Journal: Briefings in Bioinformatics

Volume 23, Issue 6

0 -- 0Anna Eames Seffernick, Krzysztof Mrózek, Deedra Nicolet, Richard M. Stone, Ann-Katherin Eisfeld, John C. Byrd, Kellie J. Archer. High-dimensional genomic feature selection with the ordered stereotype logit model
0 -- 0Yanting Zhang, Hisanori Kiryu. MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes
0 -- 0Atlas M. Sardoo, Shaoqiang Zhang, Thomas N. Ferraro, Thomas M. Keck, Yong Chen. Decoding brain memory formation by single-cell RNA sequencing
0 -- 0Siyu Han, Xiao Yang, Hang Sun, Hu Yang, Qi Zhang, Cheng Peng, Wensi Fang, Ying Li. LION: an integrated R package for effective prediction of ncRNA-protein interaction
0 -- 0César R. García-Jacas, Luis A. García-González, Felix Martinez-Rios, Issac P. Tapia-Contreras, Carlos A. Brizuela. Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?
0 -- 0Ricky Wai Tak Leung, Xiaosen Jiang, Xueqing Zong, Yanhong Zhang, Xinlin Hu, Yaohua Hu, Jing Qin 0004. CORN - Condition Orientated Regulatory Networks: bridging conditions to gene networks
0 -- 0Hui Chong, Yuguo Zha, Qingyang Yu, Mingyue Cheng, Guangzhou Xiong, Nan Wang, Xinhe Huang, Shijuan Huang, Chuqing Sun, Sicheng Wu, Wei-Hua Chen, Luís Pedro Coelho, Kang Ning 0001. EXPERT: transfer learning-enabled context-aware microbial community classification
0 -- 0Yansen Su, Minglu Wang, Pengpeng Wang, Chunhou Zheng, Yuansheng Liu, Xiangxiang Zeng. Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison
0 -- 0Vandana Ravindran, Jessica Wagoner, Paschalis Athanasiadis, Andreas B. Den Hartigh, Julia M. Sidorova, Aleksandr Ianevski, Susan L. Fink, Arnoldo Frigessi, Judith White, Stephen J. Polyak, Tero Aittokallio. Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
0 -- 0Qingxia Yang, Bo Li 0097, Panpan Wang, Jicheng Xie, Yuhao Feng, Ziqiang Liu, Feng Zhu 0004. LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data
0 -- 0Yiming Fang, Xuejun Liu, Hui Liu. Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity
0 -- 0Ziyan Feng, Zihao Shen, Honglin Li, Shiliang Li. e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature
0 -- 0Zhen Tian, Xiangyu Peng, Haichuan Fang, Wenjie Zhang, Qiguo Dai, Yangdong Ye. MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms
0 -- 0Junyan Song, Pei Fen Kuan. A systematic assessment of cell type deconvolution algorithms for DNA methylation data
0 -- 0Xudong Zhao 0002, Jingwen Zhai, Tong Liu 0013, Guohua Wang. Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins
0 -- 0Visanu Wanchai, Piroon Jenjaroenpun, Thongpan Leangapichart, Gerard Arrey, Charles M. Burnham, Maria C. Tümmler, Jesus Delgado-Calle, Birgitte Regenberg, Intawat Nookaew. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
0 -- 0Su Wang, Miran Kim, Wentao Li, Xiaoqian Jiang, Han Chen, Arif Ozgun Harmanci. Privacy-aware estimation of relatedness in admixed populations
0 -- 0Yixuan Qiao, Lianhe Zhao, Chunlong Luo, Yufan Luo, Yang Wu, Shengtong Li, Dechao Bu, Yi Zhao. Multi-modality artificial intelligence in digital pathology
0 -- 0Shidi Miao, Haobo Jia, Ke Cheng, Xiaohui Hu, Jing Li, Wenjuan Huang, Ruitao Wang. Deep learning radiomics under multimodality explore association between muscle/fat and metastasis and survival in breast cancer patients
0 -- 0Benjamin Goudey, Nicholas Geard, Karin Verspoor, Justin Zobel. Propagation, detection and correction of errors using the sequence database network
0 -- 0Binsheng He, Kun Wang, Ju Xiang, Pingping Bing, Min Tang, Geng Tian, Cheng Guo, Miao Xu, Jialiang Yang. DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network
0 -- 0Xiu-Ju George Zhao, Hui Cao. Linking research of biomedical datasets
0 -- 0Tang Li, Yanbin Yin. Critical assessment of pan-genomic analysis of metagenome-assembled genomes
0 -- 0Hanyu Zhang, Yunxia Wang, Ziqi Pan, Xiuna Sun, Minjie Mou, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu 0004. ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA
0 -- 0Yu Xu, Jiaxing Chen, Aiping Lyu, William K. Cheung, Lu Zhang. dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
0 -- 0Xiaohui Shi, Huajing Teng, Zhongsheng Sun. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops
0 -- 0Duy Pham, Buu Truong, Khai Tran, Guiyan Ni, Dat Nguyen, Trang T. H. Tran, Mai H. Tran, Duong Thuy Nguyen 0001, Nam S. Vo, Quan Nguyen. Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam
0 -- 0Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J. Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
0 -- 0Laura Marchetti, Riccardo Nifosì, Pier Luigi Martelli, Eleonora Da Pozzo, Valentina Cappello, Francesco Banterle, Maria Letizia Trincavelli, Claudia Martini, Massimo D'Elia. Quantum computing algorithms: getting closer to critical problems in computational biology
0 -- 0Dailin Gan, Guosheng Yin, Yan Dora Zhang. The GR2D2 estimator for the precision matrices
0 -- 0Jiaxin Fan, Yafei Lyu, Qihuang Zhang, Xuran Wang, Mingyao Li, Rui Xiao. MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data
0 -- 0Caimao Zhou, Dejun Peng, Bo Liao, Ranran Jia, Fang-Xiang Wu. ACP_MS: prediction of anticancer peptides based on feature extraction
0 -- 0Qianmu Yuan, Sheng Chen, Yu Wang, Huiying Zhao, Yuedong Yang. Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
0 -- 0Caiwei Zhen, Yuxian Wang, Jiaquan Geng, Lu Han, Jingyi Li, Jinghao Peng, Tao Wang, Jianye Hao, Xuequn Shang, Zhongyu Wei, Peican Zhu, Jiajie Peng. A review and performance evaluation of clustering frameworks for single-cell Hi-C data
0 -- 0Peng Zhang, Shikui Tu, Wen Zhang, Lei Xu. Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism
0 -- 0Hao Zhang, Nan Zhang, Wantao Wu, Ran Zhou, Shuyu Li, Zeyu Wang, Ziyu Dai, Liyang Zhang, Zaoqu Liu, Jian Zhang, Peng Luo, Zhixiong Liu, Quan Cheng. Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma
0 -- 0Zeynab Maghsoudi, Ha Nguyen, Alireza Tavakkoli, Tin Nguyen. A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
0 -- 0Jiacheng Leng, Ling-Yun Wu. Interaction-based transcriptome analysis via differential network inference
0 -- 0Kai-Yao Huang, Hui-Ju Kao, Tzu-Hsiang Weng, Chia-Hung Chen, Shun-Long Weng. iDVIP: identification and characterization of viral integrase inhibitory peptides
0 -- 0Meng Zhang, Jian Zhao 0034, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song. csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames
0 -- 0Li Peng, Yuan Tu, Li Huang, Yang Li, Xiangzheng Fu, Xiang Chen. DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder
0 -- 0Linlin Zhuo, Bosheng Song, Yuansheng Liu, Zejun Li, Xiangzheng Fu. Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning
0 -- 0Julio Vera, Xin Lai 0002, Andreas Baur, Michael Erdmann, Shailendra K. Gupta, Cristiano Guttà, Lucie Heinzerling, Markus V. Heppt, Philipp Maximilian Kazmierczak, Manfred Kunz, Christopher Lischer, Brigitte M. Pützer, Markus Rehm, Christian Ostalecki, Jimmy Retzlaff, Stephan Witt, Olaf Wolkenhauer, Carola Berking. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence
0 -- 0Lijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie 0003, Tao Qin, Tie-Yan Liu. SPRoBERTa: protein embedding learning with local fragment modeling
0 -- 0Menglan Cai, Anna Vesely, Xu Chen, Limin Li, Jelle J. Goeman. NetTDP: permutation-based true discovery proportions for differential co-expression network analysis
0 -- 0Bodhayan Prasad, Anthony J. Bjourson, Priyank Shukla. Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity
0 -- 0Jitong Feng, Shengbo Wu, Hongpeng Yang, Chengwei Ai, Jianjun Qiao, Junhai Xu, Fei Guo 0001. Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion
0 -- 0Yangyang Hao, Liang Lu, Anna Liu, Xue Lin, Li Xiao, Xiaoyue Kong, Kai Li, Fengji Liang, Jianghui Xiong, Lina Qu, Yinghui Li, Jian Li. Integrating bioinformatic strategies in spatial life science research
0 -- 0Anna Christine Haber, Ulrich Sax, Fabian Prasser. Open tools for quantitative anonymization of tabular phenotype data: literature review
0 -- 0Yang Li, Xue-Gang Hu, Lei Wang 0121, Pei-Pei Li, Zhu-Hong You. MNMDCDA: prediction of circRNA-disease associations by learning mixed neighborhood information from multiple distances
0 -- 0Medha Pandey, P. Anoosha, Dhanusha Yesudhas, M. Michael Gromiha. Identification of potential driver mutations in glioblastoma using machine learning
0 -- 0Elias Orouji, Ayush T. Raman. Computational methods to explore chromatin state dynamics
0 -- 0Xing Chen 0001, Li Huang. Computational model for ncRNA research
0 -- 0Hongwei Tu, Yanqiang Han, Zhilong Wang, Jinjin Li. Clustered tree regression to learn protein energy change with mutated amino acid
0 -- 0Yi Zhou, Xinyi Wang, Lin Yao, Min Zhu. LDAformer: predicting lncRNA-disease associations based on topological feature extraction and Transformer encoder
0 -- 0Yaojia Chen, Jiacheng Wang, Chuyu Wang, Mingxin Liu, Quan Zou. Deep learning models for disease-associated circRNA prediction: a review
0 -- 0. Correction to: A comprehensive benchmarking of WGS-based deletion structural variant callers
0 -- 0Trishala Das, Harbinder Kaur, Pratibha Gour, Kartikay Prasad, Andrew M. Lynn, Amresh Prakash, Vijay Kumar. Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
0 -- 0Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender 0002, Charles Tapley Hoyt, William L. Hamilton. A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
0 -- 0Bo-Wei Zhao, Xiao-Rui Su, Peng-Wei Hu, Yu-Peng Ma, Xi Zhou, Lun Hu. A geometric deep learning framework for drug repositioning over heterogeneous information networks
0 -- 0Julien Tremblay, Lars Schreiber, Charles W. Greer. High-resolution shotgun metagenomics: the more data, the better?
