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

W. Saelens; O. Pushkarev; B. Deplancke 

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

A. Loft; M. P. Emont; A. Weinstock; A. Divoux; A. Ghosh et al. 

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

Y. Zouaghi; D. Alpern; V. Gardeux; J. Russeil; B. Deplancke et al. 

Leveraging chromatin modules to explore the impact of regulatory variation on disease

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

O. Pushkarev; G. van Mierlo; J. F. Kribelbauer; W. Saelens; V. Gardeux et al. 

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

E. Erdil; A. S. Becker; M. Schwyzer; B. Martinez-Tellez; J. R. Ruiz et al. 

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

V. Gardeux; R. P. Bevers; F. P. David; E. Rosschaert; R. Rochepeau et al. 

Context transcription factors establish cooperative environments and mediate enhancer communication

J. F. Kribelbauer-Swietek; O. Pushkarev; V. Gardeux; K. Faltejskova; J. Russeil et al. 

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

R. Ferrero; P. Y. Rainer; M. Rumpler; J. Russeil; M. Zachara et al. 

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

S. Boder-Pasche; M. Demir; S. Heub; M. Garzuel; R. Ischer et al. 

The evolution of DNA sequencing with microfluidics

C. L. G. Lambert; G. van Mierlo; J. J. Bues; O. J. Guillaume-Gentil; B. Deplancke 

Systematic benchmarking of single-cell ATAC-sequencing protocols

F. V. De Rop; G. Hulselmans; C. Flerin; P. Soler-Vila; A. Rafels et al. 

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

T. Rossy; T. Distler; L. Meirelles; J. Pezoldt; J. Kim et al. 

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

L. Weiss; J. Weiden; Y. Dolen; E. M. Grad; E. A. W. van Dinther et al. 

Single-cell biology: what does the future hold?

M. Polychronidou; J. Hou; M. M. Babu; P. Liberali; I. Amit et al. 

Chromatin modules and their implication in genomic organization and gene regulation

G. van Mierlo; O. Pushkarev; J. F. Kribelbauer; B. Deplancke 

Cross-anatomical single-cell definition and characterization of human adipose progenitor niche

Novel quantitative bioengineered tools to track human bone marrow niche cellular constituents in health and disease

A single-cell-based characterization of mammalian adipose stem and progenitor cell heterogeneity and function

