List of works - Carsten O Daub

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

scientific article published on 29 October 2013

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

scientific article

A promoter-level mammalian expression atlas

scientific article

A putative silencer variant in a spontaneous canine model of retinitis pigmentosa

scientific article published on 09 March 2020

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth

scientific article published on 13 September 2017

Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.

scientific article published on 30 December 2013

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

scientific article

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of active enhancers across human cell types and tissues

scientific article

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An atlas of human long non-coding RNAs with accurate 5' ends.

scientific article

An integrated expression atlas of miRNAs and their promoters in human and mouse.

scientific article

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

scientific article

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

scientific article published on 14 December 2015

Beyond the FANTOM4.

scientific article

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

scientific article

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

scientific article

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

scientific article

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

scientific article published on 01 August 2018

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

scientific article

Correction to: Relatively frequent switching of transcription start sites during cerebellar development

scientific article

Corrigendum: Tiny RNAs associated with transcription start sites in animals

scholarly article published in Nature Genetics

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

scientific article

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.

scientific article

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

scientific article published on 4 November 2015

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.

scientific article published on 19 May 2016

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

scientific article published on 6 January 2018

Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue

scientific article

Employing conservation of co-expression to improve functional inference

scientific article

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data

scientific article

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

scientific article published on 19 April 2009

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

scientific article

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals

scientific article

Hidden layers of human small RNAs

scientific article

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

scientific article published on 26 March 2014

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

scientific article published on 18 September 2019

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

scientific article published in March 2014

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

scientific article

Long-term improvement in aortic pulse wave velocity after weight loss can be predicted by white adipose tissue factors.

scientific article published on 21 November 2017

MOIRAI: a compact workflow system for CAGE analysis

scientific article

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data

scientific article

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

scientific article

MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines.

scientific article

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins

scientific article

NGSView: an extensible open source editor for next-generation sequencing data

scientific article

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

scientific article

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes

scientific article published on 30 January 2012

Optimization of turn-back primers in isothermal amplification

scientific article published on 9 February 2011

Prediction of function divergence in protein families using the substitution rate variation parameter alpha

scientific article published on 3 May 2006

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

scientific article

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β

scientific article published in Scientific Reports

Promoter architecture of mouse olfactory receptor genes

scientific journal article

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

scientific article published on 16 July 2015

Regional differences in gene expression and promoter usage in aged human brains.

scientific article

SAMStat: monitoring biases in next generation sequencing data

scientific article

SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes

scientific article

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

scientific article published in March 2018

TagDust--a program to eliminate artifacts from next generation sequencing data

scientific article

Telomerase reverse transcriptase regulates microRNAs

scientific article

Ten simple rules for annotating sequencing experiments

scientific article published on 05 October 2020

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

scientific article published on 17 August 2016

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 19 April 2009

The mutual information: detecting and evaluating dependencies between variables.

scientific article

The regulated retrotransposon transcriptome of mammalian cells

scientific article (publication date: May 2009)

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Tiny RNAs associated with transcription start sites in animals

scientific article published on 19 April 2009

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.

scientific article

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response

scientific article

Transcriptional features of genomic regulatory blocks

scientific article published on 19 April 2009

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles

scientific article published on 9 April 2015

Unamplified cap analysis of gene expression on a single-molecule sequencer.

scientific article

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 12 November 2010

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns

scientific article published on 3 November 2011

List of works by Carsten O Daub

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

A promoter-level mammalian expression atlas

A putative silencer variant in a spontaneous canine model of retinitis pigmentosa

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth

Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of active enhancers across human cell types and tissues

An atlas of combinatorial transcriptional regulation in mouse and man

An atlas of human long non-coding RNAs with accurate 5' ends.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

Beyond the FANTOM4.

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Correction to: Relatively frequent switching of transcription start sites during cerebellar development

Corrigendum: Tiny RNAs associated with transcription start sites in animals

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue

Employing conservation of co-expression to improve functional inference

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

FANTOM5 CAGE profiles of human and mouse samples

Gateways to the FANTOM5 promoter level mammalian expression atlas

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals

Hidden layers of human small RNAs

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Long-term improvement in aortic pulse wave velocity after weight loss can be predicted by white adipose tissue factors.

MOIRAI: a compact workflow system for CAGE analysis

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines.

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins

NGSView: an extensible open source editor for next-generation sequencing data

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes

Optimization of turn-back primers in isothermal amplification

Prediction of function divergence in protein families using the substitution rate variation parameter alpha

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β

Promoter architecture of mouse olfactory receptor genes

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

Regional differences in gene expression and promoter usage in aged human brains.

SAMStat: monitoring biases in next generation sequencing data

SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

TagDust--a program to eliminate artifacts from next generation sequencing data

Telomerase reverse transcriptase regulates microRNAs

Ten simple rules for annotating sequencing experiments

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The mutual information: detecting and evaluating dependencies between variables.

The regulated retrotransposon transcriptome of mammalian cells

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Tiny RNAs associated with transcription start sites in animals

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response

Transcriptional features of genomic regulatory blocks

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles

Unamplified cap analysis of gene expression on a single-molecule sequencer.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns