Publications by Bart Deplancke

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Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription ...

Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic ...

Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors ...

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said meth ...

Molecular insights into the genetic control of development have been mainly derived from single gene mutant studies. Francesconi and Lehner (2013) report now in Nature a genome-wide map of natural sequence variants that affect the temporal expression dynam ...

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3 cDNA libraries for dozens of sample ...

The present invention concerns a biological material pooling device for biological or biomolecule purification comprising a receptacle including a first orifice comprising ordefining a rectangular opening, the receptacle being configured to receive at leas ...

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

Although the gut is a central organ of Eumetazoans and is essential for organismal health, our understanding of its morphological and molecular determinants remains rudimentary. Here, we provide a comprehensive atlas of Drosophila adult midgut. Specificall ...

The present invention concerns a microfluidic device or chip including at least one inlet for introducing at least one object into the device; an oil inlet for introducing an oil that supports droplet formation into the device or a droplet forming substanc ...

Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed wit ...

Trajectory inference methods have emerged as a novel class of single-cell bioinformatics tools to study cellular dynamics at unprecedented resolution. Initial development focused on adapting methods based on clustering or graph traversal, but recent advanc ...

In this Editorial, our Chief Editor and members of our Advisory Editorial Board discuss recent breakthroughs, current challenges, and emerging opportunities in single-cell biology and share their vision of "where the field is headed." ...

The present invention concerns a microfluidic device for mechanically induced trapping of molecular interactions comprising at least a first unit cell and a second unit cell, each unit cell comprising - a membrane chamber comprising a membrane, - a flow ch ...

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Bart Deplancke

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Context transcription factors establish cooperative environments and mediate enhancer communication

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

Primer-initiated sequence synthesis to detect and assemble structural variants

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Rounding Up Natural Gene Expression Variation during Development

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Biological material pooling device for biological or biomolecule purification

Systematic benchmarking of single-cell ATAC-sequencing protocols

Epigenomic landscape defines immuno-modulatory properties across lymph node stromal cell subsets

A Label-Free, High-Throughput Phenotypic Screen Of Adipocytic Differentiation Modulators To Accelerate Hematopoietic Recovery

Morphological and Molecular Characterization of Adult Midgut Compartmentalization in Drosophila

Device for high throughput single-cell studies

The NAD plus Salvage Pathway Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance and Asymmetric Division

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

MarrowQuant 2.0: clinical application of a user-friendly digital hematopathology tool for human bone marrow trephine biopsies

Recent advances in trajectory inference from single-cell omics data

Single-cell biology: what does the future hold?

Microfluidic device and method for isolation of nucleic acids

Differential regulation of RNA polymerase III genes during liver regeneration