Journal: Briefings in Bioinformatics

Volume 26, Issue 3

0 -- 0Jun Hu, Yu Zhou, Wen-yi Zhang, Xiao-gen Zhou. RLEAAI: improving antibody-antigen interaction prediction using protein language model and sequence order information
0 -- 0Bingying Luo, Fei Teng, Guo Tang, Weixuan Cen, Xing Liu, Jinmiao Chen, Chi Qu, Xuanzhu Liu, Xin Liu, Wenyan Jiang, Huaqiang Huang, Yu Feng, Xue Zhang, Min Jian, Mei Li, Feng Xi, Guibo Li, Sha Liao, Ao Chen, Weimiao Yu, Xun Xu, Jiajun Zhang. StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images
0 -- 0Xin Li, Fan Yang, Yibo Zhang, Zijian Yang, Ruanqi Chen, Meng Zhou 0003, Lin Yang. DeepTFtyper: an interpretable morphology-aware graph neural network for translating histopathology images into molecular subtypes in small cell lung cancer
0 -- 0Yuehua Ou, Qiyi Chen, Ningyu Zhong, Zhihua Du. ProtPhage: a deep learning framework for phage viral protein identification and functional annotation
0 -- 0Fei Ye, Mao Chen, Yixuan Huang, Ruihao Zhang, Xuqi Li, Xiuyuan Wang, Sanyang Han, Lan Ma, Xiao Liu. LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt
0 -- 0Zehua Sun, Jing Xu, Yumeng Zhang, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang 0016, Shanshan Li, Yuming Guo 0001, Hsin-Hui Shen, Jiangning Song. Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features
0 -- 0Xichen Liao, Qi Liu, Guohui Chuai. PrimeNet: rational design of Prime editing pegRNAs by deep learning
0 -- 0Kanglin Hsieh, Kai Zhang, Yan Chu, Lishan Yu, Xiaoyang Li, Nuo Hu, Isha Kawosa, Patrick G. Pilié, Pratip K. Bhattacharya, Degui Zhi, Xiaoqian Jiang, Zhongming Zhao, Yulin Dai. iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics
0 -- 0Chen Chen, Yong Xu, Jian Ouyang, Xiangyi Xiong, Pawel P. Labaj, Agnieszka Chmielarczyk, Anna Rózanska, Hao Zhang, Keyang Liu, Tieliu Shi, Jun Wu. VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts
0 -- 0Asish Kumar Swain, Rajveer Singh Shekhawat, Pankaj Yadav. ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics
0 -- 0Yangyang Wang, Xinyu Yue, Shenghan Lou, Peinan Feng, Binbin Cui, Yanlong Liu. Gene Swin transformer: new deep learning method for colorectal cancer prognosis using transcriptomic data
0 -- 0Yuxin Lin, Zongming Jia, Jixiang Wu, Hubo Yang, Xin Chen, He Wang, Xuedong Wei, Wenying Yan, Xin Qi, Yuhua Huang. Knowledge-guided multi-level network modeling with experimental characterization identifies PRKCA as a novel biomarker and tumor suppressor triggering ferroptosis in prostate cancer
0 -- 0Lauren Theunissen, Thomas Mortier, Yvan Saeys, Willem Waegeman. Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics
0 -- 0Tae-Hyun Kim, Harim Kim, Hyunjin Hwang, Shinwhan Kang, Kijung Shin, Inwha Baek. Gene expression inference based on graph neural networks using L1000 data
0 -- 0Sriniketh Vangaru, Debswapna Bhattacharya. To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era
0 -- 0Jing Wang 0057, Junfeng Xia, Dayu Tan, Yunjie Ma, Yansen Su, Chun-Hou Zheng 0001. Multi-view clustering for single-cell RNA-seq data based on graph fusion
0 -- 0Lili Liu, Haixiang Zhang, Yinan Zheng, Tao Gao, Cheng Zheng 0005, Kai Zhang, Lifang Hou, Lei Liu 0004. High-dimensional mediation analysis for longitudinal mediators and survival outcomes
0 -- 0. Correction to: ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs
