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Bart Deplancke

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Publications associées (115)

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Vincent Roland Julien Gardeux

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 ...

2023

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke, Sandy Lee

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 ...

Nature Portfolio2022

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Bart Deplancke, Wouter Saelens

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 ...

CELL PRESS2022

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

Bart Deplancke, Olaia Maria Naveiras Torres-Quiroga, Rita Sarkis

SPRINGER2022

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

Bart Deplancke, Fabrice David, Vincent Roland Julien Gardeux

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 ...

American Association for the Advancement of Science2022

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

Bart Deplancke, Mustafa Demir, Riccardo Dainese, Daniel Alpern

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 ...

2022

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

Gerardo Turcatti, Damiano Banfi, Bart Deplancke, Fabien Kuttler, Aurélien Laurent Jean-Charles Oggier, Pernille Yde Rainer, Vasco Ledebur de Antas de Campos, Vincent Roland Julien Gardeux

ELSEVIER SCIENCE INC2022

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner

Bart Deplancke, Pernille Yde Rainer, Radiana Ferrero, Julie Marie Russeil, Horia Hashimi, Magda Zachara, Daniel Alpern, Maria Litovchenko

Adipose stem and precursor cells (ASPCs) give rise to adipocytes and determine the composition and plasticity of adipose tissue. Recently, several studies have demonstrated that ASPCs partition into at least three distinct cell subpopulations, including th ...

WILEY2022

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Matthias Lütolf, Bart Deplancke, Saba Rezakhani, Esther Amstad, Riccardo Dainese, Julie Marie Russeil, Antonius Chrisnandy, Vincent Roland Julien Gardeux, Johannes Julius Bues, Marjan Biocanin, Rita Sarkis, Jörn Pezoldt

DisCo is a deterministic droplet microfluidics tool for single-cell analysis on low cell input samples, which is demonstrated to profile individual intestinal organoids and in vivo-derived small tissues. ...

NATURE PORTFOLIO2022

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

Bart Deplancke, Maria Deak, Sonia Karaz, Umji Lee, Julie Marie Russeil, Benjamin D. Cosgrove

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 ...

CELL PRESS2022

Live-seq enables temporal transcriptomic recording of single cells

Bart Deplancke, Pernille Yde Rainer, Riccardo Dainese, Wanze Chen, Magda Zachara, Vincent Roland Julien Gardeux, Wouter Saelens, Orane Josiane Guillaume-Gentil

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Liv ...

NATURE PORTFOLIO2022

Current challenges in understanding the role of enhancers in disease

Bart Deplancke

Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing eviden ...

NATURE PORTFOLIO2022

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

Bart Deplancke, Julie Marie Russeil, Wanze Chen, Vincent Roland Julien Gardeux, Maria Litovchenko, Marjan Biocanin, Jörn Pezoldt, Guido Van Mierlo

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 ...

Nature Portfolio2022

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

Freddy Radtke, Ute Koch, Bart Deplancke, Riccardo Dainese, Julie Marie Russeil, Daniel Alpern, Vincent Roland Julien Gardeux, Maria Litovchenko, Gerard Llimos Aubach, Jörn Pezoldt, Judith Franziska Kribelbauer

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of h ...

Nature Portfolio2022

Recent advances in trajectory inference from single-cell omics data

Bart Deplancke, Wouter Saelens

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 ...

ELSEVIER2021

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

Bastien Mangeat, Bart Deplancke, Julie Marie Russeil, Daniel Alpern, Vincent Roland Julien Gardeux, Elisa Cora, Jörn Pezoldt

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- ...

2021

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis

Bart Deplancke, Petra Catalina Schwalie

The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remai ...

WILEY2021

Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection

Bart Deplancke

Our understanding of the composition and functions of splenic stromal cells remains incomplete. Here, based on analysis of over 20,000 single cell transcriptomes of splenic fibroblasts, we characterized the phenotypic and functional heterogeneity of these ...

NATURE PORTFOLIO2021

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior

Michael Vincent Frochaux, Bart Deplancke, Matteo Dal Peraro, Antonio Carlos Alves Meireles Filho, Roel Paulus Josephus Bevers, Alessio Prunotto, Julie Marie Russeil, Virginie Sandra Braman, Vincent Roland Julien Gardeux, Maria Litovchenko, Brian Dennis Hollis

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transc ...

2021

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

Bart Deplancke, Julie Marie Russeil, Daniel Alpern

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 ...

2021

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