DLBWE-Cys: a deep-learning-based tool for identifying cysteine S-carboxyethylation sites using binary-weight encoding

Authors: Zhengtao Luo, Qingyong Wang, Yingchun Xia, Xiaolei Zhu, Shuai Yang, Zhaochun Xu, Lichuan Gu

Source: Frontiers in Genetics, Vol 15 (2025)

Subject Terms: S-carboxyethylation, post-translational modification, bahdanau attention mechanism, binary-weight encoding, deep learning, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2024.1464976/full; https://doaj.org/toc/1664-8021

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Dimension reduction, cell clustering, and cell–cell communication inference for single-cell transcriptomics with DcjComm

Authors: Qian Ding, Wenyi Yang, Guangfu Xue, Hongxin Liu, Yideng Cai, Jinhao Que, Xiyun Jin, Meng Luo, Fenglan Pang, Yuexin Yang, Yi Lin, Yusong Liu, Haoxiu Sun, Renjie Tan, Pingping Wang, Zhaochun Xu, Qinghua Jiang

Source: Genome Biology, Vol 25, Iss 1, Pp 1-36 (2024)

Subject Terms: Single-cell, Cell clustering, Cell–cell communication, Joint learning, Non-negative matrix factorization, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/1acf3ecb89144f69bb113bc2a6df2a95

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

Authors: Wenyi Yang, Pingping Wang, Shouping Xu, Tao Wang, Meng Luo, Yideng Cai, Chang Xu, Guangfu Xue, Jinhao Que, Qian Ding, Xiyun Jin, Yuexin Yang, Fenglan Pang, Boran Pang, Yi Lin, Huan Nie, Zhaochun Xu, Yong Ji, Qinghua Jiang

Source: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d5f02cc0b72b462c9dd2a7d430e53925

Comprehensive Review and Assessment of Computational Methods for Prediction of N6-Methyladenosine Sites

Authors: Zhengtao Luo, Liyi Yu, Zhaochun Xu, Kening Liu, Lichuan Gu

Source: Biology, Vol 13, Iss 10, p 777 (2024)

Subject Terms: m6A site identification, deep learning, machine learning, performance evaluation, independent test datasets, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2079-7737/13/10/777; https://doaj.org/toc/2079-7737

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Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor

Authors: Lixing Xiao, Haoxiu Sun, Rui Cheng, Rongrong Yang, Xiyun Jin, Zhaochun Xu, Yideng Cai, Yuexin Yang, Fenglan Pang, Guangfu Xue, Pingping Wang, Qinghua Jiang, Huan Nie

Source: Molecular Therapy: Nucleic Acids, Vol 35, Iss 1, Pp 102129- (2024)

Subject Terms: MT: Bioinformatics, alternative splicing, circulating tumor cell, epithelial-to-mesenchymal transition, pancreatic ductal adenocarcinoma, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2162253124000167; https://doaj.org/toc/2162-2531

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Identification of shared characteristics in tumor-infiltrating T cells across 15 cancers

Authors: Xiyun Jin, Yideng Cai, Guangfu Xue, Jinhao Que, Rui Cheng, Yuexin Yang, Lixing Xiao, Xiaoyu Lin, Chang Xu, Pingping Wang, Zhaochun Xu, Huan Nie, Qinghua Jiang

Source: Molecular Therapy: Nucleic Acids, Vol 32, Iss , Pp 189-202 (2023)

Subject Terms: MT: Bioinformatics, tumor-infiltrating T cells, pan-cancer, single-cell sequencing, TF regulon, state transition, Therapeutics. Pharmacology, RM1-950

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Relation: http://www.sciencedirect.com/science/article/pii/S2162253123000665; https://doaj.org/toc/2162-2531

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Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease

Authors: Pingping Wang, Lifen Yao, Meng Luo, Wenyang Zhou, Xiyun Jin, Zhaochun Xu, Shi Yan, Yiqun Li, Chang Xu, Rui Cheng, Yan Huang, Xiaoyu Lin, Kexin Ma, Huimin Cao, Hongxin Liu, Guangfu Xue, Fang Han, Huan Nie, Qinghua Jiang

Source: Cell Discovery, Vol 7, Iss 1, Pp 1-16 (2021)

Subject Terms: Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/2056-5968

Access URL: https://doaj.org/article/e479b76060ba44c7bf9bf381d3313824

Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma

Authors: Lixing Xiao, Guoying Zou, Rui Cheng, Pingping Wang, Kexin Ma, Huimin Cao, Wenyang Zhou, Xiyun Jin, Zhaochun Xu, Yan Huang, Xiaoyu Lin, Huan Nie, Qinghua Jiang

Source: BMC Cancer, Vol 21, Iss 1, Pp 1-13 (2021)

Subject Terms: Alternative splicing, Stemness, Machine learning, KIRC, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2407