0 -- 0Maider Aguerralde-Martin, Mónica Clemente-Císcar, Ana Conesa, Sonia Tarazona. MORE interpretable multi-omic regulatory networks to characterise phenotypes
0 -- 0Sina Majidian, Stephen Hwang, Mohsen Zakeri, Ben Langmead. EvANI benchmarking workflow for evolutionary distance estimation
0 -- 0Alex McSweeney-Davis, Chengran Fang, Emmanuel Caruyer, Anne Kerbrat, Jing-Rebecca Li. Alpha_Mesh_Swc: automatic and robust surface mesh generation from the skeleton description of brain cells
0 -- 0. Editor's Note on 'Bioinformatics in Russia: history and present-day landscape'
0 -- 0Su Xu, Duan Chen, Xue Wang, Shaoyu Li. Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data
0 -- 0Runtian Gao, Heng Hu, Zhongjun Jiang, Shuqi Cao, Guohua Wang, Yuming Zhao, Tao Jiang 0021. SVHunter: long-read-based structural variation detection through the transformer model
0 -- 0Tianhao Li, Zixuan Wang, Yuhang Liu, Sihan He, Quan Zou 0001, Yongqing Zhang. An overview of computational methods in single-cell transcriptomic cell type annotation
0 -- 0Jingchen Zhai, Xiguang Qi, Lianjin Cai, Yue Liu, Haocheng Tang, Lei Xie, Junmei Wang. NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling
0 -- 0Suresh Pokharel, Kepha Barasa, Pawel Pratyush, Dukka B. Kc. PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models
0 -- 0Xiaoyan Yu, Yixuan Ren, Min Xia, Zhenqiu Shu, Liehuang Zhu. Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering
0 -- 0Xun Wang 0010, Tongyu Han, Runqiu Feng, Zhijun Xia, Hanyu Wang, Wenqian Yu, Huanhuan Dai, Haonan Song, Tao Song 0001. GTE-PPIS: a protein-protein interaction site predictor based on graph transformer and equivariant graph neural network
0 -- 0Himansu Kumar, Zikang Chen, Abayomi Adegunlehin, Loren Trowbridge, Leonardo Aguilar, Pora Kim. KinaseFusionDB: an integrative knowledge of kinase fusion proteins in multi-scales
0 -- 0Li Huang, Weikang Gong, Dongsheng Chen. scValue: value-based subsampling of large-scale single-cell transcriptomic data for machine and deep learning tasks
0 -- 0Jingjing Wang, Yanpeng Zhao, Zhijiang Yang, Ge Yao, Penggang Han, Jiajia Liu, Chang Chen, Peng Zan, Xiukun Wan, Xiaochen Bo, Hui Jiang. IECata: interpretable bilinear attention network and evidential deep learning improve the catalytic efficiency prediction of enzymes
0 -- 0Maren Hackenberg, Laia Canal Guitart, Rolf Backofen, Harald Binder. Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data
0 -- 0Jianwei Huang, Youli Zhang, Shulin Ren, Ziyang Wang, Xiaocheng Jin, Xiaoli Lu, Yu Zhang, Xiaoping Min, Shengxiang Ge, Jun Zhang, Ningshao Xia. MambaPhase: deep learning for liquid-liquid phase separation protein classification
0 -- 0Fulan Deng, Jiawei Zou, Miaochen Wang, Yida Gu, Jiale Wu, Lianchong Gao, Yuan Ji, Henry H. Y. Tong, Jie Chen, Wantao Chen, Lianjiang Tan, Yaoqing Chu, Xin Zou, Jie Hao. DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle
0 -- 0Hao Tang, Feng Jiang, Zhi Zhang, Jiaojiao Yang, Lu Li, Qingye Zhang. Metabolism-associated protein network constructing and host-directed anti-influenza drug repurposing
0 -- 0Rhys Gillman, Matt A. Field, Ulf Schmitz, Lionel Hebbard. TARGET-SL: precision essential gene prediction using driver prioritisation and synthetic lethality
0 -- 0Mingxuan Zhang, Yinglei Lai. An order-preserving batch-effect correction method based on a monotonic deep learning framework
