Volume 25(4); 2024 Jul

Editorial

Attention mechanism models for precision medicine

Liang Cheng

Brief Bioinform. 2024 Jul; 25(4): bbae156. Published online 2024 May 29. doi: 10.1093/bib/bbae156

PMCID:: PMC11136616

Abstract Article PDF–168K

Problem Solving Protocol

SPIN: sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis

Euiseong Ko, Youngsoon Kim, Farhad Shokoohi, Tesfaye B Mersha, Mingon Kang

Brief Bioinform. 2024 Jul; 25(4): bbae239. Published online 2024 May 28. doi: 10.1093/bib/bbae239

PMCID:: PMC11133003

Abstract Article PDF–2.0M

A comprehensive benchmarking of machine learning algorithms and dimensionality reduction methods for drug sensitivity prediction

Lea Eckhart, Kerstin Lenhof, Lisa-Marie Rolli, Hans-Peter Lenhof

Brief Bioinform. 2024 Jul; 25(4): bbae242. Published online 2024 May 26. doi: 10.1093/bib/bbae242

PMCID:: PMC11128483

Abstract Article PDF–1.2M

irGSEA: the integration of single-cell rank-based gene set enrichment analysis

Chuiqin Fan, Fuyi Chen, Yuanguo Chen, Liangping Huang, Manna Wang, Yulin Liu, Yu Wang, Huijie Guo, Nanpeng Zheng, Yanbing Liu, Hongwu Wang, Lian Ma

Brief Bioinform. 2024 Jul; 25(4): bbae243. Published online 2024 May 27. doi: 10.1093/bib/bbae243

PMCID:: PMC11129768

Abstract Article PDF–1.1M

Accurate prediction of antibody function and structure using bio-inspired antibody language model

Hongtai Jing, Zhengtao Gao, Sheng Xu, Tao Shen, Zhangzhi Peng, Shwai He, Tao You, Shuang Ye, Wei Lin, Siqi Sun

Brief Bioinform. 2024 Jul; 25(4): bbae245. Published online 2024 May 26. doi: 10.1093/bib/bbae245

PMCID:: PMC11128484

Abstract Article PDF–1.5M

Predicting RNA polymerase II transcriptional elongation pausing and associated histone code

Lixin Ren, Wanbiao Ma, Yong Wang

Brief Bioinform. 2024 Jul; 25(4): bbae246. Published online 2024 May 23. doi: 10.1093/bib/bbae246

PMCID:: PMC11116834

Abstract Article PDF–1.9M

Predicting functional UTR variants by integrating region-specific features

Guangyu Li, Jiayu Wu, Xiaoyue Wang

Brief Bioinform. 2024 Jul; 25(4): bbae248. Published online 2024 May 23. doi: 10.1093/bib/bbae248

PMCID:: PMC11116830

Abstract Article PDF–1.7M

Mutational signatures of colorectal cancers according to distinct computational workflows

Paolo Battuello, Giorgio Corti, Alice Bartolini, Annalisa Lorenzato, Alberto Sogari, Mariangela Russo, Federica Di Nicolantonio, Alberto Bardelli, Giovanni Crisafulli

Brief Bioinform. 2024 Jul; 25(4): bbae249. Published online 2024 May 23. doi: 10.1093/bib/bbae249

PMCID:: PMC11116831

Abstract Article PDF–1.7M

Benchmarking mapping algorithms for cell-type annotating in mouse brain by integrating single-nucleus RNA-seq and Stereo-seq data

Quyuan Tao, Yiheng Xu, Youzhe He, Ting Luo, Xiaoming Li, Lei Han

Brief Bioinform. 2024 Jul; 25(4): bbae250. Published online 2024 May 25. doi: 10.1093/bib/bbae250

PMCID:: PMC11128029

Abstract Article PDF–2.5M

RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data

Sandeep Singh, Xinrui Shi, Samuel Haddox, Justin Elfman, Syed Basil Ahmad, Sarah Lynch, Tommy Manley, Claire Piczak, Christopher Phung, Yunan Sun, Aadi Sharma, Hui Li

Brief Bioinform. 2024 Jul; 25(4): bbae251. Published online 2024 May 25. doi: 10.1093/bib/bbae251

PMCID:: PMC11128028

Abstract Article PDF–1.8M

A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data

Lei Zhang, Shu Liang, Lin Wan

Brief Bioinform. 2024 Jul; 25(4): bbae255. Published online 2024 May 27. doi: 10.1093/bib/bbae255

PMCID:: PMC11129769

Abstract Article PDF–2.3M

Complementary multi-modality molecular self-supervised learning via non-overlapping masking for property prediction

Ao Shen, Mingzhi Yuan, Yingfan Ma, Jie Du, Manning Wang

Brief Bioinform. 2024 Jul; 25(4): bbae256. Published online 2024 May 27. doi: 10.1093/bib/bbae256

PMCID:: PMC11129775

Abstract Article PDF–2.0M

Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics

Lequn Wang, Yaofeng Hu, Kai Xiao, Chuanchao Zhang, Qianqian Shi, Luonan Chen

Brief Bioinform. 2024 Jul; 25(4): bbae257. Published online 2024 May 31. doi: 10.1093/bib/bbae257

PMCID:: PMC11141295

Abstract Article PDF–2.3M

IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA–miRNA interaction network constructed through gene expression data

Jiashuo Wu, Xilong Zhao, Yalan He, Bingyue Pan, Jiyin Lai, Miao Ji, Siyuan Li, Junling Huang, Junwei Han

Brief Bioinform. 2024 Jul; 25(4): bbae258. Published online 2024 May 27. doi: 10.1093/bib/bbae258

PMCID:: PMC11129766

Abstract Article PDF–3.0M

SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network

Zhihao Si, Hanshuang Li, Wenjing Shang, Yanan Zhao, Lingjiao Kong, Chunshen Long, Yongchun Zuo, Zhenxing Feng

Brief Bioinform. 2024 Jul; 25(4): bbae259. Published online 2024 May 29. doi: 10.1093/bib/bbae259

PMCID:: PMC11136618

Abstract Article PDF–2.6M

PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data

Xinjia Ruan, Yu Cheng, Yuqing Ye, Yuhang Wang, Xinyi Chen, Yuqing Yang, Tiantian Liu, Fangrong Yan

Brief Bioinform. 2024 Jul; 25(4): bbae260. Published online 2024 May 31. doi: 10.1093/bib/bbae260

PMCID:: PMC11141296

Abstract Article PDF–2.5M

Correction

Correction to: Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model

Brief Bioinform. 2024 Jul; 25(4): bbae252. Published online 2024 May 23. doi: 10.1093/bib/bbae252

Corrects:: Brief Bioinform. 2024 Jan; 25(1): bbad478.

PMCID:: PMC11116818

Correction PDF–74K

Articles from Briefings in Bioinformatics are provided here courtesy of Oxford University Press