-wide: 835
    • In genomics: 74
  • Year to date:
    • Site-wide: 1,841
  • Since beginning of last month:
    • Site-wide: 1,406

Single-cell epigenomic identification of inherited risk loci in Alzheimer's and Parkinson's disease

genomics more details view paper
  • Downloaded 5,109 times
  • Download rankings, all-time:
    • Site-wide: 1,677
    • In genomics: 177
  • Year to date:
    • Site-wide: 2,921
  • Since beginning of last month:
    • Site-wide: 3,815

Transcriptome-wide association studies: opportunities and challenges

genetics more details view paper
  • Downloaded 4,675 times
  • Download rankings, all-time:
    • Site-wide: 1,899
    • In genetics: 73
  • Year to date:
    • Site-wide: 12,516
  • Since beginning of last month:
    • Site-wide: 10,382

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

genomics more details view paper
  • Downloaded 4,344 times
  • Download rankings, all-time:
    • Site-wide: 2,113
    • In genomics: 248
  • Year to date:
    • Site-wide: 17,633
  • Since beginning of last month:
    • Site-wide: 45,520

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

bioinformatics more details view paper
  • Downloaded 3,845 times
  • Download rankings, all-time:
    • Site-wide: 2,526
    • In bioinformatics: 247
  • Year to date:
    • Site-wide: 11,410
  • Since beginning of last month:
    • Site-wide: 19,197

Reverse-complement parameter sharing improves deep learning models for genomics

bioinformatics more details view paper
  • Downloaded 3,782 times
  • Download rankings, all-time:
    • Site-wide: 2,586
    • In bioinformatics: 255
  • Year to date:
    • Site-wide: 6,458
  • Since beginning of last month:
    • Site-wide: 11,131

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

bioinformatics more details view paper
  • Downloaded 3,496 times
  • Download rankings, all-time:
    • Site-wide: 2,899
    • In bioinformatics: 305
  • Year to date:
    • Site-wide: 25,077
  • Since beginning of last month:
    • Site-wide: 20,361

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

bioinformatics more details view paper
  • Downloaded 3,137 times
  • Download rankings, all-time:
    • Site-wide: 3,415
    • In bioinformatics: 377
  • Year to date:
    • Site-wide: 20,575
  • Since beginning of last month:
    • Site-wide: 34,266

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

genomics more details view paper
  • Downloaded 3,122 times
  • Download rankings, all-time:
    • Site-wide: 3,440
    • In genomics: 407
  • Year to date:
    • Site-wide: 60,365
  • Since beginning of last month:
    • Site-wide: 71,813

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

genomics more details view paper
  • Downloaded 3,024 times
  • Download rankings, all-time:
    • Site-wide: 3,605
    • In genomics: 432
  • Year to date:
    • Site-wide: 22,428
  • Since beginning of last month:
    • Site-wide: 31,169

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

genomics more details view paper
  • Downloaded 2,956 times
  • Download rankings, all-time:
    • Site-wide: 3,689
    • In genomics: 443
  • Year to date:
    • Site-wide: 33,918
  • Since beginning of last month:
    • Site-wide: 69,114

Measuring the reproducibility and quality of Hi-C data

genomics more details view paper
  • Downloaded 2,658 times
  • Download rankings, all-time:
    • Site-wide: 4,294
    • In genomics: 511
  • Year to date:
    • Site-wide: 77,783
  • Since beginning of last month:
    • Site-wide: 92,997

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

genomics more details view paper
  • Downloaded 2,303 times
  • Download rankings, all-time:
    • Site-wide: 5,340
    • In genomics: 638
  • Year to date:
    • Site-wide: 11,796
  • Since beginning of last month:
    • Site-wide: 15,393

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

genomics more details view paper
  • Downloaded 2,143 times
  • Download rankings, all-time:
    • Site-wide: 5,904
    • In genomics: 698
  • Year to date:
    • Site-wide: 20,317
  • Since beginning of last month:
    • Site-wide: 75,253