0 -- 0Zequn Zhang, Huijun Li, Yuxi Chen, Xiaoli Li, Dongqing Wei, Hongyan Wu. HGCMLDA: predicting lncRNA-disease associations using hypergraph contrastive learning and multi-scale attentional feature fusion
0 -- 0Shangwei Guo, Shengming Zhou, Guohua Wang, Fang Wang. SCPline: An interactive framework for the single-cell proteomics data preprocessing
0 -- 0Jing Yang, Minggui Song, Yifan Bu, Haonan Zhao, Chenghui Liu, Ting Zhang, Chujun Zhang, Shutu Xu, Chuang Ma. Machine learning-augmented m6A-Seq analysis without a reference genome
0 -- 0Saiyam Jogani, Anand Santosh Pol, Mayur Prajapati, Amit Samal, Kriti Bhatia, Jayendra Parmar, Urvik Patel, Falak Shah, Nisarg Vyas, Saurabh Gupta. scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery
0 -- 0Sunghong Park, Dong-Gi Lee, Juhyeon Kim, Seung Ho Kim, Hyeon Jin Hwang, Hyunjung Shin, Hyun Goo Woo. PPIxGPN: plasma proteomic profiling of neurodegenerative biomarkers with protein-protein interaction-based eXplainable graph propagational network
0 -- 0Mofan Feng, Liangjie Liu, Zhuo-Ning Xian, Xiaoxi Wei, Keyi Li, Wenqian Yan, Qing Lu, Yi Shi, Guang He. PSTP: accurate residue-level phase separation prediction using protein conformational and language model embeddings
0 -- 0Abrar Rahman Abir, Md Toki Tahmid, Rafiqul Islam Rayan, M. Saifur Rahman. DeepRNA-Twist: language-model-guided RNA torsion angle prediction with attention-inception network
0 -- 0Yijie He, Yaqin Tang, Pengcheng Tan, Dongyu Huang, Yongheng Wang, Tong Wen, Lin Huang, Jia Wang, Lizhen Shao, Qinyu Cai, Zhimou Li, Yueyang Wang, Taihang Liu, Zhijie Han. Genetic regulation of lncRNA expression in whole human brain and their contribution to CNS disorders
0 -- 0Jing Li, Jia Mi, Wei Lin, Fengjuan Tian, Jing Wan, Jingyang Gao, Yigang Tong. VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models
0 -- 0Mikhail S. Gelfand. On "Bioinformatics in Russia: history and present-day landscape" by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast
0 -- 0Li-Mei Qian, Shi-Xiang Wang, Wen Zhou, Zi-Xin Qin, Ying-nan Wang, Qi Zhao, Rui-Hua Xu. Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology
0 -- 0Lis Arend, Klaudia Adamowicz, Johannes R. Schmidt, Yuliya Burankova, Olga I. Zolotareva, Olga Tsoy, Josch Konstantin Pauling, Stefan Kalkhof, Jan Baumbach, Markus List, Tanja Laske. Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE
0 -- 0Hailong Yang, Jia Wang, Wenyan Wang, Shufang Shi, Lijing Liu, Yuhua Yao, Geng Tian, Peizhen Wang, Jialiang Yang. MMsurv: a multimodal multi-instance multi-cancer survival prediction model integrating pathological images, clinical information, and sequencing data
0 -- 0Xianglin Zhang, Wei Zhang 0241, Jinyi Zhang, Xiuhong Lyu, Haoran Pan, Tianwei Jia, Ting Wang, Xiaowo Wang, Haiyang Guo. Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity
0 -- 0Yuhuan Liu, Xueying Wang, Haitian Zhong, Jixiu Zhai, Xiaojuan Gong, Tianchi Lu. PhosF3C: a feature fusion architecture with fine-tuned protein language model and conformer for prediction of general phosphorylation site
0 -- 0Anas Bilal, Muhammad Taseer Suleman, Khalid Almohammadi, Abdulkareem Alzahrani, Xiaowen Liu. O-methylation sites in ribonucleic acid using diverse classifiers
0 -- 0Keisuke Yamada, Kanta Suga, Naoko Abe, Koji Hashimoto, Susumu Tsutsumi, Masahito Inagaki, Fumitaka Hashiya, Hiroshi Abe, Michiaki Hamada. Multi-objective computational optimization of human 5′ UTR sequences
