Pierre‐Luc Germain

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

The paper presents a Python implementation of scDblFinder with GPU support for faster doublet detection in single-cell RNA sequencing data.

The paper identifies miR-1229-3p as a human-specific microRNA that delays neuronal synaptogenesis by reducing mitochondrial metabolism.

The paper predicts transcription factor binding across 43 human cell types using ATAC-seq data and a new platform, revealing promiscuous occupancy and chromatin contacts.

The paper shows that inhibiting miR-495-3p in mice rescues mTORC1 hyperactivation-driven autistic-like behaviors and memory impairments.

The paper improves single-cell differential expression analysis by integrating bulk RNA-seq data through bulk-based hypothesis weighing, enhancing power and robustness.

This paper provides a framework for selecting and understanding validation metrics for subpopulation detection in single-cell and spatial omics data, developing new metrics and implementing them in a Bioconductor package.

This study shows that miR-138-5p suppresses excitatory synaptic strength in the cerebellum by affecting both pre- and postsynaptic mechanisms.

The paper identifies circRNAs that regulate excitatory synaptogenesis in rat hippocampal neurons by modulating miR-128-3p activity.

This study investigates how repeated stress affects molecular responses in the mouse hippocampus, finding widespread habituation without new adaptive responses or baseline gene expression changes.

This study shows that an EDC mixture linked to lower birth weight increases adipogenesis and induces transcriptomic changes associated with birth weight and diabetes.

This study introduces a robust multiplex DIA-MS workflow with machine learning and statistical filtering to profile protein turnover in cisplatin-resistant cancer cells, revealing correlations between transcript regulation and protein degradation.

The paper benchmarks methods for identifying differentially-active transcription factors from ATAC-seq data using curated and simulated datasets, identifying three promising approaches.

The paper benchmarks computational methods for analyzing scATAC-seq data, finding that SnapATAC and SnapATAC2 outperform other methods in cell-type discrimination and scalability.

NanoTag is an IgG-free method for mapping DNA-protein interactions using a nanobody-Tn5 transposase fusion, showing high correlation with CUT&Tag data in mouse embryonic stem cells.

This study shows that miR-379-410 regulates sociability in mice by inhibiting an actomyosin network, with implications for neurodevelopmental disorders.

The paper identifies miR-708-5p as a biomarker for bipolar disorder and shows its role in regulating mood disorder-associated behaviors through targeting Nnat.

This paper introduces a novel GR degrader, KH-103, which selectively degrades glucocorticoid receptors and shows improved efficacy over existing inhibitors.

The paper shows that noradrenaline release from the locus coeruleus regulates gene expression in the hippocampus via beta-adrenergic receptors, with astrocyte-specific genes as key targets.

This study investigates how 7q11.23 CNVs affect protein synthesis and neuronal excitability in neurodevelopmental disorders using patient-derived neurons and multi-omics approaches.

This paper meta-analyzes single-cell method benchmarks to identify challenges in extensibility, interoperability, and reproducibility.

This study identifies miR-138-5p as a regulator of short-term memory and inhibitory synaptic transmission in hippocampal interneurons, with implications for schizophrenia.

scanMiR predicts microRNA targets using a biochemical model and k-mer affinity, offering tools for binding site scanning, affinity estimation, and repression prediction.

This study identifies compartment-specific gene expression changes during synaptic scaling in rat hippocampal neurons, revealing distinct regulatory mechanisms in somatic and process compartments.

The paper identifies gene regulatory network disruptions caused by LSD1 mutations in early differentiation, showing impaired transcription factor activity and potential therapeutic targets through HDAC inhibition.

treeclimbR identifies optimal hierarchical resolutions for detecting entities associated with phenotypes in multi-resolution data.

This study investigates how KMT2D mutations in Kabuki Syndrome disrupt neuronal function through chromatin and transcriptional changes, independent of H3K4me1.

diffUTR is a Bioconductor package that improves differential exon and 3' UTR usage analysis by integrating existing tools and databases, showing better flexibility and accuracy.

This study characterizes the molecular changes in the mouse hippocampus during the acute stress response using multiomic profiling and identifies rapid resolution of molecular events within 4 hours.