Carsten O. Daub
YOU?
Author Swipe
View article: Distinct Phenotypes of Peripheral Innate Lymphoid Cells and T Cells in Type 2 and Non‐Type 2 Asthma
Distinct Phenotypes of Peripheral Innate Lymphoid Cells and T Cells in Type 2 and Non‐Type 2 Asthma Open
Background Investigation of T cell and innate lymphoid cell (ILC) subsets in type 2 (T2) and non‐type 2 (non‐T2) asthma are needed to elucidate disease mechanisms. In this study, we aimed to identify ILC, CD4+, and CD8+ T cell populations …
View article: P-129 Oxygen levels alter energy metabolism in bovine preimplantation embryos
P-129 Oxygen levels alter energy metabolism in bovine preimplantation embryos Open
Study question What is the effect of oxygen (O2) levels on the transcriptomic profile and embryonic genome activation of bovine embryos during the in vitro culture? Summary answer Normoxia (20% O2) delayed transcriptomic reprogramming and …
View article: Oxygen level alters energy metabolism in bovine preimplantation embryos
Oxygen level alters energy metabolism in bovine preimplantation embryos Open
View article: Oxygen level alters energy metabolism in bovine preimplantation embryos
Oxygen level alters energy metabolism in bovine preimplantation embryos Open
STUDY QUESTION What is the effect of different oxygen (O 2 ) levels on the transcriptomic profile of bovine embryos during the in vitro culture? SUMMARY ANSWER Embryos grown in hypoxia (6% O 2 ) from zygotes until the blastocyst stage had …
View article: The DoGA consortium expression atlas of promoters and genes in 100 canine tissues
The DoGA consortium expression atlas of promoters and genes in 100 canine tissues Open
The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disea…
View article: Enhancers regulate genes linked to severe and mild childhood asthma
Enhancers regulate genes linked to severe and mild childhood asthma Open
View article: Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training
Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training Open
Exercise training has tremendous systemic tissue-specific health benefits, but the molecular adaptations to long-term exercise training are not completely understood. We investigated the skeletal muscle proteome of highly endurance-trained…
View article: Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human Open
Background Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiol…
View article: Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements Open
View article: Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics
Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics Open
Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, w…
View article: Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network Open
View article: Sequence determinants of human gene regulatory elements
Sequence determinants of human gene regulatory elements Open
DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger se…
View article: Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog
Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog Open
View article: Dog colour patterns explained by modular promoters of ancient canid origin
Dog colour patterns explained by modular promoters of ancient canid origin Open
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps r…
View article: Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish Open
Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-…
View article: Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements"
Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements" Open
This record contains the training, test and validation datasets used to train and evaluate the machine learning models in manuscript: Sahu, Biswajyoti, et al. "Sequence determinants of human gene regulatory elements." (2021).
View article: Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements"
Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements" Open
This record contains the training, test and validation datasets used to train and evaluate the machine learning models in manuscript: Sahu, Biswajyoti, et al. "Sequence determinants of human gene regulatory elements." (2021).
View article: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network Open
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a spe…
View article: The RNA content of human sperm reflects prior events in spermatogenesis and potential post-fertilization effects
The RNA content of human sperm reflects prior events in spermatogenesis and potential post-fertilization effects Open
Transcriptome analyses using high-throughput methodologies allow a deeper understanding of biological functions in different cell types/tissues. The present study provides an RNA-seq profiling of human sperm mRNAs and lncRNAs (messenger an…
View article: Micro-biopsy for detection of gene expression changes in ischemic swine myocardium: A pilot study
Micro-biopsy for detection of gene expression changes in ischemic swine myocardium: A pilot study Open
Micro-endomyocardial biopsy (micro-EMB) is a novel catheter-based biopsy technique, aiming to increase flexibility and safety compared to conventional EMB. The technique was developed and evaluated in healthy swine. Therefore, the ability …
View article: Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State
Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State Open
Selective hepatic insulin resistance is a feature of obesity and type 2 diabetes. Whether similar mechanisms operate in white adipose tissue (WAT) of obese subjects and to what extent these are normalized by weight loss is unknown. We dete…
View article: Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State
Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State Open
Selective hepatic insulin resistance is a feature of obesity and type 2 diabetes. Whether similar mechanisms operate in white adipose tissue (WAT) of obese subjects and to what extent these are normalized by weight loss is unknown. We dete…
View article: Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State
Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State Open
Selective hepatic insulin resistance is a feature of obesity and type 2 diabetes. Whether similar mechanisms operate in white adipose tissue (WAT) of those with obesity and to what extent these are normalized by weight loss are unknown. We…
View article: Sequence determinants of human gene regulatory elements
Sequence determinants of human gene regulatory elements Open
DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. To obtain a global and unbiased view of the relative importance of different sequence determinants in g…
View article: Ten simple rules for annotating sequencing experiments
Ten simple rules for annotating sequencing experiments Open
View article: Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma Open
View article: A putative silencer variant in a spontaneous canine model of retinitis pigmentosa
A putative silencer variant in a spontaneous canine model of retinitis pigmentosa Open
Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30-80% of the RP patients the genetic cause remains unknown. A similar phenotype, …
View article: *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments Open
Background Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotati…
View article: Identification and transfer of spatial transcriptomics signatures for cancer diagnosis
Identification and transfer of spatial transcriptomics signatures for cancer diagnosis Open
Background Distinguishing ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC) regions in clinical biopsies constitutes a diagnostic challenge. Spatial transcriptomics (ST) is an in situ capturing method, which allows quant…
View article: Referee report. For: COPO: a metadata platform for brokering FAIR data in the life sciences [version 1; peer review: 1 approved, 1 approved with reservations]
Referee report. For: COPO: a metadata platform for brokering FAIR data in the life sciences [version 1; peer review: 1 approved, 1 approved with reservations] Open