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. 

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. 

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

R. Sarkis; O. Burri; C. Royer-Chardon; F. Schyrr; S. Blum et al. 

Chromatin modules and their implication in genomic organization and gene regulation

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

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

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

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

R. Dainese; D. Alpern; V. Gardeux; B. Deplancke 

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

J. Bues; J. Pezoldt; B. Deplancke 

Biological material pooling device for biological or biomolecule purification

R. Dainese; D. Alpern; B. Deplancke; K. Ragios 

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. 

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

R. Sarkis; O. Burri; C. Royer-Chardon; S. Blum; F. Schyrr 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. 

Molecular Regulation of Muscle Stem Cell Fate during Skeletal Muscle Regeneration and Aging

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

D. Alpern; R. Dainese; B. Deplancke; M. Demir 

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. 

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

Towards scalable and deterministic single cell gene expression profiling

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. 

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow

P-E. M. Thiriet; J. Pezoldt; G. Gambardella; K. Keim; B. Deplancke 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. 

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

M. Weger; D. Alpern; A. Cherix; S. Ghosal; J. Grosse et al. 

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

R. Ferrero; P. Rainer; B. Deplancke 

Computational study of transcription factor binding sites

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

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 

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

D. Alpern; V. Gardeux; J. Russeil; B. Mangeat; A. C. A. Meireles-Filho et al. 

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. 

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

J. Pezoldt; C. Wiechers; M. Zou; M. Litovchenko; K. Sitnik et al. 

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

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

Mechanistic insights into AMP-activated protein kinase-dependent gene expression

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

System for capture or immunoprecipitation of a protein-dna complex

B. Deplancke; R. Dainese 

Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases?

G. Etienne; A. Vian; M. Biočanin; B. Deplancke; E. Amstad 

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. 

Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation

Q. Wang; A. Song; W. Chen; P. Schwalie; F. Zhang et al. 

A stromal cell population that inhibits adipogenesis in mammalian fat depots

P. Schwalie; H. Dong; M. Zachara; J. Russeil; D. Alpern 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. 

Genetic determinants of healthy human immune variance: from humoral response to microbiome diversity

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 

Profiling of Single-Cell Transcriptomes

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

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 

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. 

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 

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. 

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. 

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

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

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

F. P. A. David; J. Rougemont; 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. 

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

A. Isakova; R. Groux; M. Imbeault; P. Rainer; D. Alpern 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. 

Gene regulatory mechanisms underlying the intestinal innate immune response

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

A systems perspective on brown adipogenesis and metabolic activation

R. N. Pradhan; M. Zachara; B. Deplancke 

Transcription factor proteomics – Tools, applications, and challenges

J. Simicevic; 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 

The Drosophila gut response to infection

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. 

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.