multiome

SACNet: A Multiscale Diffeomorphic Convolutional Registration Network with Prior Neuroanatomical Constraints for Flexible Susceptibility Artifact Correction in Echo Planar Imaging

SACNet corrects susceptibility artifacts in dMRI scans using a registration network with neuroanatomical constraints, showing improved performance across diverse datasets.

Universal preprocessing of single-cell genomics data

The paper describes a universal preprocessing workflow for single-cell genomics data using the cellatlas package.

Partitioning heritability using single-cell multi-omics identifies a novel macrophage subpopulation conveying genetic risks of coronary artery disease.

The paper identifies a novel macrophage subpopulation, lipid-handling macrophages, that is enriched with CAD genetic risk and shows how a risk variant affects FDX1 through AP-1 and C/EBP-beta recruitment.

Representation of Protein Dynamics Disentangled by Time-structure-based Prior

The paper introduces two methods with a time-structure-based prior to disentangle protein dynamics from MD simulations, improving the representation of conformational transitions.

B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters

The paper identifies B cells as drivers of T cell immunosenescence and aging, showing that targeting B cells with CD20 antibodies can reverse age-related T cell dysfunction.

Reviving immunogenic cell death upon targeting TACC3 enhances T-DM1 response in HER2-positive breast cancer

This study shows that T-DM1 induces immunogenic cell death (ICD) in HER2-positive breast cancer, which is lost in resistance, and that targeting TACC3 restores ICD and enhances T-DM1 response.

m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation

The paper shows m6A methylation guides IMP1's regulation of microtubule-related mRNAs during human neuronal differentiation.

Selective advantage of mutant stem cells in clonal hematopoiesis occurs by attenuating the deleterious effects of inflammation and aging

This study identifies how DNMT3A and TET2 mutations in hematopoietic stem cells confer a selective advantage by reducing inflammation and aging effects.

Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress

The paper identifies a human HSC subset with inflammatory memory that accumulates with age and clonal hematopoiesis, potentially increasing cancer and infection risks.

PlexinD1 deficiency in CD11c+ dendritic cells exacerbates airway hyperresponsiveness and enhances IgE and mucus production in allergic asthma

SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis

SnapATAC2 is a fast, scalable dimensionality reduction tool for single-cell omics data that improves accuracy and efficiency in capturing cellular heterogeneity across multiple modalities.

Multilevel regulation of NF-kappa B signaling by NSD2 suppresses Kras-driven pancreatic tumorigenesis

This study shows NSD2 acts as a tumor suppressor in Kras-driven pancreatic cancer by regulating NF-kappa B signaling through multiple mechanisms.

Enhanced Omicron subvariant cross-neutralization efficacy of a monovalent SARS-CoV-2 BA.4/5 mRNA vaccine encoding a noncleaved, nonfusogenic spike antigen

This study develops a modified SARS-CoV-2 spike antigen that enhances cross-neutralization against Omicron subvariants, despite reduced neutralizing potency.

NAD+ depletion and altered mitochondrial function are key to the establishment of placental dysfunction in an inflammatory-driven subclass of preeclampsia

Boosting NAD+ levels prevent inflammatory-driven preeclampsia by improving placental mitochondrial function.

Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations

The paper adjusts the AMBER OL3 force field to improve RNA simulations by fixing intra-nucleotide steric clashes in base-phosphate interactions.

Single nuclei multiomic analyses identify human cardiac lymphatic endothelial cells associated with coronary arteries in the epicardium

The paper identifies a novel population of cardiac lymphatic endothelial cells in human fetal hearts associated with coronary arteries using single nuclei multiomic analysis.

CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems

The paper introduces a tool for automated molecular assembly under periodic boundary conditions, demonstrating its application on six complex systems.

Effect of number of diffusion encoding directions in Neonatal Diffusion Tensor Imaging using Tract-Based Spatial Statistical analysis

The paper evaluates the effect of diffusion encoding directions on DTI scalar estimates in neonates using TBSS analysis and finds negligible differences with 24 or more directions.

A systems vaccinology resource to develop and test computational models of immunity

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

SIMVI reveals intrinsic and spatial-induced states in spatial omics data

SIMVI disentangles intrinsic and spatial-induced variations in spatial omics data, revealing spatial effects and biological dynamics across multiple datasets.

Overlapping and distinct cis-acting requirements for oskar mRNA localization pathways

This study investigates cis-acting elements and trans-acting factors required for the late-phase localization of oskar mRNA in Drosophila oocytes, finding that the SOLE structure and sequence, along with the 3 UTR, are essential for this process.

Role of Caveolin 1 in metabolic programming of fetal brain

This study investigates how the absence of Caveolin-1 in fetal brain affects metabolism, epigenetics, and aging in mice by integrating metabolomics, transcriptomics, and single-cell data.

hnRNP A1 induces aberrant CFTR exon 9 splicing via a newly discovered Exonic Splicing Silencer element.

This study identifies an exonic splicing silencer element in CFTR exon 9 that is bound by hnRNP A1, leading to exon skipping and non-functional CFTR protein.

Situating the oxytocin receptor gene polymorphisms in the context of structural and connectome-level substrates and association with endogenous oxytocin

The paper examines sex-specific structural and connectome-level differences associated with OXTR SNPs and their relationship with endogenous oxytocin in young adults.

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamicload balancing for heterogeneous biomolecular systems

The paper introduces GENESIS CGDYN, a large-scale coarse-grained MD simulation tool with dynamic load balancing for heterogeneous biomolecular systems, demonstrating its application to IDP droplet fusions and large droplet formation.

Homeostasis of mRNA concentrations through coupling transcription, exportation, and degradation

The paper proposes a mechanistic model of mRNA buffering that couples transcription, exportation, and degradation, explaining constant mRNA concentrations under various perturbations.

A longitudinal resource for population neuroscience of school-age children and adolescents in China

The paper introduces a longitudinal dataset of school-age children and adolescents in China, detailing its design, sampling, and neuroimaging measurements.

Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images

This paper develops an automated deep learning method for ischemic stroke lesion segmentation in mouse MRI, achieving high agreement with manual segmentation.

tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation

This paper applies tICA-metadynamics to identify slow dynamics in trimethoprim permeation through a multicomponent membrane, improving convergence efficiency and correcting artifacts in collective variables.

Proteogenomic characterization reveals antitumor mechanisms of intrahepatic cholangiocarcinoma

This study identifies two NRG-related clusters in iCCA using multi-omics data and develops a prognostic signature model, NPS, which correlates with drug response and immunotherapy outcomes.