multiome

Latent-Space Residue-Pair Networks from Molecular Dynamics Distinguish Ligand-Activated and SAVI-Associated STING

The paper uses MD simulations and machine learning to compare residue-pair fluctuations in STING under different conditions, identifying distinct dynamic patterns.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

Autoregulation of RNase E synthesis: Predominant impact of a branched RNA stem-loop to which the nuclease binds

The paper identifies a branched RNA stem-loop (hp3) as a major regulator of RNase E synthesis in Escherichia coli, showing it binds RNase E with high affinity and functions additively with hp2.

Antisense oligonucleotides targeting transcription termination windows disrupt mRNA 3' end processing and decrease gene expression

This study shows that antisense oligonucleotides targeting transcription termination windows can decrease gene expression by disrupting mRNA 3' end processing and causing off-target effects.

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

The paper identifies NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity in bladder cancer, linking its expression to response to enfortumab vedotin and checkpoint inhibitors.

High-throughput identification of chromatin-opening transcription factors

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

Inhibitory Nectin-2/TIGIT interactions between CD163+ macrophages and CD8+ T cells in spatially defined immune niches associate with poor outcomes in neuroblastoma

The paper identifies inhibitory Nectin-2/TIGIT interactions between CD163+ macrophages and CD8+ T cells in neuroblastoma tumor niches, linking them to poor patient outcomes.

Automated Segmentation and Tractography of Brainstem and Subcortical White Matter

The paper develops an automated pipeline for segmenting and parcellating brainstem and subcortical white matter pathways using diffusion MRI data.

Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex

This study links glymphatic clearance, neural activity, and amyloid-β deposition in the cortex using MRI and transcriptomic data, showing spatial associations and potential vulnerability to neurodegeneration.

Pumilio proteins license viral noncoding RNA engagement with target mRNAs

The paper identifies PUM1 and PUM2 as cofactors for viral noncoding RNAs HSUR1 and HSUR2 in mRNA repression, showing PUM binding is required for productive HSUR-mRNA engagement.

Lung surfactants as a component of lipid nanoparticles for pulmonary mRNA delivery

This study shows that adding lung surfactant Poractant alfa to lipid nanoparticles improves their performance for pulmonary mRNA delivery, increasing transfection efficiency and particle concentration.

A circRNA-derived IRES-like element enables programmable translational activation of the endogenous chaperone HSP90

The paper describes a synthetic circRNA-derived IRES-like element, SynFarsa, that enhances translation of an endogenous protein, HSP90, in trans by targeting its 3'UTR.

An Open Test--Retest Dataset of Rapid Myelin Mapping Acquisitions

The paper introduces a multimodal MRI dataset to evaluate myelin-sensitive imaging methods across test-retest acquisitions and metrics.

Dysregulation of FMR1 Splicing in Human Fragile X Syndrome

This study identifies FMR1-217 mis-splicing in FXS as a result of CGG repeat expansion, R-loop formation, and impaired Pol II elongation, with potential therapeutic rescue via splice-switching ASOs.

Pumilio and Brain tumor regulate the expression of Smaug during the Drosophila maternal-to-zygotic transition

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.

HIV-1 prime-boost vaccination shapes distinct clonal trajectories and memory precursor states of Env- and Gag-specific T cells

This study shows that HIV-1 DNA/rAd5 vaccination leads to distinct clonal expansion and memory precursor states in Env- and Gag-specific CD8 T cells.

P-body sequestration of clock transcripts delays repressor synthesis to set circadian period in Drosophila

The paper identifies P-body sequestration of clock transcripts as a mechanism delaying repressor synthesis, which sets the circadian period in Drosophila.

Single Cell Cytometry of Mouse Brain Tissue

This study compares methods for generating single-cell suspensions from mouse brain tissue using mass cytometry, finding that mechanical dissociation with enzymes yields viable cells while Percoll reduces viability, and cryopreservation preserves cell composition.

Frequency Shift Imaging Using an Adiabatic SLR Self-Refocused Pulse for Positive-Contrast SPION Imaging at 7T

This paper introduces Frequency Shift Imaging (FSI), a positive-contrast MRI technique for SPION detection, showing improved specificity and signal intensity compared to conventional negative-contrast methods.

BiomiX 3.0: A user-friendly platform for democratized multi-omics integration with graph-based learning.

BiomiX 3.0 is a multi-omics integration platform that introduces PRAMIGO, a supervised heterogeneous graph transformer, and benchmarks five methods on CLL and PTB datasets, showing that no single method captures all biologically relevant signals.

Spatially resolved contrastive analysis of perturbation-driven microenvironmental heterogeneity across tissues and conditions

Haruka identifies condition-specific and shared spatial domains across tissues and conditions using contrastive learning, demonstrating improved detection of spatially heterogeneous perturbation responses.

A spectral framework for measuring diversity in multiple sequence alignments

This paper introduces Leff, a spectral measure to quantify effective information in multiple sequence alignments, showing evolutionary constraints reduce sequence diversity in RNA and proteins.

Layer-to-cell-class correspondence is gene-specific for pyroptosis-related transcription in human skin

Epidermal NLRP1, PYCARD and CASP4 versus dermal GSDMD polarity in systemic sclerosis skin is reproduced by same-donor cell-class pseudobulk for PYCARD and GSDMD, but rarely NLRP1.

Dual-targeted nanoparticles enable the ex vivo generation of cytotoxic and phagocytic CAR effector cells

This study develops dual-targeted lipid nanoparticles to enhance the ex vivo generation of CAR-T cells and CAR-monocytes, showing improved cytotoxic and phagocytic activity.

A Wolbachia pipientis protein confers resistance to virus infection in Drosophila melanogaster

The paper identifies a Wolbachia protein that enhances Drosophila resistance to virus infection via the IMD pathway.

DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference

DeepSCENIC uses transfer learning from sequence-to-function models to infer causal gene regulatory networks from single-cell multiome data.

Spatially-resolved multimodal profiling identifies functionally-heterogeneous cancer-associated fibroblasts associated with poor radiotherapy outcomes in muscle-invasive bladder cancer.

This study identifies functionally heterogeneous cancer-associated fibroblasts in muscle-invasive bladder cancer linked to poor radiotherapy outcomes.

ZNF121 recruits YTHDF2 to modulate mRNA stability

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

Reprogramming mRNA localization by targeted RNA-protein interference reveals roles in oncogenesis

This study uses CRISPR/dCas13 to interfere with RNA-RBP interactions, showing that disrupting mRNA localization reduces cancer cell invasiveness and metastasis.