|
0
|
|
Cross-cohort projection of clinically anchored latent risk enables multi-omics interpretation without refitting.
(academic.oup.com)
|
Huang Z
…
Chen M
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#multi-omics
#prognostication
#prostate
#deconvolution
|
|
0
|
|
MitoClipSplice: a machine learning framework for resolving mitochondrial RNA cleavage sites from strand-specific RNA-seq soft-clips.
(academic.oup.com)
|
Yuan Q
…
Zhou K
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#rna-seq
#mitochondrial
#machine learning
#rna processing
|
|
0
|
|
Functional motif detection via in silico ablation using AlphaGenome.
(academic.oup.com)
|
Liang Y
…
Wang G
Briefings in Bioinformatics
2026-07-03
|
#regulation
#sequencing
#machine learning
#enhancer
#transcriptomics
|
|
0
|
|
Data-intensive immune network modelling for One Health.
(academic.oup.com)
|
Hillis R
…
Overton IM
Briefings in Bioinformatics
2026-07-03
|
#immunology
#transcriptomics
#bioinformatics
#network-biology
#machine learning
|
|
0
|
|
Exploring cell-type associations of rare disease phenotypes using non-diseased cell atlases.
(academic.oup.com)
|
Novoa J
…
Chagoyen M
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#single-cell
#rare disease
#phenotype
#cell-atlas
|
|
0
|
|
STRESS: spatial transcriptomics resolution enhancing method based on the state-space model.
(academic.oup.com)
|
Wang X
…
Liu X
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#deep learning
#gene expression
#tissue
|
|
0
|
|
TopoMetry systematically learns and evaluates the latent geometry of single-cell data.
(elifesciences.org)
|
Sidarta-Oliveira D
…
Velloso LA
eLife
2026-07-03
|
#transcriptomics
#single-cell
#clustering
#visualization
|
|
0
|
|
DeSpaST: deconvoluting spatial transcriptomics signals to cell-level resolution using histology images.
(academic.oup.com)
|
Zhou Q
…
Xie Y
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#deconvolution
#histology
#cancer
|
|
0
|
|
scGenoByte: a GenoByte embedding transformer with biological priors for cell type annotation.
(academic.oup.com)
|
Yao J
…
Wu S
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#single-cell
#cell annotation
#representation learning
#pathway analysis
|
|
0
|
|
Foundation models in omics research: a comprehensive survey.
(academic.oup.com)
|
Liu H
…
Sun J
Briefings in Bioinformatics
2026-07-03
|
#omics
#machine learning
#multi-omics
#transcriptomics
#biomarker
|
|
0
|
|
The Lomb-Scargle periodogram-based differentially expressed gene detection along pseudotime.
(academic.oup.com)
|
Iuchi H
…
Hamada M
Nucleic Acids Research
2026-07-03
|
#transcriptomics
#single-cell
#trajectory
#differentiation
|
|
0
|
|
Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.
(academic.oup.com)
|
Yang J
…
Liu Q
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#cell-communication
#computational
#signaling
|
|
0
|
|
miRSiC: a regulatory-aware machine learning framework for microRNA expression inference across bulk and single-cell transcriptomes.
(academic.oup.com)
|
Chen GT
…
Lee TY
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#microrna
#machine learning
#cancer
#gene regulation
|
|
0
|
|
Deep learning models for cell cycle phase prediction from single-cell RNA sequencing data.
(academic.oup.com)
|
Akhter H
…
Adjeroh DA
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#machine learning
#cell cycle
#deep learning
|
|
0
|
|
scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.
(academic.oup.com)
|
Xiao Z
…
Guo L
Nucleic Acids Research
2026-07-03
|
#transcriptomics
#single-cell
#annotation
#diffusion models
#denoising
|
|
0
|
|
IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.
(academic.oup.com)
|
Shen C
…
Zhang R
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#splicing
#machine learning
#non-model-organisms
|
|
0
|
|
Efficient evidence-based genome annotation with EviAnn.
(nature.com)
|
Zimin AV
…
Salzberg SL
Nature Methods
2026-07-03
|
#annotation
#sequencing
#transcriptomics
#genomics
|
|
0
|
|
Imaging-anchored multiomics in cardiovascular disease: integrating cardiac imaging, bulk, single-cell, and spatial transcriptomics.
(academic.oup.com)
|
Le MHN
…
Quoc Khanh Le N
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#multi-omics
#cardiovascular
#imaging
|
|
0
|
|
A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.
(academic.oup.com)
|
Qi Y
…
Kaiser S
Nucleic Acids Research
2026-07-03
|
#mass spectrometry
#rna modification
#transcriptomics
#chromatography
|
|
0
|
|
STGBench: sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic alterations.
(academic.oup.com)
|
Wang S
…
Wang J
Briefings in Bioinformatics
2026-07-03
|
#sequencing
#transcriptomics
#simulation
#cnv
|
|
0
|
|
The case for caution in the application of whole-exome sequencing data for immune repertoire analysis.
(academic.oup.com)
|
Gong Z
…
Li S
Briefings in Bioinformatics
2026-07-03
|
#sequencing
#immunology
#repertoire
#methodology
#transcriptomics
|
|
0
|
|
Computational analysis in spatial transcriptomics: methods and perspectives.
(academic.oup.com)
|
Zhou Q
…
Xie Y
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#computational
#gene expression
|
|
0
|
|
SOPA and SIMPA: normalized single-sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers.
(academic.oup.com)
|
Alsharoh H
…
Bender A
Briefings in Bioinformatics
2026-07-03
|
#multi-omics
#pathway
#cancer
#heterogeneity
#transcriptomics
|
|
0
|
|
Enhancing the performance and interpretability of epigenetic clocks.
