Journal: Briefings in Bioinformatics

Volume 24, Issue 6

0 -- 0Hajar Saihi, Conrad Bessant, William Alazawi. Automated and reproducible cell identification in mass cytometry using neural networks
0 -- 0Siyao Wu, Yushan Qiu, Xiaoqing Cheng. ConSpaS: a contrastive learning framework for identifying spatial domains by integrating local and global similarities
0 -- 0Yue Jiang, Xuejiao Hu, Shu Fan, Weijiang Liu, Jingjing Chen, Liang Wang, Qianyun Deng, Jing Yang, Aimei Yang, Zheng Lou, Yuanlin Guan, Han-xia, Bing Gu. RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome
0 -- 0Saisai Tian, Yanan Li, Jia Xu, Lijun Zhang, Jinbo Zhang, Jinyuan Lu, Xike Xu, Xin Luan, Jing Zhao, Weidong Zhang. COIMMR: a computational framework to reveal the contribution of herbal ingredients against human cancer via immune microenvironment and metabolic reprogramming
0 -- 0Yuxing Lu, Rui Peng, Lingkai Dong, Kun Xia, Renjie Wu, Shuai Xu, Jinzhuo Wang. Multiomics dynamic learning enables personalized diagnosis and prognosis for pancancer and cancer subtypes
0 -- 0Jie Pan, Zhuhong You, Wencai You, Tian Zhao, Chenlu Feng, Xuexia Zhang, Fengzhi Ren, Sanxing Ma, Fan Wu, Shiwei Wang, Yanmei Sun. PTBGRP: predicting phage-bacteria interactions with graph representation learning on microbial heterogeneous information network
0 -- 0Chi Zhang, Yiliang Zhang, Yunxuan Zhang, Hongyu Zhao. Benchmarking of local genetic correlation estimation methods using summary statistics from genome-wide association studies
0 -- 0Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang, Lei Wei. Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics
0 -- 0Lei Zhang, Sheng Wang, Jie Hou 0001, Dong-Si, JunYong Zhu, Renzhi Cao. ComplexQA: a deep graph learning approach for protein complex structure assessment
0 -- 0Xiaowen Hu, Dayun Liu, Jiaxuan Zhang, Yanhao Fan, Tianxiang Ouyang, Yue Luo, Yuanpeng Zhang, Lei Deng. A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations
0 -- 0Guishan Zhang, Ye Luo, Xianhua Dai, Zhiming Dai. Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities
0 -- 0Mehrsa Mardikoraem, Zirui Wang, Nathaniel Pascual, Daniel R. Woldring. Generative models for protein sequence modeling: recent advances and future directions
0 -- 0Mingguang Shi, Xuefeng Li, Mingna Li, Yichong Si. Attention-based generative adversarial networks improve prognostic outcome prediction of cancer from multimodal data
0 -- 0Jiangyi Shao, Qi Zhang, Ke Yan, Bin Liu. PreHom-PCLM: protein remote homology detection by combing motifs and protein cubic language model
0 -- 0Yang Cao, Dan Wang, Jin Wu, Zhanxin Yao, Si Shen, Chao Niu, Ying Liu, Pengcheng Zhang, Quannian Wang, Jinhao Wang, Hua Li, Xi Wei, Xinxing Wang, Qingyang Dong. MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection
0 -- 0Jiaojiao Guan, Cheng Peng, Jiayu Shang, Xubo Tang, Yanni Sun. PhaGenus: genus-level classification of bacteriophages using a Transformer model
0 -- 0Michal Kubacki, Mahesan Niranjan. Quantum annealing-based clustering of single cell RNA-seq data
0 -- 0Zhuo Wang, Yuxuan Pang, Chia-Ru Chung, Hsin-Yao Wang, Haiyan Cui, Ying-Chih Chiang, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee. Staphylococcus aureus using machine learning and mass spectrometry technology
0 -- 0Tao Wang 0082, Hui Zhao, Yungang Xu, Yongtian Wang, Xuequn Shang, Jiajie Peng, Bing Xiao 0001. scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks
0 -- 0Bo Li, Chen Peng, Zeran You, Xiaolong Zhang, Shihua Zhang. Single-cell RNA-sequencing data clustering using variational graph attention auto-encoder with self-supervised leaning