0 -- 0Jie Wang, Zihao Shen, Yichen Liao, Zhen Yuan, Shiliang Li, Gaoqi He, Man Lan, Xuhong Qian, Kai Zhang, Honglin Li. Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space
0 -- 0Qiao Ning, Zedong Qi, Yue Wang, Ansheng Deng, Chen Chen. FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites
0 -- 0Zena Cai, Ping Fu, Ye Qiu, Aiping Wu, Gaihua Zhang, Yirong Wang, Taijiao Jiang, Xing-Yi Ge, Haizhen Zhu, Yousong Peng. vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data
0 -- 0Yuyao Huang, Jiesi Luo, Runyu Jing, Menglong Li. Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism
0 -- 0Yue Gao 0004, Shipeng Shang, Shuang Guo, Xinyue Wang, Hanxiao Zhou, Yue Sun, Jing Gan, Yakun Zhang, Xia Li, Shangwei Ning, Yunpeng Zhang. AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species
0 -- 0Ebony Rose Watson, Ariane Mora, Atefeh Taherian-Fard, Jessica Cara Mar. How does the structure of data impact cell-cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data
0 -- 0Xia-an Bi, Yuhua Mao, Sheng Luo, Hao Wu, Lixia Zhang, Xun Luo, Luyun Xu. A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection
0 -- 0Shamima Rashid, Teng Ann Ng, Chee-Keong Kwoh 0001. Jupytope: computational extraction of structural properties of viral epitopes
0 -- 0Lei Huang, Jiecong Lin, Rui Liu, Zetian Zheng, Lingkuan Meng, Xingjian Chen, Xiangtao Li, Ka Chun Wong. CoaDTI: multi-modal co-attention based framework for drug-target interaction annotation
0 -- 0Jiannan Yang, Zhen Li, William Ka Kei Wu, Shi Yu, Zhongzhi Xu, Qian Chu, Qingpeng Zhang. Deep learning identifies explainable reasoning paths of mechanism of action for drug repurposing from multilayer biological network
0 -- 0Yuhua Yao, Yaping Lv, Ling Tong, Yuebin Liang, Shuxue Xi, Binbin Ji, Guanglu Zhang, Ling Li, Geng Tian, Min Tang, Xiyue Hu, Shijun Li, Jialiang Yang. ICSDA: a multi-modal deep learning model to predict breast cancer recurrence and metastasis risk by integrating pathological, clinical and gene expression data
0 -- 0Meihong Gao, Shuhui Liu, Yang Qi, Xinpeng Guo, Xuequn Shang. GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA-PCG associations
0 -- 0Li Huang, Li Zhang, Xing Chen 0001. Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models
0 -- 0Timothy Warwick, Sandra Seredinski, Nina M. Krause, Jasleen Kaur Bains, Lara Althaus, James A Oo, Alessandro Bonetti, Anne Dueck, Stefan Engelhardt, Harald Schwalbe, Matthias S. Leisegang, Marcel H. Schulz, Ralf P. Brandes. A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions
0 -- 0Tianyang Zhang, Qiang Tang, Fulei Nie, Qi Zhao, Wei Chen. DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters
0 -- 0Bao-Min Liu, Ying-Lian Gao, Dai-Jun Zhang, Feng Zhou, Juan Wang 0003, Chun-Hou Zheng 0001, Jin-Xing Liu. A new framework for drug-disease association prediction combing light-gated message passing neural network and gated fusion mechanism
0 -- 0Jian Ruan, Shuaishuai Xu, Ruyin Chen, Wenxin Qu, Qiong Li, Chanqi Ye, Wei Wu, Qi Jiang, Feifei Yan, Enhui Shen, Qinjie Chu, Yunlu Jia, Xiaochen Zhang, Wenguang Fu, Jinzhang Chen, Michael P. Timko, Peng Zhao, Longjiang Fan, Yifei Shen. EMLI-ICC: an ensemble machine learning-based integration algorithm for metastasis prediction and risk stratification in intrahepatic cholangiocarcinoma
0 -- 0Kai Zheng 0020, Xin-Lu Zhang, Lei Wang 0121, Zhu-Hong You, Zhao-Hui Zhan, Hao-Yuan Li. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs
0 -- 0Li Huang, Li Zhang, Xing Chen 0001. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion
0 -- 0Chengkui Zhao, Nan Xu, Jingwen Tan, Qi Cheng, Weixin Xie, Jiayu Xu, Zhenyu Wei, Jing Ye, Lei Yu, Weixing Feng. ILGBMSH: an interpretable classification model for the shRNA target prediction with ensemble learning algorithm
0 -- 0. Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
0 -- 0Liang Cheng. Omics data analysis and integration for COVID-19 patients - editorial
0 -- 0Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart. binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
0 -- 0Wenkai Yan, Zutan Li, Cong Pian, Yufeng Wu. PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites
0 -- 0Hock Chuan Yeo, Kumar Selvarajoo. Machine learning alternative to systems biology should not solely depend on data
0 -- 0Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao 0001, Cangzhi Jia, Jiangning Song. Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations
0 -- 0Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang 0012, Hoifung Poon, Tie-Yan Liu. BioGPT: generative pre-trained transformer for biomedical text generation and mining
0 -- 0Jiahui Ji, Maryam Anwar, Enrico Petretto, Costanza Emanueli, Prashant Kumar Srivastava. PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
0 -- 0Dong Ou-Yang, Yong Liang 0001, Jianjun Wang, Xiao-Ying Liu 0001, Shengli Xie, Rui Miao, Ning Ai, Le Li, Qi Dang. Predicting multiple types of miRNA-disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization
0 -- 0Hang Cheng, Yuhong Sun, Qing Yang, Minggui Deng, Zhijian Yu, Gang Zhu, Jiuxin Qu, Lei Liu, Liang Yang, Yu Xia. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method
0 -- 0Siqi Chen, Tiancheng Li, Luna Yang, Fei Zhai, Xiwei Jiang, Rongwu Xiang, Guixia Ling. Artificial intelligence-driven prediction of multiple drug interactions
0 -- 0Xizhi Luo, Fei Qin, Feifei Xiao, Guoshuai Cai. BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data
0 -- 0Yanzheng Meng, Lin Zhang, Laizhi Zhang, Ziyu Wang, Xuanwen Wang, Chan Li, Yu Chen, Shipeng Shang, Lei Li 0013. CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications
0 -- 0Wenya Wang, Li Zhang, Jianqiang Sun, Qi Zhao, Jianwei Shuai. Predicting the potential human lncRNA-miRNA interactions based on graph convolution network with conditional random field
0 -- 0Hanxuan Cai, Huimin Zhang, Duancheng Zhao, Jingxing Wu, Ling Wang 0008. FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction
0 -- 0Daniel Rivas-Barragan, Daniel Domingo-Fernández, Yojana Gadiya, David Healey. Ensembles of knowledge graph embedding models improve predictions for drug discovery
0 -- 0Peihao Fan, Julia Kofler, Ying Ding, Michael Marks, Robert A Sweet, Lirong Wang. Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia: explained with network efficiency and pathway analysis methods
0 -- 0Yuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. Identification of drug-side effect association via restricted Boltzmann machines with penalized term
0 -- 0Li Zhang, Chun-Chun Wang, Xing Chen 0001. Predicting drug-target binding affinity through molecule representation block based on multi-head attention and skip connection
0 -- 0Yuan Zhang, Qiaoyan Jiang, Ling Li, Zutan Li, Zhihui Xu, Yuanyuan Chen, Yang Sun, Cheng Liu, Zhengsheng Mao, Feng Chen, Hualan Li, Yue Cao, Cong Pian. Predicting the structure of unexplored novel fentanyl analogues by deep learning model
0 -- 0Chong Jin, Brian Lee, Li Shen, Qi Long. Integrating multi-omics summary data using a Mendelian randomization framework

Volume 23, Issue 5

0 -- 0Giovanna Carpi, Lev Gorenstein, Timothy T. Harkins, Mehrzad Samadi, Pankaj Vats. A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study
0 -- 0Ping Xuan, Xiaowen Zhang, Yu Zhang, Kaimiao Hu, Toshiya Nakaguchi, Tiangang Zhang. multi-type neighbors enhanced global topology and pairwise attribute learning for drug-protein interaction prediction
0 -- 0Lingling Zhao, Huiting Sun, Xinyi Cao, Naifeng Wen, Junjie Wang 0005, Chunyu Wang. Learning representations for gene ontology terms by jointly encoding graph structure and textual node descriptors
0 -- 0Siyu Hou, Peng Zhang, Kuo Yang, Lan Wang, Changzheng Ma, Yanda Li, Shao Li. Decoding multilevel relationships with the human tissue-cell-molecule network
0 -- 0Jiping Wang, Hongmin Liang, Qingzhao Zhang, Shuangge Ma. Replicability in cancer omics data analysis: measures and empirical explorations
0 -- 0Guanhua Zou, Yilong Lin, Tianyang Han, Le Ou-Yang. DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data
0 -- 0Lu Liang, Ye Liu, Bo Kang, Ru Wang, Meng-Yu Sun, Qi Wu, Xiang-Fei Meng, Jianping Lin. Large-scale comparison of machine learning algorithms for target prediction of natural products
0 -- 0Qiguo Dai, Ziqiang Liu, Zhaowei Wang, Xiaodong Duan, Maozu Guo 0001. GraphCDA: a hybrid graph representation learning framework based on GCN and GAT for predicting disease-associated circRNAs
0 -- 0Xudong Zhao 0002, Tong Liu, Guohua Wang. Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms
0 -- 0Biqing Zhu, HongYu Li, Le Zhang, Sreeganga S. Chandra, Hongyu Zhao. A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data
0 -- 0Tianjiao Zhang, Jie Zhou, Wentao Gao, Yuran Jia, Yanan Wei, Guohua Wang. Complex genome assembly based on long-read sequencing
0 -- 0Hao Liu, Jiaqi Dai, Ke Li, Yang Sun, Haoran Wei, Hong Wang, Chunxia Zhao, Dao Wen Wang. Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework
0 -- 0Xilin Shen, Hongru Shen, Dan Wu, Mengyao Feng, Jiani Hu, Jilei Liu, Yichen Yang 0004, Meng Yang, Yang Li, Lei Shi, Kexin Chen, Xiangchun Li. Scalable batch-correction approach for integrating large-scale single-cell transcriptomes
0 -- 0Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-bin Shen, Kup-Sze Choi, Shitong Wang 0001, Jing Wu, Dong-jun Yu. MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction
0 -- 0Zhi Ma, Yang Young Lu, Yiwen Wang, Renhao Lin, Zizi Yang, Fang Zhang, Ying Wang 0005. Metric learning for comparing genomic data with triplet network
0 -- 0Kai Zheng, Haochen Zhao, Qichang Zhao, Bin Wang, Xin Gao, Jianxin Wang 0001. NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks
0 -- 0Gui-Yan Xie, Chun-Jie Liu, An-Yuan Guo. EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets
0 -- 0Tianjiao Zhang, Yuran Jia, Hongfei Li, Dali Xu, Jie Zhou, Guohua Wang. CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins
0 -- 0Natàlia Segura-Alabart, Francesc Serratosa, Sergio Gómez, Alberto Fernández 0003. Nonunique UPGMA clusterings of microsatellite markers
0 -- 0Mingyuan Ma, Sen Na, Xiaolu Zhang, Congzhou Chen, Jin Xu. SFGAE: a self-feature-based graph autoencoder model for miRNA-disease associations prediction
0 -- 0Wenkai Han, Yuqi Cheng, Jiayang Chen, Huawen Zhong, Zhihang Hu, Siyuan Chen, Licheng Zong, Liang Hong, Ting-Fung Chan, Irwin King, Xin Gao 0001, Yu Li 0006. Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
0 -- 0Han Sun, Xiaoyun Huang, Ban Huo, Yuting Tan, Tingting He, Xingpeng Jiang. Detecting sparse microbial association signals adaptively from longitudinal microbiome data based on generalized estimating equations
0 -- 0Jian Liu, Yichen Pan, Zhihan Ruan, Jun Guo. SCDD: a novel single-cell RNA-seq imputation method with diffusion and denoising
0 -- 0Mingyan Fang, Zheng Su, Hassan Abolhassani, Yuval Itan, Xin Jin, Lennart Hammarström. VIPPID: a gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases
0 -- 0Sumeet Patiyal, Anjali Dhall, Gajendra P. S. Raghava. A deep learning-based method for the prediction of DNA interacting residues in a protein
0 -- 0Bin Liu 0058, Dimitrios Papadopoulos 0004, Fragkiskos D. Malliaros, Grigorios Tsoumakas, Apostolos N. Papadopoulos. Multiple similarity drug-target interaction prediction with random walks and matrix factorization
0 -- 0Zhong-Hao Ren, Zhu-Hong You, Changqing Yu, Li-ping Li, Yongjian Guan, Lu-Xiang Guo, Jie Pan. A biomedical knowledge graph-based method for drug-drug interactions prediction through combining local and global features with deep neural networks
0 -- 0Qian Ding, Wenyi Yang, Meng Luo, Chang Xu, Zhaochun Xu, Fenglan Pang, Yideng Cai, Anastasia A. Anashkina, Xi Su, Na Chen, Qinghua Jiang. CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data
0 -- 0Chanwoo Park, Boram Kim, Taesung Park. DeepHisCoM: deep learning pathway analysis using hierarchical structural component models
0 -- 0Rui Zhang 0065, Xumin Ni, Kai Yuan, Yuwen Pan, Shuhua Xu. MultiWaverX: modeling latent sex-biased admixture history
0 -- 0Li Huang, Li Zhang, Xing Chen 0001. Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models
0 -- 0Xiao Yuan, Peng Zhang 0050. Revisiting benchmark study for response to methodological critiques of 'Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases'
0 -- 0Hui Liu 0026, Yibiao Huang, Xuejun Liu, Lei Deng 0002. Attention-wise masked graph contrastive learning for predicting molecular property
0 -- 0Fabrício Martins Lopes, Matheus Henrique Pimenta-Zanon. Letter on the results of the BASiNET method in the paper 'A systematic evaluation of computational tools for lncRNA identification'
0 -- 0Yaqi Zhang, Gancheng Zhu, Kewei Li, Fei Li, Lan Huang 0002, Meiyu Duan, Fengfeng Zhou. HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction
