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Convolutional neural network architectures for predicting DNA-protein binding

Bioinformatics, 2016-06, Vol.32 (12), p.i121-i127

2016

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High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

PLoS computational biology, 2012-08, Vol.8 (8), p.e1002638-e1002638

2012

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Predictable and precise template-free CRISPR editing of pathogenic variants

Nature (London), 2018-11, Vol.563 (7733), p.646-651

2018

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Antibody complementarity determining region design using high-capacity machine learning

Bioinformatics, 2020-04, Vol.36 (7), p.2126-2133

2020

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Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Nature biotechnology, 2014-02, Vol.32 (2), p.171-178

2014

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Discovering differential genome sequence activity with interpretable and efficient deep learning

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009282-e1009282

2021

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Differentiated human stem cells resemble fetal, not adult, β cells

Proceedings of the National Academy of Sciences - PNAS, 2014-02, Vol.111 (8), p.3038-3043

2014

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MARIS: method for analyzing RNA following intracellular sorting

PloS one, 2014-03, Vol.9 (3), p.e89459-e89459

2014

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Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Nature neuroscience, 2013-09, Vol.16 (9), p.1219-1227

2013

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Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions

Nature communications, 2021-05, Vol.12 (1), p.3222-3222, Article 3222

2021

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Visualizing complex feature interactions and feature sharing in genomic deep neural networks

BMC bioinformatics, 2019-07, Vol.20 (1), p.401-401, Article 401

2019

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IDR2D identifies reproducible genomic interactions

Nucleic acids research, 2020-04, Vol.48 (6), p.e31-e31

2020

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Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

Cell reports (Cambridge), 2019-05, Vol.27 (8), p.2281-2291.e5

2019

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An improved map of conserved regulatory sites for Saccharomyces cerevisiae

BMC bioinformatics, 2006-03, Vol.7 (1), p.113-113, Article 113

2006

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Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro

Nature communications, 2022-09, Vol.13 (1), p.5427-5427, Article 5427

2022

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Differential chromatin profiles partially determine transcription factor binding

PloS one, 2017-07, Vol.12 (7), p.e0179411-e0179411

2017

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A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding

eLife, 2022-07, Vol.11

2022

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Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

Proceedings of the National Academy of Sciences - PNAS, 2009-10, Vol.106 (43), p.18321-18326

2009

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Genotype to Phenotype: A Complex Problem

Science (American Association for the Advancement of Science), 2010-04, Vol.328 (5977), p.469-469

2010

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Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency

Nature communications, 2021-08, Vol.12 (1), p.5111-5111, Article 5111

2021

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Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Nature neuroscience, 2013-09, Vol.16 (9), p.1191-1198

2013

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An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

PLoS computational biology, 2014-03, Vol.10 (3), p.e1003501-e1003501

2014

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Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

Science (American Association for the Advancement of Science), 2012-09, Vol.337 (6100), p.1353-1356

2012

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Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

Nature neuroscience, 2014-08, Vol.17 (8), p.1046-1054

2014

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Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Cell, 2005-08, Vol.122 (4), p.517-527

2005

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Convolutional neural network architectures for predicting DNA-protein binding

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

Predictable and precise template-free CRISPR editing of pathogenic variants

Antibody complementarity determining region design using high-capacity machine learning

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

Discovering differential genome sequence activity with interpretable and efficient deep learning

Differentiated human stem cells resemble fetal, not adult, β cells

MARIS: method for analyzing RNA following intracellular sorting

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions

Visualizing complex feature interactions and feature sharing in genomic deep neural networks

IDR2D identifies reproducible genomic interactions

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro

Differential chromatin profiles partially determine transcription factor binding

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

Genotype to Phenotype: A Complex Problem

Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

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