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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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Convolutional neural network architectures for predicting DNA-protein binding

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

2016

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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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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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Predicting the impact of non-coding variants on DNA methylation

Nucleic acids research, 2017-06, Vol.45 (11), p.e99

2017

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DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

Bioinformatics, 2019-07, Vol.35 (14), p.i278-i283

2019

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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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MARIS: method for analyzing RNA following intracellular sorting

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

2014

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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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Comment on: The Impact of Nursing Home Socioeconomic and Racial Composition

Journal of the American Geriatrics Society (JAGS), 2020-05, Vol.68 (5), p.1111-1112

Gifford, David R.

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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seqgra: principled selection of neural network architectures for genomics prediction tasks

Bioinformatics (Oxford, England), 2022-04, Vol.38 (9), p.2381-2388

2022

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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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Differential chromatin profiles partially determine transcription factor binding

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

2017

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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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IDR2D identifies reproducible genomic interactions

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

2020

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Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets

Cell systems, 2021-01, Vol.12 (1), p.102-107.e4

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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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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High-resolution genetic mapping with pooled sequencing

BMC bioinformatics, 2012-04, Vol.13 Suppl 6 (Suppl 6), p.S8-S8, Article S8

2012

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A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets

Cell, 2019-02, Vol.176 (4), p.790-804.e13

2019

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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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Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design

Cell systems, 2019-08, Vol.9 (2), p.159-166.e3

2019

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Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

BMC genomics, 2017-01, Vol.18 (1), p.45-45, Article 45

2017

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

Convolutional neural network architectures for predicting DNA-protein binding

Antibody complementarity determining region design using high-capacity machine learning

Predictable and precise template-free CRISPR editing of pathogenic variants

Predicting the impact of non-coding variants on DNA methylation

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

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

MARIS: method for analyzing RNA following intracellular sorting

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

Comment on: The Impact of Nursing Home Socioeconomic and Racial Composition

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

seqgra: principled selection of neural network architectures for genomics prediction tasks

Discovering differential genome sequence activity with interpretable and efficient deep learning

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

Differential chromatin profiles partially determine transcription factor binding

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

IDR2D identifies reproducible genomic interactions

Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets

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

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

High-resolution genetic mapping with pooled sequencing

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets

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

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design

Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

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