0 -- 0Paula J. Gómez-González, Susana G. Campino, Jody Phelan, Taane G. Clark. Mycobacterium tuberculosis for clinical and epidemiological applications
0 -- 0Weijie Zhang, Pengyun Gong, Yichu Shan, Lili Zhao, Hongke Hu, Qiushi Wei, Zhen Liang, Chao Liu, Lihua Zhang, Yukui Zhang. SpotLink enables sensitive and precise identification of site nonspecific cross-links at the proteome scale
0 -- 0Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma. Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
0 -- 0Qiang Tang, Fulei Nie, Qi Zhao, Wei Chen 0064. A merged molecular representation deep learning method for blood-brain barrier permeability prediction
0 -- 0Jing Hu, Jie Gao, Xiaomin Fang, Zijing Liu, Fan Wang, Weili Huang, Hua Wu 0003, Guodong Zhao. DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations
0 -- 0Leroy Bondhus, Roshni Varma, Yenifer Hernandez, Valerie A. Arboleda. Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity
0 -- 0Rui Yin, Xianghe Zhu, Min Zeng, Pengfei Wu, Min Li, Chee-Keong Kwoh 0001. A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods
0 -- 0Li Peng, Cheng Yang, Li Huang, Xiang Chen, Xiangzheng Fu, Wei Liu. RNMFLP: Predicting circRNA-disease associations based on robust nonnegative matrix factorization and label propagation
0 -- 0Ling Luo 0001, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu. BioRED: a rich biomedical relation extraction dataset
0 -- 0Pei Chen, Jiayuan Zhong, Kun Yang, Xuhang Zhang, Yingqi Chen, Rui Liu 0009. TPD: a web tool for tipping-point detection based on dynamic network biomarker
0 -- 0Chien Lee, Bo-Han Su, Yufeng Jane Tseng. Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors
0 -- 0Zhengzheng Lou, Zhaoxu Cheng, Hui Li, Zhixia Teng, Yang Liu, Zhen Tian. Predicting miRNA-disease associations via learning multimodal networks and fusing mixed neighborhood information
0 -- 0Hongyu Ding, Junwei Luo. MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach
0 -- 0Xudong Zhang, Gan Wang, Xiangyu Meng 0005, Shuang Wang, Ying Zhang, Alfonso Rodríguez-Patón, Jianmin Wang, Xun Wang. Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug-drug interactions prediction
0 -- 0Tanmaya Kumar Sahu, Amit Kumar Singh, Shikha Mittal, Shailendra Kumar Jha, Sundeep Kumar, Sherry Rachel Jacob, Kuldeep Singh. G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data
0 -- 0Kang Jin, Daniel J. Schnell, Guangyuan Li, Nathan Salomonis, V. B. Surya Prasath, Rhonda Szczesniak, Bruce J. Aronow. CellDrift: inferring perturbation responses in temporally sampled single-cell data
0 -- 0Huihui Yan, Yuanyuan Xie, Yao Liu, Leer Yuan, Rong Sheng. ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery
0 -- 0Rong Gao, Jinling Yan, Peiluan Li, Luonan Chen. Detecting the critical states during disease development based on temporal network flow entropy
0 -- 0Wei Liu, Xingen Sun, Li Yang, Kaiwen Li, Yu Yang, Xiangzheng Fu. NSCGRN: a network structure control method for gene regulatory network inference
0 -- 0Gang Xu, Yilin Wang, Qinghua Wang, Jianpeng Ma. Studying protein-protein interaction through side-chain modeling method OPUS-Mut
0 -- 0Tao Zeng, Bernard Andes Hess Jr., Fan Zhang, Ruibo Wu. Bio-inspired chemical space exploration of terpenoids
0 -- 0Yun Zuo, Yue Hong, Xiangxiang Zeng, Qiang Zhang, Xiangrong Liu. MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites
0 -- 0Lei Wang 0121, Leon Wong, Zheng-Wei Li, Yuan Huang, Xiao-Rui Su, Bo-Wei Zhao, Zhuhong You. A machine learning framework based on multi-source feature fusion for circRNA-disease association prediction
0 -- 0Congxue Hu, Yingqi Xu, Feng Li, Wanqi Mi, He Yu, Xinran Wang, Xin Wen, Shuaijun Chen, Xia Li 0004, Yanjun Xu, Yunpeng Zhang. Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets
0 -- 0Jiawei Zou, Fulan Deng, Miaochen Wang, Zhen Zhang, Zheqi Liu, Xiaobin Zhang, Rong Hua, Ke Chen, Xin Zou, Jie Hao. scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data
0 -- 0Wei Li, Han Zhang, Minghe Li, Mingjing Han, Yanbin Yin. MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN
0 -- 0Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, Jörg Hackermüller. AI for predicting chemical-effect associations at the chemical universe level - <tt>deepFPlearn</tt>
0 -- 0Sujie Zhu, Weikaixin Kong, Jie Zhu, Liting Huang, Shixin Wang, Suzhen Bi, Zhengwei Xie. The genetic algorithm-aided three-stage ensemble learning method identified a robust survival risk score in patients with glioma
0 -- 0Pedro Blecua, Veronica Davalos, Izar de Villasante, Angelika Merkel, Eva Musulen, Laia Coll-Sanmartin, Manel Esteller. Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary
0 -- 0Fei Liu, Xiangkang Jiang, Jingyuan Yang, Jiawei Tao, Mao Zhang. A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia
0 -- 0Hansi Zheng, Xiaoman Li, Haiyan Hu. Letter to the editor: evaluating computational tools for lncRNA identification on independent datasets
0 -- 0Tanmaya Kumar Sahu, Prabina Kumar Meher, Nalini Kanta Choudhury, Atmakuri Ramakrishna Rao. A comparative analysis of amino acid encoding schemes for the prediction of flexible length linear B-cell epitopes
0 -- 0Yongsan Yang, Fengcui Qian, Xuecang Li, Yanyu Li, Liwei Zhou, Qiuyu Wang, Xinyuan Zhou, Jian Zhang, Chao Song, Zhengmin Yu, Ting Cui, Chenchen Feng, Jiang Zhu, Desi Shang, Jiaqi Liu, Mengfei Sun, Yuexin Zhang, Huifang Tang, Chunquan Li 0002. GREAP: a comprehensive enrichment analysis software for human genomic regions
0 -- 0Qingjian Chen, Qi-Nian Wu, Yu-Ming Rong, Shixiang Wang, Zhixiang Zuo, Long Bai, Bei Zhang, Shuqiang Yuan, Qi Zhao. Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol
0 -- 0Qiaoming Liu, Ximei Luo, Jie Li 0055, Guohua Wang. scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells
0 -- 0Jiani Ma, Hui Liu, Yumeng Mao, Lin Zhang. N6-methylation (m6A)-mediated diseases
0 -- 0Ofir Yaish, Maor Asif, Yaron Orenstein. A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
0 -- 0Nick Keur, Isis Ricaño-Ponce, Vinod Kumar, Vasiliki Matzaraki. A systematic review of analytical methods used in genetic association analysis of the X-chromosome
0 -- 0Md. Sohrawordi, Md. Ali Hossain, Md. Al Mehedi Hasan. PLP_FS: prediction of lysine phosphoglycerylation sites in protein using support vector machine and fusion of multiple F_Score feature selection
0 -- 0Shuo Shi, Qi Wang, Yunfei Shang, Congfan Bu, Mingming Lu, Meiye Jiang, Hao Zhang, Shuhuan Yu, Jingyao Zeng, Zaichao Zhang, Zhenglin Du, Jing-Fa Xiao. TSomVar: a tumor-only somatic and germline variant identification method with random forest
0 -- 0Jiye Wang, Chaofeng Lou, Guixia Liu, Weihua Li 0005, Zengrui Wu, Yun Tang. Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening
0 -- 0Sini Junttila, Johannes Smolander, Laura L. Elo. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
0 -- 0Annika L. Gable, Damian Szklarczyk, David Lyon, João F. Matias Rodrigues, Christian von Mering. Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments
0 -- 0Gang Xu, Qinghua Wang, Jianpeng Ma. Corrigendum to 'OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors'
0 -- 0Xuhua Yan, Ruiqing Zheng, Min Li 0007. GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets
0 -- 0Yi Cao, Zhen-Qun Yang, Xu-Lu Zhang, Wenqi Fan, Yaowei Wang, Jiajun Shen, Dong-Qing Wei, Qing Li, Xiao-Yong Wei. Identifying the kind behind SMILES - anatomical therapeutic chemical classification using structure-only representations
0 -- 0Renchu Guan, Haoyu Pang, Yanchun Liang 0001, Zhongjun Shao, Xin Gao, Dong Xu 0002, Xiaoyue Feng. Discovering trends and hotspots of biosafety and biosecurity research via machine learning
0 -- 0Daniele Mercatelli, Chiara Cabrelle, Pierangelo Veltri, Federico M. Giorgi, Pietro H. Guzzi. Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data
0 -- 0Vinícius de Almeida Paiva, Murillo Ventura Mendonça, Sabrina de Azevedo Silveira, David B. Ascher, Douglas E. V. Pires, Sandro C. Izidoro. GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms
0 -- 0Wei-Xin Hu, Yu Rong, Yan Guo, Feng Jiang, Wen Tian, Hao Chen, Shan-Shan Dong, Tie-Lin Yang. ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA
0 -- 0Laura Zaragoza-Infante, Valentin Junet, Nikos Pechlivanis, Styliani-Christina Fragkouli, Serovpe Amprachamian, Triantafyllia Koletsa, Anastasia Chatzidimitriou, Maria Papaioannou, Kostas Stamatopoulos, Andreas Agathangelidis, Fotis E. Psomopoulos. IgIDivA: immunoglobulin intraclonal diversification analysis
0 -- 0Zhe Wang, Hong Pan, Huiyong Sun, Yu Kang 0002, Huanxiang Liu, Dongsheng Cao 0001, Tingjun Hou. fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation
0 -- 0Katarzyna Sidorczuk, Przemyslaw Gagat, Filip Pietluch, Jakub Kala, Dominik Rafacz, Laura Bakala, Jadwiga Slowik, Rafal Kolenda, Stefan Rödiger, Legana C. H. W. Fingerhut, Ira Cooke, Pawel Mackiewicz, Michal Burdukiewicz. Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data
0 -- 0Shaokai Wang, Haochen Zhao. SADeepcry: a deep learning framework for protein crystallization propensity prediction using self-attention and auto-encoder networks
0 -- 0Sandeep Kumar Dhanda, Jitendra Malviya, Sudheer Gupta. in silico tools for the prediction of cytokine-inducing potential of T-cell epitopes
0 -- 0Jingsi Ming, Zhixiang Lin, Jia Zhao, Xiang Wan, Tabula Microcebus Consortium, C. Ezran, S. Liu, Can Yang, Angela Ruohao Wu. FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets
0 -- 0Sanjay Kumar, Geethu S. Kumar, Subhrangsu Sundar Maitra, Petr Malý, Shiv Bharadwaj, Pradeep Sharma, Vivek Dhar Dwivedi. Viral informatics: bioinformatics-based solution for managing viral infections
0 -- 0Chenyang Zhang, Minjie Mou, Ying Zhou, Wei Zhang, Xichen Lian, Shuiyang Shi, Mingkun Lu, Huaicheng Sun, Fengcheng Li, Yunxia Wang, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Yunqing Qiu, Feng Zhu 0004, Jianqing Gao. Biological activities of drug inactive ingredients
0 -- 0Hao Peng, Jiayuan Zhong, Pei Chen, Rui Liu 0009. Identifying the critical states of complex diseases by the dynamic change of multivariate distribution
0 -- 0Ji Lv, Guixia Liu, Junli Hao, Yuan Ju, Binwen Sun, Ying Sun. Computational models, databases and tools for antibiotic combinations
0 -- 0Bernardina Scafuri, Anna Verdino, Nancy D'Arminio, Anna Marabotti. Computational methods to assist in the discovery of pharmacological chaperones for rare diseases
0 -- 0Guanjin Qu, Zihui Yan, Huaming Wu. Clover: tree structure-based efficient DNA clustering for DNA-based data storage
0 -- 0Lu-Xiang Guo, Zhu-Hong You, Lei Wang 0121, Changqing Yu, Bo-Wei Zhao, Zhong-Hao Ren, Jie Pan. A novel circRNA-miRNA association prediction model based on structural deep neural network embedding
0 -- 0Feng Zhang, Chen Yang, Yihao Wang, Huiyuan Jiao, Zhiming Wang, Jianfeng Shen, Lingjie Li. FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight
0 -- 0Asli Boyraz, Vera Pawlowsky-Glahn, Juan José Egozcue, Aybar Can Acar. Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data
0 -- 0Suruchi Aggarwal, Anurag Raj, Dhirendra Kumar, Debasis Dash, Amit Kumar Yadav. False discovery rate: the Achilles' heel of proteogenomics
0 -- 0LiJuan Yang, Guanghui Yang, Zhi-Tong Bing, Yuan Tian, Liang Huang, Yuzhen Niu, Lei Yang 0021. Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm
0 -- 0Shouzhi Chen, Qing Li, Jianping Zhao, Yannan Bin, Chunhou Zheng 0001. NeuroPred-CLQ: incorporating deep temporal convolutional networks and multi-head attention mechanism to predict neuropeptides
0 -- 0Fan Yang, Shuaijie Zhang, Wei Pan, Ruiyuan Yao, Weiguo Zhang, Yanchun Zhang, Guoyin Wang, Qianghua Zhang, Yunlong Cheng, Jihua Dong, Chunyang Ruan, LiZhen Cui, Hao Wu, Fuzhong Xue. Signaling repurposable drug combinations against COVID-19 by developing the heterogeneous deep herb-graph method
0 -- 0Vishakha Gautam, Rahul Gupta, Deepti Gupta, Anubhav Ruhela, Aayushi Mittal, Sanjay Kumar Mohanty, Sakshi Arora, Ria Gupta, Chandan Saini, Debarka Sengupta, Natarajan Arul Murugan, Gaurav Ahuja. deepGraphh: AI-driven web service for graph-based quantitative structure-activity relationship analysis
0 -- 0Wengang Wang, Hailin Chen. Predicting miRNA-disease associations based on graph attention networks and dual Laplacian regularized least squares
0 -- 0Abhishek Vijayan, Shadma Fatima, Arcot Sowmya, Fatemeh Vafaee. Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods
0 -- 0Xiangmei Li, Yalan He, Jiashuo Wu, Jiayue Qiu, Ji Li, Qian Wang, Ying Jiang, Junwei Han. A novel pathway mutation perturbation score predicts the clinical outcomes of immunotherapy
0 -- 0Giuseppe Agapito, Chiara Pastrello, Yun Niu, Igor Jurisica. Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture
0 -- 0Patryk Jarnot, Joanna Ziemska-Legiecka, Marcin Grynberg, Aleksandra Gruca. Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