0 -- 0. Correction to: DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data
0 -- 0Yuting Hu, Feng Hu, Hongwen Zhang 0008, Hongling Xu, Jixiang Gao, Wenshuai Deng, Zijing Tian, Qiaoyu Hu, Honglin Li 0003, Yanyan Diao. RPSubAlign: a novel sequence-based molecular representation method for retrosynthesis prediction with improved validity and robustness
0 -- 0Tung Dang, Yushiro Fuji, Kie Kumaishi, Erika Usui, Shungo Kobori, Takumi Sato, Megumi Narukawa, Yusuke Toda, Kengo Sakurai, Yuji Yamasaki, Hisashi Tsujimoto, Masami Yokota Hirai, Yasunori Ichihashi, Hiroyoshi Iwata. I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data
0 -- 0Osafu Augustine Egbon, John W. Hickey, Benedict Anchang. Fusion of spatiotemporal and network models to prioritize multiscale effects in single-cell perturbations
0 -- 0Ana Stolnicu, Nensi Ikonomi, Peter Eckhardt-Bellmann, Johann M. Kraus, Hans A. Kestler. Robust signalling entropy estimation for biological process characterisation
0 -- 0Alvira Ajadee, Sabkat Mahmud, Md. Ahad Ali, Md. Manir Hossain Mollah, Reaz Ahmmed, Md. Nurul Haque Mollah. In-silico discovery of type-2 diabetes-causing host key genes that are associated with the complexity of monkeypox and repurposing common drugs
0 -- 0Luxuan Wang, Beihong Ji, Jingchen Zhai, Junmei Wang. Advancing promiscuous aggregating inhibitor analysis with intelligent machine learning classification
0 -- 0Hong-Qi Zhang, Xin-Ran Lin, Yan-Ting Wang, Wen-Fang Pei, Guang-Ji Ma, Ze-Xu Zhou, Ke-Jun Deng, Dan Yan, Tian-Yuan Liu. EDS-Kcr: deep supervision based on large language model for identifying protein lysine crotonylation sites across multiple species
0 -- 0Xiao Ding, Yun Ma, Shicheng Li, Jingze Liu, Luyao Qin, Aiping Wu. Influenza virus reassortment patterns exhibit preference and continuity while uncovering cross-species transmission events
0 -- 0Zhiwei Cheng, Yongyong Ren, Xinbo Wang, Yuening Zhang, Yingqi Hua, Hongyu Zhao 0003, Hui Lu 0004. A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics
0 -- 0Ning Wang, Minghui Wu, Wenchao Gu, Chenglong Dai, Zongru Shao, K. P. Subbalakshmi. MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data
0 -- 0Xudong Liu, Zhiwei Nie, Haorui Si, Xurui Shen, Yutian Liu 0004, Xiansong Huang, Tianyi Dong, Fan Xu, Zhixiang Ren, Peng Zhou, Jie Chen 0001. in silico virus evolution
0 -- 0Xianjun Han, Zhenglong Zhang, Can Bai, Zijian Wu. Integrated multimodal hierarchical fusion and meta-learning for enhanced molecular property prediction
0 -- 0Liye Chen, Biaoshun Li, Yihao Chen, MuJie Lin, Shipeng Zhang, Chenxin Li, Yu Pang, Ling Wang. ADCNet: a unified framework for predicting the activity of antibody-drug conjugates
0 -- 0Muhammad A Nawaz, Igor E. Pamirsky, Kirill S. Golokhvast. Response to letter to editor "On 'Bioinformatics in Russia: history and present-day landscape' by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast" by Mikhail Gelfand
0 -- 0Jiahui Guan, Lantian Yao, Peilin Xie, Zhihao Zhao, Dian Meng, Tzong-Yi Lee, Junwen Wang, Ying-Chih Chiang. Graph-RPI: predicting RNA-protein interactions via graph autoencoder and self-supervised learning strategies
0 -- 0Fangyu Mo, Qinghong Qian, Xiaolin Lu, Dihuai Zheng, Wenjie Cai, Jie Yao, Hongyu Chen, Yujie Huang, Xiang Zhang, Sanling Wu, Yifei Shen, Yinqi Bai, Yongcheng Wang, Weiqin Jiang, Longjiang Fan. K-mer embedding of microbiomic single-microbe RNA sequencing data