Access URL: https://doaj.org/article/79e91d703bcc420fb2d0b3bc36e4e39f

Global Characterization of Peripheral B Cells in Parkinson’s Disease by Single-Cell RNA and BCR Sequencing

Authors: Pingping Wang, Meng Luo, Wenyang Zhou, Xiyun Jin, Zhaochun Xu, Shi Yan, Yiqun Li, Chang Xu, Rui Cheng, Yan Huang, Xiaoyu Lin, Lifen Yao, Huan Nie, Qinghua Jiang

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: Parkinson’s disease, B cells, scRNA-seq, scBCR-seq, adaptive immune response, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.814239/full; https://doaj.org/toc/1664-3224

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N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation

Authors: Wenyang Zhou, Chang Xu, Pingping Wang, Meng Luo, Zhaochun Xu, Rui Cheng, Xiyun Jin, Yu Guo, Guangfu Xue, Liran Juan, Anastasia A. Anashkina, Huan Nie, Qinghua Jiang

Source: Frontiers in Cell and Developmental Biology, Vol 9 (2021)

Subject Terms: SARS-CoV-2, N439K, molecular dynamics, binding free energy, neutralizing antibody, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2021.697035/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/37ba098766774e3f8f952d10746acd84

Identification of potential vaccine targets for COVID‐19 by combining single‐cell and bulk TCR sequencing

Authors: Pingping Wang, Zhaochun Xu, Wenyang Zhou, Xiyun Jin, Chang Xu, Meng Luo, Kexin Ma, Huimin Cao, Yan Huang, Xiaoyu Lin, Fenglan Pang, Yiqun Li, Qinghua Jiang

Source: Clinical and Translational Medicine, Vol 11, Iss 5, Pp n/a-n/a (2021)

Subject Terms: Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/2001-1326

Access URL: https://doaj.org/article/b63bb316436d4b6ba927e8ecad861d8d

Comprehensive Analysis of Copy Number Variations in Kidney Cancer by Single-Cell Exome Sequencing

Authors: Wenyang Zhou, Fan Yang, Zhaochun Xu, Meng Luo, Pingping Wang, Yu Guo, Huan Nie, Lifen Yao, Qinghua Jiang

Source: Frontiers in Genetics, Vol 10 (2020)

Subject Terms: copy number variations, single-cell exome sequencing, clear-cell renal cell carcinoma, receptor protein tyrosine kinase, signaling transduction pathway, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fgene.2019.01379/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/53f6ce2acbbd4002aed5280f3068c8c1

Identification of D Modification Sites by Integrating Heterogeneous Features in Saccharomyces cerevisiae

Authors: Pengmian Feng, Zhaochun Xu, Hui Yang, Hao Lv, Hui Ding, Li Liu

Source: Molecules, Vol 24, Iss 3, p 380 (2019)

Subject Terms: dihydrouridine, nucleotide physicochemical property, pseudo dinucleotide composition, RNA secondary structure, ensemble classifier, Organic chemistry, QD241-441

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Relation: https://www.mdpi.com/1420-3049/24/3/380; https://doaj.org/toc/1420-3049

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Design and analysis of photonic crystal spectral diversity filters for biosensing

Authors: Badieirostami, M., Reid, C.M., Momtahan, O., Momeni, B., Alibi, A., Zhaochun Xu, Zhanglei Wang, Sullivan, M.E., Brady, D.J., Foulger, S.H.

Source: Conference on Lasers and Electro-Optics, 2004. (CLEO). Lasers and Electro-optics Lasers and Electro-Optics, 2004. (CLEO). Conference on. 2:2 pp. vol.2 2004

Relation: Conference on Lasers and Electro-Optics (CLEO)

PAI-SAE: Predicting Adenosine To Inosine Editing Sites Based On Hybrid Features By Using Spare Auto-Encoder.

Authors: Xuan Xiao, Peng Wang, Zhaochun Xu, Wangren Qiu, Xinzhu Fang

Source: IOP Conference Series: Earth & Environmental Science; July2018, Vol. 170 Issue 5, p1-1, 1p

Toxicity and Hypolipidemic Activity of Lansiumamide B in Mice

Authors: CHEN Danni, WANG Sainan, YIN Zhaochun, XU Zewen, GUO Xiaomin, LI Kangyuan, WANG Jiawei, CHEN Liping, CAO Yong, XIAO Suyao

Source: Shipin Kexue, Vol 45, Iss 7, Pp 145-154 (2024)

Subject Terms: lansiumamide b, no observed adverse effect level, hypolipidemic, insulin resistance, oxidative stress, Food processing and manufacture, TP368-456

File Description: electronic resource

Relation: https://www.spkx.net.cn/fileup/1002-6630/PDF/2024-45-7-018.pdf; https://doaj.org/toc/1002-6630

Access URL: https://doaj.org/article/9e5ad0468ffc4029b2bacd26d53350a9