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sTPLS: identifying common and specific correlated patterns under multiple biological conditions

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Jinyu Chen and Wenwen Min
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf195, https://doi.org/10.1093/bib/bbaf195
Published: 26 April 2025
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GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning

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Wengyu Zhang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf194, https://doi.org/10.1093/bib/bbaf194
Published: 26 April 2025
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Deep learning in GPCR drug discovery: benchmarking the path to accurate peptide binding

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Luuk R Hoegen Dijkhof and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf186, https://doi.org/10.1093/bib/bbaf186
Published: 26 April 2025
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MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human

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Yun Zuo and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf189, https://doi.org/10.1093/bib/bbaf189
Published: 26 April 2025
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WheatGP, a genomic prediction method based on CNN and LSTM

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Chunying Wang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf191, https://doi.org/10.1093/bib/bbaf191
Published: 25 April 2025
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Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types

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Gen Li and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf190, https://doi.org/10.1093/bib/bbaf190
Published: 24 April 2025
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Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer

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Fabio Cumbo and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf177, https://doi.org/10.1093/bib/bbaf177
Published: 24 April 2025
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DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks

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Yizhen Wang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf187, https://doi.org/10.1093/bib/bbaf187
Published: 24 April 2025
Journal Article

PathSynergy: a deep learning model for predicting drug synergy in liver cancer

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Fengyue Zhang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf192, https://doi.org/10.1093/bib/bbaf192
Published: 24 April 2025
Journal Article

MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variants

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Zeyin Li and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf196, https://doi.org/10.1093/bib/bbaf196
Published: 24 April 2025
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Carmna: classification and regression models for nitrogenase activity based on a pretrained large protein language model

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Anqiang Ye and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf197, https://doi.org/10.1093/bib/bbaf197
Published: 24 April 2025
Journal Article

Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data

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Xinyi Mou and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf141, https://doi.org/10.1093/bib/bbaf141
Published: 21 April 2025
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Mutual-assistance learning for trustworthy biomarker discovery and disease prediction

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Jin Zhang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf178, https://doi.org/10.1093/bib/bbaf178
Published: 21 April 2025
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IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning

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Junxi Xie and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf182, https://doi.org/10.1093/bib/bbaf182
Published: 21 April 2025
Journal Article

Self-awareness of retrosynthesis via chemically inspired contrastive learning for reinforced molecule generation

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Yi Zhang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf185, https://doi.org/10.1093/bib/bbaf185
Published: 21 April 2025
Journal Article

Nonlinear embedding and integration of omics data: a fast and tuning-free approach

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Shengjie Liu and Tianwei Yu
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf184, https://doi.org/10.1093/bib/bbaf184
Published: 21 April 2025
Journal Article

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases

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Cong M Pham and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf173, https://doi.org/10.1093/bib/bbaf173
Published: 21 April 2025
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STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics

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Yuxuan Pang and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf174, https://doi.org/10.1093/bib/bbaf174
Published: 21 April 2025
Journal Article

SCANER: robust and sensitive identification of malignant cells from the scRNA-seq profiled tumor ecosystem

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Peng Xia and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf175, https://doi.org/10.1093/bib/bbaf175
Published: 20 April 2025
Journal Article

A graph neural network approach for accurate prediction of pathogenicity in multi-type variants

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Hongtao Yu and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf151, https://doi.org/10.1093/bib/bbaf151
Published: 19 April 2025