0 -- 0Anjali Dhall, Sumeet Patiyal, Gajendra P. S. Raghava. HLAncPred: a method for predicting promiscuous non-classical HLA binding sites
0 -- 0Tianjian Liang, Chen Jiang, Jiayi Yuan, Yasmin Othman, Xiang-Qun Xie, Zhiwei Feng. Differential performance of RoseTTAFold in antibody modeling
0 -- 0Yuansong Zeng, Zhuoyi Wei, Fengqi Zhong, Zixiang Pan, Yutong Lu, Yuedong Yang. A parameter-free deep embedded clustering method for single-cell RNA-seq data
0 -- 0Yuansong Zeng, Zhuoyi Wei, Weijiang Yu, Rui Yin, Yuchen Yuan, Bingling Li, Zhonghui Tang, Yutong Lu, Yuedong Yang. Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks
0 -- 0Haiyue Wang, Xiaoke Ma. Learning discriminative and structural samples for rare cell types with deep generative model
0 -- 0Minghao Yang, Zhi-an Huang, Wenhao Gu, Kun Han, Wenying Pan, Xiao Yang, Zexuan Zhu. Prediction of biomarker-disease associations based on graph attention network and text representation
0 -- 0Ping Xuan, Shuai Wang, Hui Cui 0002, Yue Zhao, Tiangang Zhang, Peiliang Wu. Learning global dependencies and multi-semantics within heterogeneous graph for predicting disease-related lncRNAs
0 -- 0Xuwen Wang, Ying Xu, Ruoyu Liu, Xin Lai 0003, Yuqian Liu, Shenjie Wang, Xuanping Zhang, Jiayin Wang. PEcnv: accurate and efficient detection of copy number variations of various lengths
0 -- 0Xinghu Qin, Charleston W. K. Chiang, Oscar E. Gaggiotti. Deciphering signatures of natural selection via deep learning
0 -- 0Qiao Ning, Jinmou Li. DLF-Sul: a multi-module deep learning framework for prediction of S-sulfinylation sites in proteins
0 -- 0Zhao-Yue Zhang, Lin Ning, Xiucai Ye, Yu-He Yang, Yasunori Futamura, Tetsuya Sakurai, Hao Lin 0001. iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism
0 -- 0Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin 0001, Nanning Zheng 0001, Tie-Yan Liu, Tong Wang. Improved drug-target interaction prediction with intermolecular graph transformer
0 -- 0Xiaotao Shen, Wei Shao 0008, Chuchu Wang, Liang Liang, Songjie Chen, Sai Zhang, Mirabela Rusu, Michael P. Snyder. Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine
0 -- 0Stephen Bonner, Ufuk Kirik, Ola Engkvist, Jian Tang, Ian P. Barrett. Implications of topological imbalance for representation learning on biomedical knowledge graphs
0 -- 0Quan Xu, Yueyue Liu, Jifang Hu, Xiaohong Duan, Niuben Song, Jiale Zhou, Jincheng Zhai, Junyan Su, Siyao Liu, Fan Chen, Wei Zheng, Zhongjia Guo, Hexiang Li, Qiming Zhou, Beifang Niu. OncoPubMiner: a platform for mining oncology publications
0 -- 0Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng 0002, Chen Wu, Dachuan Zhang, Hui Liu. Contrastive learning-based computational histopathology predict differential expression of cancer driver genes
0 -- 0Junhao Su, Zhenxian Zheng, Syed Shakeel Ahmed, Tak Wah Lam, Ruibang Luo. Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks
0 -- 0Sreya Vadapalli, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed. Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine
0 -- 0Jing Liang, Zong-Wei Li, Cai-Tong Yue, Zhuo Hu, Han Cheng, Zexian Liu, Wei-feng Guo. Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer
0 -- 0Xiaobin Wu, Yuan Zhou. GE-Impute: graph embedding-based imputation for single-cell RNA-seq data
0 -- 0Yujie Wang, Gang Zhou, Tianhao Guan, Yan Wang, Chenxu Xuan, Tao Ding, Jie Gao. A network-based matrix factorization framework for ceRNA co-modules recognition of cancer genomic data
0 -- 0Alex G. C. de Sá, Yangyang Long, Stephanie Portelli, Douglas E. V. Pires, David B. Ascher. toxCSM: comprehensive prediction of small molecule toxicity profiles
0 -- 0Daniel Toro-Domínguez, Jordi Martorell-Marugan, Manuel Martínez-Bueno, Raúl López-Domínguez, Elena Carnero-Montoro, Guillermo Barturen, Daniel Goldman, Michelle Petri, Pedro Carmona-Saez, Marta E. Alarcón-Riquelme. Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression
0 -- 0Julius O. B. Jacobsen, Catherine Kelly, Valentina Cipriani, Peter N. Robinson, Damian Smedley. Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases
0 -- 0Hongyan Shi, Shengli Zhang, Xinjie Li. R5hmCFDV: computational identification of RNA 5-hydroxymethylcytosine based on deep feature fusion and deep voting
0 -- 0Neelam Sharma, Naorem Leimarembi Devi, Shipra Jain, Gajendra P. S. Raghava. ToxinPred2: an improved method for predicting toxicity of proteins
0 -- 0Jiayu Shang, Yanni Sun. CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model

Volume 23, Issue 4

0 -- 0Wang Ruohan, Zhang Yuwei, Wang Mengbo, Feng Xikang, Wang Jianping, Li Shuai Cheng. Resolving single-cell copy number profiling for large datasets
0 -- 0Yanglan Gan, Cheng Guo, Wenjing Guo, Guangwei Xu, Guobing Zou. Entropy-based inference of transition states and cellular trajectory for single-cell transcriptomics
0 -- 0Hiroyuki Kurata, Sho Tsukiyama, Balachandran Manavalan. iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model
0 -- 0Xinyi Xu, Xiaokang Yu, Gang Hu, Kui Wang, Jingxiao Zhang, Xiangjie Li. Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis
0 -- 0Zhi-Zheng Wang, Ming-Shu Wang, Fan Wang, Xing-Xing Shi, Wei Huang, Ge-Fei Hao, Guangfu Yang. Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations
0 -- 0Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo. Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs
0 -- 0Fengcheng Li, Jiayi Yin, Mingkun Lu, Qingxia Yang, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Yunqing Qiu, Haibin Dai, Yuzong Chen, Feng Zhu 0004. ConSIG: consistent discovery of molecular signature from OMIC data
0 -- 0Mathew Karikomi, Peijie Zhou, Qing Nie. DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data
0 -- 0Xiaqiong Wang, Yalu Wen. A penalized linear mixed model with generalized method of moments for prediction analysis on high-dimensional multi-omics data
0 -- 0Emilio Fenoy, Alejandro A. Edera, Georgina Stegmayer. Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks
0 -- 0Leandro A Bugnon, Alejandro A. Edera, S. Prochetto, Matias Gerard, Jonathan Raad, E. Fenoy, Mariano Rubiolo, Uciel Chorostecki, Toni Gabaldón, Federico Ariel, Leandro E. Di Persia, Diego H. Milone, Georgina Stegmayer. Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches
0 -- 0Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Elayaraja Kolanthai, Craig J. Neal, Sudipta Seal, Özlem Özmen Garibay. AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification
0 -- 0Dong Lu, Rongrong Pan, Wenxuan Wu, Yanyan Zhang, Shensuo Li, Hong Xu, Jialan Huang, Jianhua Xia, Qun Wang, Xin Luan, Chao Lv, Weidong Zhang, Guofeng Meng. FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis
0 -- 0Dezhong Lv, Kang Xu, Changbo Yang, Yujie Liu, Ya Luo, Weiwei Zhou, Haozhe Zou, Yangyang Cai, Na Ding, Xia Li 0004, Tingting Shao, Yongsheng Li, Juan Xu. PRES: a webserver for decoding the functional perturbations of RNA editing sites
0 -- 0Guiying Dong, Zi-Chao Zhang 0001, Jianfeng Feng, Xing-Ming Zhao. MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network
0 -- 0Ryuji Hamamoto, Ken Takasawa, Hidenori Machino, Kazuma Kobayashi, Satoshi Takahashi, Amina Bolatkan, Norio Shinkai, Akira Sakai, Rina Aoyama, Masayoshi Yamada, Ken Asada, Masaaki Komatsu, Koji Okamoto, Hirokazu Kameoka, Syuzo Kaneko. Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine
0 -- 0Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T. Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu. ggmsa: a visual exploration tool for multiple sequence alignment and associated data
0 -- 0Priya Gupta, Sureshkumar Venkadesan, Debasisa Mohanty. Plasmodium proteins
0 -- 0Pâmela M. Rezende, Joicymara S. Xavier, David B. Ascher, Gabriel R. Fernandes, Douglas E. V. Pires. Evaluating hierarchical machine learning approaches to classify biological databases
0 -- 0Hyunho Kim, Minsu Park, Ingoo Lee, Hojung Nam. BayeshERG: a robust, reliable and interpretable deep learning model for predicting hERG channel blockers
0 -- 0Wiktoria Wilman, Sonia Wróbel, Weronika Bielska, Piotr Deszynski, Pawel Dudzic, Igor Jaszczyszyn, Jedrzej Kaniewski, Jakub Mlokosiewicz, Anahita Rouyan, Tadeusz Satlawa, Sandeep Kumar, Victor Greiff, Konrad Krawczyk. Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery
0 -- 0Xin Wang, Xia Cao, Yuantao Feng, Maozu Guo 0001, Guoxian Yu, Jun Wang. ELSSI: parallel SNP-SNP interactions detection by ensemble multi-type detectors
0 -- 0Xianglin Zhang, Xiaodong Jia, Bixi Zhong, Lei Wei, Jiaqi Li, Wei Zhang, Huan Fang 0003, Yanda Li, Yinying Lu, Xiaowo Wang. Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA
0 -- 0Yunda Si, Chengfei Yan. Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2
0 -- 0Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun. Accurate identification of bacteriophages from metagenomic data using Transformer
0 -- 0Wei Zhang, Qiaozhen Meng, Jianxin Wang, Fei Guo 0001. HDIContact: a novel predictor of residue-residue contacts on hetero-dimer interfaces via sequential information and transfer learning strategy
0 -- 0Teemu J. Rintala, Arindam Ghosh, Vittorio Fortino. Network approaches for modeling the effect of drugs and diseases
0 -- 0Zhe Zhang, Miaomiao Zhu, Qi Xie, Robert M. Larkin, Xueping Shi, Bo Zheng. CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences
0 -- 0Zhi-Hui Luo, Li-Da Zhu, Ya-min Wang, Sheng Hu Qian, Menglu Li, Wen Zhang, Zhen-Xia Chen. DSEATM: drug set enrichment analysis uncovering disease mechanisms by biomedical text mining
0 -- 0Tiago Pereira, Maryam Abbasi, Rita I Oliveira, Romina A. Guedes, Jorge A. R. Salvador, Joel P. Arrais. Deep generative model for therapeutic targets using transcriptomic disease-associated data - USP7 case study
0 -- 0Raquel Pagano-Márquez, José Córdoba-Caballero, Beatriz Martínez-Poveda, Ana R. Quesada, Elena Rojano, Pedro Seoane, Juan A. G. Ranea, Miguel Ángel Medina. Deepening the knowledge of rare diseases dependent on angiogenesis through semantic similarity clustering and network analysis
0 -- 0Hongyu Luo, Yingfei Xiang, Xiaomin Fang, Wei Li 0176, Fan Wang, Hua Wu 0003, Haifeng Wang 0001. BatchDTA: implicit batch alignment enhances deep learning-based drug-target affinity estimation
0 -- 0Jianhua Dai, Chao Jiang, Ruoyao Peng, Daojian Zeng, Yangding Li. Chinese medical dialogue information extraction via contrastive multi-utterance inference
0 -- 0Saritha Kodikara, Susan Ellul, Kim-Anh Lê Cao. Statistical challenges in longitudinal microbiome data analysis
0 -- 0Boris Vishnepolsky, Maya Grigolava, Grigol Managadze, Andrei Gabrielian, Alex Rosenthal, Darrell E. Hurt, Michael Tartakovsky, Malak Pirtskhalava. Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction
0 -- 0Pietro Hiram Guzzi, Francesco Petrizzelli, Tommaso Mazza. Disease spreading modeling and analysis: a survey
0 -- 0Qiang Wei, Chao Jin, Yang Wang, Shanshan Guo, Xu Guo, Xiaonan Liu, Jiaze An, Jinliang Xing, Bingshan Li. A computational framework to unify orthogonal information in DNA methylation and copy number aberrations in cell-free DNA for early cancer detection
0 -- 0Young Jun Jeon, Md. Mehedi Hasan 0002, Hyun Woo Park, Ki-Wook Lee, Balachandran Manavalan. TACOS: a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization
0 -- 0Yunhee Jeong, Lisa Barros de Andrade e Sousa, Dominik Thalmeier, Reka Toth, Marlene Ganslmeier, Kersten Breuer, Christoph Plass, Pavlo Lutsik. Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes
0 -- 0Klaudia Adamowicz, Andreas Maier 0009, Jan Baumbach, David B. Blumenthal. in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST
0 -- 0Jessica Gliozzo, Marco Mesiti, Marco Notaro, Alessandro Petrini, Alex Patak, Antonio Puertas Gallardo, Alberto Paccanaro, Giorgio Valentini, Elena Casiraghi. Heterogeneous data integration methods for patient similarity networks
0 -- 0Madhu Sharma, Indra Prakash Jha, Smriti Chawla, Neetesh Pandey, Omkar Chandra, Shreya Mishra, Vibhor Kumar. Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs
0 -- 0Qifan He, Jian Yang, Yonghai Jin. Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma
0 -- 0Zhichao Liu, Ting Li, Skylar Connor, Shraddha Thakkar, Ruth Roberts, Weida Tong. Best practice and reproducible science are required to advance artificial intelligence in real-world applications
0 -- 0Xinghu Qin, Charleston W. K. Chiang, Oscar E. Gaggiotti. KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis
0 -- 0Mengfei Liu, Linlin Hao, Sien Yang, Xiaohui Wu. PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data
0 -- 0Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Minyoung Kim, Aditya Sarkar, Sei Chang, Angela Lu, Neha Rajkumar, Nicholas Darfci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul. A comprehensive benchmarking of WGS-based deletion structural variant callers