(academic.oup.com)
|
Patel T
…
van Bommel A
Nucleic Acids Research
2026-07-03
|
#epigenetics
#methylation
#aging
#transcriptomics
#biomarker
|
|
0
|
|
Decoding apoptosis, ferroptosis, and inflammatory cell death in adenomyosis at single-cell resolution.
(academic.oup.com)
|
Sheng Q
…
He X
Briefings in Bioinformatics
2026-07-03
|
#single-cell
#transcriptomics
#apoptosis
#adenomyosis
#ferroptosis
|
|
0
|
|
Multi-task spatial distillation reveals cell-type-resolved programmed cell death landscapes in the human kidney.
(academic.oup.com)
|
Wu C
…
Zuo N
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#kidney
#apoptosis
#deconvolution
#pyroptosis
|
|
0
|
|
Generalizable AI predicts immunotherapy outcomes across cancers and treatments.
(nature.com)
|
Shen W
…
Zitnik M
Nature Medicine
2026-07-03
|
#immunotherapy
#transcriptomics
#cancer
#biomarker
#machine learning
|
|
0
|
|
FerroScore: a statistical approach for quantifying tumor-related ferroptosis based on omics data.
(academic.oup.com)
|
Teng J
…
Zhou T
Briefings in Bioinformatics
2026-07-03
|
#ferroptosis
#transcriptomics
#cancer
#immunology
#biomarker
|
|
0
|
|
A comprehensive survey on graph neural networks for gene regulatory network inference.
(academic.oup.com)
|
Jamal Alkhateeb N
…
Awad M
Briefings in Bioinformatics
2026-07-03
|
#gene-regulatory-networks
#graph-neural-networks
#inference
#transcriptomics
|
|
0
|
|
scImmuneCo: a compendium of cell-type-specific functional modules for decoding immune responses from single-cell RNA-seq data.
(academic.oup.com)
|
Wang FQ
…
Yang W
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#immunity
#single-cell
#co-expression
#interferon
|
|
0
|
|
MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.
(academic.oup.com)
|
Zhang Z
…
Gao X
Bioinformatics
2026-07-03
|
#transcriptomics
#clustering
#graph-neural-networks
#tissue
|
|
0
|
|
Multi-modal data integration reveals functionally credible predictive biomarkers in ovarian cancer.
(link.springer.com)
|
Muranen TA
…
Hynninen J
Genome Medicine
2026-07-03
|
#transcriptomics
#cancer
#biomarker
#sequencing
#precision medicine
|
|
0
|
|
Cap 2'-O-methyltransferase CMTR2 regulates male meiosis independent of its methyltransferase activity.
(academic.oup.com)
|
Zheng B
…
Sun F
Nucleic Acids Research
2026-07-03
|
#meiosis
#infertility
#recombination
#transcriptomics
|
|
0
|
|
scHashFormer: a hash-driven graph transformer for scalable scRNA-seq clustering.
(academic.oup.com)
|
Lu Z
…
Liang J
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#clustering
#single-cell sequencing
#deep learning
|
|
0
|
|
Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.
(academic.oup.com)
|
Villemin JP
…
Colinge J
Nucleic Acids Research
2026-07-03
|
#proteomics
#transcriptomics
#single-cell
#bioinformatics
|
|
0
|
|
RAG: a regularized adaptive graph-based method for rare-cell identification from single-cell expression data.
(academic.oup.com)
|
Wang X
…
Feng S
Briefings in Bioinformatics
2026-07-03
|
#single-cell
#transcriptomics
#clustering
#cell identification
#graph-based
|
|
0
|
|
CTMAP: an adversarial cross-modal learning framework for accurate and robust cell-type annotation in single-cell resolution spatial transcriptomics.
(academic.oup.com)
|
Wang Y
…
Sun D
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#cell-type
#deep learning
#integration
|
|
0
|
|
Annotation-free phenotype prediction using knowledge-augmented clustering from single-cell RNA sequencing data.
(academic.oup.com)
|
Noh J
…
Oh M
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#clustering
#phenotype
#machine learning
|
|
0
|
|
Variational sparse Gaussian-process method for detecting spatially variable genes and cellular interactions in spatial transcriptomics.
(academic.oup.com)
|
Wang Z
…
Hu J
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#gene expression
#cell-communication
#cancer
|
|
0
|
|
Graph-based contrastive learning enables unified integration and niche transfer across single-cell and spatial multi-omics.
(academic.oup.com)
|
Zhou W
…
Tian L
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#single-cell
#embedding
#proteomics
|
|
0
|
|
PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.
(academic.oup.com)
|
Zhai W
…
Ji J
Bioinformatics
2026-07-03
|
#transcriptomics
#single-cell
#networks
#neurodegeneration
#cancer
|
|
0
|
|
Screening of cell-type-specific meta-programs for drug repurposing in Alzheimer's disease.
(academic.oup.com)
|
Zhang C
…
Zhang Y
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#neurodegeneration
#neuroinflammation
#drug-repurposing
#single-cell
|
|
0
|
|
Multi-tissue integrated Mendelian randomization method identifies disease risk genes.
(academic.oup.com)
|
Cheng Y
…
Yan F
Briefings in Bioinformatics
2026-07-03
|
#mendelian randomization
#transcriptomics
#causal inference
#genetics
#disease-risk
|
|
0
|
|
PromptSTG: prototype-guided prompting for few-shot spatial transcriptomics annotation.
(academic.oup.com)
|
Guan R
…
Han X
Briefings in Bioinformatics
2026-07-03
|
#transcriptomics
#annotation
#cell-type
#graph learning
|