|
0
|
|
Fault-tolerant pedigree reconstruction from pairwise kinship relations.
(academic.oup.com)
|
Huang EC
…
Narasimhan VM
Bioinformatics
2026-05-04
|
#phylogenomics
#sequencing
#modeling
|
|
0
|
|
MDCDR: predicting cancer drug response via multimodal feature fusion and feature disentanglement.
(academic.oup.com)
|
Zhang J
…
Shen X
Briefings in Bioinformatics
2026-05-04
|
#drug response
#cancer
#modeling
#personalized medicine
#machine learning
|
|
0
|
|
Proximal regularization of deep residual neural networks applied to high-dimensional genomic data.
(academic.oup.com)
|
Fan Y
…
Waldmann P
Briefings in Bioinformatics
2026-05-04
|
#modeling
#genomics
#regularization
#prediction
|
|
0
|
|
Foundation models and deep learning for cancer drug response prediction: a framework for data, metrics, and validation.
(academic.oup.com)
|
Sada Del Real K
…
Rubio A
Briefings in Bioinformatics
2026-05-04
|
#modeling
#cancer
#drug response
#machine learning
#omics
|
|
0
|
|
The next paradigm in bioinformatics: a review of multi-agent systems and foundational models for end-to-end scientific discovery.
(academic.oup.com)
|
Branda F
…
Scarpa F
Briefings in Bioinformatics
2026-05-04
|
#modeling
#transcriptomics
#drug discovery
#personalized medicine
|
|
0
|
|
Quantum ensembling methods for healthcare and life science.
(academic.oup.com)
|
Rhrissorrakrai K
…
Parida L
Briefings in Bioinformatics
2026-05-04
|
#classification
#modeling
#immunotherapy
#cancer
|
|
0
|
|
StackAge: an ensemble-based clock for precise quantification of biological age using multi-omics data.
(academic.oup.com)
|
Jiang Y
…
Qin Y
Briefings in Bioinformatics
2026-05-04
|
#proteomics
#metabolomics
#aging
#modeling
#inflammation
|
|
0
|
|
CanLRHI: a multimodal pretraining model for cell death analysis in cancer pathology based on long-text representation and high-resolution images.
(academic.oup.com)
|
Zhang T
…
Ma J
Briefings in Bioinformatics
2026-05-04
|
#cancer
#pathology
#modeling
#apoptosis
|
|
0
|
|
Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.
(academic.oup.com)
|
Wang K
…
Zhou J
Briefings in Bioinformatics
2026-05-04
|
#metabolism
#modeling
#machine learning
#synthetic biology
|
|
0
|
|
Porcine MutBERT: a family of lightweight genomic foundation models for functional element prediction in pigs.
(academic.oup.com)
|
Long W
…
Wang Z
Briefings in Bioinformatics
2026-05-04
|
#genomics
#modeling
#transcriptomics
#livestock
|
|
0
|
|
ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation.
(academic.oup.com)
|
Wang P
…
Sun Z
Briefings in Bioinformatics
2026-05-04
|
#eqtl
#transcriptomics
#transcription factor
#genomics
#modeling
|
|
0
|
|
MMP3C v2: a network-based framework decoding metabolic plasticity in rheumatoid arthritis, enabling accurate diagnosis and uncovering cell-type-specific metabolic rewiring.
(academic.oup.com)
|
Chen X
…
Huang C
Briefings in Bioinformatics
2026-05-04
|
#metabolism
#rheumatoid arthritis
#transcriptomics
#immunity
#modeling
|
|
0
|
|
RNA design: update on computational frameworks and programs for inverse RNA folding.
(academic.oup.com)
|
Mukherjee S
…
Barash D
Briefings in Bioinformatics
2026-05-04
|
#rna design
#inverse folding
#computational
#secondary structure
#modeling
|
|
0
|
|
DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.
(academic.oup.com)
|
Wang J
…
Liu Y
Briefings in Bioinformatics
2026-05-04
|
#metagenomics
#assembly
#binning
#microbiome
#modeling
|
|
0
|
|
Predicting protein-protein interaction sites based on dynamic perception mechanism within a hierarchical E(n)-equivariant graph.
(academic.oup.com)
|
Li X
…
Cao B
Briefings in Bioinformatics
2026-05-04
|
#protein-protein interaction
#structure prediction
#modeling
#graph neural network
|
|
0
|
|
From mechanistic modeling to AI-driven design: computational strategies for targeting the gamma-secretase complex.
