- Minghao Fang, Jingwen Fang, Songwen Luo, Ke Liu, Qiaoni Yu, Jiaxuan Yang, Youyang Zhou, Zongkai Li, Ruoming Sun, Chuang Guo, Kun Qu. eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data. Briefings in Bioinformatics, 25(2), January 2024.
- Jingxuan Qiu, Wanchun Nie, Hao Ding, Jia Dai, Yiwen Wei, Dezhi Li, Yuxi Zhang, Junting Xie, Xinxin Tian, Nannan Wu, Tianyi Qiu. PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy. Briefings in Bioinformatics, 25(2), January 2024.
- Yi-Heng Zhu, Zi Liu, Yan Liu 0038, Zhiwei Ji, Dong-jun Yu. ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings in Bioinformatics, 25(2), January 2024.
- Hangjia Zhao, Michael Baudis. labelSeg: segment annotation for tumor copy number alteration profiles. Briefings in Bioinformatics, 25(2), January 2024.
- Qiuchen Meng, Lei Wei, Kun Ma, Ming Shi, Xinyi Lin, Joshua W. K. Ho, Yinqing Li, Xuegong Zhang. scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. Briefings in Bioinformatics, 25(2), January 2024.
- Yaofeng Hu, Kai Xiao, Hengyu Yang, Xiaoping Liu 0002, Chuanchao Zhang, Qianqian Shi. Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics. Briefings in Bioinformatics, 25(2), January 2024.
- Aleksandra E. Badaczewska-Dawid, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik. Structure prediction of linear and cyclic peptides using CABS-flex. Briefings in Bioinformatics, 25(2), January 2024.
- Lijuan Wang, Ying Lu, Doudou Li, Yajing Zhou, Lili Yu, Ines Mesa Eguiagaray, Harry Campbell, Xue Li, Evropi Theodoratou. The landscape of the methodology in drug repurposing using human genomic data: a systematic review. Briefings in Bioinformatics, 25(2), January 2024.
- Shi Zhang, Rui Zhang 0065, Kai Yuan, Lu Yang, Chang Liu 0059, Yuting Liu, Xumin Ni, Shuhua Xu. Reconstructing complex admixture history using a hierarchical model. Briefings in Bioinformatics, 25(2), January 2024.
- Rajesh Kumar Pathak, Jun-Mo Kim. Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare. Briefings in Bioinformatics, 25(2), January 2024.