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Authors: Fuyi Li
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Journal Article

Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis

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Zhenhao Zhang and others
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae558, https://doi.org/10.1093/bib/bbae558
Published: 01 November 2024
Journal Article

scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks

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Tianxiang Liu and others
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae486, https://doi.org/10.1093/bib/bbae486
Published: 05 October 2024
Journal Article

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects

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Xiaoyu Wang and others
Briefings in Bioinformatics, Volume 25, Issue 5, September 2024, bbae446, https://doi.org/10.1093/bib/bbae446
Published: 13 September 2024
Journal Article

Advancing microRNA target site prediction with transformer and base-pairing patterns

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Yue Bi and others
Nucleic Acids Research, Volume 52, Issue 19, 28 October 2024, Pages 11455–11465, https://doi.org/10.1093/nar/gkae782
Published: 13 September 2024
Journal Article

Variable calling of m6A and associated features in databases: a guide for end-users

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Renhua Song and others
Briefings in Bioinformatics, Volume 25, Issue 5, September 2024, bbae434, https://doi.org/10.1093/bib/bbae434
Published: 11 September 2024
Journal Article

Advancing mRNA subcellular localization prediction with graph neural network and RNA structure

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Fuyi Li and others
Bioinformatics, Volume 40, Issue 8, August 2024, btae504, https://doi.org/10.1093/bioinformatics/btae504
Published: 12 August 2024
Journal Article

MERITS: a web-based integrated Mycobacterial PE/PPE protein database

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Zhijie He and others
Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae035, https://doi.org/10.1093/bioadv/vbae035
Published: 02 March 2024
Journal Article

ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction

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Fuyi Li and others
Briefings in Bioinformatics, Volume 24, Issue 6, November 2023, bbad372, https://doi.org/10.1093/bib/bbad372
Published: 24 October 2023
Journal Article

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities

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Jing Xu and others
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad240, https://doi.org/10.1093/bib/bbad240
Published: 27 June 2023
Journal Article

TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters

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Yan Zhu and others
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad209, https://doi.org/10.1093/bib/bbad209
Published: 08 June 2023
Journal Article

ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species

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Ruyi Chen and others
Briefings in Bioinformatics, Volume 24, Issue 3, May 2023, bbad170, https://doi.org/10.1093/bib/bbad170
Published: 06 May 2023
Journal Article

ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning

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Xiaoti Jia and others
Briefings in Bioinformatics, Volume 24, Issue 2, March 2023, bbad063, https://doi.org/10.1093/bib/bbad063
Published: 04 March 2023
Journal Article

VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants

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Fang Ge and others
Briefings in Bioinformatics, Volume 24, Issue 1, January 2023, bbac535, https://doi.org/10.1093/bib/bbac535
Published: 18 December 2022
Journal Article

COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants

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Yuanyuan Bu and others
Briefings in Functional Genomics, Volume 22, Issue 3, May 2023, Pages 274–280, https://doi.org/10.1093/bfgp/elac049
Published: 17 December 2022
Journal Article

Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations

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Yue Bi and others
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac467, https://doi.org/10.1093/bib/bbac467
Published: 05 November 2022
Journal Article

DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions

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Quanzhong Liu and others
Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4053–4061, https://doi.org/10.1093/bioinformatics/btac454
Published: 07 July 2022
Journal Article

RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins

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Xinxin Peng and others
Briefings in Bioinformatics, Volume 23, Issue 4, July 2022, bbac215, https://doi.org/10.1093/bib/bbac215
Published: 02 June 2022
Journal Article

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets

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Zhen Chen and others
Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W434–W447, https://doi.org/10.1093/nar/gkac351
Published: 07 May 2022
Journal Article

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning

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Xiaoyu Wang and others
Briefings in Bioinformatics, Volume 23, Issue 2, March 2022, bbac031, https://doi.org/10.1093/bib/bbac031
Published: 17 February 2022
Journal Article

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction

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Meng Zhang and others
Briefings in Bioinformatics, Volume 23, Issue 2, March 2022, bbab551, https://doi.org/10.1093/bib/bbab551
Published: 11 January 2022