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Author: Anshul Kundaje

Rankings

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    • bioinformatics: 72,482 (rank: 9 out of 31,557)
    • genetics: 4,812 (rank: 3,324 (tie) out of 34,226)
    • genomics: 37,997 (rank: 166 out of 39,410)
    • molecular biology: 700 (rank: 5,145 (tie) out of 18,752)

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Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

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Deep learning at base-resolution reveals cis-regulatory motif syntax

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Transcriptome-wide association studies: opportunities and challenges

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

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

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

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Reverse-complement parameter sharing improves deep learning models for genomics

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

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

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Separable Fully Connected Layers Improve Deep Learning Models For Genomics

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Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

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

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Measuring the reproducibility and quality of Hi-C data

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

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Semi-automated genome annotation using epigenomic data and Segway

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

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

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Impact of regulatory variation across human iPSCs and differentiated cells

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

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

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

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Umap and Bismap: quantifying genome and methylome mappability

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

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Impact of the X chromosome and sex on regulatory variation

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

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Targeted optimization of regulatory DNA sequences with neural editing architectures

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

molecular biology more details view paper
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A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization

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Cell cycle dynamics of human pluripotent stem cells primed for differentiation

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

genomics more details view paper
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PyBoost: A parallelized Python implementation of 2D boosting with hierarchies

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