Bart Deplancke

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

COSMIC, a generative model, quantifies the relationship between nuclear morphology and gene expression using paired single-cell data, revealing morphology-associated genes in prostate cancer and spatial transcriptomics of zebrafish embryos.

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

This study shows that growth factor-free synthetic matrices reveal donor-specific differences in human skeletal progenitor cell osteogenic potential, which are masked by conventional methods.

The paper shows pneumococcal infection activates innate immune genes in only 1-4% of lung epithelial cells, contrasting with E. coli's 40% response, and identifies prostaglandin signaling as protective during invasive disease.

The scFAIR Consortium develops a unified metadata schema and portal to improve FAIRness of scRNA-seq data through standardized annotations and semantic search.

The paper introduces IRIS, a platform integrating high-resolution imaging and single-cell RNA sequencing to link morphology with transcriptomes, revealing new nuclear-ER architectures in CD8+ T cells.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

The paper identifies shared and unique transcriptional changes in Drosophila melanogaster upon individual essential amino acid deprivation, revealing mechanisms linking nutrient scarcity to behavioral and physiological responses.

The paper introduces scTF-seq, a method to study TF dose-dependent reprogramming in mouse MSCs, revealing heterogeneity in cell fate and TF sensitivity.

The paper shows that mitochondrial metabolic activity determines ER stress signaling activation in neurons, conserved across Drosophila and human brains.

This paper develops a 3D ex vivo model of bone marrow to study childhood ALL, finding increased drug resistance in certain subtypes compared to 2D models.

This study identifies VGLL4 as a regulator of classical brown adipose tissue development by modulating the Hippo-YAP pathway and adipogenic gene expression.

ChromatinHD uses raw ATAC-seq data to predict gene expression and detect differential accessibility, outperforming existing methods by capturing functional accessibility changes.

EXTRA-seq quantifies enhancer-promoter communication in endogenous contexts, revealing the TATA-box's role in modulating expression and improving gene expression prediction when integrated with deep learning models.

The paper systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

DGRPool is a web tool that harmonizes DGRP phenotyping data to enable GWAS and PheWAS, revealing correlations between longevity and other traits.

The paper investigates how gustatory organs contribute to food texture preference in Drosophila larvae, showing their role in texture evaluation and ingestion decisions.

This study identifies JAK/STAT, GATA, and NF-κB pathways as regulators of lectin-24A, a gene involved in Drosophila's humoral immune response to parasitoid wasps.

The paper evaluates CM mapping tools, shows cell type-specific CRE interactions, and demonstrates how non-coding variants affect CM activity in a cell type-specific manner.

This study profiles GnRH neurons in mice to uncover developmental gene expression patterns linked to human reproductive processes.

The paper identifies 'context-only' transcription factors that contribute to enhancer communication by forming cooperative environments with pioneer factors.

The paper identifies marmite (mmt) as a conserved neuropeptide family mediating protein appetite and nutritional homeostasis across species.

The paper creates a single-cell transcriptomic atlas of the adult fruit fly, identifying over 250 cell types and analyzing gene signatures and sexual dimorphism across tissues.

This study uses human minibrain models and BRB-seq to analyze TMT-induced neurotoxicity, identifying key molecular events and pathways involved in adverse outcomes.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

The paper introduces Live-seq, a method for single-cell transcriptome profiling that preserves cell viability, enabling temporal analysis of gene expression and cell behavior.

This study identifies the Hippo pathway's role in regulating sarcomeric gene expression to control myofibril assembly and muscle fiber growth in Drosophila.

The paper investigates multimodal and multisensory coding in Drosophila larval taste neurons using calcium imaging and single-cell transcriptomics, revealing complex integration of taste and mechanical stimuli.