0 -- 0Ning Wang, Ke Yan 0003, Jun Zhang, Bin Liu 0014. iDRNA-ITF: identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework
0 -- 0Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen 0001, Bjoern Peters. A comprehensive analysis of the IEDB MHC class-I automated benchmark
0 -- 0Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong 0001, Nam S. Vo. LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays
0 -- 0Weikang Gong, Junjie Wee, Min-Chun Wu, Xiaohan Sun, Chunhua Li, Kelin Xia. Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation
0 -- 0Zijie Sun, Qinlai Huang, Yuhe Yang, Shihao Li, Hao Lv, Yang Zhang, Hao Lin 0001, Lin Ning. PSnoD: identifying potential snoRNA-disease associations based on bounded nuclear norm regularization
0 -- 0Xiao-Shuang Li, Xiang Liu, Le Lu 0009, Xian-Sheng Hua 0001, Ying Chi, Kelin Xia. Multiphysical graph neural network (MP-GNN) for COVID-19 drug design
0 -- 0Jun Bai, Renbo Tan, Zheng An, Ying Xu. Quantitative estimation of intracellular oxidative stress in human tissues
0 -- 0Kandasamy Saravanakumar, Sugavaneswaran Siva Santosh, Mohamedali Afaan Ahamed, Anbazhagan Sathiyaseelan, Ghazala Sultan, Navabshan Irfan, Davoodbasha Mubarak Ali, Myeong-Hyeon Wang. Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses
0 -- 0Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan 0001, John Z. H. Zhang. de novo compounds against given targets using ultrafast deep learning models as core components
0 -- 0Xingxin Pan, L. Frank Huang. Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression
0 -- 0Artem Danilevsky, Avital Luba Polsky, Noam Shomron. Adaptive sequencing using nanopores and deep learning of mitochondrial DNA
0 -- 0Polina Suter, Jack Kuipers, Niko Beerenwinkel. Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks
0 -- 0Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone. barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
0 -- 0Tianjiao Zhang, Liang Chen 0021, Rongzhen Li, Ning Liu, Xiaobing Huang, Garry Wong. PIWI-interacting RNAs in human diseases: databases and computational models
0 -- 0Nansu Zong, Ning Li, Andrew Wen, Victoria Ngo, Yue Yu, Ming Huang, Shaika Chowdhury, Chao Jiang, Sunyang Fu, Richard Weinshilboum, Guoqian Jiang, Lawrence Hunter, Hongfang Liu. BETA: a comprehensive benchmark for computational drug-target prediction
0 -- 0Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li 0021. PCfun: a hybrid computational framework for systematic characterization of protein complex function
0 -- 0Wenjuan Nie, Lei Deng 0002. TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach
0 -- 0Anthony Huffman, Edison Ong, Junguk Hur, Adonis D'mello, Hervé Tettelin, Yongqun He. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning
0 -- 0Sirvan Khalighi, Peronne Joseph, Deepak Babu, Salendra Singh, Thomas LaFramboise, Kishore Guda, Vinay Varadan. SYSMut: decoding the functional significance of rare somatic mutations in cancer
0 -- 0Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher. Structural landscapes of PPI interfaces
0 -- 0Teng Zhang, Shao-Wu Zhang 0001, Jian Feng, Bei Zhang. Aexpress-BHM: predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model
0 -- 0Pietro di Lena, Claudia Sala, Christine Nardini. Evaluation of different computational methods for DNA methylation-based biological age
0 -- 0Shangbo Ning, Huiwen Wang, Chen Zeng, Yunjie Zhao. Prediction of allosteric druggable pockets of cyclin-dependent kinases
0 -- 0Daniel N. Sosa, Russ B. Altman. Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference
0 -- 0Jianfeng Li, Benben Miao, Shixiang Wang, Wei Dong, Houshi Xu, Chenchen Si, Wei Wang, Songqi Duan, Jiacheng Lou, Zhiwei Bao, Hailuan Zeng, Zengzeng Yang, Wenyan Cheng, Fei Zhao, Jianming Zeng, Xue-Song Liu, Renxie Wu, Yang Shen, Zhu Chen, Saijuan Chen, Mingjie Wang. Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization
0 -- 0Hongzhun Wang, Feng Huang, Zhankun Xiong, Wen Zhang. A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions
0 -- 0Tri Minh Nguyen 0005, Thin Nguyen, Truyen Tran 0001. Mitigating cold-start problems in drug-target affinity prediction with interaction knowledge transferring
0 -- 0Hui Yu, Shiyu Zhao, Jianyu Shi. STNN-DDI: a Substructure-aware Tensor Neural Network to predict Drug-Drug Interactions
0 -- 0Lihong Peng, Feixiang Wang, Zhao Wang, Jingwei Tan, Li Huang, Xiongfei Tian, Guangyi Liu, Liqian Zhou. Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies
0 -- 0Xinxin Peng, Xiaoyu Wang, Yuming Guo, ZongYuan Ge, Fuyi Li, Xin Gao, Jiangning Song. RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins
0 -- 0Wenxiang Zhang, Hang Wei, Bin Liu 0014. idenMD-NRF: a ranking framework for miRNA-disease association identification
0 -- 0Mengyun Jiang, Weidong Ning, Shishi Wu, Xingwei Wang 0012, Kun Zhu 0019, Aomei Li, Yongyao Li, Shifeng Cheng, Bo Song. Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames
0 -- 0Ho-Jin Gwak, Mina Rho. ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data
0 -- 0Feiyue Sun, Jianqiang Sun, Qi Zhao. A deep learning method for predicting metabolite-disease associations via graph neural network
0 -- 0Bing Wang, Yue Wang, Yu Chen, Mengmeng Gao, Jie Ren, Yueshuai Guo, Chenghao Situ, Yaling Qi, Hui Zhu, Yan Li, Xuejiang Guo. DeepSCP: utilizing deep learning to boost single-cell proteome coverage
0 -- 0Xin Dong, Ke Chen 0013, Wenbo Chen, Jun Wang, Liuping Chang, Jin Deng, Lei Wei, Leng Han, Chunhua Huang, Chunjiang He. circRIP: an accurate tool for identifying circRNA-RBP interactions
0 -- 0Zhao Chen, Yin Jiang, Xiaoyu Zhang, Rui Zheng, Ruijin Qiu, Yang Sun, Chen Zhao, Hongcai Shang. The prediction approach of drug-induced liver injury: response to the issues of reproducible science of artificial intelligence in real-world applications
0 -- 0Tong Yang, Feng Gao 0001. Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands
0 -- 0Wennan Chang, Chi Zhang 0021, Sha Cao. et al.
0 -- 0Grete Francesca Privitera, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti. Virus finding tools: current solutions and limitations
0 -- 0Robson Bonidia, Anderson P. Avila-Santos, Breno Lívio Silva de Almeida, Peter F. Stadler, Ulisses Nunes da Rocha, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho. BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria
0 -- 0Qian Gao, Yu Zhang, Hongwei Sun, Tong Wang. Evaluation of propensity score methods for causal inference with high-dimensional covariates
0 -- 0Jianmin Wang, Yanyi Chu, Jiashun Mao, Hyeon-Nae Jeon, Haiyan Jin, Amir Zeb, Yuil Jang, Kwang-Hwi Cho, Tao Song, Kyoung Tai No. De novo molecular design with deep molecular generative models for PPI inhibitors
0 -- 0Jiawen Chen, Weifang Liu, Tianyou Luo, Zhentao Yu, Minzhi Jiang, Jia Wen, Gaorav P. Gupta, Paola Giusti, Hongtu Zhu, Yuchen Yang, Yun Li. A comprehensive comparison on cell-type composition inference for spatial transcriptomics data

Volume 23, Issue 3

0 -- 0Xiaozhe Wan, Xiaolong Wu, Dingyan Wang, Xiaoqin Tan, Xiaohong Liu, Zunyun Fu, Hualiang Jiang, Mingyue Zheng, Xutong Li. An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph
0 -- 0Zimo Huang, Jun Wang, Zhongmin Yan, Maozu Guo 0001. Differentially expressed genes prediction by multiple self-attention on epigenetics data
0 -- 0Wei Liu, Hui Lin, Li Huang, Li Peng, Ting Tang, Qi Zhao, Li Yang. Identification of miRNA-disease associations via deep forest ensemble learning based on autoencoder
0 -- 0Cheng-Hong Yang 0001, Yu-Huei Cheng, Li-Yeh Chuang, Yu-Da Lin. Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer
0 -- 0Eric Van Buren, Ming Hu, Liang Cheng, John Wrobel, Kirk Wilhelmsen, Lishan Su, Yun Li, Di Wu. TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation
0 -- 0Lei Wang, Yaqin Tan, Xiaoyu Yang, Linai Kuang, Pengyao Ping. Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models
0 -- 0Xue Zhang, Chen Guang Liu, Shi-Hui Yang, Xia Wang, Feng-Wu Bai, Zhuo Wang. Benchmarking of long-read sequencing, assemblers and polishers for yeast genome
0 -- 0Kanghao Shao, Yunhao Zhang, Yuqi Wen, Zhongnan Zhang, Song He, Xiaochen Bo. DTI-HETA: prediction of drug-target interactions based on GCN and GAT on heterogeneous graph
0 -- 0Wenze Ding, Kenta Nakai, Haipeng Gong. Protein design via deep learning
0 -- 0Ruibo Zhang, Souparno Ghosh, Ranadip Pal. Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations
0 -- 0Rashmie Abeysinghe, Yuntao Yang, Mason Bartels, W. Jim Zheng, Licong Cui. An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations
0 -- 0Qiongqiong Feng, Minghua Hou, Jun Liu, Kai-Long Zhao, Guijun Zhang. Construct a variable-length fragment library for de novo protein structure prediction
0 -- 0Qiang Kang, Jun Meng, Yushi Luan. RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA-RNA interaction
0 -- 0Weizhong Zhao, Shujie Luo, Haifang Wu, Xingpeng Jiang, Tingting He, Xiaohua Hu 0001. A multi-label learning framework for predicting antibiotic resistance genes via dual-view modeling
0 -- 0Xia-an Bi, Wenyan Zhou, Sheng Luo, Yuhua Mao, Xi Hu, Bin Zeng 0001, Luyun Xu. Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease
0 -- 0Peng Zhou 0003, Li Wen, Jing Lin, Li Mei, Qian Liu, Shuyong Shang, Juelin Li, Jianping Shu. Integrated unsupervised-supervised modeling and prediction of protein-peptide affinities at structural level
0 -- 0Ziwei Chen, Fuzhou Gong, Lin Wan, Liang Ma. BiTSC 2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
0 -- 0Zi-Yi Yang, Zhaofeng Ye, Yijia Xiao, Chang-Yu Hsieh, Sheng-yu Zhang. SPLDExtraTrees: robust machine learning approach for predicting kinase inhibitor resistance
0 -- 0Gang Xu, Qinghua Wang, Jianpeng Ma. Expression of Concern to: OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors
0 -- 0Meidan Zhao, Pengqian Wang, Kai Zhang. Bioinformatics/network topology analysis of acupuncture in the treatment of COVID-19: response to methodological issues
0 -- 0Ju Xiang, Xiangmao Meng, Yichao Zhao, Fang-Xiang Wu, Min Li 0007. HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure
0 -- 0Ye Hong, Dani Flinkman, Tomi Suomi, Sami Pietilä, Peter James, Eleanor Coffey, Laura L. Elo. Correction to: PhosPiR: an automated phosphoproteomic pipeline in R
0 -- 0Sare Amerifar, Mahammad Norouzi, Mahmoud Ghandi. A tool for feature extraction from biological sequences
0 -- 0Yixin Yan, Mengyun Yang, Haochen Zhao, Guihua Duan, Xiaoqing Peng, Jianxin Wang 0001. Drug repositioning based on multi-view learning with matrix completion
0 -- 0Wajdi Alghamdi, Muhammad Attique, Ebraheem Alzahrani, Malik Zaka Ullah, Yaser Daanial Khan. LBCEPred: a machine learning model to predict linear B-cell epitopes
0 -- 0Martin Bartas, Adriana Volná, Christopher A. Beaudoin, Ebbe Toftgaard Poulsen, Jirí Cerven, Václav Brázda, Vladimír Spunda, Tom L. Blundell, Petr Pecinka. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA
0 -- 0Axel Kowald, Israel Barrantes, Steffen Möller, Daniel Palmer, Hugo Murua Escobar, Anne Schwerk, Georg Fuellen. Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives
0 -- 0Anqi Lin, Chang Qi, Ting Wei, Mengyao Li, Quan Cheng, Zaoqu Liu, Peng Luo, Jian Zhang. CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer
0 -- 0Xiaoyi Guo, Yizhang Jiang, Quan Zou. Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides
0 -- 0Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen 0004, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng. Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
0 -- 0Hongchao Ji, Xue Lu, Zhenxiang Zheng, Siyuan Sun, Chris Soon Heng Tan. ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data
0 -- 0Yuanyuan Ma, Zexuan Sun, Pengcheng Zeng, Wenyu Zhang, Zhixiang Lin. JSNMF enables effective and accurate integrative analysis of single-cell multiomics data
0 -- 0Xiaocong Yang, Yang Liu 0236, Jianhong Gan, Zhixiong Xiao, Yang Cao. FitDock: protein-ligand docking by template fitting
0 -- 0Xiangwen Wang, Yonggang Lu, Xianghong Lin. Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures
0 -- 0Xingyu Li, Xue Lin, Xueyin Mei, Pin Chen, Anna Liu, Weicheng Liang, Shan Chang, Jian Li. HLA3D: an integrated structure-based computational toolkit for immunotherapy
0 -- 0Haiyue Wang, Xiaoke Ma. Learning deep features and topological structure of cells for clustering of scRNA-sequencing data
0 -- 0Han-Jing Jiang, Yabing Huang, Qianpeng Li. Spectral clustering of single cells using Siamese nerual network combined with improved affinity matrix
0 -- 0Xuanjin Cheng, Yongxing Liu, Jiahe Wang, Yujie Chen, Andrew Gordon Robertson, Xuekui Zhang, Steven J. M. Jones, Stefan Taubert. cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines
0 -- 0César R. García-Jacas, Sergio A. Pinacho-Castellanos, Luis A. García-González, Carlos A. Brizuela. Do deep learning models make a difference in the identification of antimicrobial peptides?
