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Author: Anshul B. Kundaje

Rankings

  • All-time downloads: 166,348 (rank: 744 )
  • Categories:
    • bioinformatics: 84,929 (rank: 10 )
    • cell biology: 1,024 (rank: 11,743 (tie) )
    • genetic and genomic medicine: 312 (rank: 11,929 (tie) )
    • genetics: 11,788 (rank: 1,459 )
    • genomics: 60,426 (rank: 168 )
    • molecular biology: 1,131 (rank: 6,695 (tie) )
    • neuroscience: 6,738 (rank: 3,296 (tie) )

Downloads per author, site-wide

Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

bioinformatics more details view paper
  • Downloaded 56,335 times
  • Download rankings, all-time:
    • Site-wide: 148
    • In bioinformatics: 3
  • Year to date:
    • Site-wide: 1,543
  • Since beginning of last month:
    • Site-wide: 3,502

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

genomics more details view paper
  • Downloaded 11,260 times
  • Download rankings, all-time:
    • Site-wide: 1,001
    • In genomics: 63
  • Year to date:
    • Site-wide: 2,760
  • Since beginning of last month:
    • Site-wide: 5,956

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

genomics more details view paper
  • Downloaded 6,087 times
  • Download rankings, all-time:
    • Site-wide: 2,166
    • In genomics: 167
  • Year to date:
    • Site-wide: 14,073
  • Since beginning of last month:
    • Site-wide: 16,387

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

neuroscience more details view paper
  • Downloaded 5,687 times
  • Download rankings, all-time:
    • Site-wide: 2,362
    • In neuroscience: 117
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 5,294

Transcriptome-wide association studies: opportunities and challenges

genetics more details view paper
  • Downloaded 5,181 times
  • Download rankings, all-time:
    • Site-wide: 2,694
    • In genetics: 77
  • Year to date:
    • Site-wide: 25,132
  • Since beginning of last month:
    • Site-wide: 81,900

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

genomics more details view paper
  • Downloaded 4,616 times
  • Download rankings, all-time:
    • Site-wide: 3,142
    • In genomics: 291
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 23,060

Reverse-complement parameter sharing improves deep learning models for genomics

bioinformatics more details view paper
  • Downloaded 4,449 times
  • Download rankings, all-time:
    • Site-wide: 3,314
    • In bioinformatics: 259
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 23,133

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

bioinformatics more details view paper
  • Downloaded 4,376 times
  • Download rankings, all-time:
    • Site-wide: 3,396
    • In bioinformatics: 273
  • Year to date:
    • Site-wide: 5,120
  • Since beginning of last month:
    • Site-wide: 20,513

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

bioinformatics more details view paper
  • Downloaded 3,683 times
  • Download rankings, all-time:
    • Site-wide: 4,298
    • In bioinformatics: 385
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 46,671

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

genomics more details view paper
  • Downloaded 3,374 times
  • Download rankings, all-time:
    • Site-wide: 4,864
    • In genomics: 467
  • Year to date:
    • Site-wide: 136,059
  • Since beginning of last month:
    • Site-wide: 46,534

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

genetics more details view paper
  • Downloaded 3,309 times
  • Download rankings, all-time:
    • Site-wide: 4,991
    • In genetics: 179
  • Year to date:
    • Site-wide: 44,835
  • Since beginning of last month:
    • Site-wide: 36,558

Separable Fully Connected Layers Improve Deep Learning Models For Genomics

bioinformatics more details view paper
  • Downloaded 3,306 times
  • Download rankings, all-time:
    • Site-wide: 5,000
    • In bioinformatics: 456
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 152,207

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

genomics more details view paper
  • Downloaded 3,270 times
  • Download rankings, all-time:
    • Site-wide: 5,077
    • In genomics: 486
  • Year to date:
    • Site-wide: 43,342
  • Since beginning of last month:
    • Site-wide: 101,786

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

genomics more details view paper
  • Downloaded 3,093 times
  • Download rankings, all-time:
    • Site-wide: 5,481
    • In genomics: 533
  • Year to date:
    • Site-wide: 16,603
  • Since beginning of last month:
    • Site-wide: 16,400

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

genomics more details view paper
  • Downloaded 3,087 times
  • Download rankings, all-time:
    • Site-wide: 5,494
    • In genomics: 534
  • Year to date:
    • Site-wide: 31,139
  • Since beginning of last month:
    • Site-wide: 68,708