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

J. Pezoldt; C. Wiechers; M. Zou; M. Litovchenko; M. Biocanin et al. 

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

S. Lee; Y-C. Chen; A. E. Gillen; J. M. Taliaferro; B. Deplancke et al. 

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

M. Zachara; P. Y. Rainer; H. Hashimi; J. M. Russeil; D. Alpern et al. 

Live-seq enables temporal transcriptomic recording of single cells

W. Chen; O. Guillaume-Gentil; P. Y. Rainer; C. G. Gaebelein; W. Saelens et al. 

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

U. Lee; P. Stuelsatz; S. Karaz; D. W. McKellar; J. Russeil et al. 

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

G. Llimos; V. Gardeux; U. Koch; J. F. Kribelbauer; A. Hafner et al. 

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

H. Li; J. Janssens; M. De Waegeneer; S. S. Kolluru; K. Davie et al. 

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

J. Bues; M. Biocanin; J. Pezoldt; R. Dainese; A. Chrisnandy et al. 

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

M. Guilliams; J. Bonnardel; B. Haest; B. Vanderborght; C. Wagner et al. 

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

O. Naveiras; F. Schyrr; V. Campos; A. Alonso-Calleja; B. von der Weid et al. 

Current challenges in understanding the role of enhancers in disease

J. B. Zaugg; P. Sahlen; R. Andersson; M. Alberich-Jorda; W. de Laat et al. 

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

J. Pezoldt; C. Wiechers; F. Erhard; U. Rand; T. Bulat et al. 

Recent advances in trajectory inference from single-cell omics data

L. Deconinck; R. Cannoodt; W. Saelens; B. Deplancke; Y. Saeys 

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis

A. Bast-Habersbrunner; C. Kiefer; P. Weber; T. Fromme; A. Schiessl et al. 

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

P. V’kovski; M. Gultom; J. N. Kelly; S. Steiner; J. Russeil et al. 

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

A. Kaya-Copur; F. Marchiano; M. Y. Hein; D. Alpern; J. Russeil et al. 

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

M. Litovchenko; A. C. A. Meireles-Filho; M. Frochaux; R. P. J. Bevers; A. Prunotto et al. 

Towards scalable and deterministic single cell gene expression profiling

Toward a mechanistic understanding of variable chromatin modules

The role and transcriptional regulation of FAM46A in adipocyte differentiation

Developing new tools to study and program cell fate at the single-cell level

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

J. Liu; M. Frochaux; V. Gardeux; B. Deplancke; M. Robinson-Rechavi 

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

M. Kapun; M. G. Barron; F. Staubach; D. J. Obbard; R. A. W. Wiberg et al. 

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

P. Turelli; C. Playfoot; D. Grun; C. Raclot; J. Pontis et al. 

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

F. P. A. David; M. Litovchenko; B. Deplancke; V. Gardeux 

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

R. Dainese; V. Gardeux; G. Llimos; D. Alpern; J. Y. Jiang et al. 

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

M. V. Frochaux; M. B. Sleiman; V. Gardeux; R. Dainese; B. Hollis et al. 

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

M. Bou Sleiman; M. V. Frochaux; T. Andreani; D. Osman; R. Guigo et al. 

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity

R. Ferrero; P. Rainer; B. Deplancke 

A single-cell-based identification and characterisation of Aregs, an inhibitory subpopulation of adipose stem and precursor cells

Computational study of transcription factor binding sites

Multi-omics reveals abundant mitochondrial genomic and circadian expression variation in the Drosophila Genetic Reference Panel

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning

Y. Li; P. C. Schwalie; A. Bast-Habersbrunner; S. Mocek; J. Russeil et al. 

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

E. T. Friman; C. Deluz; A. C. A. Meireles-Filho; S. Govindan; V. Gardeux et al. 

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel

R. P. J. Bevers; M. Litovchenko; A. Kapopoulou; V. S. Braman; M. R. Robinson et al. 

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

H. Okada; R. Yagi; V. Gardeux; B. Deplancke; E. Hafen 

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress

D. Ma; M. Bou-Sleiman; P. Joncour; C-E. Indelicato; M. Frochaux et al. 

Multilevel regulation of the glass locus during Drosophila eye development

C. Fritsch; F. J. Bernardo-Garcia; T-H. Humberg; A. K. Mishra; S. Miellet et al. 

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip

M. Biocanin; J. Bues; R. Dainese; E. Amstad; B. Deplancke 

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer

W. Chen; P. C. Schwalie; E. V. Pankevich; C. Gubelmann; S. K. Raghav et al. 

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

L. Shokri; S. Inukai; A. Hafner; K. Weinand; K. Hens et al. 

The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance

N. Vannini; V. Campos; M. Girotra; V. Trachsel; S. Rojas-Sutterlin et al. 

Differential regulation of RNA polymerase III genes during liver regeneration

M. Yeganeh; V. Praz; C. Carmeli; D. Villeneuve; L. Rib et al. 

Elucidating regulatory mechanisms shaping the transcriptome and proteome of the gut immune response in Drosophila melanogaster

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

The role of the transcriptional regulator BCL6 in adipose tissue development and remodeling

System for capture or immunoprecipitation of a protein-dna complex

B. Deplancke; R. Dainese 

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells

A. M-F. Delachat; N. Guidotti; A. L. Bachmann; A. C. Meireles-Filho; H. Pick et al. 

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

N. Vannini; V. Campos; M. Girotra; S. Rojas-Sutterlin; J. Tratwal et al. 

The phenotypic impact of naturally occurring genetic and molecular mitochondrial variation in a Drosophila Genetic Reference Population

