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Identification of transcription factor binding sites using ATAC-seq

Genome Biology, 2019-02, Vol.20 (1), p.45-21, Article 45

2019

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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Bioinformatics, 2009-11, Vol.25 (21), p.2865-2871

2009

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Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction

Nature communications, 2021-01, Vol.12 (1), p.681-681, Article 681

2021

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The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

Developmental cell, 2019-09, Vol.50 (5), p.644-657.e8

2019

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Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

Science (American Association for the Advancement of Science), 2008-08, Vol.321 (5891), p.956-960

2008

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A systematic analysis of circRNAs in subnuclear compartments

RNA biology, 2024-12, Vol.21 (1), p.1-16

2024

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Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

Immunity (Cambridge, Mass.), 2016-11, Vol.45 (5), p.1148-1161

2016

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Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection

PloS one, 2023-11, Vol.18 (11), p.e0287725-e0287725

2023

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A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes

Scientific reports, 2021-03, Vol.11 (1), p.6518-6518, Article 6518

2021

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Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Genome research, 2022-04, Vol.32 (4), p.710-725

2022

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Integrative prediction of gene expression with chromatin accessibility and conformation data

Epigenetics & chromatin, 2020-02, Vol.13 (1), p.4-17, Article 4

2020

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CpG content-dependent associations between transcription factors and histone modifications

PloS one, 2021-04, Vol.16 (4), p.e0249985-e0249985

2021

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Fiona: a parallel and automatic strategy for read error correction

Bioinformatics, 2014-09, Vol.30 (17), p.i356-i363

2014

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Integrative analysis of epigenetics data identifies gene-specific regulatory elements

Nucleic acids research, 2021-10, Vol.49 (18), p.10397-10418

2021

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DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

BMC systems biology, 2012-08, Vol.6 (1), p.104-104

2012

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DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal

Nature communications, 2022-12, Vol.13 (1), p.7444-19, Article 7444

2022

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HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Nature communications, 2022-11, Vol.13 (1), p.6563-6563, Article 6563

2022

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Fostering accessible online education using Galaxy as an e-learning platform

PLoS computational biology, 2021-05, Vol.17 (5), p.e1008923-e1008923

2021

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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Bioinformatics (Oxford, England), 2012-04, Vol.28 (8), p.1086-1092

2012

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Bayesian ontology querying for accurate and noise-tolerant semantic searches

Bioinformatics (Oxford, England), 2012-10, Vol.28 (19), p.2502-2508

2012

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Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4

Cell reports (Cambridge), 2023-08, Vol.42 (8), p.112824-112824, Article 112824

2023

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Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages

EBioMedicine, 2021-10, Vol.72, p.103578-103578, Article 103578

2021

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Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival

Cellular physiology and biochemistry, 2019, Vol.52 (4), p.787-801

2019

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Multimodal analysis methods in predictive biomedicine

Computational and structural biotechnology journal, 2023-01, Vol.21, p.5829-5838

2023

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Reconstructing dynamic microRNA-regulated interaction networks

Proceedings of the National Academy of Sciences - PNAS, 2013-09, Vol.110 (39), p.15686-15691

2013

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Identification of transcription factor binding sites using ATAC-seq

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

A systematic analysis of circRNAs in subnuclear compartments

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection

A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Integrative prediction of gene expression with chromatin accessibility and conformation data

CpG content-dependent associations between transcription factors and histone modifications

Fiona: a parallel and automatic strategy for read error correction

Integrative analysis of epigenetics data identifies gene-specific regulatory elements

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal

HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Fostering accessible online education using Galaxy as an e-learning platform

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Bayesian ontology querying for accurate and noise-tolerant semantic searches

Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4

Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages

Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival

Multimodal analysis methods in predictive biomedicine

Reconstructing dynamic microRNA-regulated interaction networks

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