0 -- 0Zhongshen Li, Junru Jin, WenJia He, Wentao Long, Haoqing Yu, Xin Gao 0001, Kenta Nakai, Quan Zou 0001, Leyi Wei. CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides
0 -- 0Ran Zhang 0008, Xuezhi Wang 0004, Pengfei Wang 0008, Zhen Meng, Wenjuan Cui, Yuanchun Zhou. HTCL-DDI: a hierarchical triple-view contrastive learning framework for drug-drug interaction prediction
0 -- 0Hongxin Xiang, Shuting Jin, Xiangrong Liu, Xiangxiang Zeng, Li Zeng. Chemical structure-aware molecular image representation learning
0 -- 0Siddharth Sinha, Jiaheng Li, Benjamin Tam, San Ming Wang. Classification of PTEN missense VUS through exascale simulations
0 -- 0Jiaying Zhao, Chi-Wing Wong, Wai-Ki Ching, Xiaoqing Cheng. NG-SEM: an effective non-Gaussian structural equation modeling framework for gene regulatory network inference from single-cell RNA-seq data
0 -- 0Tiago O. Pereira 0001, Maryam Abbasi, Joel P. Arrais. de novo molecular design applying self-attention mechanisms
0 -- 0Xin Dai, Longlong Wu, Shinjae Yoo, Qun Liu. Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
0 -- 0Simon Boutry, Raphaël Helaers, Tom Lenaerts, Miikka Vikkula. Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations
0 -- 0Anupam Gautam, Debaleena Bhowmik, Sayantani Basu, Wenhuan Zeng, Abhishake Lahiri, Daniel H. Huson, Sandip Paul. Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
0 -- 0Qizhi Pei, Lijun Wu, Jinhua Zhu 0001, Yingce Xia, Shufang Xie 0003, Tao Qin 0001, Haiguang Liu, Tie-Yan Liu, Rui Yan 0001. Breaking the barriers of data scarcity in drug-target affinity prediction
0 -- 0Ruifen Cao, Weiling Hu, Pi-Jing Wei, Yun Ding, Yannan Bin, Chun-Hou Zheng 0001. FFMAVP: a new classifier based on feature fusion and multitask learning for identifying antiviral peptides and their subclasses
0 -- 0Wen Tao, Yuansheng Liu, Xuan Lin, Bosheng Song, Xiangxiang Zeng. Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning
0 -- 0Chunwei Ma, Russ Wolfinger. A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing
0 -- 0Quanbao Zhang, Lei Cao, Hongtao Song, Kui Lin, Erli Pang. MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome
0 -- 0Qiang Su, Yi Long, Jun Wang, Deming Gou. CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation
0 -- 0Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang 0053, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song. SMG: self-supervised masked graph learning for cancer gene identification
0 -- 0Gang Xu, Zhenwei Luo, Ruhong Zhou, Qinghua Wang, Jianpeng Ma. OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow
0 -- 0Pengfei Gao, Haonan Zhao, Zheng Luo, Yifan Lin, Wanjie Feng, Yaling Li, Fanjiang Kong, Xia Li, Chao Fang, Xutong Wang. SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding
0 -- 0Biaoshun Li, MuJie Lin, Tiegen Chen, Ling Wang. FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction
0 -- 0Hoon Je Seong, Jin Ju Kim, Woo Jun Sul. ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool
0 -- 0Wentao Zhang, Yanchao Xu, Aowen Wang, Gang Chen 0001, Junbo Zhao. Fuse feeds as one: cross-modal framework for general identification of AMPs
0 -- 0Pourya Naderi Yeganeh, Yue Y. Teo, Dimitra Karagkouni, Yered Pita-Juárez, Sarah L. Morgan, Frank J. Slack, Ioannis S. Vlachos, Winston A. Hide. PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs
0 -- 0Jing Liang, Zong-Wei Li, Ze-Ning Sun, Ying Bi, Han Cheng, Tao Zeng, Weifeng Guo. Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction
0 -- 0Tuoyu Liu, Han Gao, Xiaopu Ren, Guoshun Xu, Bo Liu, Ningfeng Wu, Huiying Luo, Yuan Wang, Tao Tu, Bin Yao, Feifei Guan, Yue Teng, Huoqing Huang, Jian Tian. Protein-protein interaction and site prediction using transfer learning