(academic.oup.com)
|
Das S
…
Pandurangan AP
Briefings in Bioinformatics
2026-05-04
|
#modeling
#drug discovery
#protease
#neurodegeneration
#simulation
|
|
0
|
|
Modeling DNA storage retrieval reliability via sequencing coverage depth.
(academic.oup.com)
|
Cao R
…
Chen X
Briefings in Bioinformatics
2026-05-04
|
#sequencing
#modeling
#reliability
|
|
0
|
|
Carcinogenicity prediction via multi-task learning of cross-organ representations with attention mechanisms.
(academic.oup.com)
|
Song Y
…
Yoo S
Briefings in Bioinformatics
2026-05-04
|
#carcinogenicity
#modeling
#prediction
#cancer
|
|
0
|
|
SE(3)-PROTACs: Geometric deep learning for PROTAC degradation prediction.
(academic.oup.com)
|
Kothakapu AR
…
Kondaparthi V
Briefings in Bioinformatics
2026-05-04
|
#modeling
#proteomics
#protein
#degradation
|
|
0
|
|
Graph-based RNA structural representation reveals determinants of subcellular localization.
(academic.oup.com)
|
Hao Y
…
Li F
Briefings in Bioinformatics
2026-05-04
|
#rna
#localization
#modeling
#prediction
|
|
0
|
|
Digital twins of ex vivo human lungs enable accurate and personalized evaluation of therapeutic efficacy.
(nature.com)
|
Zhou X
…
Sage AT
Nature Biotechnology
2026-05-04
|
#modeling
#transcriptomics
#proteomics
#metabolomics
#therapeutics
|
|
0
|
|
scHILL: deciphering individual-level immune cell heterogeneity with single-cell RNA sequencing data.
(academic.oup.com)
|
Wang Y
…
Song S
Briefings in Bioinformatics
2026-05-04
|
#transcriptomics
#immunity
#modeling
#heterogeneity
|
|
0
|
|
GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method.
(academic.oup.com)
|
Wang S
…
Huang DS
Briefings in Bioinformatics
2026-05-04
|
#modeling
#chromatin
#machine learning
#gene regulation
|
|
0
|
|
Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.
(academic.oup.com)
|
Hossain E
…
Yousefi N
Briefings in Bioinformatics
2026-05-04
|
#amr
#machine learning
#genomics
#prediction
#modeling
|
|
0
|
|
Untangling or further entangling? Theoretical expansion of the structural landscape of nucleic acid quadruplexes and modeling with 3D-NuS-Qplex.
(academic.oup.com)
|
Rathinavelan T
…
Sundaresan S
Briefings in Bioinformatics
2026-05-04
|
#modeling
#quadruplex
#nucleic acid
|
|
0
|
|
Semi-supervised disentangled representation learning for single-cell RNA sequencing data.
(academic.oup.com)
|
Liu H
…
Wei Z
Briefings in Bioinformatics
2026-05-04
|
#transcriptomics
#clustering
#modeling
#sequencing
|
|
0
|
|
SwiftTCR: efficient computational docking protocol of TCRpMHC-I complexes using restricted rotation matrices.
(academic.oup.com)
|
Parizi FM
…
Xue LC
Briefings in Bioinformatics
2026-05-04
|
#modeling
#docking
#immunity
#immunotherapy
|
|
0
|
|
Benchmarking TCR-pMHC structure prediction: a unified evaluation and CDR3-based functional insights.
(academic.oup.com)
|
Lu J
…
Feng F
Briefings in Bioinformatics
2026-05-04
|
#structure prediction
#immunity
#modeling
#benchmarking
|
|
0
|
|
Identification and characterization of lncRNA-stemness-immune regulatory patterns.
(academic.oup.com)
|
Qian Z
…
Zhao Y
Briefings in Bioinformatics
2026-05-04
|
#ncrna
#stemness
#immunity
#cancer
#modeling
|
|
0
|
|
GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles.
(academic.oup.com)
|
Dong H
…
Du PF
Briefings in Bioinformatics
2026-05-04
|
#chromatin
#modeling
#sequencing
#gene regulation
#deep learning
|
|
0
|
|
HighRes_Builder: improved access and modeling of noncanonical residues for protein structure prediction.
(academic.oup.com)
|
Han Y
…
Wang X
Briefings in Bioinformatics
2026-05-04
|
#structure prediction
#protein
#modeling
#peptide
|
|
0
|
|
Reply to "Letter to the editor: methodological considerations in the benchmarking of AI-based protein-aptamer complex prediction".
