multiome

Pandemic Coronavirus Genome Packaging Relies on Multiple Dispersed Packaging Signals

This study identifies multiple dispersed packaging signals in the SARS-CoV-2 genome that cooperate to direct RNA packaging into virions, revealing a dynamic mechanism for coronavirus genome assembly.

A conserved in-frame stop codon acts as a multipotent defense mechanism in alphaviruses

This study shows that an in-frame stop codon in alphaviruses helps evade innate immune defenses in both mosquito and vertebrate hosts.

Multicellular Spatial Programs Define the Histopathological Architecture of Meningioma

This study identifies multicellular spatial molecular programs in meningiomas using multi-omic data and develops a model to infer these programs from histopathology.

A Glycosylation-Dependent Checkpoint Restrains Intestinal Intra-Epithelial Lymphocyte Activation

This study identifies GCNT2 as a glycosylation-dependent checkpoint that restrains intestinal intra-epithelial lymphocyte (IEL) activation by modifying CD45 and dampening TCR signaling.

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

OmicOS provides an agent-operable omics ecosystem that enables AI systems to execute and verify analyses using community methods, achieving high performance in benchmark tasks.

Efficient heterologous mRNA production in E. coli via protein-facilitated protection

This paper develops a method to produce stable eukaryotic mRNA in E. coli by creating protein-mRNA complexes that protect against RNase degradation.

NO modulates human airway smooth muscle function by altering glucose-6-phosphate dehydrogenase effects on sGC function in asthma

This study shows that NO modulates airway smooth muscle function in asthma by altering G6PD effects on sGC function through redox regulation and heme-maturation.

Circular RNA vaccine performance is determined by RNA quality and epitranscriptomic tuning rather than innate activation

This study shows that circRNA vaccine performance depends on RNA quality and epitranscriptomic modifications rather than innate immune activation.

Cell Cycle Sensing Shapes Human T Cell Fate and Exhaustion Programs

This study investigates how cell cycle dynamics influence T cell fate and exhaustion by analyzing single-cell data and manipulating cell cycle progression and signaling.

mRNA-based tuberculosis vaccines BNT164a1 and BNT164b1 are immunogenic, well-tolerated and efficacious in rodent models

This paper describes two mRNA vaccines for tuberculosis that are immunogenic, well-tolerated, and effective in rodent models, entering clinical trials.

Fitness-driven scaling laws between mRNA and protein levels

The paper identifies optimal scaling laws between mRNA and protein levels that maximize cell fitness, showing a universal lower bound of 0.5 for the scaling exponent across organisms.

MYC-Driven Activation of USP39 Enhances SRSF1 Stability and Promotes PDAC Progression

The paper identifies a MYC-USP39-SRSF1 regulatory axis in PDAC that stabilizes SRSF1 and promotes tumor progression, suggesting USP39 as a therapeutic target.

JASMINE: A powerful representation learning method for enhanced analysis of incomplete multi-omics data

JASMINE improves analysis of incomplete multi-omics data by learning representations that preserve modality-specific and shared information, achieving better performance across tasks.

Type I IFN reprograms CD4⁺ T cell lipid metabolism as an antiviral effector mechanism during acute HIV/SIV infection

The paper investigates how type I IFN reprograms CD4⁺ T cell lipid metabolism during acute HIV/SIV infection and identifies metabolic changes linked to viral reservoir establishment.

Expression of four mitochondrial tRNAs from only two loci

The paper identifies mirror tRNA pairs produced from opposite strands of the same locus, demonstrating a novel mechanism for maintaining tRNA diversity in mitochondrial genomes.

Evaluating agentic AI for biological discovery in autonomous and copilot settings

This study evaluates agentic AI's ability to support biological discovery in autonomous and human-AI copilot settings using multi-omic cancer datasets.

PRIME: scalable, robust inference of mechanistic cell states from multimodal single-cell counts via probability generating functions

PRIME infers mechanistic cell states from multimodal single-cell data by embedding counts in a probability generating function space, enabling robust kinetic analysis and clustering.

Choriodecidual Ureaplasma parvum infection induces fetal lung inflammation prior to intra-amniotic infection in a nonhuman primate model

This study shows that choriodecidual Ureaplasma parvum infection causes fetal lung inflammation before detectable intra-amniotic infection in a nonhuman primate model.

The Host DHX29 RNA Helicase Regulates HCMV Immediate Early Protein Synthesis

This study shows DHX29 is required for efficient translation of HCMV immediate early proteins IE1 and IE2, which are critical for viral replication and reactivation.

Metadata Collector: An Open-Source Platform for Standardized Metadata Management in Multi Centre Sequencing Projects

Metadata Collector is an open-source platform designed to standardize metadata management in multi-centre sequencing projects, ensuring FAIR-aligned and reproducible metadata across distributed research groups.

mRNA 3'UTRs chaperone intrinsically disordered regions to control protein activity

The paper shows that mRNA 3'UTRs act as chaperones for intrinsically disordered regions (IDRs) to regulate protein activity by promoting IDR-IDR interactions and preventing domain folding interference.

Decoding Hierarchical Cell-Cell Communication in Spatial Multi-Omics with CellSTIC

CellSTIC decodes hierarchical cell-cell communication in spatial multi-omics data by integrating multimodal evidence and organizing interactions into a hierarchical semantic representation.

Collecting Duct-Targeted Lipid Nanoparticles Deliver Pkd2 mRNA to Restore Polycystin-2 and Attenuate ADPKD

This study develops lipid nanoparticles targeting collecting duct cells to deliver Pkd2 mRNA, restoring polycystin-2 and reducing cysts in ADPKD models.

Protein-state dysregulation and sex-specific neurodevelopmental signatures in schizophrenia forebrain organoids

This study uses forebrain organoids to show that schizophrenia involves sex-specific protein-state dysregulation, with changes in post-translational modifications and proteomic pathways rather than transcript levels.

MAGI: Mechanistic Consequences of Genetic Variants via Genomic Foundation Models

MAGI provides mechanistic insights into genetic variants by integrating genomic data and clinical annotations to improve variant interpretation and generate testable hypotheses.

mRNA-Encoded TLR5 Agonist as an Immune Adjuvant

This study tests an mRNA-encoded TLR5 agonist as an adjuvant to enhance mRNA vaccine immunogenicity and efficacy.

The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in early Caenorhabditis elegans embryos

The paper identifies SPN-4 as a specificity factor for CCR4-NOT-dependent clearance of maternal mRNAs in C. elegans embryos, showing its role in targeting specific transcripts for decay.

CeSpGRN: Inferring cell-specific gene regulatory networks from single cell multi-omics and spatial data

CeSpGRN infers cell-specific gene regulatory networks from single-cell multi-omics and spatial data, showing improved accuracy over existing methods.

High concordance between genetic effects on mRNA and protein abundance

The paper analyzes genetic effects on mRNA and protein abundance across multiple yeast datasets, finding high concordance with few exceptions.

In vivo reprogramming of cytotoxic effector CD8+ T cells via fractalkine-conjugated mRNA-LNP

This study shows fractalkine-conjugated mRNA-LNP can target and modify CD8+ T cells in vivo, enabling transient expression of proteins like IL-2 and CD62L.