0 -- 0Kaizhuang Jing, Tingchu Wei, Xuedie Gu, Guoliang Lin, Lin Liu, Jing Luo. Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids
0 -- 0Liangcan Li, Xin Li, Hao Wu. A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation
0 -- 0Peidong Zhang, Xingang Peng, Rong Han, Ting Chen 0006, Jianzhu Ma. Rag2Mol: structure-based drug design based on retrieval augmented generation
0 -- 0Yuanyuan Zeng, Zhiyu You, Jiayang Guo, Jialin Zhao 0005, Ying Zhou, Jialiang Huang, Xiaowen Lyu, Longbiao Chen, Qiyuan Li. Chrombus-XMBD: a graph convolution model predicting 3D-genome from chromatin features
0 -- 0Mike van Santvoort, Federica Eduati. An algorithmic perspective on deciphering cell-cell interactions with spatial omics data
0 -- 0Pi-Jing Wei, Huaiwan Jin, Zhen Gao, Yansen Su, Chun-Hou Zheng 0001. GAEDGRN: reconstruction of gene regulatory networks based on gravity-inspired graph autoencoders
0 -- 0Chen Yang, Yingqi Zhao, Boyuan Xue, Shaojie Wang, Haijia Su. Escherichia coli microbial consortia
0 -- 0Rym Bouriga, Caroline Bailleux, Jocelyn Gal, Emmanuel Chamorey, Baharia Mograbi, Jean-Michel Hannoun-Levi, Gérard Milano. Advances and critical aspects in cancer treatment development using digital twins
0 -- 0Fengyi Guo, Yuanbo Li, Hongyuan Zhao, Xiaogang Liu, Jian Mao, Dongna Ma, Shuangping Liu. GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection
0 -- 0Zhixia Teng, Zhaowen Tian, Murong Zhou, Guohua Wang, Zhen Tian, Yuming Zhao. Enhancing LncRNA-miRNA interaction prediction with multimodal contrastive representation learning
0 -- 0. Correction to: ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics
0 -- 0Mingjuan Wang, Xuetong Chen, Mingxing Liu, Huiying Luo, Shuangshuang Zhang, Jie Guo, Jinghui Wang, Li Zhou, Na Zhang, Hongyan Li, Chao Wang, Liang Li, Zhenzhong Wang, Haiqing Wang, Zihu Guo, Yan Li 0025, Yonghua Wang. Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory
0 -- 0Giulia Cesaro, James Shiniti Nagai, Nicolò Gnoato, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, Carmelo Vittorio Musumarra, Ettore Mosca, Ivan G. Costa, Barbara Di Camillo, Enrica Calura, Giacomo Baruzzo. Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions
0 -- 0Alain J. Mbebi, Facundo Mercado, David Hobby, Hao Tong, Zoran Nikoloski. Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives
0 -- 0Kun Wu, Zixu Wang, Xiulong Yang, Yangyang Chen 0006, Fulvio Mastrogiovanni, Jialu Zhang, Lizhuang Liu. TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery
0 -- 0Murong Zhou, Zeyu Luo, Yu-Hang Yin, Qiaoming Liu, Guohua Wang, Yuming Zhao. scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification
0 -- 0Xuchao Zhang, Jing Chen, Yongtian Wang, Xiaofeng Wang, Jialu Hu, Jiajie Peng, Xuequn Shang 0001, Yanpu Wang, Tao Wang 0082. cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling
0 -- 0Xin Gao, Hanqun Cao, Jinpeng Li 0004, Jiezhong Qiu, Guangyong Chen, Pheng-Ann Heng. Gated-GPS: enhancing protein-protein interaction site prediction with scalable learning and imbalance-aware optimization
0 -- 0Guliang Wang, Ioannis Mouratidis, Kimonas Provatas, Nikol Chantzi, Michail Patsakis, Ilias Georgakopoulos-Soares, Karen M. Vasquez. ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences
0 -- 0Rui Zhang, Huaming Wu. GC-balanced polar codes correcting insertions, deletions and substitutions for DNA storage