Genome-wide maps of enhancer regulation connect risk variants to disease genes

genetics more details view paper
  • Downloaded 2,122 times
  • Download rankings, all-time:
    • Site-wide: 5,999
    • In genetics: 302
  • Year to date:
    • Site-wide: 2,130
  • Since beginning of last month:
    • Site-wide: 2,457

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

genomics more details view paper
  • Downloaded 2,065 times
  • Download rankings, all-time:
    • Site-wide: 6,244
    • In genomics: 735
  • Year to date:
    • Site-wide: 31,306
  • Since beginning of last month:
    • Site-wide: 58,271

Semi-automated genome annotation using epigenomic data and Segway

bioinformatics more details view paper
  • Downloaded 2,039 times
  • Download rankings, all-time:
    • Site-wide: 6,367
    • In bioinformatics: 785
  • Year to date:
    • Site-wide: 39,706
  • Since beginning of last month:
    • Site-wide: 88,651

Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics

bioinformatics more details view paper
  • Downloaded 1,924 times
  • Download rankings, all-time:
    • Site-wide: 6,936
    • In bioinformatics: 875
  • Year to date:
    • Site-wide: 10,172
  • Since beginning of last month:
    • Site-wide: 3,057

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

genomics more details view paper
  • Downloaded 1,913 times
  • Download rankings, all-time:
    • Site-wide: 6,992
    • In genomics: 797
  • Year to date:
    • Site-wide: 56,492
  • Since beginning of last month:
    • Site-wide: 81,623

High-throughput discovery and characterization of human transcriptional effectors

genetics more details view paper
  • Downloaded 1,868 times
  • Download rankings, all-time:
    • Site-wide: 7,239
    • In genetics: 355
  • Year to date:
    • Site-wide: 3,843
  • Since beginning of last month:
    • Site-wide: 1,130

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

genomics more details view paper
  • Downloaded 1,782 times
  • Download rankings, all-time:
    • Site-wide: 7,737
    • In genomics: 883
  • Year to date:
    • Site-wide: 103,223
  • Since beginning of last month:
    • Site-wide: 101,591

Impact of regulatory variation across human iPSCs and differentiated cells

genomics more details view paper
  • Downloaded 1,764 times
  • Download rankings, all-time:
    • Site-wide: 7,859
    • In genomics: 901
  • Year to date:
    • Site-wide: 77,996
  • Since beginning of last month:
    • Site-wide: 110,072

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

bioinformatics more details view paper
  • Downloaded 1,758 times
  • Download rankings, all-time:
    • Site-wide: 7,905
    • In bioinformatics: 1,003
  • Year to date:
    • Site-wide: 32,805
  • Since beginning of last month:
    • Site-wide: 97,814

Umap and Bismap: quantifying genome and methylome mappability

genomics more details view paper
  • Downloaded 1,359 times
  • Download rankings, all-time:
    • Site-wide: 11,686
    • In genomics: 1,314
  • Year to date:
    • Site-wide: 52,795
  • Since beginning of last month:
    • Site-wide: 64,867

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

bioinformatics more details view paper
  • Downloaded 1,230 times
  • Download rankings, all-time:
    • Site-wide: 13,572
    • In bioinformatics: 1,706
  • Year to date:
    • Site-wide: 28,125
  • Since beginning of last month:
    • Site-wide: 108,022

Impact of the X chromosome and sex on regulatory variation

genomics more details view paper
  • Downloaded 1,144 times
  • Download rankings, all-time:
    • Site-wide: 15,121
    • In genomics: 1,641
  • Year to date:
    • Site-wide: 122,171
  • Since beginning of last month:
    • Site-wide: 91,193

Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics

bioinformatics more details view paper
  • Downloaded 1,107 times
  • Download rankings, all-time:
    • Site-wide: 15,920
    • In bioinformatics: 1,991
  • Year to date:
    • Site-wide: 6,294
  • Since beginning of last month:
    • Site-wide: 14,398

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

genomics more details view paper
  • Downloaded 1,016 times
  • Download rankings, all-time:
    • Site-wide: 18,108
    • In genomics: 1,905
  • Year to date:
    • Site-wide: 3,358
  • Since beginning of last month:
    • Site-wide: 4,690

Targeted optimization of regulatory DNA sequences with neural editing architectures

bioinformatics more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 20,279
    • In bioinformatics: 2,506
  • Year to date:
    • Site-wide: 17,589
  • Since beginning of last month:
    • Site-wide: 98,587

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

molecular biology more details view paper
  • Downloaded 925 times
  • Download rankings, all-time:
    • Site-wide: 20,731
    • In molecular biology: 572
  • Year to date:
    • Site-wide: 24,509
  • Since beginning of last month:
    • Site-wide: 24,971

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

bioinformatics more details view paper
  • Downloaded 872 times
  • Download rankings, all-time:
    • Site-wide: 22,630
    • In bioinformatics: 2,754
  • Year to date:
    • Site-wide: 51,525
  • Since beginning of last month:
    • Site-wide: 59,113

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

neuroscience more details view paper
  • Downloaded 755 times
  • Download rankings, all-time:
    • Site-wide: 27,723
    • In neuroscience: 3,837
  • Year to date:
    • Site-wide: 185
  • Since beginning of last month:
    • Site-wide: 2,477

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

genomics more details view paper
  • Downloaded 728 times
  • Download rankings, all-time:
    • Site-wide: 29,127
    • In genomics: 2,689
  • Year to date:
    • Site-wide: 90,462
  • Since beginning of last month:
    • Site-wide: 94,754

Transcription-dependent domain-scale 3D genome organization in dinoflagellates

genomics more details view paper
  • Downloaded 685 times
  • Download rankings, all-time:
    • Site-wide: 31,587
    • In genomics: 2,855
  • Year to date:
    • Site-wide: 26,203
  • Since beginning of last month:
    • Site-wide: 20,660

Cell cycle dynamics of human pluripotent stem cells primed for differentiation

genetics more details view paper
  • Downloaded 685 times
  • Download rankings, all-time:
    • Site-wide: 31,629
    • In genetics: 1,591
  • Year to date:
    • Site-wide: 102,592
  • Since beginning of last month:
    • Site-wide: 113,414

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

genomics more details view paper
  • Downloaded 653 times
  • Download rankings, all-time:
    • Site-wide: 33,753
    • In genomics: 2,991
  • Year to date:
    • Site-wide: 53,401
  • Since beginning of last month:
    • Site-wide: 67,295

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

bioinformatics more details view paper
  • Downloaded 638 times
  • Download rankings, all-time:
    • Site-wide: 34,800
    • In bioinformatics: 3,939
  • Year to date:
    • Site-wide: 106,228
  • Since beginning of last month:
    • Site-wide: 120,105

Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell

cell biology more details view paper
  • Downloaded 544 times
  • Download rankings, all-time:
    • Site-wide: 42,508
    • In cell biology: 1,804
  • Year to date:
    • Site-wide: 20,012
  • Since beginning of last month:
    • Site-wide: 32,104

MTSplice predicts effects of genetic variants on tissue-specific splicing

genomics more details view paper
  • Downloaded 451 times
  • Download rankings, all-time:
    • Site-wide: 52,768
    • In genomics: 4,089
  • Year to date:
    • Site-wide: 16,069
  • Since beginning of last month:
    • Site-wide: 30,446

fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks

bioinformatics more details view paper
  • Downloaded 207 times
  • Download rankings, all-time:
    • Site-wide: 95,881
    • In bioinformatics: 8,348
  • Year to date:
    • Site-wide: 23,349
  • Since beginning of last month:
    • Site-wide: 34,239

Genetic architectures of proximal and distal colorectal cancer are partly distinct

genetic and genomic medicine more details view paper
  • Downloaded 207 times
  • Download rankings, all-time:
    • Site-wide: 95,847
    • In genetic and genomic medicine: 323
  • Year to date:
    • Site-wide: 56,543
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    • Site-wide: 36,361

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