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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Bioinformatics, 2011-12, Vol.27 (24), p.3423-3424

2011

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Role of LDB1 in the transition from chromatin looping to transcription activation

Genes & development, 2014-06, Vol.28 (12), p.1278-1290

2014

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The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions

Cell reports (Cambridge), 2017-06, Vol.19 (12), p.2490-2502

2017

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Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

Developmental cell, 2014-12, Vol.31 (6), p.761-773

2014

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Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Nature communications, 2023-07, Vol.14 (1), p.3931-3931, Article 3931

2023

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Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages

Nature communications, 2022-07, Vol.13 (1), p.4257-18, Article 4257

2022

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Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

eLife, 2021-01, Vol.10

2021

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An epigenome atlas of neural progenitors within the embryonic mouse forebrain

Nature communications, 2022-07, Vol.13 (1), p.4196-4196, Article 4196

2022

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Cerebrospinal Fluid Protein Biomarker Discovery in CLN3

Journal of proteome research, 2023-07, Vol.22 (7), p.2493-2508

2023

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Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis

Nature communications, 2023-09, Vol.14 (1), p.5687-15, Article 5687

2023

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Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

PLoS genetics, 2018-03, Vol.14 (3), p.e1007276-e1007276

2018

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Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain

eLife, 2022-02, Vol.11

2022

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RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function

Genes & development, 2011-08, Vol.25 (16), p.1686-1701

2011

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Profiles of Wnt pathway gene expression during tooth morphogenesis

Frontiers in physiology, 2024-01, Vol.14, p.1316635-1316635

2024

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Tissue-specific regulation of chromatin insulator function

PLoS genetics, 2012-11, Vol.8 (11), p.e1003069

2012

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Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1

International journal of molecular sciences, 2019-12, Vol.21 (1), p.292

2019

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Correlation of age of onset and clinical severity in Niemann-Pick disease type C1 with lysosomal abnormalities and gene expression

Scientific reports, 2022-02, Vol.12 (1), p.2162-2162, Article 2162

2022

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Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles

Frontiers in cellular neuroscience, 2024-02, Vol.18, p.1334244-1334244

2024

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Mediation of Drosophila autosomal dosage effects and compensation by network interactions

Genome biology, 2012-01, Vol.13 (4), p.r28-r28

2012

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SMAD3 mutation in LDS3 causes bone fragility by impairing the TGF-β pathway and enhancing osteoclastogenesis

Bone Reports, 2022-12, Vol.17, p.101603-101603, Article 101603

2022

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Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1

Biomarker research, 2023-01, Vol.11 (1), p.14-14, Article 14

2023

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Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization

Nucleic acids research, 2020-10, Vol.48 (18), p.10226-10240

2020

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The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila

Journal of cell science, 2019-03, Vol.132 (5)

2019

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Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

Nature genetics, 2023-02, Vol.55 (2), p.280-290

2023

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A compendium of RNA-binding motifs for decoding gene regulation

Nature (London), 2013-07, Vol.499 (7457), p.172-177

2013

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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Role of LDB1 in the transition from chromatin looping to transcription activation

The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions

Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

An epigenome atlas of neural progenitors within the embryonic mouse forebrain

Cerebrospinal Fluid Protein Biomarker Discovery in CLN3

Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function

Profiles of Wnt pathway gene expression during tooth morphogenesis

Tissue-specific regulation of chromatin insulator function

Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1

Correlation of age of onset and clinical severity in Niemann-Pick disease type C1 with lysosomal abnormalities and gene expression

Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles

Mediation of Drosophila autosomal dosage effects and compensation by network interactions

SMAD3 mutation in LDS3 causes bone fragility by impairing the TGF-β pathway and enhancing osteoclastogenesis

Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1

Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization

The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila

Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

A compendium of RNA-binding motifs for decoding gene regulation

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