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Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data

PloS one, 2022-01, Vol.17 (1), p.e0263344-e0263344

2022

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A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

Nature communications, 2020-08, Vol.11 (1), p.4318-4318, Article 4318

2020

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A universal tool for predicting differentially active features in single-cell and spatial genomics data

Scientific reports, 2023-07, Vol.13 (1), p.11830-11830, Article 11830

2023

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The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

Nature immunology, 2010-10, Vol.11 (10), p.936-944

2010

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Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1

The European respiratory journal, 2021-03, Vol.57 (3), p.2000018

2021

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Regnase-1 Prevents Pulmonary Arterial Hypertension Through mRNA Degradation of Interleukin-6 and Platelet-Derived Growth Factor in Alveolar Macrophages

Circulation (New York, N.Y.), 2022-09, Vol.146 (13), p.1006-1022

2022

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Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

Proceedings of the National Academy of Sciences - PNAS, 2016-04, Vol.113 (17), p.E2393-E2402

2016

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Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

Genome Biology, 2018-09, Vol.19 (1), p.138-15, Article 138

2018

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Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

BMC genomics, 2016-12, Vol.17 (Suppl 13), p.1032-1032, Article 1032

2016

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Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs

Cell reports (Cambridge), 2017-05, Vol.19 (8), p.1614-1630

2017

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The Transcription Factor Jdp2 Controls Bone Homeostasis and Antibacterial Immunity by Regulating Osteoclast and Neutrophil Differentiation

Immunity (Cambridge, Mass.), 2012-12, Vol.37 (6), p.1024-1036

2012

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Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism

Science signaling, 2022-04, Vol.15 (729), p.eabm5011

2022

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A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster

PloS one, 2014-08, Vol.9 (8), p.e104342-e104342

2014

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Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages

Cell reports (Cambridge), 2020-07, Vol.32 (2), p.107906-107906, Article 107906

2020

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Modeling tissue-specific structural patterns in human and mouse promoters

Nucleic acids research, 2010-01, Vol.38 (1), p.17-25

2010

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The N 6 -methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity

Nature communications, 2022-10, Vol.13 (1), p.6435-17

2022

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IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18

Proceedings of the National Academy of Sciences - PNAS, 2010-10, Vol.107 (41), p.17680-17685

2010

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Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression

Nucleic acids research, 2024-02, Vol.52 (3), p.1107-1119

2024

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A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

BMC genomics, 2012, Vol.13 Suppl 7 (Suppl 7), p.S11-S11

2012

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Modeling the cis -regulatory modules of genes expressed in developmental stages of Drosophila melanogaster

PeerJ (San Francisco, CA), 2017-05, Vol.5, p.e3389-e3389, Article e3389

2017

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Murine breast cancers disorganize the liver transcriptome in a zonated manner

Communications biology, 2023-01, Vol.6 (1), p.97-97, Article 97

2023

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Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment

Nature immunology, 2017-02, Vol.18 (2), p.173-183

2017

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A Parzen window-based approach for the detection of locally enriched transcription factor binding sites

BMC bioinformatics, 2013-01, Vol.14 (1), p.26-26, Article 26

2013

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Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation

Cell, 2013-05, Vol.153 (5), p.1036-1049

2013

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Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

Cell, 2015-05, Vol.161 (5), p.1058-1073

2015

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Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data

A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

A universal tool for predicting differentially active features in single-cell and spatial genomics data

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1

Regnase-1 Prevents Pulmonary Arterial Hypertension Through mRNA Degradation of Interleukin-6 and Platelet-Derived Growth Factor in Alveolar Macrophages

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs

The Transcription Factor Jdp2 Controls Bone Homeostasis and Antibacterial Immunity by Regulating Osteoclast and Neutrophil Differentiation

Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism

A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster

Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages

Modeling tissue-specific structural patterns in human and mouse promoters

The N 6 -methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity

IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

Modeling the cis -regulatory modules of genes expressed in developmental stages of Drosophila melanogaster

Murine breast cancers disorganize the liver transcriptome in a zonated manner

Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites

Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

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