Briefings Bioinform.

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Publications

volume 25, number 2, 2024

Shi Zhang, Rui Zhang, Kai Yuan, Lu Yang, Chang Liu, Yuting Liu, Xumin Ni, Shuhua Xu
Reconstructing complex admixture history using a hierarchical model. Briefings Bioinform. 25 (2) (2024)
Seokjin Han, Ji Eun Lee, Seolhee Kang, Minyoung So, Hee Jin, Jang Ho Lee, Sunghyeob Baek, Hyungjin Jun, Tae Yong Kim, Yun-Sil Lee
Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis. Briefings Bioinform. 25 (2) (2024)
Junxiang Zeng, Xiupan Gao, Limei Gao, Youyou Yu, Lisong Shen, Xiujun Pan
Recognition of rare antinuclear antibody patterns based on a novel attention-based enhancement framework. Briefings Bioinform. 25 (2) (2024)
Wenyuan Ma, Hui Wu, Yiran Chen, Hongxia Xu, Junjie Jiang, Bang Du, Mingyu Wan, Xiaolu Ma, Xiaoyu Chen, Lili Lin, Xinhui Su, Xuanwen Bao, Yifei Shen, Nong Xu, Jian Ruan, Haiping Jiang, Yongfeng Ding
New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Briefings Bioinform. 25 (2) (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 Bioinform. 25 (2) (2024)
Yury A Barbitoff, Mikhail O. Ushakov, Tatyana E. Lazareva, Yulia A Nasykhova, Andrey S. Glotov, Alexander V. Predeus
Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges. Briefings Bioinform. 25 (2) (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 Bioinform. 25 (2) (2024)
Yan Miao, Zhenyuan Sun, Chenjing Ma, Chen Lin, Guohua Wang, Chunxue Yang
VirGrapher: a graph-based viral identifier for long sequences from metagenomes. Briefings Bioinform. 25 (2) (2024)
Lingyan Zheng, Shuiyang Shi, Xiuna Sun, Mingkun Lu, Yang Liao, Sisi Zhu, Hongning Zhang, Ziqi Pan, Pan Fang, Zhenyu Zeng, Honglin Li, Zhaorong Li, Weiwei Xue, Feng Zhu
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Briefings Bioinform. 25 (2) (2024)
Giovanni Visonà, Emmanuelle Bouzigon, Florence Demenais, Gabriele Beate Schweikert
Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery. Briefings Bioinform. 25 (2) (2024)
Yaofeng Hu, Kai Xiao, Hengyu Yang, Xiaoping Liu, Chuanchao Zhang, Qianqian Shi
Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics. Briefings Bioinform. 25 (2) (2024)
Hangjia Zhao, Michael Baudis
labelSeg: segment annotation for tumor copy number alteration profiles. Briefings Bioinform. 25 (2) (2024)
Songqi Zhou, Yang Li, Wenyuan Wu, Li Li
scMMT: a multi-use deep learning approach for cell annotation, protein prediction and embedding in single-cell RNA-seq data. Briefings Bioinform. 25 (2) (2024)
Zeyu Luo, Rui Wang, Yawen Sun, Junhao Liu, Herman Z. Q. Chen, Yu-Juan Zhang
Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction. Briefings Bioinform. 25 (2) (2024)
Sowmya Ramaswamy Krishnan, Arijit Roy, M. Michael Gromiha
Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning. Briefings Bioinform. 25 (2) (2024)
Yue Guo, Haitao Hu, Wenbo Chen, Hao Yin, Jian Wu, Chang-Yu Hsieh, Qiaojun He, Ji Cao
SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction. Briefings Bioinform. 25 (2) (2024)
Youngjune Park, Nils P. Muttray, Anne-Christin Hauschild
Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology. Briefings Bioinform. 25 (2) (2024)
Shuang Gu, Chaoliang Wen, Zhen Xiao, Qiang Huang, Zheyi Jiang, Honghong Liu, Jia Gao, Junying Li, Congjiao Sun, Ning Yang
MyoV: a deep learning-based tool for the automated quantification of muscle fibers. Briefings Bioinform. 25 (2) (2024)
Aleksandra E. Badaczewska-Dawid, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik
Structure prediction of linear and cyclic peptides using CABS-flex. Briefings Bioinform. 25 (2) (2024)
Chengcheng Zhang, Tianyi Zang, Tianyi Zhao
KGE-UNIT: toward the unification of molecular interactions prediction based on knowledge graph and multi-task learning on drug discovery. Briefings Bioinform. 25 (2) (2024)
Fabio N. de Mello, Ana C. Tahira, Maria Gabriela Berzoti-Coelho, Sergio Verjovski-Almeida
The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping. Briefings Bioinform. 25 (2) (2024)
Jing Meng, Jingze Liu, Wenkai Song, Honglei Li, Jiangyuan Wang, Le Zhang, Yousong Peng, Aiping Wu, Taijiao Jiang
PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network. Briefings Bioinform. 25 (2) (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, 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 Bioinform. 25 (2) (2024)
Zhen-Hao Guo, Yan-Bin Wang, Siguo Wang, Qinhu Zhang, De-Shuang Huang