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

Device for high throughput single-cell studies

B. Deplancke; J. Bues; R. Dainese; M. Biocanin 

Hippo, TGF-beta, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection

P. Houtz; A. Bonfini; X. Liu; J. Revah; A. Guillou et al. 

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

F. P. A. David; J. Rougemont; B. Deplancke 

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

V. Gardeux; F. P. A. David; A. Shajkofci; P. C. Schwalie; B. Deplancke 

Dissecting the brown adipogenic regulatory network using integrative genomics

R. N. Pradhan; J. J. Bues; V. Gardeux; P. C. Schwalie; D. Alpern et al. 

Tissue-specific enhancer repression through molecular integration of cell signaling inputs

L. H. Mojica-Vazquez; M. H. Benetah; A. Baanannou; S. Bernat-Fabre; B. Deplancke et al. 

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

P. C. Schwalie; P. Ordonez-Moran; J. Huelsken; B. Deplancke 

Profiling of Single-Cell Transcriptomes

W. Chen; V. Gardeux; A. Meireles-Filho; B. Deplancke 

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

J. A. Sobel; I. Krier; T. Andersin; S. Raghav; D. Canella et al. 

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

A. F. Mcdaid; P. K. Joshi; E. Porcu; A. Komljenovic; H. Li et al. 

Disease-Informed Bayesian Association Scan Reveals Novel Loci Associated with Human Lifespan and Linked Biomarkers

A. F. Mcdaid; P. K. Joshi; N. Mounier; E. Porcu; A. Komljenovic et al. 

Transcription factor proteomics – Tools, applications, and challenges

J. Simicevic; B. Deplancke 

Gene regulatory mechanisms underlying the intestinal innate immune response

A. C. A. Meireles-Filho; B. Deplancke 

Gene regulatory dynamics underlying brown fat cell differentiation

Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens

G. Kalay; R. Lusk; M. Dome; K. Hens; B. Deplancke et al. 

PDF Signaling Is an Integral Part of the Drosophila Circadian Molecular Oscillator

S. Mezan; J. D. Feuz; B. Deplancke; S. Kadener 

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

A. Isakova; Y. Berset; V. Hatzimanikatis; B. Deplancke 

The Genetics of Transcription Factor DNA Binding Variation

B. Deplancke; D. Alpern; V. Gardeux 

Microfluidic device and method for isolation of nucleic acids

A. Isakova; B. Deplancke 

Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence

M. S. B. Sleiman; D. Osman; A. Massouras; A. A. Hoffmann; B. Lemaitre et al. 

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

C. Schertel; M. Albarca; C. Rockel-Bauer; N. W. Kelley; J. Bischof et al. 

A mammalian transcription factor-specific peptide repository for targeted proteomics

J. Simicevic; M. Moniatte; R. Hamelin; E. Ahrne; B. Deplancke 

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

K. R. Nitta; A. Jolma; Y. Yin; E. Morgunova; T. Kivioja et al. 

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

S. M. Waszak; O. Delaneau; A. R. Gschwind; H. Kilpinen; S. K. Raghav et al. 

Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research

N. Moullan; L. Mouchiroud; X. Wang; D. Ryu; E. G. Williams et al. 

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

S. M. Waszak; H. Kilpinen; A. R. Gschwind; A. Orioli; S. K. Raghav et al. 

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

W. Huang; A. Massouras; Y. Inoue; J. Peiffer; M. Ramia et al. 

Dissecting the DNA binding principles of transcription factor monomers and heterodimers

Context-specific regulation of BMAL1 target genes during the circadian rhythm in mouse

An integrative genomics approach toward deciphering the regulatory logic of phase-specific circadian transcription in the mouse liver