0 -- 0Sara H. Mohamed, Mohamed Hamed, Hussain A Alamoudi, Zayd Jastaniah, Fadhl M. Al-Akwaa, Asmaa Reda. Helicobacter pylori-associated gastric cancer identifies hub genes as a novel therapeutic biomarker
0 -- 0Yu Shi, Wei Xu, Pingzhao Hu. Out of distribution learning in bioinformatics: advancements and challenges
0 -- 0Wenbo Guo, Zeyu Chen, Jin Gu. Computational modeling of single-cell dynamics data
0 -- 0Hongqiang Lyu, Pei Cao, Wenyao Long, Xiaoran Yin, Shengjun Xu, Laiyi Fu. DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data
0 -- 0Feifei Xia, Max A. Verbiest, Oxana Lundström, Tugce Bilgin Sonay, Michael Baudis, Maria Anisimova. Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms
0 -- 0Tianjiao Zhang, Saihong Shao, Hongfei Zhang, Zhongqian Zhao, Xingjie Zhao, Zhao-Xiang Zhang 0001, Zhenxing Wang, Guohua Wang. KansformerEPI: a deep learning framework integrating KAN and transformer for predicting enhancer-promoter interactions
0 -- 0Jelard Aquino, Daniel Witoslawski, Steve Park, Jessica Holder, Amei Amei, Mira V. Han. A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection
0 -- 0Zhiyue Tom Hu, Yaodong Yu, Ruoqiao Chen, Shan-Ju Yeh, Bin Chen, Haiyan Huang. Large-scale information retrieval and correction of noisy pharmacogenomic datasets through residual thresholded deep matrix factorization
0 -- 0Hao Mei, Zhiyuan Wang, Hang Yang, Xiaoke Li, Yaqing Xu. Network analysis of multivariate time series data in biological systems: methods and applications
0 -- 0Partha Pratim Ray. Should LLMs be over empowered for high-stake regulatory research?
0 -- 0Ting Li, Henghui Fan, Jianping Zhao 0001, Xiaomei Yang, Junfeng Xia. MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning
0 -- 0. Correction to: Bioinformatics in Russia: history and present-day landscape
0 -- 0Yan Zhao, Huaiyu Wang. Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications
0 -- 0Yihe Yang, Noah Lorincz-Comi, Mengxuan Li, Xiaofeng Zhu. cis-Mendelian randomization method robust to weak instrument bias and horizontal pleiotropy bias
0 -- 0Ruilin Su, Binyang Huang, Junyan Tan, Zhencai Shen, Ping Zhong 0003, Jianfeng Liu. Mutual information stacking method for prediction of the growth traits in pigs
0 -- 0Cheng Zhu, Sen Cao, Tianfeng Shang, Jingjing Guo, An Su, Chengxi Li, Hongliang Duan. Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2
0 -- 0Xinyi Tang, Ran Liu. De-motif sampling: an approach to decompose hierarchical motifs with applications in T cell recognition
0 -- 0Xiang Lian, Xia Kuang, Dong-Dong Zhang, Qian Xu, Anqiang Ye, Cheng-Yu Wang, Hong-Tu Cui, Hai-Xia Guo, Ji-Yun Zhang, Yuan Liu, Ge-Fei Hao, Zhenshun Cheng, Feng-Biao Guo. Systematic identification of cancer-type-specific drugs based on essential genes and validations in lung adenocarcinoma
0 -- 0Lianchong Gao, Yujun Liu, Jiawei Zou, Fulan Deng, Zheqi Liu, Zhen Zhang, Xinran Zhao, Lei Chen, Henry H. Y. Tong, Yuan Ji, Huangying Le, Xin Zou, Jie Hao. Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data
0 -- 0Yu Cheng, Xinjia Ruan, Xiaofan Lu, YuQing Yang, Yuhang Wang, Shangjin Yan, Yuzhe Sun, Fangrong Yan, Liyun Jiang, Tiantian Liu. Accounting for the impact of rare variants on causal inference with RARE: a novel multivariable Mendelian randomization method
0 -- 0Hongyu Zhang, Weining Li, Jinting Guan. scTsI: an effective two-stage imputation method for single-cell RNA-seq data