Measuring the reproducibility and quality of Hi-C data

genomics more details view paper
  • Downloaded 2,786 times
  • Download rankings, all-time:
    • Site-wide: 6,382
    • In genomics: 626
  • Year to date:
    • Site-wide: 33,322
  • Since beginning of last month:
    • Site-wide: 121,206

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

genomics more details view paper
  • Downloaded 2,656 times
  • Download rankings, all-time:
    • Site-wide: 6,854
    • In genomics: 673
  • Year to date:
    • Site-wide: 6,884
  • Since beginning of last month:
    • Site-wide: 8,396

Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics

bioinformatics more details view paper
  • Downloaded 2,616 times
  • Download rankings, all-time:
    • Site-wide: 7,013
    • In bioinformatics: 712
  • Year to date:
    • Site-wide: 11,192
  • Since beginning of last month:
    • Site-wide: 11,350

High-throughput discovery and characterization of human transcriptional effectors

genetics more details view paper
  • Downloaded 2,538 times
  • Download rankings, all-time:
    • Site-wide: 7,338
    • In genetics: 301
  • Year to date:
    • Site-wide: 9,872
  • Since beginning of last month:
    • Site-wide: 12,367

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

genomics more details view paper
  • Downloaded 2,292 times
  • Download rankings, all-time:
    • Site-wide: 8,531
    • In genomics: 841
  • Year to date:
    • Site-wide: 79,598
  • Since beginning of last month:
    • Site-wide: 101,051

Semi-automated genome annotation using epigenomic data and Segway

bioinformatics more details view paper
  • Downloaded 2,272 times
  • Download rankings, all-time:
    • Site-wide: 8,640
    • In bioinformatics: 938
  • Year to date:
    • Site-wide: 62,870
  • Since beginning of last month:
    • Site-wide: 31,055

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

genomics more details view paper
  • Downloaded 2,169 times
  • Download rankings, all-time:
    • Site-wide: 9,206
    • In genomics: 895
  • Year to date:
    • Site-wide: 60,171
  • Since beginning of last month:
    • Site-wide: 101,578

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

genomics more details view paper
  • Downloaded 2,062 times
  • Download rankings, all-time:
    • Site-wide: 9,919
    • In genomics: 970
  • Year to date:
    • Site-wide: 14,281
  • Since beginning of last month:
    • Site-wide: 102,083

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

genomics more details view paper
  • Downloaded 2,029 times
  • Download rankings, all-time:
    • Site-wide: 10,162
    • In genomics: 988
  • Year to date:
    • Site-wide: 48,166
  • Since beginning of last month:
    • Site-wide: 24,428

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

bioinformatics more details view paper
  • Downloaded 1,868 times
  • Download rankings, all-time:
    • Site-wide: 11,522
    • In bioinformatics: 1,266
  • Year to date:
    • Site-wide: 40,642
  • Since beginning of last month:
    • Site-wide: 68,068

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

genomics more details view paper
  • Downloaded 1,864 times
  • Download rankings, all-time:
    • Site-wide: 11,569
    • In genomics: 1,126
  • Year to date:
    • Site-wide: 118,444
  • Since beginning of last month:
    • Site-wide: 144,586

Impact of regulatory variation across human iPSCs and differentiated cells

genomics more details view paper
  • Downloaded 1,817 times
  • Download rankings, all-time:
    • Site-wide: 12,007
    • In genomics: 1,168
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 147,724

Umap and Bismap: quantifying genome and methylome mappability

genomics more details view paper
  • Downloaded 1,532 times
  • Download rankings, all-time:
    • Site-wide: 15,553
    • In genomics: 1,493
  • Year to date:
    • Site-wide: 80,461
  • Since beginning of last month:
    • Site-wide: 121,316

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

bioinformatics more details view paper
  • Downloaded 1,424 times
  • Download rankings, all-time:
    • Site-wide: 17,386
    • In bioinformatics: 1,940
  • Year to date:
    • Site-wide: 93,989
  • Since beginning of last month:
    • Site-wide: 75,593

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

bioinformatics more details view paper
  • Downloaded 1,322 times
  • Download rankings, all-time:
    • Site-wide: 19,433
    • In bioinformatics: 2,172
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 120,532

Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)

genomics more details view paper
  • Downloaded 1,233 times
  • Download rankings, all-time:
    • Site-wide: 21,575
    • In genomics: 1,976
  • Year to date:
    • Site-wide: 108,507
  • Since beginning of last month:
    • Site-wide: 25,926