0 -- 0Xiaoyu Guan, Yuqin Wang, Wei Shao 0005, Zhongnian Li, Shuo Huang, Daoqiang Zhang. S2Snet: deep learning for low molecular weight RNA identification with nanopore
0 -- 0Ping Xuan, XiangFeng Meng, Ling Gao, Tiangang Zhang, Toshiya Nakaguchi. Heterogeneous multi-scale neighbor topologies enhanced drug-disease association prediction
0 -- 0Zhihua Du, Yang-Han Wu, Yu-An Huang, Jie Chen, Gui-Qing Pan, Lun Hu, Zhu-Hong You, Jian-qiang Li. GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions
0 -- 0Ping Xuan, Meng Wang, Yong Liu, Dong Wang, Tiangang Zhang, Toshiya Nakaguchi. Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction
0 -- 0Fei Wu, Yao-Zhong Liu, Binhua Ling. MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
0 -- 0Yaowen Gu, Si Zheng, Zidu Xu, Qijin Yin, Liang Li, Jiao Li. An efficient curriculum learning-based strategy for molecular graph learning
0 -- 0Naveen Duhan, Jeanette M. Norton, Rakesh Kaundal. deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning
0 -- 0Zhonghua Jiang, Yongmei Lu, Zhuochong Liu, Wei Wu, Xinyi Xu, András Dinnyés, Zhonghua Yu, Li Chen, Qun Sun. Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants
0 -- 0Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao, Tingjun Hou, Huiyong Sun. Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations
0 -- 0Paul R. Buckley, Chloe H. Lee, Ruichong Ma, Isaac Woodhouse, Jeongmin Woo, Vasily Tsvetkov, Dmitrii S. Shcherbinin, Agne Antanaviciute, Mikhail Shughay, Margarida Rei, Alison Simmons, Hashem Koohy. Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens
0 -- 0Yifan Shang, Xiucai Ye, Yasunori Futamura, Liang Yu, Tetsuya Sakurai. Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving
0 -- 0Mengya Liu, Zhan-Li Sun, Zhigang Zeng, Kin-Man Lam 0001. MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block
0 -- 0Liang Yu, Yujia Zheng, Bingyi Ju, Chunyan Ao, Lin Gao 0006. Research progress of miRNA-disease association prediction and comparison of related algorithms
0 -- 0Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives
0 -- 0Fuxu Wang, Haoyan Wang, Lizhuang Wang, Haoyu Lu, Shizheng Qiu, Tianyi Zang, Xinjun Zhang, Yang Hu 0008. MHCRoBERTa: pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences
0 -- 0Anna Dal Molin, Enrico Gaffo, Valeria Difilippo, Alessia Buratin, Caterina Tretti Parenzan, Silvia Bresolin, Stefania Bortoluzzi. Correction to: CRAFT a bioinformatics software for custom prediction of circular RNA functions
0 -- 0Xia-an Bi, Lou Li, Zizheng Wang, Yu Wang, Xun Luo, Luyun Xu. IHGC-GAN: influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data
0 -- 0Jing Wang, Qinglong Zhang, Junshan Han, Yanpeng Zhao, Caiyun Zhao, Bowei Yan, Chong Dai, Lianlian Wu, Yuqi Wen, Yixin Zhang, Dongjin Leng, Zhongming Wang, Xiaoxi Yang, Song He, Xiaochen Bo. Computational methods, databases and tools for synthetic lethality prediction
0 -- 0Le Huang, Yuchen Yang, Gang Li 0034, Minzhi Jiang, Jia Wen, Armen Abnousi, Jonathan D. Rosen, Ming Hu 0001, Yun Li. A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data
0 -- 0Wenjing Ma, Sumeet Sharma, Peng Jin, Shannon L. Gourley, Zhaohui S. Qin. LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data
0 -- 0Matteo Tiberti, Thilde Terkelsen, Kristine Degn, Ludovica Beltrame, Tycho Canter Cremers, Isabelle da Piedade, Miriam Di Marco, Emiliano Maiani, Elena Papaleo. in silico saturation mutagenesis of protein structures and structural ensembles
0 -- 0Mingsheng Tang, Tong Wang, Xuefen Zhang. A review of SNP heritability estimation methods
0 -- 0Ping Xuan, Zhe Gong, Hui Cui 0002, Bochong Li, Tiangang Zhang. Fully connected autoencoder and convolutional neural network with attention-based method for inferring disease-related lncRNAs
0 -- 0Likun Jiang, Changzhi Jiang, Xinyu Yu, Rao Fu, Shuting Jin, Xiangrong Liu. DeepTTA: a transformer-based model for predicting cancer drug response
0 -- 0Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández. On the influence of several factors on pathway enrichment analysis
0 -- 0Dafei Xie, Song He, Lu Han, Lianlian Wu, Hai Huang, Huan Tao, Pingkun Zhou, Xunlong Shi, Hui Bai, Xiaochen Bo. Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs
0 -- 0Ettayapuram Ramaprasad Azhagiya Singam, Martyn T. Smith, David McCoy, Alan E. Hubbard, Michele A. La Merrill, Kathleen A. Durkin. Predicting the binding of small molecules to nuclear receptors using machine learning
0 -- 0Zuguang Gu, Daniel Hübschmann. Improve consensus partitioning via a hierarchical procedure
0 -- 0Dietmar Fernández-Orth, Manuel Rueda, Babita Singh, Mauricio Moldes, Aina Jene, Marta Ferri, Claudia Vasallo, Lauren A. Fromont, Arcadi Navarro, Jordi Rambla. A quality control portal for sequencing data deposited at the European genome-phenome archive
0 -- 0Liangzhen Zheng, Jintao Meng, Kai Jiang, Haidong Lan, Zechen Wang, Mingzhi Lin, Weifeng Li, Hongwei Guo, Yanjie Wei, Yuguang Mu. Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term
0 -- 0Yu Liu. scDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data
0 -- 0Yi-Yang Feng, Hui Yu, Yue-Hua Feng, Jian-Yu Shi. Directed graph attention networks for predicting asymmetric drug-drug interactions
0 -- 0Fei Liu 0006, Monika Heiner, David R. Gilbert. Hybrid modelling of biological systems: current progress and future prospects
0 -- 0Mengya Chai, YaJuan Guo, Liu Yang, Jianhui Li, Shuo Liu, Lei Chen, Yuelei Shen, Yi Yang, Youchun Wang, Lida Xu, Changyuan Yu. A high-throughput single cell-based antibody discovery approach against the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing antibodies targeting the highly conserved S2 domain
0 -- 0Yueming Yin, Haifeng Hu 0004, Zhen Yang 0001, Feihu Jiang, Yihe Huang, Jiansheng Wu. AFSE: towards improving model generalization of deep graph learning of ligand bioactivities targeting GPCR proteins
0 -- 0Liheng Luo, Michael Gribskov, Sufang Wang. Bibliometric review of ATAC-Seq and its application in gene expression
0 -- 0Yachen Liu, Yalan Lin, Wenxian Yang, Yuxiang Lin, Yujuan Wu, Zheyang Zhang, Nuoqi Lin, Xianlong Wang, Mengsha Tong, Rongshan Yu. Application of individualized differential expression analysis in human cancer proteome
0 -- 0Jing Liu, Xinghua Tang, Shuanglong Cui, Xiao Guan. Predicting the function of rice proteins through Multi-instance Multi-label Learning based on multiple features fusion
0 -- 0Mariella Bonomo, Raffaele Giancarlo, Daniele Greco, Simona E. Rombo. Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis
0 -- 0Talal Ahmed, Mark A. Carty, Stephane Wenric, Jonathan R. Dry, Ameen A. Salahudeen, Aly A. Khan, Eric Lefkofsky, Martin C. Stumpe, Raphael Pelossof. Privacy preserving validation for multiomic prediction models
0 -- 0Rakesh Kaundal, Cristian D. Loaiza, Naveen Duhan, Nicholas Flann. deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions
0 -- 0Yulian Ding, Xiujuan Lei, Bo Liao, Fang-Xiang Wu. MLRDFM: a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations
0 -- 0Muhammad Toseef, Xiangtao Li, Ka Chun Wong. Reducing healthcare disparities using multiple multiethnic data distributions with fine-tuning of transfer learning
0 -- 0Han-Yuan Zhang, Lei Wang, Zhu-Hong You, Lun Hu, Bo-Wei Zhao, Zheng-Wei Li, Yang-Ming Li. iGRLCDA: identifying circRNA-disease association based on graph representation learning
0 -- 0Yongqing Zhang, Qiang Zhang, Jiliu Zhou, Quan Zou 0001. A survey on the algorithm and development of multiple sequence alignment
0 -- 0Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Chang-Yu Hsieh, Dongsheng Cao 0001, Tingjun Hou. Knowledge-based BERT: a method to extract molecular features like computational chemists
0 -- 0Ying Yang, Sha Tian, Yushan Qiu, Pu Zhao, Quan Zou 0001. MDICC: novel method for multi-omics data integration and cancer subtype identification
0 -- 0Anna Torkamannia, Yadollah Omidi, Reza Ferdousi. A review of machine learning approaches for drug synergy prediction in cancer
0 -- 0Wenjian Xu, Haochen He, Zhengguang Guo, Wei Li. Evaluation of machine learning models on protein level inference from prioritized RNA features
0 -- 0Yanqing Yang, Deshan Zhou, XinBen Zhang, Yulong Shi, Jiaxin Han, Liping Zhou, Leyun Wu, Minfei Ma, Jintian Li, Shaoliang Peng, Zhijian Xu, Weiliang Zhu. D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19
0 -- 0Shengpeng Yu, Hong Wang, Tianyu Liu, Cheng Liang, Jiawei Luo 0001. A knowledge-driven network for fine-grained relationship detection between miRNA and disease
0 -- 0Yidi Deng, Jarny Choi, Kim-Anh Lê Cao. Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references
0 -- 0Jing Li, Ya-Nan Wu, Sen Zhang, Xiao-Ping Kang, Tao Jiang. Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants
0 -- 0Renan Andrades, Mariana Recamonde Mendoza. Machine learning methods for prediction of cancer driver genes: a survey paper
0 -- 0Xiaoman Wang, Lifei Ma, Xiaoya Pei, Heping Wang, Xiaoqiang Tang, Jian-Fei Pei, Yang-Nan Ding, Siyao Qu, Zi-Yu Wei, Hui-Yu Wang, Xiaoyue Wang, Gong-Hong Wei, De-Pei Liu, Houzao Chen. Comprehensive assessment of cellular senescence in the tumor microenvironment
0 -- 0Xiao-Rui Su, Lun Hu, Zhuhong You, Pengwei Hu, Bo-Wei Zhao. Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions
0 -- 0Keilash Chirom, Md. Zubbair Malik, Irengbam Rocky Mangangcha, Pallavi Somvanshi, R. K. Brojen Singh. Network medicine in ovarian cancer: topological properties to drug discovery
0 -- 0Mingsheng Tang, Tingting Hou, Xiaoran Tong, Xiaoxi Shen, Xuefen Zhang, Tong Wang, Qing Lu. Fast heritability estimation based on MINQUE and batch training
0 -- 0Liwen Xu, Shiwei Zhu, Yujia Lan, Min Yan, Zedong Jiang, Jiali Zhu, Gaoming Liao, Yanyan Ping, Jinyuan Xu, Bo Pang, Yunpeng Zhang, Yun Xiao 0001, Xia Li 0004. Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment
0 -- 0Miao-Hsia Lin, Pei-Shan Wu, Tzu-Hsuan Wong, I-Ying Lin, Johnathan Lin, Jürgen Cox, Sung-Huan Yu. Benchmarking differential expression, imputation and quantification methods for proteomics data
0 -- 0Amelia Villegas-Morcillo, Angel M. Gomez, Victoria E. Sánchez. An analysis of protein language model embeddings for fold prediction
0 -- 0Yusong Liu, Tongxin Wang, Ben Duggan, Michael F. Sharpnack, Kun Huang 0001, Jie Zhang 0010, Xiufen Ye, Travis S. Johnson. SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression
0 -- 0Haohuai He, Guanxing Chen, Calvin Yu-Chian Chen. 3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction

Volume 23, Issue 2

0 -- 0Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia C. F. Prosperi. Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing
0 -- 0Yue Su, Keyu Du, Jun Wang, Jin-Mao Wei, Jian Liu. Multi-variable AUC for sifting complementary features and its biomedical application
0 -- 0Yuansong Zeng, Zhuoyi Wei, Zixiang Pan, Yutong Lu, Yuedong Yang. A robust and scalable graph neural network for accurate single-cell classification
0 -- 0Yaowen Chen, Zhen He, Yahui Men, Guohua Dong, Shuofeng Hu, Xiaomin Ying. MetaLogo: a heterogeneity-aware sequence logo generator and aligner
0 -- 0Pedro Sánchez-Sánchez, Francisco-José Santonja, Alfonso Benítez-Páez. Assessment of human microbiota stability across longitudinal samples using iteratively growing-partitioned clustering
0 -- 0Chenwei Wang, Xiaodan Tan, Dachao Tang, Yujie Gou, Cheng Han, Wanshan Ning, Shaofeng Lin, Weizhi Zhang, Miaomiao Chen, Di Peng, Yu Xue 0001. GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites
0 -- 0Vivek Bhakta Mathema, Kassaporn Duangkumpha, Kwanjeera Wanichthanarak, Narumol Jariyasopit, Esha Dhakal, Nuankanya Sathirapongsasuti, Chagriya Kitiyakara, Yongyut Sirivatanauksorn, Sakda Khoomrung. CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics
