Publications by Bart Deplancke

Engineering next-generation microfluidic technologies for single-cell phenomics

Bart Deplancke, Johannes Julius Bues, Guido Van Mierlo, Camille Lucie Germaine Lambert, Orane Josiane Guillaume-Gentil

Springer Science and Business Media LLC2025

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw a ...

Nature Research2025

Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Bart Deplancke

Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves a ...

Springer Science and Business Media LLC2025

Transcriptomic profiling of murine GnRH neurons reveals developmental trajectories linked to human reproduction and infertility

Bart Deplancke, Vincent Roland Julien Gardeux, Julie Marie Russeil, Daniel Alpern

Rationale: Neurons producing Gonadotropin-Releasing Hormone (GnRH) are essential for human reproduction and have to migrate from nose to brain during prenatal life. Impaired GnRH neuron biology results in alterations of the reproductive axis, including del ...

2025

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

Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Daniel Alpern, Gilles Weder, Mustafa Demir, Dariia Gudkova, Hüseyin Baris Atakan

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 ...

Springer2024

Context transcription factors establish cooperative environments and mediate enhancer communication

Bart Deplancke, Vincent Roland Julien Gardeux, Julie Marie Russeil, Guido Van Mierlo, Judith Franziska Kribelbauer

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 ...

2024

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Bart Deplancke, Vincent Roland Julien Gardeux, Guido Van Mierlo, Judith Franziska Kribelbauer

Background: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify ...

2024

The evolution of DNA sequencing with microfluidics

Bart Deplancke, Johannes Julius Bues, Guido Van Mierlo, Camille Lucie Germaine Lambert

The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, we reflect on the key concepts underlying microfluidics and how resulting engineering advances ...

NATURE PORTFOLIO2024

DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

Bart Deplancke, Vincent Roland Julien Gardeux

Genome-wide association studies have advanced our understanding of complex traits, but studying how a GWAS variant can affect a specific trait in the human population remains challenging due to environmental variability. Drosophila melanogaster is in this ...

2024

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

Bart Deplancke, Vincent Roland Julien Gardeux

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 ...

Nature Research2024