CUT&Tag

ORFik: a comprehensive R toolkit for the analysis of translation

ORFik is an R/Bioconductor toolkit for analyzing translation data, supporting multiple high-throughput assays and providing over 30 translation-related metrics.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

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.

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

TFEA quantifies transcription factor activity changes from perturbation data, identifying key regulators and temporal regulatory networks.

In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei

The paper develops a method to profile chromatin states in specific Drosophila cell types using GFP-tagged nuclei and applies it to photoreceptor neurons.

Neutrophil extracellular traps arm DC vaccination against NPM-mutant myeloproliferation

This study demonstrates that neutrophil extracellular traps (NETs) loaded with mutant NPMc+ can be used as a vaccine to treat NPMc-driven myeloproliferation by inducing CD8+ T cell responses and reducing leukemic expansion.

A transcription start site map in human pancreatic islets reveals functional regulatory signatures

The paper maps transcription start sites in human pancreatic islets and identifies functional regulatory elements linked to type 2 diabetes GWAS signals.

Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR

The paper introduces TSRexploreR, an R package for analyzing TSS mapping data, including TSS/TSR detection, normalization, and shift detection.

An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons.

The paper develops an integrated resource to analyze small RNA profiles in mosquitoes, revealing evolutionary dynamics and host responses to viruses and transposons.

Low Quantity single strand CAGE (LQ-ssCAGE) maps regulatory enhancers and promoters

The paper introduces LQ-ssCAGE, a cost-effective CAGE method for low quantity RNA samples, and demonstrates its use in identifying novel enhancer and promoter-derived lncRNAs.

RNA structure prediction using positive and negative evolutionary information

The paper introduces CaCoFold, a method that predicts conserved RNA structures by integrating positive and negative evolutionary information, improving accuracy over existing methods.

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

The paper performs a global analysis of transcription start sites (TSS) in the ovine reference genome using CAGE sequencing, identifying novel TSS and validating them with bisulfite sequencing.

MasterPATH: network analysis of functional genomics screening data

MasterPATH analyzes functional genomics screening data using network analysis to identify active molecular pathways associated with specific phenotypes.

IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles

IPANEMAP models RNA structure from multiple probing reactivity profiles, demonstrating improved performance through integration of diverse experimental data.

Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

SegRNA identifies unannotated transcripts by analyzing multi-experiment transcriptomic data without relying on pre-existing annotations.

Human library of cardiac promoters and enhancers

The paper presents a comprehensive CAGE atlas of human cardiac promoters and enhancers, identifying novel regulatory elements and their association with heart morphology and pathologies.

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

The paper introduces SURF, a tool for integrating CLIP-seq and RNA-seq data to identify differential alternative transcriptional regulation events linked to RNA-binding proteins.

Vascular Injury Changes Topology of Vessel Network to Adapt to Partition of Blood Flow for New Arteriovenous Specification

The paper shows that vascular injury leads to changes in vessel network topology to increase blood flow and activate Notch-ephrinb2 signaling for microcirculation restoration.

A ChIP-exo screen of 887 PCRP transcription factor antibodies in human cells

The paper evaluates 887 PCRP antibodies against human transcription factors using ChIP-exo and other assays, identifying 5% as strong candidates and 34% as warranting further testing.

Discovery of 20 novel ribosomal leaders in bacteria and archaea

The paper identifies 20 new ribosomal leader structures in bacteria and archaea, expanding the known r-leader count by over 50%.

In silico simulations of erythrocyte aquaporins with quantitative in vitro validation

This study compares TIP3P and TIP4P water models in simulating erythrocyte aquaporins using molecular dynamics and experimental validation.

Development of a honey bee RNA virus vector based on the genome of Deformed wing virus.

The paper develops a honey bee RNA virus vector using Deformed wing virus (DWV) by inserting eGFP and observes genome deletions in the progeny.

Enhancer and Promoter Usage in the Normal and Failed Human Heart

This study uses CAGE-seq to analyze promoter and enhancer usage in healthy and failed human hearts, identifying changes in gene regulation associated with heart failure.

Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for analysis of CAGE data

ADAPT-CAGE improves TSS identification from CAGE data using machine learning, outperforming existing methods and enabling accurate genome-wide annotation.

Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells

This study uses live-cell imaging to show Hfq dynamically interacts with mRNAs and sRNAs, recruiting RNase E to promote mRNA turnover and enabling sRNA-mediated gene regulation.

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures

MESSI infers coevolution rates of base-pairing interactions in nucleic acid sequences and identifies functionally important substructures.

Identification of Novel miRNAs in Mouse Embryonic Stem Cells, Embryonic Fibroblasts, and Reprogrammed Pluripotent Cells

The paper identifies nine novel miRNAs in mouse cells, including a species-specific miRNA with a unique evolutionary origin through inverted duplication.

Malaria parasite immune evasion and adaptation to its mosquito host is influenced by the acquisition of multiple blood meals

This study shows that additional blood meals affect Plasmodium parasite development differently in Anopheles mosquitoes, influencing oocyst numbers and immune evasion.

CAGEfightR: Cap Analysis of Gene Expression (CAGE) in R/Bioconductor

CAGEfightR is an R/Bioconductor package for analyzing CAGE data, enabling TSS and enhancer identification, annotation, quantification, and visualization.

Control of human testis-specific gene expression

The paper analyzes testis-specific genes to identify regulatory features and patterns associated with differentiation levels in human testis cells.

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

This study identifies molecular mechanisms of translational stalling caused by inhibitory codon pairs and poly(A) tracts using in vitro biochemistry, ribosome profiling, and cryo-EM.