0 -- 0Alexey N. Davydov, Dmitry Bolotin, Stanislav V. Poslavsky, Dmitry M. Chudakov. Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'
0 -- 0Zihan Zheng, Ling Chang, Yinong Li, Kun Liu, Jie Mu, Song Zhang, Jingyi Li, Yuzhang Wu, Liyun Zou, Qingshan Ni, Ying Wan. Screening single-cell trajectories via continuity assessments for cell transition potential
0 -- 0Fuyu Li, Wenlong Ming, Wenxiang Lu, Ying Wang, Xiaohan Li, Xianjun Dong, Yunfei Bai. FLED: a full-length eccDNA detector for long-reads sequencing data
0 -- 0Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Takuro Nakayama, Goro Tanifuji, Ryoma Kamikawa, Yasukazu Nakamura. A practical assembly guideline for genomes with various levels of heterozygosity
0 -- 0Yidong Song, Qianmu Yuan, Huiying Zhao, Yuedong Yang. Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures
0 -- 0. Correction to: An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning
0 -- 0Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomás Helikar, Bhanwar Lal Puniya. COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery
0 -- 0Zhe Li, Xinyi Tu, Yuping Chen, Wenbin Lin. HetDDI: a pre-trained heterogeneous graph neural network model for drug-drug interaction prediction
0 -- 0Xiaoshuai Zhang, Huannan Guo, Fan Zhang, Xuan Wang, Kaitao Wu, Shizheng Qiu, Bo Liu, Yadong Wang, Yang Hu, Junyi Li. HNetGO: protein function prediction via heterogeneous network transformer
0 -- 0Rahul Brahma, Jae-Min Shin, Kwang-Hwi Cho. KinScan: AI-based rapid profiling of activity across the kinome
0 -- 0Xiaoyi Liu, Hongpeng Yang, Chengwei Ai, Yijie Ding, Fei Guo 0001, Jijun Tang. MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference
0 -- 0Kathi Zarnack, Eduardo Eyras. 'Artificial intelligence and machine learning in RNA biology'
0 -- 0Andy J. Wu, Akila Perera, Linganesan Kularatnarajah, Anna Korsakova, Jason J. Pitt. Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches
0 -- 0Haoran Sun, Zhaoqi Song, Qiuming Chen, Meiling Wang, Furong Tang, Lijun Dou, Quan Zou 0001, Fenglong Yang. MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactions
0 -- 0Sugam Budhraja, Maryam Gholami Doborjeh, Balkaran Singh, Samuel Tan, Zohreh Gholami Doborjeh, Edmund Lai, Alexander Merkin, Jimmy Lee, Wilson Wen Bin Goh, Nikola K. Kasabov. Filter and Wrapper Stacking Ensemble (FWSE): a robust approach for reliable biomarker discovery in high-dimensional omics data
0 -- 0Fuyi Li, Cong Wang, Xudong Guo, Tatsuya Akutsu, Geoffrey I. Webb, Lachlan J. M. Coin, Lukasz A. Kurgan, Jiangning Song. ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction
0 -- 0Jochen Sieg, Matthias Rarey. Searching similar local 3D micro-environments in protein structure databases with MicroMiner
0 -- 0Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Salvatore Gaglio, Alfonso Urso. GOWDL: gene ontology-driven wide and deep learning model for cell typing of scRNA-seq data
0 -- 0Jiayuan Zhong, Chongyin Han, Pei Chen, Rui Liu 0009. SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development
0 -- 0Wei Li, Bin Xiang, Fan Yang, Yu Rong, Yanbin Yin, Jianhua Yao 0001, Han Zhang. scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data
0 -- 0Yu-Ning Huang, Mohammad Vahed, Kerui Peng, Houda Alachkar, Serghei Mangul. Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M
0 -- 0Zhe Lin, Yangmei Qin, Hao Chen, Dan Shi, Mindong Zhong, Te An, Linshan Chen, Yiquan Wang, Fan Lin, Guang Li, Zhi Liang Ji. TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes
