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

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

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

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, Judith Franziska Kribelbauer, Guido Van Mierlo

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

Single-Cell Transcriptomic and Spatial Characterization of Multipotent Stromal Cells in Homeostatic, Remodeled, and In Vitro Expanded Human Bone Marrow

Jessica Sordet, Bart Deplancke

2024

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

Bart Deplancke, Pernille Yde Rainer, Radiana Ferrero, Julie Marie Russeil, Magda Zachara, Daniel Alpern, Vincent Roland Julien Gardeux, Jörn Pezoldt, Guido Van Mierlo

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 ...

Cell Press2024

Single-cell biology: what does the future hold?

Bart Deplancke

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." ...

WILEY2023

Biological material pooling device for biological or biomolecule purification

Bart Deplancke, Riccardo Dainese, Daniel Alpern

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 ...

2023

Pseudomonas aeruginosa type IV pili actively induce mucus contraction to form biofilms in tissue-engineered human airways

Bart Deplancke, Lorenzo Anton-Louis Talà, Tamara Rossy, Alexandre Louis André Persat, Jörn Pezoldt

The opportunistic pathogen Pseudomonas aeruginosa causes antibiotic-recalcitrant pneumonia by forming biofilms in the respiratory tract. Despite extensive in vitro experimentation, how P. aeruginosa forms biofilms at the airway mucosa is unresolved. To inv ...

PUBLIC LIBRARY SCIENCE2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

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

NATURE PORTFOLIO2023

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

Olivier Burri, Giovanna Ambrosini, Bart Deplancke, Arne Seitz, Olaia Maria Naveiras Torres-Quiroga, Frédérica Schyrr, Rita Sarkis, Mariangela Costanza, Martin Weigert

2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Judith Franziska Kribelbauer, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

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

Bart Deplancke, Jorieke Weiden, Guido Van Mierlo

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 ...

AMER CHEMICAL SOC2023

System and method for single cell phenotypical profiling and deterministic nanoliter-droplet encapsulation and deterministic droplet consortia assemblies

Bart Deplancke, Johannes Julius Bues, Jörn Pezoldt

The present invention concerns a system for phenotypical profiling of at least one object and deterministic nanoliter-droplet encapsulation, comprising sample supplying means, buffer supplying means; a microfluidic chip comprising an encapsulation area or ...

2023