0 -- 0Xiaobo Sun, Xiaochu Lin, Ziyi Li, Hao Wu 0003. A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq
0 -- 0Snehalika Lall, Abhik Ghosh, Sumanta Ray, Sanghamitra Bandyopadhyay. sc-REnF: An entropy guided robust feature selection for single-cell RNA-seq data
0 -- 0Haizhen Zheng. Letter regarding article named 'Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy'
0 -- 0Chen Shen, Huiyu Li, Miao Li, Yu Niu, Jing Liu, Li Zhu, Hongsheng Gui, Wei Han, Huiying Wang, Wenpei Zhang, Xiaochen Wang, Xiao Luo, Yu Sun, Jiangwei Yan, Fanglin Guan. DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA-miRNA-mRNA regulatory axes
0 -- 0Elham Khalili, Shahin Ramazi, Faezeh Ghanati, Samaneh Kouchaki. Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network
0 -- 0Anna Dal Molin, Enrico Gaffo, Valeria Difilippo, Alessia Buratin, Caterina Tretti Parenzan, Silvia Bresolin, Stefania Bortoluzzi. CRAFT: a bioinformatics software for custom prediction of circular RNA functions
0 -- 0Yong Lu, Gang Xue, Ningbo Zheng, Kun Han, Wenzhong Yang, Rui-Sheng Wang, Ling-Yun Wu, Lance D. Miller, Timothy Pardee, Pierre L. Triozzi, Hui-Wen Lo, Kounosuke Watabe, Stephen T. C. Wong, Boris C. Pasche, Wei Zhang, Guangxu Jin. hDirect-MAP: projection-free single-cell modeling of response to checkpoint immunotherapy
0 -- 0Biao Zhang, Dong Liu, Yang Zhang, Hong-bin Shen, Gui-jun Zhang. Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning
0 -- 0Sazan Mahbub, Md. Shamsuzzoha Bayzid. EGRET: edge aggregated graph attention networks and transfer learning improve protein-protein interaction site prediction
0 -- 0Zhi Ruan, Shengmei Zou, Zeyu Wang, Luhan Zhang, Hangfei Chen, Yuye Wu, Huiqiong Jia, Mohamed S. Draz, Ye Feng. Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids
0 -- 0Liang Wang, Xavier Didelot, Yuhai Bi, George F. Gao. SARS-CoV-2 transmissibility compared between variants of concern and vaccination status
0 -- 0Mahwish Shahid, Maham Ilyas, Waqar Hussain, Yaser Daanial Khan. ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network
0 -- 0Tangbo Zhong, ZhengWei Li, Zhu-Hong You, Ru Nie, Huan Zhao. Predicting miRNA-disease associations based on graph random propagation network and attention network
0 -- 0Xiaoyu Wang, Fuyi Li, Jing Xu, Jia Rong, Geoffrey I. Webb, ZongYuan Ge, Jian Li, Jiangning Song. ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning
0 -- 0John D. O'Connor, Ian M. Overton, Stephen J. McMahon. RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity
0 -- 0Muhalb M. Alsaffar, Mohammad Hasan, Gavin P. McStay, Mohamed Sedky. Digital DNA lifecycle security and privacy: an overview
0 -- 0Ran Wang, Xubin Zheng, Jun Wang, Shibiao Wan, Fangda Song, Man Hon Wong 0001, Kwong-Sak Leung, Lixin Cheng. Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia
0 -- 0Shih-Kai Chu, Shilin Zhao, Yu Shyr, Qi Liu. Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data
0 -- 0Xiaopeng Jin, Xiaoling Luo, Bin Liu 0014. PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships
0 -- 0Jing Wang, Junfeng Xia, Dayu Tan, Rongxin Lin, Yansen Su, Chun-Hou Zheng 0001. scHFC: a hybrid fuzzy clustering method for single-cell RNA-seq data optimized by natural computation
0 -- 0Rick Gelhausen, Teresa Müller, Sarah L. Svensson, Omer S. Alkhnbashi, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen. RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
0 -- 0Hui Tang, Xiangtian Yu, Rui Liu 0009, Tao Zeng 0003. Vec2image: an explainable artificial intelligence model for the feature representation and classification of high-dimensional biological data by vector-to-image conversion
0 -- 0Xiao Yuan, Jing Wang, Bing Dai, Yanfang Sun, Keke Zhang, Fangfang Chen, Qian Peng, Yixuan Huang, Xinlei Zhang, Junru Chen, Xilin Xu, Jun Chuan, Wenbo Mu, Huiyuan Li, Ping Fang, Qiang Gong, Peng Zhang 0050. Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases
0 -- 0Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang. AlphaFold2-aware protein-DNA binding site prediction using graph transformer
0 -- 0Chengming Zhang, Yabin Chen, Tao Zeng 0003, Chuanchao Zhang, Luonan Chen. Deep latent space fusion for adaptive representation of heterogeneous multi-omics data
0 -- 0Alejandro A. Edera, Diego H. Milone, Georgina Stegmayer. Anc2vec: embedding gene ontology terms by preserving ancestors relationships
0 -- 0Benedict Anchang, Raul Mendez-Giraldez, Xiaojiang Xu, Trevor K. Archer, Qing Chen, Guang Hu, Sylvia K. Plevritis, Alison Anne Motsinger-Reif, Jian-Liang Li. Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures
0 -- 0Mingzhe Xie, Ludong Yang, Gennong Chen, Yan Wang, Zhi Xie, Hongwei Wang 0003. RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data
0 -- 0Yuning Yang, Zilong Hou, Yansong Wang, Hongli Ma, Pingping Sun, Zhiqiang Ma, Ka Chun Wong, Xiangtao Li. HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network
0 -- 0Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Chen Tang, Xiaohan Chen, Yunjie Li, Qi Liu, Qin Liu. PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein-protein interaction network
0 -- 0Minerva Fatimae Ventolero, Saidi Wang, Haiyan Hu, Xiaoman Li. Computational analyses of bacterial strains from shotgun reads
0 -- 0Hao Wu, Pengyu Zhang, Zhaoheng Ai, Leyi Wei, Hongming Zhang, Fan Yang, LiZhen Cui. StackTADB: a stacking-based ensemble learning model for predicting the boundaries of topologically associating domains (TADs) accurately in fruit flies
0 -- 0Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli. Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
0 -- 0Rui Cheng, Zhaochun Xu, Meng Luo, Pingping Wang, Huimin Cao, Xiyun Jin, Wenyang Zhou, Lixing Xiao, Qinghua Jiang. Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development
0 -- 0Chenjin Ma, MengYun Wu, Shuangge Ma. Analysis of cancer omics data: a selective review of statistical techniques
0 -- 0Josephine Yates, Valentina Boeva. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis
0 -- 0Yaning Yang, Xiaoqi Wang, Deshan Zhou, Dong-Qing Wei, Shaoliang Peng. SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants
0 -- 0Qisheng Pan, Thanh Binh Nguyen, David B. Ascher, Douglas E. V. Pires. Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures
0 -- 0Yuguo Zha, Kang Ning 0001. Ontology-aware neural network: a general framework for pattern mining from microbiome data
0 -- 0Alexios Chatzigoulas, Zoe Cournia. Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning
0 -- 0Fengcheng Li, Ying Zhou, Ying Zhang, Jiayi Yin, Yunqing Qiu, Jianqing Gao, Feng Zhu 0004. POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability
0 -- 0Xubo Tang, Jiayu Shang, Yanni Sun. RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data
0 -- 0Xianyu Xu, Ling Yue, Bingchun Li, Ying Liu, Yuan Wang, Wenjuan Zhang, Lin Wang. DSGAT: predicting frequencies of drug side effects by graph attention networks
0 -- 0Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte. de novo transcriptome assembly and annotation
0 -- 0Hongru Shen, Xilin Shen, Mengyao Feng, Dan Wu, Chao Zhang, Yichen Yang 0004, Meng Yang, Jiani Hu, Jilei Liu, Wei Wang, Yang Li, Qiang Zhang, Jilong Yang, Kexin Chen, Xiangchun Li. A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings
0 -- 0Douglas E. V. Pires, Keith A. Stubbs, Joshua S. Mylne, David B. Ascher. cropCSM: designing safe and potent herbicides with graph-based signatures
0 -- 0Dejun Jiang, Huiyong Sun, Jike Wang, Chang-Yu Hsieh, Yuquan Li, Zhenxing Wu, Dong-Sheng Cao 0001, Jian Wu, Tingjun Hou. Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning
0 -- 0Tingting Yang, Mingyu Gan, Qingyun Liu, Wenying Liang, Qiqin Tang, Geyang Luo, Tianyu Zuo, Yongchao Guo, Chuangyue Hong, Qibing Li, Weiguo Tan, Qian Gao. Mycobacterium tuberculosis drug resistance and transmission
0 -- 0Liang Yu, Yujia Zheng, Lin Gao 0006. MiRNA-disease association prediction based on meta-paths
0 -- 0Ran Su, Yixuan Huang, De-gan Zhang, Guobao Xiao, Leyi Wei. SRDFM: Siamese Response Deep Factorization Machine to improve anti-cancer drug recommendation
0 -- 0Ge Wang, Min-Qi Xue, Hong-bin Shen, Ying-Ying Xu. Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks
0 -- 0Yin Shen, Quan Zhong, Tian Liu, Zi Wen, Wei Shen, Li Li 0057. CharID: a two-step model for universal prediction of interactions between chromatin accessible regions
0 -- 0Yunda Si, Yi Zhang, Chengfei Yan. A reproducibility analysis-based statistical framework for residue-residue evolutionary coupling detection
0 -- 0Zhuohang Yu, Zengrui Wu, Weihua Li 0005, Guixia Liu, Yun Tang. ADENet: a novel network-based inference method for prediction of drug adverse events
0 -- 0Guiying Wu, Xiangyu Li, Wenbo Guo 0010, Zheng Wei, Tao Hu 0001, Yiran Shan, Jin Gu. JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding
0 -- 0Yajie Meng, Changcheng Lu, Min Jin, Junlin Xu, Xiangxiang Zeng, Jialiang Yang. A weighted bilinear neural collaborative filtering approach for drug repositioning
0 -- 0Shanshan Cheng, Jingjing Lyu, Xian Shi, Kai Wang, Zengmiao Wang, Minghua Deng, Baoluo Sun, Chaolong Wang. Rare variant association tests for ancestry-matched case-control data based on conditional logistic regression
0 -- 0Kaimiao Hu, Hui Cui, Tiangang Zhang, Chang Sun, Ping Xuan. ALDPI: adaptively learning importance of multi-scale topologies and multi-modality similarities for drug-protein interaction prediction
0 -- 0Guodong Li, Ping Zhang, Weicheng Sun, Chengjuan Ren, Lei Wang. Bridging-BPs: a novel approach to predict potential drug-target interactions based on a bridging heterogeneous graph and BPs2vec
0 -- 0Gil Ben-Cohen, Flora Doffe, Michal Devir, Bernard Leroy, Thierry Soussi, Shai Rosenberg. TP53
0 -- 0Lu Jiang 0007, Jiahao Sun, Yue Wang, Qiao Ning, Na Luo, Minghao Yin. Identifying drug-target interactions via heterogeneous graph attention networks combined with cross-modal similarities
0 -- 0Charles E. Mordaunt, Julia S. Mouat, Rebecca J. Schmidt, Janine M. Lasalle. Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease
0 -- 0Jinsong Shao, Qineng Gong, Zeyu Yin, Wenjie Pan, Sanjeevi Pandiyan, Li Wang. S2DV: converting SMILES to a drug vector for predicting the activity of anti-HBV small molecules
0 -- 0Zutan Li, Jingya Fang, Shining Wang, Liangyun Zhang, Yuanyuan Chen, Cong Pian. Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture
0 -- 0Xiaohui Shi, Huajing Teng, Leisheng Shi, Wenjian Bi, Wenqing Wei, Fengbiao Mao, Zhongsheng Sun. Comprehensive evaluation of computational methods for predicting cancer driver genes
0 -- 0Min Dai, Xiaobing Pei, Xiu-Jie Wang. Accurate and fast cell marker gene identification with COSG
0 -- 0Rovshan G. Sadygov. Protein turnover models for LC-MS data of heavy water metabolic labeling
0 -- 0Melivoia Rapti, Yassine Zouaghi, Jenny Meylan, Emmanuelle Ranza, Stylianos E. Antonarakis, Federico Andrea Santoni. CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications
0 -- 0Hyunsu An, Minho Eun, Jawoon Yi, Jihwan Park. CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins
0 -- 0Ya-Hui Zhou, Guo Li, Yuan-Ming Zhang. A compressed variance component mixed model framework for detecting small and linked QTL-by-environment interactions
0 -- 0Sören Richard Stahlschmidt, Benjamin Ulfenborg, Jane Synnergren. Multimodal deep learning for biomedical data fusion: a review
0 -- 0Dalang Yu, Xiao Yang, Bixia Tang, Yi-Hsuan Pan, Jianing Yang, Guangya Duan, Junwei Zhu, Zi-Qian Hao, Hailong Mu, Long Dai, Wangjie Hu, Mochen Zhang, Ying Cui, Tong Jin, Cui-Ping Li, Lina Ma, Xiao Su, Guoqing Zhang, Wenming Zhao, HaiPeng Li. Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2
