Publications by Bart Deplancke

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Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITEseq, single-nuclei sequencing, spatial tran ...

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional ...

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here ...

Adoptive T cell therapyhas successfully been implementedfor thetreatment of cancer. Nevertheless, ex vivo expansion of T cells byartificial antigen-presenting cells (aAPCs) remains cumbersome andcan compromise T cell functionality, thereby limiting their t ...

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

The present invention concerns a system for immunoprecipitation of a protein-DNA complex or for capture of a protein-DNA complex including: - a microfluidic device including a plurality of antibody units, wherein each antibody unit includes at least one mi ...

White adipose tissue (WAT) is a cellularly heterogeneous endocrine organ that not only serves as an energy reservoir, but also actively participates in metabolic homeostasis. Among the main constituents of adipose tissue are adipocytes, which arise from ad ...

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifac ...

Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is s ...

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influen ...

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revea ...

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we ...

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to- ...

DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regu ...

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

Site-specific transcription factors (TFs) play an essential role in mammalian development and function as they are vital for the majority of cellular processes. Despite their biological importance, TF proteomic data is scarce in the literature, likely due ...

Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key ...

Bart Deplancke

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Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Profiling of Single-Cell Transcriptomes

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Direct In Vivo Activation of T Cells with Nanosized Immunofilaments Inhibits Tumor Growth and Metastasis

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

System for capture or immunoprecipitation of a protein-dna complex

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Transcription factor proteomics - Tools, applications, and challenges

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer

Dissecting the brown adipogenic regulatory network using integrative genomics

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

A mammalian transcription factor-specific peptide repository for targeted proteomics

Variable Outcome of Mutations

The Genetics of Transcription Factor DNA Binding Variation