scCorrector: a robust method for integrating multi-study single-cell data. Briefings Bioinform. 25 (2) (2024)
Lu-Xiang Guo, Lei Wang, Zhu-Hong You, Chang-Qing Yu, Meng-Lei Hu, Bo-Wei Zhao, Yang Li
Likelihood-based feature representation learning combined with neighborhood information for predicting circRNA-miRNA associations. Briefings Bioinform. 25 (2) (2024)
Tingpeng Yang, Tianze Ling, Boyan Sun, Zhendong Liang, Fan Xu, Xiansong Huang, Linhai Xie, Yonghong He, Leyuan Li, Fuchu He, Yu Wang, Cheng Chang
Introducing π-HelixNovo for practical large-scale de novo peptide sequencing. Briefings Bioinform. 25 (2) (2024)
Ariadna Llop-Peiró, Gerard Pujadas, Santiago Garcia-Vallvé
Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery. Briefings Bioinform. 25 (2) (2024)
Kandarp Joshi, Dan O. Wang
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation. Briefings Bioinform. 25 (2) (2024)
Olivier Cinquin
ChIP-GPT: a managed large language model for robust data extraction from biomedical database records. Briefings Bioinform. 25 (2) (2024)
Yantong Cai, Jia Lv, Rui Li, Xiaowen Huang, Shi Wang, Zhenmin Bao, Qifan Zeng
Deqformer: high-definition and scalable deep learning probe design method. Briefings Bioinform. 25 (2) (2024)
Gulam Sarwar Chuwdhury, Yunshan Guo, Chi-Leung Chiang, Ka-On Lam, Ngar-Woon Kam, Zhonghua Liu, Wei Dai
ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction. Briefings Bioinform. 25 (2) (2024)
Yue Zang, Xia Ran, Jie Yuan, Hao Wu, Youya Wang, He Li, Huajing Teng, Zhongsheng Sun
Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer. Briefings Bioinform. 25 (2) (2024)
Musu Yuan, Hui Wan, Zihao Wang, Qirui Guo, Minghua Deng
SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data. Briefings Bioinform. 25 (2) (2024)
Merve Vural-Ozdeniz, Kubra Calisir, Rana Acar, Aysenur Yavuz, Mustafa M. Ozgur, Ertugrul Dalgic, Ozlen Konu
CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters. Briefings Bioinform. 25 (2) (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 Bioinform. 25 (2) (2024)
Jin Zhang, Zikang Ma, Yan Yang, Lei Guo, Lei Du
Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study. Briefings Bioinform. 25 (2) (2024)
Sheng-Yong Xu, Shanshan Cai, Zhi-Qiang Han
Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species. Briefings Bioinform. 25 (2) (2024)
Yuyao Zhai, Liang Chen, Minghua Deng
scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data. Briefings Bioinform. 25 (2) (2024)
Mona Nourbakhsh, Kristine Degn, Astrid Saksager, Matteo Tiberti, Elena Papaleo
Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks. Briefings Bioinform. 25 (2) (2024)
Albert Katchborian-Neto, Matheus F. Alves, Paula C. P. Bueno, Karen de Jesus Nicácio, Miller S. Ferreira, Tiago B. Oliveira, Henrique Barbosa, Michael Murgu, Ana C. C. de Paula Ladvocat, Danielle F. Dias, Marisi G. Soares, João H. G. Lago, Daniela A Chagas-Paula
Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data. Briefings Bioinform. 25 (2) (2024)
Simone Maestri, Mattia Furlan, Logan Mulroney, Lucia Coscujuela Tarrero, Camilla Ugolini, Fabio Dalla Pozza, Tommaso Leonardi, Ewan Birney, Francesco Nicassio, Mattia Pelizzola
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing. Briefings Bioinform. 25 (2) (2024)
Qingyue Wei, Md Tauhidul Islam, Yuyin Zhou, Lei Xing
Self-supervised deep learning of gene-gene interactions for improved gene expression recovery. Briefings Bioinform. 25 (2) (2024)
Xinyu Guo, Liang Chen
From G1 to M: a comparative study of methods for identifying cell cycle phases. Briefings Bioinform. 25 (2) (2024)
Min Sun, Jing Chen, Chang Zhao, Lihua Zhang, Maili Liu, Yukui Zhang, Qun Zhao, Zhou Gong
Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers. Briefings Bioinform. 25 (2) (2024)
Jiaxuan Liu, Yonggang Lu, Li Zhu
Cryo-EM 3D reconstruction. Briefings Bioinform. 25 (2) (2024)
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 Bioinform. 25 (2) (2024)
Céline Brouard, Raphaël Mourad, Nathalie Vialaneix
Should we really use graph neural networks for transcriptomic prediction? Briefings Bioinform. 25 (2) (2024)
Wang Xu, Houfang Zhang, Wenhan Guo, Lijun Jiang, Yunjie Zhao, Yunhui Peng
Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis. Briefings Bioinform. 25 (2) (2024)
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Lei Xu
Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2. Briefings Bioinform. 25 (2) (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 Bioinform. 25 (2) (2024)