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PMC Full-Text Search Results

Items: 1 to 20 of 1503

1.
RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method
Lai Heng Tan, Chee Keong Kwoh, Yuguang Mu
Brief Bioinform. 2024 May; 25(3): bbae166. Published online 2024 May 1. doi: 10.1093/bib/bbae166
PMCID:
PMC11063749
ArticlePDF–2.5M
2.
Scoring alignments by embedding vector similarity
Sepehr Ashrafzadeh, G Brian Golding, Silvana Ilie, Lucian Ilie
Brief Bioinform. 2024 May; 25(3): bbae178. Published online 2024 May 1. doi: 10.1093/bib/bbae178
PMCID:
PMC11063651
ArticlePDF–1.3M
3.
DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery
Wei Lan, Haibo Liao, Qingfeng Chen, Lingzhi Zhu, Yi Pan, Yi-Ping Phoebe Chen
Brief Bioinform. 2024 May; 25(3): bbae185. Published online 2024 Apr 27. doi: 10.1093/bib/bbae185
PMCID:
PMC11056029
ArticlePDF–5.7M
4.
CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides
Lei Liu, Liu Yang, Suqi Cao, Zhigang Gao, Bin Yang, Guoqing Zhang, Ruixin Zhu, Dingfeng Wu
Brief Bioinform. 2024 May; 25(3): bbae190. Published online 2024 Apr 27. doi: 10.1093/bib/bbae190
PMCID:
PMC11056021
ArticlePDF–1.9M
5.
CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data
Furui Liu, Fangyuan Shi, Fang Du, Xiangmei Cao, Zhenhua Yu
Brief Bioinform. 2024 May; 25(3): bbae187. Published online 2024 Apr 25. doi: 10.1093/bib/bbae187
PMCID:
PMC11052634
ArticlePDF–1.6M
6.
DEGAP: Dynamic elongation of a genome assembly path
Yicheng Huang, Ziyuan Wang, Monica A Schmidt, Handong Su, Lizhong Xiong, Jianwei Zhang
Brief Bioinform. 2024 May; 25(3): bbae194. Published online 2024 Apr 25. doi: 10.1093/bib/bbae194
PMCID:
PMC11052632
ArticlePDF–1.2M
7.
Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms
Seyed Amir Malekpour, Laleh Haghverdi, Mehdi Sadeghi
Brief Bioinform. 2024 May; 25(3): bbae180. Published online 2024 Apr 22. doi: 10.1093/bib/bbae180
PMCID:
PMC11036345
ArticlePDF–1.9M
8.
CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses
Xue Zhang, JingCheng Wu, Yuanyuan Luo, Yilin Wang, Yujie Wu, Xiaobin Xu, Yufang Zhang, Ruiying Kong, Ying Chi, Yisheng Sun, Shuqing Chen, Qiaojun He, Feng Zhu, Zhan Zhou
Brief Bioinform. 2024 May; 25(3): bbae183. Published online 2024 Apr 22. doi: 10.1093/bib/bbae183
PMCID:
PMC11036340
ArticlePDF–2.1M
9.
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network
Xiaowen Hu, Pan Zhang, Dayun Liu, Jiaxuan Zhang, Yuanpeng Zhang, Yihan Dong, Yanhao Fan, Lei Deng
Brief Bioinform. 2024 May; 25(3): bbae179. Published online 2024 Apr 21. doi: 10.1093/bib/bbae179
PMCID:
PMC11033953
ArticlePDF–1.2M
10.
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu
Brief Bioinform. 2024 May; 25(3): bbae172. Published online 2024 Apr 21. doi: 10.1093/bib/bbae172
PMCID:
PMC11033846
ArticlePDF–1.8M
11.
Eravacycline, an antibacterial drug, repurposed for pancreatic cancer therapy: insights from a molecular-based deep learning model
Adi Jabarin, Guy Shtar, Valeria Feinshtein, Eyal Mazuz, Bracha Shapira, Shimon Ben-Shabat, Lior Rokach
Brief Bioinform. 2024 May; 25(3): bbae108. Published online 2024 Apr 21. doi: 10.1093/bib/bbae108
PMCID:
PMC11033730
ArticlePDF–1.2M
12.
TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples
Shenjie Wang, Xiaoyan Zhu, Xuwen Wang, Yuqian Liu, Minchao Zhao, Zhili Chang, Xiaonan Wang, Yang Shao, Jiayin Wang
Brief Bioinform. 2024 May; 25(3): bbae159. Published online 2024 Apr 18. doi: 10.1093/bib/bbae159
PMCID:
PMC11024516
ArticlePDF–1.1M
13.
Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg
Ting-He Zhang, Sumin Jo, Michelle Zhang, Kai Wang, Shou-Jiang Gao, Yufei Huang
Brief Bioinform. 2024 May; 25(3): bbae170. Published online 2024 Apr 15. doi: 10.1093/bib/bbae170
PMCID:
PMC11018547
ArticlePDF–817K
14.
MGCNSS: miRNA–disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy
Zhen Tian, Chenguang Han, Lewen Xu, Zhixia Teng, Wei Song
Brief Bioinform. 2024 May; 25(3): bbae168. Published online 2024 Apr 15. doi: 10.1093/bib/bbae168
PMCID:
PMC11018511
ArticlePDF–2.9M
15.
Correction to: Inflated false discovery rate due to volcano plots: problem and solutions
Brief Bioinform. 2024 May; 25(3): bbae149. Published online 2024 Apr 15. doi: 10.1093/bib/bbae149
Corrects:
Brief Bioinform. 2021 Sep; 22(5): bbab053.
PMCID:
PMC11017513
CorrectionPDF–85K
16.
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
Ming-Siang Huang, Jen-Chieh Han, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai, Wen-Lian Hsu
Brief Bioinform. 2024 May; 25(3): bbae132. Published online 2024 Apr 12. doi: 10.1093/bib/bbae132
PMCID:
PMC11014787
ArticlePDF–1.0M
17.
MUSCLE: multi-view and multi-scale attentional feature fusion for microRNA–disease associations prediction
Boya Ji, Haitao Zou, Liwen Xu, Xiaolan Xie, Shaoliang Peng
Brief Bioinform. 2024 May; 25(3): bbae167. Published online 2024 Apr 11. doi: 10.1093/bib/bbae167
PMCID:
PMC11009512
ArticlePDF–1.5M
18.
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication
Akram Vasighizaker, Sheena Hora, Raymond Zeng, Luis Rueda
Brief Bioinform. 2024 May; 25(3): bbae160. Published online 2024 Apr 11. doi: 10.1093/bib/bbae160
PMCID:
PMC11009470
ArticlePDF–416K
19.
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
Ken Chen, Yue Zhou, Maolin Ding, Yu Wang, Zhixiang Ren, Yuedong Yang
Brief Bioinform. 2024 May; 25(3): bbae163. Published online 2024 Apr 11. doi: 10.1093/bib/bbae163
PMCID:
PMC11009468
ArticlePDF–1.7M
20.
DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework
Hongyuan Zhao, Suyi Zhang, Hui Qin, Xiaogang Liu, Dongna Ma, Xiao Han, Jian Mao, Shuangping Liu
Brief Bioinform. 2024 May; 25(3): bbae157. Published online 2024 Apr 9. doi: 10.1093/bib/bbae157
PMCID:
PMC11007113
ArticlePDF–1.6M

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