List of works - Carsten O Daub

An atlas of active enhancers across human cell types and tissues

scientific article

A promoter-level mammalian expression atlas

scientific article

The regulated retrotransposon transcriptome of mammalian cells

scientific article (publication date: May 2009)

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

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

scientific article

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

scientific article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Tiny RNAs associated with transcription start sites in animals

scientific article published on 19 April 2009

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

The mutual information: detecting and evaluating dependencies between variables.

scientific article

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

scientific article

Hidden layers of human small RNAs

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

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

scientific article

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

scientific article

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

scientific article

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

scientific article

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

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

scientific article

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

scientific article

SAMStat: monitoring biases in next generation sequencing data

scientific article

Transcriptional features of genomic regulatory blocks

scientific article published on 19 April 2009

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

scientific article published on 19 April 2009

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

scientific article published on 19 April 2009

Promoter architecture of mouse olfactory receptor genes

scientific journal article

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

scientific article published on 30 January 2012

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

scientific article published on 12 November 2010

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

scientific article

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

scientific article

Optimization of turn-back primers in isothermal amplification

scientific article published on 9 February 2011

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

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals

scientific article

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

scientific article

MOIRAI: a compact workflow system for CAGE analysis

scientific article

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data

scientific article

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

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

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

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

scientific article

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

scientific article

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

scientific article published on 30 December 2013

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

scientific article published on 17 August 2016

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

scientific article published on 9 April 2015

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

scientific 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

List of works by Carsten O Daub

An atlas of active enhancers across human cell types and tissues

A promoter-level mammalian expression atlas

The regulated retrotransposon transcriptome of mammalian cells

An atlas of combinatorial transcriptional regulation in mouse and man

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

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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Tiny RNAs associated with transcription start sites in animals

Gateways to the FANTOM5 promoter level mammalian expression atlas

The mutual information: detecting and evaluating dependencies between variables.

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

Hidden layers of human small RNAs

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

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

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

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

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

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

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

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

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

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

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

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

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

SAMStat: monitoring biases in next generation sequencing data

Transcriptional features of genomic regulatory blocks

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

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

Promoter architecture of mouse olfactory receptor genes

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

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

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

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

Optimization of turn-back primers in isothermal amplification

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

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals

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

MOIRAI: a compact workflow system for CAGE analysis

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data

FANTOM5 CAGE profiles of human and mouse samples

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

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

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

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

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

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

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

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

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