Impact of the X chromosome and sex on regulatory variation

genomics more details view paper
  • Downloaded 1,206 times
  • Download rankings, all-time:
    • Site-wide: 22,324
    • In genomics: 2,041
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 121,461

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

molecular biology more details view paper
  • Downloaded 1,131 times
  • Download rankings, all-time:
    • Site-wide: 24,642
    • In molecular biology: 646
  • Year to date:
    • Site-wide: 133,128
  • Since beginning of last month:
    • Site-wide: 76,813

Targeted optimization of regulatory DNA sequences with neural editing architectures

bioinformatics more details view paper
  • Downloaded 1,127 times
  • Download rankings, all-time:
    • Site-wide: 24,752
    • In bioinformatics: 2,751
  • Year to date:
    • Site-wide: 125,365
  • Since beginning of last month:
    • Site-wide: 51,763

Chromatin accessibility dynamics of neurogenic niche cells reveal a reversible decline in neural stem cell migration during aging

neuroscience more details view paper
  • Downloaded 1,051 times
  • Download rankings, all-time:
    • Site-wide: 27,497
    • In neuroscience: 3,407
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 19,871

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 1,024 times
  • Download rankings, all-time:
    • Site-wide: 28,559
    • In cell biology: 1,046
  • Year to date:
    • Site-wide: 10,016
  • Since beginning of last month:
    • Site-wide: 30,788

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

bioinformatics more details view paper
  • Downloaded 989 times
  • Download rankings, all-time:
    • Site-wide: 30,107
    • In bioinformatics: 3,298
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 68,262

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

genomics more details view paper
  • Downloaded 939 times
  • Download rankings, all-time:
    • Site-wide: 32,547
    • In genomics: 2,723
  • Year to date:
    • Site-wide: 72,598
  • Since beginning of last month:
    • Site-wide: 78,254

Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

genomics more details view paper
  • Downloaded 873 times
  • Download rankings, all-time:
    • Site-wide: 36,104
    • In genomics: 2,958
  • Year to date:
    • Site-wide: 9,222
  • Since beginning of last month:
    • Site-wide: 7,325

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

genomics more details view paper
  • Downloaded 777 times
  • Download rankings, all-time:
    • Site-wide: 42,733
    • In genomics: 3,353
  • Year to date:
    • Site-wide: 80,403
  • Since beginning of last month:
    • Site-wide: 121,256

Cell cycle dynamics of human pluripotent stem cells primed for differentiation

genetics more details view paper
  • Downloaded 760 times
  • Download rankings, all-time:
    • Site-wide: 44,148
    • In genetics: 1,876
  • Year to date:
    • Site-wide: 86,823
  • Since beginning of last month:
    • Site-wide: 141,945

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

genomics more details view paper
  • Downloaded 705 times
  • Download rankings, all-time:
    • Site-wide: 49,052
    • In genomics: 3,712
  • Year to date:
    • Site-wide: 136,380
  • Since beginning of last month:
    • Site-wide: 121,412

MTSplice predicts effects of genetic variants on tissue-specific splicing

genomics more details view paper
  • Downloaded 699 times
  • Download rankings, all-time:
    • Site-wide: 49,617
    • In genomics: 3,749
  • Year to date:
    • Site-wide: 110,583
  • Since beginning of last month:
    • Site-wide: 134,490

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

bioinformatics more details view paper
  • Downloaded 696 times
  • Download rankings, all-time:
    • Site-wide: 49,869
    • In bioinformatics: 5,056
  • Year to date:
    • Site-wide: 127,495
  • Since beginning of last month:
    • Site-wide: 152,532

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

bioinformatics more details view paper
  • Downloaded 466 times
  • Download rankings, all-time:
    • Site-wide: 81,948
    • In bioinformatics: 7,401
  • Year to date:
    • Site-wide: 68,111
  • Since beginning of last month:
    • Site-wide: 37,017

Genetic architectures of proximal and distal colorectal cancer are partly distinct

genetic and genomic medicine more details view paper
  • Downloaded 312 times
  • Download rankings, all-time:
    • Site-wide: 117,221
    • In genetic and genomic medicine: 688
  • Year to date:
    • Site-wide: 97,645
  • Since beginning of last month:
    • Site-wide: 112,807

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