0 -- 0Dongmei Ai, Lulu Chen, Jiemin Xie, Longwei Cheng, Fang Zhang, Yihui Luan, Yang Li, Shengwei Hou, Fengzhu Sun, Li Charlie Xia. Identifying local associations in biological time series: algorithms, statistical significance, and applications
0 -- 0Yongjian Yang, Yu-Te Lin, Guanxun Li, Yan Zhong, Qian Xu, James J. Cai. Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet
0 -- 0Mark Ziemann, Pierre Poulain, Anusuiya Bora. The five pillars of computational reproducibility: bioinformatics and beyond
0 -- 0Mingyi Hu, Jinlin Zhu, Guohao Peng, Wenwei Lu, Hongchao Wang, Zhenping Xie. IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification
0 -- 0Jingjing Zhang, Huiling Zhang, Zhen Ju, Yin Peng, Yi Pan 0001, Wenhui Xi, Yanjie Wei. JCcirc: circRNA full-length sequence assembly through integrated junction contigs
0 -- 0Chao Xu, Runduo Liu, Shuheng Huang, Wenchao Li, Zhe Li, Hai-Bin Luo. 3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation
0 -- 0Ying Wang, Min Zhang, Jian Shi, Yue Zhu, Xin Wang, Shaojun Zhang, Fang Wang. Cracking the pattern of tumor evolution based on single-cell copy number alterations
0 -- 0Anna Ketteler, David B. Blumenthal. Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer
0 -- 0Zihan Liu, Jiaqi Wang, Yun Luo, Shuang Zhao, Wenbin Li, Stan Z. Li. Efficient prediction of peptide self-assembly through sequential and graphical encoding
0 -- 0Maryam Yassi, Aniruddha Chatterjee, Matthew Parry. Application of deep learning in cancer epigenetics through DNA methylation analysis
0 -- 0Kai Jing, Yewen Xu, Yang Yang, Pengfei Yin, Duo Ning, Guangyu Huang, Yuqing Deng, Gengzhan Chen, Guoliang Li 0002, Simon Zhongyuan Tian, Meizhen Zheng. ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis
0 -- 0Guo Mao, Zhengbin Pang, Ke Zuo, Qinglin Wang, Xiangdong Pei, Xinhai Chen, Jie Liu 0002. Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
0 -- 0Ziyang Tang, Xiang Liu, Zuotian Li, Tonglin Zhang, Baijian Yang 0001, Jing Su, Qianqian Song. SpaRx: elucidate single-cell spatial heterogeneity of drug responses for personalized treatment
0 -- 0Musun Park, Su-Jin Baek, Sang-Min Park, Jin-Mu Yi, Seongwon Cha. in silico herbal medicine experimentations
0 -- 0. Correction to: CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
0 -- 0Haonan Wu, Jiyun Han, Shizhuo Zhang, Xin Gao 0001, Chaozhou Mou, Juntao Liu. Spatom: a graph neural network for structure-based protein-protein interaction site prediction
0 -- 0Tianyuan Lei, Ruoyu Chen, Shaoqiang Zhang, Yong Chen. Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations
0 -- 0Alison K. Adams, Brandon D. Kristy, Myranda Gorman, Peter Balint-Kurti, G. Craig Yencho, Bode A. Olukolu. Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes
0 -- 0Yanglan Gan, Wenxiao Liu, Guangwei Xu, Cairong Yan, Guobing Zou. DMFDDI: deep multimodal fusion for drug-drug interaction prediction
0 -- 0Chi Xiao, Jun Wang, Shenrong Yang, Minxin Heng, Junyi Su, Hao Xiao, Jingdong Song, Weifu Li. VISN: virus instance segmentation network for TEM images using deep attention transformer
0 -- 0Wentai Ma, Leisheng Shi, Mingkun Li. A fast and accurate method for SARS-CoV-2 genomic tracing
0 -- 0Marie-Pier Scott-Boyer, Pascal Dufour, François Belleau, Régis Ongaro-Carcy, Clément Plessis, Olivier Périn, Arnaud Droit. Use of Elasticsearch-based business intelligence tools for integration and visualization of biological data
0 -- 0Abbas Shojaee, Shao-Shan Carol Huang. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions
0 -- 0Chao Zhang, Zhi-Wei Duan, Yun-Pei Xu, Jin Liu, Hong-Dong Li. FEED: a feature selection method based on gene expression decomposition for single cell clustering