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TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

Nucleic acids research, 2016-07, Vol.44 (13), p.e117-e117

2016

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A systematic evaluation of single-cell RNA-sequencing imputation methods

Genome Biology, 2020-08, Vol.21 (1), p.218-218, Article 218

2020

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Single-cell ATAC-seq signal extraction and enhancement with SCATE

Genome Biology, 2020-07, Vol.21 (1), p.161-161, Article 161

2020

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Single-cell regulome data analysis by SCRAT

Bioinformatics (Oxford, England), 2017-09, Vol.33 (18), p.2930-2932

2017

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Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

Nature communications, 2021-01, Vol.12 (1), p.652-652, Article 652

2021

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Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth

eLife, 2017-09, Vol.6

2017

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GLI transcriptional repression is inert prior to Hedgehog pathway activation

Nature communications, 2022-02, Vol.13 (1), p.808-808, Article 808

2022

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A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

Nature communications, 2023-11, Vol.14 (1), p.7286-7286, Article 7286

2023

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An integrated software system for analyzing ChIP-chip and ChIP-seq data

Nature biotechnology, 2008-11, Vol.26 (11), p.1293-1300

2008

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Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina

Proceedings of the National Academy of Sciences - PNAS, 2017-05, Vol.114 (18), p.E3719-E3728

2017

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ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

Nature communications, 2018-04, Vol.9 (1), p.1364-13, Article 1364

2018

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Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

Nature communications, 2023-01, Vol.14 (1), p.296-296, Article 296

2023

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GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

eLife, 2020-01, Vol.9

2020

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Sex differences in gene regulation in the dorsal root ganglion after nerve injury

BMC genomics, 2019-02, Vol.20 (1), p.147-18, Article 147

2019

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Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis

Developmental cell, 2010-11, Vol.19 (5), p.765-777

2010

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Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects

Nature communications, 2023-10, Vol.14 (1), p.6317-6317, Article 6317

2023

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Hedgehog regulation of epithelial cell state and morphogenesis in the larynx

eLife, 2022-11, Vol.11

2022

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Metabolic programs define dysfunctional immune responses in severe COVID-19 patients

Cell reports (Cambridge), 2021-03, Vol.34 (11), p.108863, Article 108863

2021

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ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

Nature protocols, 2016-12, Vol.11 (12), p.2432-2453

2016

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A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

Genes & development, 2008-10, Vol.22 (19), p.2651-2663

2008

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Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology

Clinical infectious diseases, 2022-01, Vol.74 (2), p.254-262

2022

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Genome-wide prediction of DNase I hypersensitivity using gene expression

Nature communications, 2017-10, Vol.8 (1), p.1038-17, Article 1038

2017

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NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation

Nature methods, 2022-02, Vol.19 (2), p.205-215

2022

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Reconstruction of Single-Cell Trajectories Using Stochastic Tree Search

Genes, 2023-01, Vol.14 (2), p.318

2023

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Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

PLoS biology, 2018-09, Vol.16 (9), p.e2006347-e2006347

2018

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TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

A systematic evaluation of single-cell RNA-sequencing imputation methods

Single-cell ATAC-seq signal extraction and enhancement with SCATE

Single-cell regulome data analysis by SCRAT

Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth

GLI transcriptional repression is inert prior to Hedgehog pathway activation

A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

An integrated software system for analyzing ChIP-chip and ChIP-seq data

Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis

Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects

Hedgehog regulation of epithelial cell state and morphogenesis in the larynx

Metabolic programs define dysfunctional immune responses in severe COVID-19 patients

ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology

Genome-wide prediction of DNase I hypersensitivity using gene expression

NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation

Reconstruction of Single-Cell Trajectories Using Stochastic Tree Search

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

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