Publications by Bart Deplancke

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Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research gr ...

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewi ...

Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and meta-bolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator ...

Although several mouse and human adipose SVF cellular subpopulations have by now been identified, we still lack an understanding of the cellular and functional variability of adipose stem and progenitor cell (ASPC) populations across human fat depots. To a ...

Background RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study ...

Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription factors encoded by the genome ...

Gut-draining mesenteric lymph nodes (LN) provide the framework to shape intestinal adaptive immune responses. Based on the transcriptional signatures established by our previous work, the composition and immunomodulatory function of LN stromal cells (SC) v ...

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently ...

Skeletal muscles are composed of gigantic cells called muscle fibers, packed with force-producing myofibrils. During development, the size of individual muscle fibers must dramatically enlarge to match with skeletal growth. How muscle growth is coordinated ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling. This makes these fat cells attractive therapeutic targets to tackle the burgeoning issue of obesity, which itself is coupled to insulin resistance, type 2 diabetes, cardiovascular a ...

During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segme ...

The standard method for identifying active Brown Adipose Tissue (BAT) is [18F]-Fluorodeoxyglucose ([18F]-FDG) PET/CT imaging, which is costly and exposes patients to radiation, making it impractical for population studies. These issues can be addressed wit ...

Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to contr ...

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed ti ...

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

A long-standing question in biology is whether multipotent somatic stem and progenitor cells (SSPCs) feature molecular properties that could guide their system-independent identification. Population-based transcriptomic studies have so far not been able to ...

Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sex ...

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing geneand transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification o ...

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Bart Deplancke

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ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle

A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Global and stage specific patterns of krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells

Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34(+) stromal cell subsets

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

A systems perspective on brown adipogenesis and metabolic activation

Topology and dynamics of the zebrafish segmentation clock core circuit

Predicting standardized uptake value of brown adipose tissue from CT scans using convolutional neural networks

Multilevel regulation of the glass locus during Drosophila eye development

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Cross-Tissue Identification of Somatic Stem and Progenitor Cells Using a Single-Cell RNA-Sequencing Derived Gene Signature

Sex-dependent and sex-independent regulatory systems of size variation in natural populations

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

Diverse cell-specific patterns of alternative polyadenylation in Drosophila