CUT&Tag

Local administration of a novel siRNA modality into the CNS extends survival and improves motor function in the SOD1G93A mouse model for ALS

This study demonstrates that a novel siRNA modality, conjugated with an accessory oligonucleotide, improves survival and motor function in a mouse model of ALS when delivered locally to the CNS.

FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression

This study shows FUS regulates snoRNA expression, affecting rRNA modifications like 2-O-Me and pseudouridylation, which may contribute to ALS pathology.

Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting

The paper tracks the coreceptor switch of HIV-1 in early infection, finding that a single mutation can drive X4 variants and co-evolution of antigenicity and tropism.

EpiCompare: R package for the comparison and quality control of epigenomic peak files

EpiCompare is an R package that compares and quality controls epigenomic peak files, providing an interactive HTML report with minimal user input.

An apicomplexan bromodomain, TgBDP1 associates with diverse epigenetic factors to regulate essential transcriptional processes in Toxoplasma gondii.

This paper identifies TgBDP1, a bromodomain protein in Toxoplasma gondii, as essential for gene regulation by interacting with epigenetic factors and influencing transcriptional processes.

The microRNomes of Chinese Hamster Ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress

This study characterizes miRNA profiles in CHO cells and their extracellular vesicles under normal and stress conditions, revealing shifts in miRNA enrichment associated with osmotic and ammonia stress.

A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell therapy applications

The paper introduces a method for CRISPR-targeted genome integration of a barcoded gene into antigen-specific T cells to enhance traceability and monitoring in adoptive cell therapy.

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP

The paper introduces PEKA, a tool for analyzing CLIP data to assess motif specificity, and shows that technical biases affect motif detection.

A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency

This study uses a CRISPR screen to identify pathways involved in HIV-1 latency, finding that ING3 and AZD5582 combination activates proviruses.

Visualizing conformational space of functional biomolecular complexes by deep manifold learning

This paper introduces AlphaCryo4D, a deep learning framework for atomic-level cryo-EM reconstructions of conformational continua in biomolecular complexes, demonstrating its ability to visualize dynamic components and hidden conformational space.

Alternative promoters in CpG depleted regions pervasively account for epigenetic misregulation of cancer transcriptomes

The paper identifies alternative promoters in cancer transcriptomes that are associated with epigenetic misregulation due to DNA methylation changes in CpG-depleted regions.

Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut

This study identifies MafB and cMaf as transcription factors essential for neonatal gut nutrient uptake, showing their role in endo-lysosomal programs and metabolic pathway changes.

Bridging the gap between in vitro and in silico single-molecule force spectroscopy

The paper bridges the gap between in vitro and in silico single-molecule force spectroscopy by combining coarse-grained and all-atom SMD simulations with DHS theory.

Profiling dynamic RNA-protein interactions using small molecule-induced RNA editing

This study introduces TRIBE-ID, a method to profile RNA-protein interactions with temporal control, showing stress granules enhance G3BP1-RNA interactions and stabilize RNA clients.

MaD: Macromolecular Descriptors for Integrative Dynamic Modeling Supported by Cryo-EM Data

MaD improves integrative modeling of large flexible macromolecular complexes by using conformation-invariant descriptors from cryo-EM data and molecular simulations.

CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy

This paper engineers an influenza A virus with increased CpG content, showing it is attenuated in mice but replication competent in vaccine propagation systems, suggesting a new strategy for live attenuated vaccines.

IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy

The paper shows IPMK binds to the SWI/SNF complex, regulates BRG1 localization, and affects chromatin accessibility in mouse embryonic stem cells.

Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells

The paper tracks chromosomal instability in iPSCs during culture, finding trisomy 12 dominance and novel structural variations acquired over time.

Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells

The paper investigates transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells, identifying TE-derived transcripts and ISGs with novel exons.

Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

The paper presents a refinement method using HADDOCK2.4 to reduce atomic clashes in low-to-medium resolution cryo-EM complexes by optimizing protein-protein interfaces.

HOXD13 is a direct EWS-FLI1 target and moderates fusion-dependent transcriptional states

The paper identifies HOXD13 as a direct target of EWS-FLI1 and shows it modulates transcriptional states in Ewing sarcoma by antagonizing EWS-FLI1-dependent gene repression.

Deep learning based on multi-omics integration identifies potential therapeutic targets in breast cancer

The paper develops a deep learning model integrating multi-omics data to stratify breast cancer patients by prognosis and identify potential therapeutic targets.

Long dsRNA mediated RNA interference (dsRNAi) is antiviral in interferon competent mammalian cells

The paper shows that low-concentration dsRNA can inhibit viral replication in IFN-competent mammalian cells via RNAi, independent of IFN induction.

FILER: large-scale, harmonized FunctIonaL gEnomics Repository

FILER provides a large-scale, harmonized functional genomics data catalog with streamlined access to over 50,000 datasets and efficient querying capabilities.

Multi-omics Topic Modeling for Breast Cancer Classification

This paper uses multi-omics topic modeling to classify breast cancer subtypes, showing improved accuracy by integrating mRNA, microRNA, and copy number variation data.

Sterilization of drug-resistant influenza virus through genetic interference: use of unnatural amino acid-engineered virions

This paper presents a method using unnatural amino acid-engineered drug-resistant influenza virus to sterilize drug-resistant strains, validated in vitro and in animal models.

RBPSpot: Learning on Appropriate Contextual Information for RBP Binding Sites Discovery

RBPSpot identifies RBP binding sites using contextual sequence features and a DNN, achieving ~90% accuracy and outperforming existing tools across multiple datasets.

Investigating the Role of Chromatin Remodeler FOXA1 in Ferroptotic Cell Death

This study investigates the role of FOXA1 in ferroptotic cell death in multiple myeloma cells, finding that FOXA1 is upregulated and binds to pericentromeric regions during ferroptosis.

Long-range single-molecule mapping of chromatin modification in eukaryotes

The paper introduces a method called BIND&MODIFY to map histone modifications at the single-molecule level using long-read sequencing, revealing long-range chromatin states and heterogeneity.

CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis

CUT&RUNTools 2.0 is a computational pipeline for analyzing single-cell and bulk CUT&RUN and CUT&Tag data, offering alignment, quality control, clustering, and visualization tools.