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Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks

Developmental cell, 2012-09, Vol.23 (3), p.637-651

2012

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gene regulatory network in mouse embryonic stem cells

Proceedings of the National Academy of Sciences - PNAS, 2007-10, Vol.104 (42), p.16438-16443

2007

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Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons

Biological psychiatry (1969), 2021-03, Vol.89 (5), p.497-509

2021

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Statistical inferences for isoform expression in RNA-Seq

Bioinformatics, 2009-04, Vol.25 (8), p.1026-1032

2009

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DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

Nucleic acids research, 2019-06, Vol.47 (10), p.e60-e60

2019

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SeqMap: mapping massive amount of oligonucleotides to the genome

Bioinformatics, 2008-10, Vol.24 (20), p.2395-2396

2008

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Modeling gene regulation from paired expression and chromatin accessibility data

Proceedings of the National Academy of Sciences - PNAS, 2017-06, Vol.114 (25), p.E4914-E4923

2017

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CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

Genomics, proteomics & bioinformatics, 2023-06, Vol.21 (3), p.632-648

2023

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ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Proceedings of the National Academy of Sciences - PNAS, 2009-12, Vol.106 (51), p.21521-21526

2009

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Genetic effects of sequence-conserved enhancer-like elements on human complex traits

Genome Biology, 2024-01, Vol.25 (1), p.1-28, Article 1

2024

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Modeling regulatory network topology improves genome-wide analyses of complex human traits

Nature communications, 2021-05, Vol.12 (1), p.2851-2851, Article 2851

2021

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DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

Nature communications, 2019-10, Vol.10 (1), p.4613-11, Article 4613

2019

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Improving PacBio long read accuracy by short read alignment

PloS one, 2012-10, Vol.7 (10), p.e46679-e46679

2012

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CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data

Nucleic acids research, 2018-09, Vol.46 (15), p.e89-e89

2018

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Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Genome Biology, 2022-05, Vol.23 (1), p.114-19, Article 114

2022

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Unsupervised clustering and epigenetic classification of single cells

Nature communications, 2018-06, Vol.9 (1), p.2410-8, Article 2410

2018

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Learning Causal Bayesian Network Structures From Experimental Data

Journal of the American Statistical Association, 2008-06, Vol.103 (482), p.778-789

2008

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Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

Proceedings of the National Academy of Sciences - PNAS, 2018-07, Vol.115 (30), p.7723-7728

2018

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Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Nature communications, 2017-07, Vol.8 (1), p.59-59, Article 59

2017

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Characterization of the human ESC transcriptome by hybrid sequencing

Proceedings of the National Academy of Sciences - PNAS, 2013-12, Vol.110 (50), p.E4821-E4830

2013

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Functional annotation and network reconstruction through cross-platform integration of microarray data

Nature biotechnology, 2005-02, Vol.23 (2), p.238-243

2005

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CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

Cell stem cell, 2018-11, Vol.23 (5), p.758-771.e8

2018

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Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection

Proceedings of the National Academy of Sciences - PNAS, 2001-01, Vol.98 (1), p.31-36

2001

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Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Genome Biology, 2022-10, Vol.23 (1), p.1-213, Article 213

2022

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Completely phased genome sequencing through chromosome sorting

Proceedings of the National Academy of Sciences - PNAS, 2011-01, Vol.108 (1), p.12-17

2011

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Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks

gene regulatory network in mouse embryonic stem cells

Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons

Statistical inferences for isoform expression in RNA-Seq

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

SeqMap: mapping massive amount of oligonucleotides to the genome

Modeling gene regulation from paired expression and chromatin accessibility data

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Genetic effects of sequence-conserved enhancer-like elements on human complex traits

Modeling regulatory network topology improves genome-wide analyses of complex human traits

DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

Improving PacBio long read accuracy by short read alignment

CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Unsupervised clustering and epigenetic classification of single cells

Learning Causal Bayesian Network Structures From Experimental Data

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Characterization of the human ESC transcriptome by hybrid sequencing

Functional annotation and network reconstruction through cross-platform integration of microarray data

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection

Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Completely phased genome sequencing through chromosome sorting

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