CUT&Tag

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data

DUETT identifies RNA structural transitions from chemical probing data by using a feedback control-inspired method and linear regression to detect known and novel events.

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

The paper develops a computational method, mCross, to model RBP binding specificity using precise crosslink site registration and validates it with ENCODE eCLIP data.

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning

The paper shows CTCF binding and nucleosome positioning at CTCF sites change during the cell cycle, with loss of binding in prometaphase and rearrangement of chromatin structure.

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

The paper shows that the transcription start site landscape in Saccharomyces cerevisiae remains stable across different environmental conditions and identifies a negative correlation between TSS shape index and expression levels.

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

SLIC-CAGE enables high-resolution transcription start site mapping using nanogram-level total RNA, significantly reducing the required input compared to existing CAGE methods.

One drug multiple targets: An approach to predict drug efficacies on bacterial strains differing in membrane composition

The paper develops a model to predict daptomycin activity against Streptococcus aureus strains with varying membrane compositions, suggesting interaction with the inner membrane.

Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution

The paper develops a method to profile spliceosome-bound RNA at nucleotide resolution in yeast, revealing non-canonical splicing events and substrate features influencing catalytic efficiency.

An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns

The paper introduces FOCS, a method to infer enhancer-promoter links using activity patterns, and presents an extensive E-P map covering over 300,000 links.

Estimating RNA structure chemical probing reactivities from reverse transcriptase stops and mutations.

The paper develops a statistical model to estimate RNA structure chemical probing reactivity using reverse transcriptase stops and mutations from a single experiment.

SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data

SARNAclust identifies RNA motifs from immunoprecipitation data by combining structure/sequence analysis, revealing known and novel motifs including a new ILF3 motif similar to hnRNPC.

Module analysis captures pancancer (epi)genetically deregulated cancer driver genes for smoking and antiviral response

This paper introduces AMARETTO, a multi-omics integration algorithm that identifies pancancer driver genes related to smoking and antiviral responses by analyzing eleven cancer types.

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

The paper introduces seqOutBias to correct enzymatic sequence bias in sequencing data, improving the identification of molecular signatures from protein/DNA interactions.

TruePaiR: Software for the Accurate Identification of Complementary piRNA Read Pairs in High-Throughput Sequencing Data

TruePaiR identifies complementary piRNA read pairs in sRNA sequencing data to assess piRNA amplification across species and tissues.

Integrative Deep Models for Alternative Splicing

This paper improves AS prediction models by integrating diverse data sources and introduces a new target function that enhances model accuracy.

Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan

The paper introduces circScan, a method to identify circRNA-RBP interactions from CLIP-seq data, finding thousands of novel interactions in human and mouse genomes.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach

The paper introduces iDeep, a hybrid deep learning framework that improves RNA-protein binding motif prediction by integrating cross-domain knowledge, achieving better performance and interpretability.

Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5′-mRNA ends

This study uses CAGE to profile 5′-mRNA ends in Daphnia pulex, revealing promoter architecture and sex-specific gene expression patterns, including novel cis-regulatory elements and insights into cyclical parthenogenesis.

OncoScape: Exploring the cancer aberration landscape by genomic data fusion

OncoScape integrates five genomic data types across 11 cancer types to identify new candidate cancer genes and reveals discrepancies between cell line and tumor aberrations.

RNA structure through multidimensional chemical mapping

This paper introduces multidimensional chemical mapping methods to determine RNA structures and shows they accurately resolve secondary and tertiary structures of various RNA molecules.