multiome

multiDEGGs: a multi-omic differential network analysis package for biomarker discovery and predictive modeling

multiDEGGs performs differential network analysis across multi-omic data to identify biomarkers and improve predictive modeling in rheumatoid arthritis treatment response.

Hydroxychloroquine-functionalized Ionizable Lipids Mitigate Inflammatory Responses in mRNA Therapeutics

This study introduces HCQ-functionalized LNPs that reduce inflammation while maintaining mRNA delivery efficiency, showing promise for repeated dosing applications.

NTX250: A Modular mRNA-Based Immunotherapy Platform for HPV-Associated Cancers with Broad Applicability.

This paper introduces NTX250, an mRNA-based immunotherapy platform for HPV-associated cancers that induces tumor regression and durable immune memory in preclinical models.

Mutual homeostasis of charged proteins

The paper identifies a homeostatic mechanism called interstasis that co-regulates the dosage of proteins with low complexity domains through RNA-based negative feedback.

CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data

CLUEY improves cell type detection and clustering in single-cell omics by integrating biological knowledge to guide clustering and enhance interpretability.

Regulation of NFKBIZ by precise Regnase-1 endoribonuclease cleavage and subsequent uridylation

The paper shows Regnase-1 cleaves and uridylates NFKBIZ mRNA, enhancing its decay and linking this process to lymphoma and viral pathogenesis.

Loss of Brain Structural qMRI Signatures in Aging

This study examines age-related changes in brain microstructure using qMRI, finding increased regional similarity and individual variability in older adults.

CGBack: Diffusion Model for Backmapping Large-Scale and Complex Coarse-Grained Molecular Systems

CGBack uses a diffusion model to accurately backmap coarse-grained molecular systems to all-atom structures, improving upon existing methods by preserving stereochemistry and handling complex systems.

mRNA-Based Designer APCs Elicit Robust CD8⁺ and CD4⁺ T Cell Responses

This paper develops an mRNA-based platform that reprograms somatic cells into designer APCs, enhancing T cell responses against tumors and demonstrating translational potential in human and mouse models.

Exploiting TGF-β-mediated Stromal Programming in Homologous Recombination-Deficient Pancreatic Cancer

This study shows that ATM-deficient pancreatic cancers reprogram the tumor microenvironment via TGF-β-driven myCAF enrichment, and targeting this stromal axis with chemotherapy improves therapeutic efficacy.

Neurodevelopmental deviations in schizophrenia: Evidences from multimodal connectome-based brain ages

This study uses multimodal MRI data to estimate brain age in early-onset schizophrenia patients and finds increased brain age gaps correlated with symptom severity.

Differentiation hierarchy in adult B cell acute lymphoblastic leukemia at clonal resolution

This study uses barcoding and multiome single-cell data to show a unidirectional differentiation hierarchy in B-ALL with an immature population having high leukemogenic potential.

Dietary isoleucine content defines the metabolic and molecular response to a Western diet

This study shows that reducing dietary isoleucine improves metabolic health in mice on a Western diet, with distinct molecular responses across sexes and strains.

N1-methylpseudouridine mRNA modification enhances efficiency and specificity of gene overexpression by preventing Prkra-mediated global translation repression

This study shows that N1-methylpseudouridine modification of IVT mRNA reduces dsRNA-induced translation repression and immune responses in zebrafish embryos.

Integrative multi-omics combined with functional pharmacological profiling in patient-derived organoids identifies personalized therapeutic vulnerabilities of adult high-grade gliomas

This study integrates multi-omics and functional drug screening in patient-derived organoids to identify personalized therapeutic vulnerabilities in adult high-grade gliomas, finding distinct drug responses in IDH1 mutant and MYCN-amplified tumors.

Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

OmicsFUSION: A Pretrained Hyena-Based Framework for Encoding, Reconstruction, and Representation of the Omics and DNA Data

The paper introduces a framework that integrates DNA sequences with omics data using a pretrained model, enabling reconstruction and unified representation of genomic and functional information.

Integrated Genomic Profiling Reveals Mechanisms of Broad Drug Resistance and Opportunities for Phenotypic Reprogramming in Cancer Cells

This study identifies mechanisms of broad drug resistance in cancer and proposes strategies to reverse it using integrated genomic and computational approaches.

Mechanistic insights into RAN translation within the Huntingtin coding sequence

The paper investigates RAN translation from HTT CAG repeats, showing it occurs in multiple reading frames without AUG start codons and is detectable in neurons.

Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics

This study creates a single-cell multiomics atlas of B cell development in prenatal and adult bone marrow and in vitro models, identifying novel cell subsets and molecular signatures.

PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression

This study shows PYM1 regulates EJC occupancy in a gene architecture-dependent manner, affecting mRNA stability and decay, and is exploited by flaviviruses to alter host mRNA regulation.

Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms

This study designs and tests dimeric RSV F-subunit vaccines in protein and mRNA forms, showing enhanced immunogenicity and protection against RSV infection in rodent models.

Unveiling causal regulatory mechanisms through cell-state parallax

The paper introduces GrID-Net, a graph neural network that detects causal locus-gene associations using cell-state parallax, uncovering noncoding mechanisms affecting 132 genes in schizophrenia.

DKC1-mediated pseudouridylation of rRNA targets hnRNP A1 to sustain IRES-dependent translation and ATF4-driven metabolic adaptation

This study identifies DKC1-mediated pseudouridylation of rRNA as essential for sustaining IRES-dependent translation and ATF4-driven metabolic adaptation in neuroblastoma.

Deep generative models generate mRNA sequences with enhanced translation capacity and stability

GEMORNA generates mRNA sequences with enhanced translation capacity and stability, showing significant improvements in expression levels and therapeutic applications.

Leveraging Large Language Models for Redundancy-Aware Pathway Analysis and Deep Biological Interpretation

MAPA uses large language models to reduce redundancy in pathway analysis and improve biological interpretation of multi-omics data.

GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells

GraphVelo extends RNA velocity inference to multimodal data by using graph-based machine learning to preserve vector information across different data representations.

Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux

The paper introduces ambimux, a method to estimate and demultiplex ambient molecule contamination in single-cell RNA+ATAC multiome data, improving the detection of biologically meaningful signals.

PathPCNet: Pathway Principal Component-Based Interpretable Framework for Drug Sensitivity Prediction

PathPCNet predicts drug sensitivity using multi-omics data and biological pathways, achieving high correlation and uncovering key gene-drug interactions.

GENESIS: Generating scRNA-Seq data from Multiome Gene Expression

GENESIS converts Multiome GEX data into synthetic scRNA-Seq profiles using generative models, improving cell-type classification accuracy.