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Briefings in Bioinformatics|April 7, 2025
CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditionsAndrea Lomagno, Ishak Yusuf, Gabriele Tosadori, et al.
Briefings in Bioinformatics|April 7, 2025
Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasetsHaoyang Cheng, Zhuoran Liang, Yijin Wu, et al.
Briefings in Bioinformatics|March 10, 2025
Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencodersLiang Chen, Madison Dautle, Ruoying Gao, et al.
Briefings in Bioinformatics|December 21, 2024
scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learningLin Yuan, Shengguo Sun, Yufeng Jiang, et al.
Briefings in Bioinformatics|November 27, 2024
FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAsYan-Yu Li, Feng-Cui Qian, Guo-Rui Zhang, et al.
Briefings in Bioinformatics|December 16, 2024
Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore dataWillem Stock, Coralie Rousseau, Glen Dierickx, et al.
Briefings in Bioinformatics|December 16, 2024
THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured dataYixuan Wang, Yanfang Guan, Xin Lai, et al.
Briefings in Bioinformatics|December 23, 2024
CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq dataYi Zhang, Yin Wang, Xinyuan Liu, et al.
Briefings in Bioinformatics|December 22, 2024
Annotating publicly-available samples and studies using interpretable modeling of unstructured metadataHao Yuan, Parker Hicks, Mansooreh Ahmadian, et al.
Briefings in Bioinformatics|December 10, 2024
Understanding relationships between epigenetic marks and their application to robust assignment of chromatin statesLeandro Murgas, Gianluca Pollastri, Erick Riquelme, et al.
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