CUT&Tag

Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes

The paper uses molecular dynamics simulations to show cardiolipin increases membrane spontaneous curvature and reduces bending rigidity, leading to lateral heterogeneities through curvature sensing.

Mapping eukaryotic chromatin accessibility and histone modifications with DNA deaminase

The paper introduces two new methods, ChrODIE and ANDIE, for mapping chromatin accessibility and histone modifications without enzymatic cleavage, enabling multi-omics integration.

DreaM: A Computational Pipeline for Enhanced Short-Read Sequence Analysis in Repetitive Genomic Regions

DreaM improves short-read sequence analysis in repetitive regions by removing PCR duplicates and enhancing peak detection in ChIP-Seq and CUT&RUN data targeting centromeres.

Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation

This study investigates how Zic transcription factors regulate gene expression during cerebellar granule neuron maturation by analyzing their binding patterns and interactions with other transcription factors.

Accelerating Drug Discovery and Repurposingby Combining Transcriptional Signature Connectivity with Docking

This paper introduces ceSAR, a method combining docking and transcriptional signature connectivity to improve drug discovery and repurposing by reducing false positives and computational costs.

Examining NFκB Genomic Interactions by ChIP-seq and CUT&Tag

This study compares ChIP-seq and CUT&Tag for NFκB transcription factor genomic interactions, showing how experimental conditions affect detected interactions and their functional relevance.

Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping

Spatial tri-omic sequencing (DBiT ARP-seq and DBiT CTRP-seq) and CODEX imaging map chromatin, RNA, and protein dynamics across mammalian brain development and lysolecithin-induced neuroinflammation.

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity

This paper introduces Ribosome Decision Graphs (RDGs) to represent eukaryotic RNA translation complexity, enabling analysis of translation patterns and genetic variation effects.

Valproic Acid Treatment Enhances Chromosome Flexibility and Electron Transport in MCF7 Breast Cancer Cells

This study examines how Valproic Acid affects chromosome flexibility and electron transport in MCF7 breast cancer cells using atomic force microscopy and electron transport analysis.

Towards Parsimonious Generative Modeling of RNA Families

This paper introduces eaDCA, a sparse generative model for RNA families that efficiently predicts functional sequences and mutation effects, showing comparable performance to complex methods with fewer parameters.

The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma

The paper identifies ADA2B's role in maintaining oncogenic gene expression programs in multiple myeloma through epigenetic mechanisms.

High-throughput investigation of genetic design constraints in domesticated Influenza A Virus for transient gene delivery

The paper investigates genetic design constraints in domesticated Influenza A Virus for transient gene delivery, identifying permissible mutations and RNA level motif depletion.

Polycomb Repressive Complex 1.1 Component, BCOR, Promotes Syncytiotrophoblast Differentiation in Mice and Humans

This study shows BCOR is essential for syncytiotrophoblast differentiation in mice and humans by repressing stem cell genes and alternate lineage factors.

Prediction of DNA i-Motifs Via Machine Learning

The paper introduces a machine learning tool, iM-Seeker, to predict DNA i-Motif folding status and strength using CUT&Tag data and biophysical experiments.

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

racoon_clip - a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data

racoon_clip processes iCLIP and eCLIP data to extract single-nucleotide RNA binding signals, providing automated analysis and visualization tools.

Skeletal Muscle Satellite Cells Co-Opt the Tenogenic Gene Scleraxis to Instruct Regeneration

This study shows that Scx is required for satellite cell expansion and muscle regeneration, with distinct target genes from tendon development.

G1 length dictates H3K27me3 landscapes

The paper shows that G1 phase length regulates H3K27me3 levels in stem and tumor cells, with longer G1 increasing and shorter G1 decreasing H3K27me3.

An end-to-end approach for protein folding by integrating Cryo-EM maps and sequence evolution

This study introduces SMARTFold, a deep learning model that integrates Cryo-EM maps and sequence alignment to predict protein structures, outperforming existing methods on benchmark datasets.

Robust reprogramming of glia into neurons by inhibition of Notch signaling and NFI factors in adult mammalian retina.

This study shows that inhibiting Notch signaling and NFI factors can efficiently reprogram adult mammalian retinal glia into neurons, with enhanced effects under retinal injury.

Region-specific reversal of epidermal planar polarity in the fancy rosette mouse

The paper studies epidermal planar polarity reversal in the fancy rosette mouse, finding a region-specific rotation of the PCP axis due to a mutation in Fzd6.

Unidirectional expression of enhancers with cell type-dependent direction of transcription

The paper shows enhancers are usually unidirectionally transcribed in a cell type but may appear bidirectional when aggregated across cell types, suggesting enhancer RNAs are functional.

Reorganization of the Flagellum Scaffolding Induces a Sperm Standstill During Fertilization

This study shows that reorganization of the flagellum's F-actin network during sperm-egg fusion leads to midpiece contraction and motility cessation.

A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues.

The paper introduces a tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues to study chromatin accessibility and histone modifications during metamorphosis.

Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae

The paper introduces HyperTRIBE, an antibody-free method to identify RNA-binding protein targets in yeast by using RNA editing, and successfully applies it to two RBPs.

Uncovering transcriptional regulatory network during regeneration for boosting wheat transformation

This study identifies key transcriptional factors that enhance wheat transformation efficiency by analyzing multi-omic data during shoot regeneration.

Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

RCRUNCH improves eCLIP data analysis to identify RNA-binding protein binding sites and motifs, creating a comprehensive resource of in vivo-bound RBP sequence motifs.

Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development

This study identifies MECOM, PAX8, SOX17, and WT1 as master regulators in HGSC, showing their rewired cistromes and tumor-specific inhibition potential.

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3' UTR structure to RNA metabolism

The paper extends a hiCLIP atlas of Staufen1-bound duplexes by 10-fold using computational methods and reveals structural features of RNA binding and their impact on RNA metabolism.