0 -- 0Bosheng Song, Xiaoyan Luo, Xiaoli Luo, Yuansheng Liu, Zhangming Niu, Xiangxiang Zeng. Learning spatial structures of proteins improves protein-protein interaction prediction
0 -- 0Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li 0021, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou 0001, Lachlan J. M. Coin, Jiangning Song. Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction
0 -- 0Ting Wang, Jiahao Qiao, Shuo Zhang, Yongyue Wei, Ping Zeng. Simultaneous test and estimation of total genetic effect in eQTL integrative analysis through mixed models
0 -- 0Wenming Wu, Wensheng Zhang, Xiaoke Ma. Network-based integrative analysis of single-cell transcriptomic and epigenomic data for cell types
0 -- 0Hongda Zhang, Hui Cui, Tiangang Zhang, Yangkun Cao, Ping Xuan. Learning multi-scale heterogenous network topologies and various pairwise attributes for drug-disease association prediction
0 -- 0Yanglan Gan, Xingyu Huang, Guobing Zou, Shuigeng Zhou, Jihong Guan. Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network
0 -- 0Shiva Dahal-Koirala, Gabriel Balaban, Ralf Stefan Neumann, Lonneke Scheffer, Knut Erik Aslaksen Lundin, Victor Greiff, Ludvig Magne Sollid, Shuo-Wang Qiao, Geir Kjetil Sandve. TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
0 -- 0Mengyuan Zhao, Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo. A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data
0 -- 0Siyu Han, Jialing Huang, Francesco Foppiano, Cornelia Prehn, Jerzy Adamski, Karsten Suhre, Ying Li, Giuseppe Matullo, Freimut Schliess, Christian Gieger, Annette Peters, Rui Wang-Sattler. TIGER: technical variation elimination for metabolomics data using ensemble learning architecture
0 -- 0Yongsheng Li, Yunpeng Zhang, Tao Pan, Ping Zhou, Weiwei Zhou, Yueying Gao, Shaojiang Zheng, Juan Xu. Shedding light on the hidden human proteome expands immunopeptidome in cancer
0 -- 0Laura Balagué-Dobón, Alejandro Cáceres, Juan R. González. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure
0 -- 0Chun-Chun Wang, Tian-Hao Li, Li Huang, Xing Chen 0001. Prediction of potential miRNA-disease associations based on stacked autoencoder
0 -- 0Ramachandran Chelliah, Eric Banan-Mwinedaliri, Imran Khan, Shuai Wei, Fazle Elahi, Su-Jung Yeon, Vijayalakshmi Selvakumar, Fred Kwame Ofosu, Momna Rubab, Hum Hun Ju, Harikrishna Reddy Rallabandi, Inamul Hasan Madar, Ghazala Sultan, Deog Hwan Oh. A review on the application of bioinformatics tools in food microbiome studies
0 -- 0Ruolan Chen, Feng Xia 0001, Bing Hu, Shuting Jin, Xiangrong Liu. Drug-target interactions prediction via deep collaborative filtering with multiembeddings
0 -- 0Alejandro Rubio, Juan Jiménez, Antonio J. Pérez-Pulido. Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes
0 -- 0Yanlun Tu, Houchao Lei, Hong-bin Shen, Yang Yang 0030. SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images
0 -- 0Shuang Wang, Tao Song, Shugang Zhang, Mingjian Jiang, Zhiqiang Wei 0002, Zhen Li 0024. Molecular substructure tree generative model for de novo drug design
0 -- 0Sho Tsukiyama, Md. Mehedi Hasan 0002, Hong-Wen Deng, Hiroyuki Kurata. BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches
0 -- 0Ken Chen, Huiying Zhao, Yuedong Yang. Capturing large genomic contexts for accurately predicting enhancer-promoter interactions
0 -- 0Xiao-Chen Zhang, Jia-Cai Yi, Guo-Ping Yang, Chengkun Wu, Tingjun Hou, Dong-Sheng Cao 0001. ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images
0 -- 0Ju Xiang, Jiashuai Zhang, Yichao Zhao, Fang-Xiang Wu, Min Li 0007. Biomedical data, computational methods and tools for evaluating disease-disease associations
0 -- 0Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu 0002, Luonan Chen. Transcriptome analysis method based on differential distribution evaluation
0 -- 0Zhaohui Zhan, Lusheng Wang. Proteoform identification based on top-down tandem mass spectra with peak error corrections
0 -- 0Sheng Yang, Xiang Zhou. PGS-server: accuracy, robustness and transferability of polygenic score methods for biobank scale studies
0 -- 0Xiaotai Huang, Songwei Jia, Lin Gao 0006, Jing Wu. Reconstruction of human protein-coding gene functional association network based on machine learning
0 -- 0Xiaopeng Jin, Xiaoling Luo, Bin Liu 0014. Correction to: PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships
0 -- 0Junjie Wee, Kelin Xia. Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction
0 -- 0Lei Li, Siriruk Changrob, Yanbin Fu, Olivia Stovicek, Jenna J. Guthmiller, Joshua J. C. McGrath, Haley L. Dugan, Christopher T. Stamper, Nai-Ying Zheng, Min Huang, Patrick C. Wilson. Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens
0 -- 0Jiashuai Zhang, Huiting Xiao, Kai Song, Keru Li, Hengrui Yuan, Rongqiang Yuan, Jia Yang, Yuting Zhao, Zhiqiang Chang, Wenyuan Zhao. IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer
0 -- 0Vishakha Singh, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar 0003, Sonal Saxena. Accelerating the discovery of antifungal peptides using deep temporal convolutional networks
0 -- 0Yijie Ding, Jijun Tang, Fei Guo, Quan Zou 0001. Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization
0 -- 0Taeho Jo 0002, Kwangsik Nho, Paula Bice, Andrew J. Saykin. Deep learning-based identification of genetic variants: application to Alzheimer's disease classification
0 -- 0Nan Sheng, Lan Huang 0002, Yan Wang, Jing Zhao, Ping Xuan, Ling Gao, Yangkun Cao. Multi-channel graph attention autoencoders for disease-related lncRNAs prediction
0 -- 0Mingmin Xu, Yuanyuan Chen, Zhihui Xu, Liangyun Zhang, Hangjin Jiang, Cong Pian. MiRLoc: predicting miRNA subcellular localization by incorporating miRNA-mRNA interactions and mRNA subcellular localization
0 -- 0Weiping Lin, Lianlian Wu, Yixin Zhang, Yuqi Wen, Bowei Yan, Chong Dai, Kun-Hong Liu 0001, Song He, Xiaochen Bo. An enhanced cascade-based deep forest model for drug combination prediction
0 -- 0Yanqiang Han, Zhilong Wang, An Chen, Imran Ali, Junfei Cai, Simin Ye, Jin-Jin Li. An inductive transfer learning force field (ITLFF) protocol builds protein force fields in seconds

Volume 23, Issue 1

0 -- 0Hukam Chand Rawal, Shakir Ali, Tapan Kumar Mondal. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms
0 -- 0Chun-Chun Wang, Chi-Chi Zhu, Xing Chen 0001. Ensemble of kernel ridge regression-based small molecule-miRNA association prediction in human disease
0 -- 0Menglu Li, Wen Zhang. PHIAF: prediction of phage-host interactions with GAN-based data augmentation and sequence-based feature fusion
0 -- 0Kamil Kaminski, Jan Ludwiczak, Maciej Jasinski, Adriana Bukala, Rafal Madaj, Krzysztof Szczepaniak, Stanislaw Dunin-Horkawicz. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins
0 -- 0Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin 0001, Li Liu. A deep learning model to identify gene expression level using cobinding transcription factor signals
0 -- 0Sander N. Goossens, Tim H. Heupink, Elise De Vos, Anzaan Dippenaar, Margaretha De Vos, Rob Warren, Annelies Van Rie. Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data
0 -- 0Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-jun Yu. MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network
0 -- 0Vishakha Singh, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar 0003, Sonal Saxena. StaBle-ABPpred: a stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides
0 -- 0Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Yu-Yen Ou. mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences
0 -- 0Siqi Bao, Ke Li, Congcong Yan, Zicheng Zhang, Jia Qu, Meng Zhou 0003. Deep learning-based advances and applications for single-cell RNA-sequencing data analysis
0 -- 0Francesco Napolitano, Xiaopeng Xu, Xin Gao 0001. Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies
0 -- 0María Virginia Sabando, Ignacio Ponzoni, Evangelos E. Milios, Axel J. Soto. Using molecular embeddings in QSAR modeling: does it make a difference?
0 -- 0Haoxiang Qin, Qidong Shen, Hongyi Zhao, Guozhen Qi, Lei Gao. Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins
0 -- 0Rong Tang, Zijian Wu, Zeyin Rong, Jin Xu, Wei Wang, Bo Zhang, Xianjun Yu, Si Shi. Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma
0 -- 0Yongxian Fan, Meijun Chen, Xiaoyong Pan. GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field
0 -- 0Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma 0003, Yan Wang 0028. Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data
0 -- 0Yaqi Wang, Guoqin Mai, Min Zou, Haoyu Long, Yao-Qing Chen, Litao Sun, Dechao Tian, Yang Zhao, Guozhi Jiang, Zicheng Cao, Xiangjun Du. Heavy chain sequence-based classifier for the specificity of human antibodies
0 -- 0Xiao-Rui Su, Lun Hu, Zhuhong You, Pengwei Hu, Lei Wang 0121, Bo-Wei Zhao. A deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2
0 -- 0Neng Huang, Fan Nie, Peng Ni, Xin Gao 0001, Feng Luo, Jianxin Wang 0001. BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
0 -- 0Robson Bonidia, Douglas Silva Domingues, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho. MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors
0 -- 0Bruna Moreira da Silva, Yoochan Myung, David B. Ascher, Douglas E. V. Pires. epitope3D: a machine learning method for conformational B-cell epitope prediction
0 -- 0Bingxiang Xu, Xiaoli Li, Xiaomeng Gao, Yan Jia, Jing Liu, Feifei Li, Zhihua Zhang. DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data
0 -- 0Mario Flores, Zhentao Liu, Tinghe Zhang, Md Musaddaqui Hasib, Yu-Chiao Chiu, Zhenqing Ye, Karla Paniagua, Sumin Jo, Jianqiu Zhang, Shou-Jiang Gao, Yu-Fang Jin, Yidong Chen, Yufei Huang. Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis
0 -- 0Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen 0004, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng. Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
0 -- 0Yang Li, Guanyu Qiao, Keqi Wang, Guohua Wang. Drug-target interaction predication via multi-channel graph neural networks
0 -- 0Qinhuan Luo, Yongzhen Yu, Xun Lan. SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging
0 -- 0Qiaoming Liu, Jun Wan 0002, Guohua Wang. A survey on computational methods in discovering protein inhibitors of SARS-CoV-2
0 -- 0Fuhao Zhang, Bi Zhao, Wenbo Shi, Min Li 0007, Lukasz A. Kurgan. DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning
0 -- 0Hui-Sheng Li, Le Ou-Yang, Yuan Zhu, Hong Yan 0001, Xiao-fei Zhang. scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning
0 -- 0Kengo Sato, Yuki Kato. Prediction of RNA secondary structure including pseudoknots for long sequences
0 -- 0Maria K. Jaakkola, Laura L. Elo. Estimating cell type-specific differential expression using deconvolution
0 -- 0Héctor Buena Maizón, Francisco J. Barrantes. A deep learning-based approach to model anomalous diffusion of membrane proteins: the case of the nicotinic acetylcholine receptor
0 -- 0Yi Yang, Xingjie Shi, Wei Liu, Qiuzhong Zhou, Mai Chan Lau, Jeffrey Chun Tatt Lim, Lei Sun, Cedric Chuan Young Ng, Joe Yeong, Jin Liu. SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes
0 -- 0Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang 0008. META-DDIE: predicting drug-drug interaction events with few-shot learning
0 -- 0Umm-Kulthum Ismail Umlai, Dhinoth Kumar Bangarusamy, Xavier Estivill, Puthen Veettil Jithesh. Genome sequencing data analysis for rare disease gene discovery
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