(academic.oup.com)
|
Zhao J
…
Li Y
Briefings in Bioinformatics
2026-05-04
|
#modeling
#protein
#binding
|
|
0
|
|
Rethinking bioinformatics in liquid-liquid phase separation: data resources, predictive models, and an event-centric perspective.
(academic.oup.com)
|
Yuan ZL
…
Ning L
Briefings in Bioinformatics
2026-05-04
|
#modeling
#prediction
#bioinformatics
#machine learning
|
|
0
|
|
QTLNetwork-MP: integrative mapping of additive, epistatic, and G x E effects for complex traits in multiparent advanced generation intercross populations.
(academic.oup.com)
|
Zhu TN
…
Xu HM
Briefings in Bioinformatics
2026-05-04
|
#qtl
#epistasis
#mapping
#genetics
#modeling
|
|
0
|
|
Shoebill: an interpretable AlphaFold2-informed predictor of protein crystallization propensity using XGBoost.
(academic.oup.com)
|
Liao KJ
…
Sun YJ
Briefings in Bioinformatics
2026-05-04
|
#modeling
#protein structure
#prediction
#crystallography
|
|
0
|
|
VIRSE: a variational Bayesian framework for RNA structural ensemble inference.
(academic.oup.com)
|
Liang J
…
Song Q
Briefings in Bioinformatics
2026-05-04
|
#rna
#inference
#modeling
#sequencing
|
|
0
|
|
STORM: spatial transcriptomics optimization by resolution via matrix factorization.
(academic.oup.com)
|
Gurarslan D
…
Kahveci T
Briefings in Bioinformatics
2026-05-04
|
#transcriptomics
#modeling
#cancer
|
|
0
|
|
DeepPTMPred: a multi-modal deep learning framework for accurate prediction of protein post-translational modification sites.
(academic.oup.com)
|
Wang C
…
Wang J
Briefings in Bioinformatics
2026-05-04
|
#proteomics
#modeling
#prediction
#phosphorylation
|
|
0
|
|
KSDiffusion: conditional diffusion for kinase-specific phosphorylation site prediction under data-limited and imbalanced regimes.
(academic.oup.com)
|
Qiu S
…
Shi X
Briefings in Bioinformatics
2026-05-04
|
#phosphorylation
#modeling
#proteomics
#machine learning
|
|
0
|
|
Machine learning-guided multimodal profiling defines perturbed immune states at the time of cancer diagnosis.
(academic.oup.com)
|
Berlin P
…
Maletzki C
Briefings in Bioinformatics
2026-05-04
|
#immunity
#cancer
#transcriptomics
#modeling
#inflammation
|
|
0
|
|
Comprehensive evaluation of artificial intelligence-empowered approaches for protein-aptamer complex prediction.
(academic.oup.com)
|
Zhao J
…
Li Y
Briefings in Bioinformatics
2026-05-04
|
#modeling
#aptamer
#proteomics
#therapeutics
#binding
|
|
0
|
|
Empowering multifaceted analysis of spatial transcriptomics data with RGAST.
(academic.oup.com)
|
Gong Y
…
Yu Z
Briefings in Bioinformatics
2026-05-04
|
#transcriptomics
#clustering
#neuroimaging
#modeling
|
|
0
|
|
Pathogenicity prediction for noncanonical splice-altering variants based on multimodal feature fusion.
(academic.oup.com)
|
Li X
…
Xia J
Briefings in Bioinformatics
2026-05-04
|
#modeling
#pathogenicity
#splicing
#variants
#deep learning
|
|
0
|
|
CEDR: robust consensus cancer subtyping with multi-omics data via ensemble dimensionality reduction.
(academic.oup.com)
|
Cao H
…
Cui Y
Briefings in Bioinformatics
2026-05-04
|
#clustering
#cancer
#dimensionality reduction
#multi-omics
#modeling
|
|
0
|
|
ssNetShift: single-sample metabolic network rewiring reveals hidden prognostic subtypes beyond clinical staging in gastric cancer.
(academic.oup.com)
|
Lin G
…
Raftery D
Briefings in Bioinformatics
2026-05-04
|
#metabolism
#cancer
#modeling
#biomarker
#heterogeneity
|
|
0
|
|
Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.
(academic.oup.com)
|
Ding W
…
Jin S
Briefings in Bioinformatics
2026-05-04
|
#chromatin
#interaction
#sequencing
#modeling
#regulation
|