| 0 | -- | 0 | Sergio-Llaneza Lago, William D. Fraser, Darrell Green. Bayesian unsupervised clustering identifies clinically relevant osteosarcoma subtypes |
| 0 | -- | 0 | Lingpeng Kong, Hong Cheng, Kun Zhu, Bo Song. LOGOWheat: deep learning-based prediction of regulatory effects for noncoding variants in wheats |
| 0 | -- | 0 | Junwei Luo, Jiaojiao Wang, Jingjing Wei, Chaokun Yan, HuiMin Luo. DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering |
| 0 | -- | 0 | Juntao Li, Shan Xiang, Dongqing Wei. Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF |
| 0 | -- | 0 | Elisabet Munté, Carla Roca, Jesús del Valle, Lidia Feliubadaló, Marta Pineda, Bernat Gel, Elisabeth Castellanos, Barbara Rivera, David Cordero, Víctor Moreno, Conxi Lázaro, José Marcos Moreno-Cabrera. Detection of germline CNVs from gene panel data: benchmarking the state of the art |
| 0 | -- | 0 | Xinlong Wen, Hao Liu 0056, Wenhan Long, Shuoying Wei, Rongbo Zhu. Consistent semantic representation learning for out-of-distribution molecular property prediction |
| 0 | -- | 0 | Bo Yang, Chenxi Cui, Meng Wang, Hong Ji, Feiyue Gao. Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data |
| 0 | -- | 0 | Zhen Wang, Yizhen Feng, Qingwen Tian, Ziqi Liu, Pengju Yan, Xiaolin Li. RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models |
| 0 | -- | 0 | Yonathan Schwammenthal, Tom Rabinowitz, Lina Basel-Salmon, Reut Tomashov-Matar, Noam Shomron. Noninvasive fetal genotyping using deep neural networks |
| 0 | -- | 0 | . Correction to: HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction |
| 0 | -- | 0 | Zheng Su, Mingyan Fang, Andrei Smolnikov, Fatemeh Vafaee, Marcel E. Dinger, Emily C. Oates. Post-transcriptional regulation supports the homeostatic expression of mature RNA |
| 0 | -- | 0 | Fabio Cumbo, Simone Truglia, Emanuel Weitschek, Daniel Blankenberg. Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer |
| 0 | -- | 0 | Yiru Pan, Xingyu Ji, Jiaqi You, Lu Li, Zhenping Liu, Xianlong Zhang, Zeyu Zhang, Maojun Wang. CSGDN: contrastive signed graph diffusion network for predicting crop gene-phenotype associations |
| 0 | -- | 0 | Fatma S. Ahmed, Saleh K. H. Aly, Xiangrong Liu. NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture |
| 0 | -- | 0 | Dries Heylen, Murih Pusparum, Jurgis Kuliesius, Jim Wilson, Young-Chan Park, Jacek Jamiolkowski, Valentino D'onofrio, Dirk Valkenborg, Jan Aerts, Gökhan Ertaylan, Jef Hooyberghs. Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison |
| 0 | -- | 0 | Anna Postovskaya, Koen Vercauteren, Pieter Meysman, Kris Laukens. tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs |
| 0 | -- | 0 | Yanming Wei, Tong Zhou, Yixiao Zhai, Liang Yu 0002, Quan Zou 0001. FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity |
| 0 | -- | 0 | Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng. Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges |
| 0 | -- | 0 | Arnaud Guille, José Adélaïde, Pascal Finetti, Fabrice André, Daniel Birnbaum, Emilie Mamessier, François Bertucci, Max Chaffanet. A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing |
| 0 | -- | 0 | Zhijian Huang, Kai Chen, Xiaojun Xiao, Ziyu Fan, Yuanpeng Zhang, Lei Deng 0002. DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism |
| 0 | -- | 0 | Dao-Tran, Ha Nguyen, Van-Dung Pham, Phuong Nguyen, Hung Nguyen Luu, Liem Minh Phan, Christin Blair Destefano, Sai-Ching Jim Yeung, Tin Nguyen. A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables |
| 0 | -- | 0 | Iljung Jin, SongYeon Lee, Martin Schmuhalek, Hojung Nam. DD-PRiSM: a deep learning framework for decomposition and prediction of synergistic drug combinations |
| 0 | -- | 0 | Liu Yang, Suqi Cao, Lei Liu 0033, Ruixin Zhu, Dingfeng Wu. cyclicpeptide: a Python package for cyclic peptide drug design |
| 0 | -- | 0 | Qianwen Luo, Shanshan Zhang, Hamza Butt, Yin Chen, Hongmei Jiang, Lingling An. PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data |
| 0 | -- | 0 | Qi-xin Zhang, Tianneng Zhu, Feng Lin, Dunhuang Fang, Xuejun Chen, Xiangyang Lou, Zhijun Tong, Bingguang Xiao, Hai-ming Xu. mmGEBLUP: an advanced genomic prediction scheme for genetic improvement of complex traits in crops through integrative analysis of major genes, polygenes, and genotype-environment interactions |
| 0 | -- | 0 | Marek Nowicki, Magdalena Mroczek, Dhananjay Mukhedkar, Piotr Bala, Ville Nikolai Pimenoff, Laila Sara Arroyo Mühr. HPV-KITE: sequence analysis software for rapid HPV genotype detection |
| 0 | -- | 0 | Yun Zuo 0001, Xingze Fang, Jiankang Chen, Jiayi Ji, Yuwen Li, Zeyu Wu, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng, Hongwei Yin, Anjing Zhao. MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human |
| 0 | -- | 0 | Anna Postovskaya, Koen Vercauteren, Pieter Meysman, Kris Laukens. tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs |
| 0 | -- | 0 | Wengyu Zhang, Qi Tian 0001, Yi Cao, Wenqi Fan, Dongmei Jiang, Yaowei Wang 0001, Qing Li 0001, Xiao-Yong Wei. GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning |
| 0 | -- | 0 | Aimin Xie, Hao Wang, Jiaxu Zhao, Zhaoyang Wang, Jinyuan Xu, Yan Xu. scPAS: single-cell phenotype-associated subpopulation identifier |
| 0 | -- | 0 | Sehi Park, Kil To Chong 0001, Hilal Tayara. CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites |
| 0 | -- | 0 | Willem Stock, Coralie Rousseau, Glen Dierickx, Sofie D'hondt, Luz Amadei Martínez, Simon M. Dittami, Luna M. van der Loos, Olivier De Clerck. Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data |
| 0 | -- | 0 | Shyamsundar Ravishankar, Vilma Perez, Roberta Davidson, Xavier Roca-Rada, Divon Lan, Yassine Souilmi, Bastien Llamas. Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping |
| 0 | -- | 0 | Ezechiel B. Tibiri, Palwende R. Boua, Issiaka Soulama, Christine Dubreuil-Tranchant, Ndomassi Tando, Charlotte Tollenaere, Christophe Brugidou, Romaric K. Nanema, Fidèle Tiendrebeogo. Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso |
| 0 | -- | 0 | Tianjiao Zhang, Zhongqian Zhao, Jixiang Ren, Ziheng Zhang, Hongfei Zhang, Guohua Wang. cfDiffusion: diffusion-based efficient generation of high quality scRNA-seq data with classifier-free guidance |
| 0 | -- | 0 | Quan Lu, Jiajun Xu, Renyi Zhang, Hangcheng Liu, Meng Wang, Xiaoshuang Liu, Zhenyu Yue, Yujia Gao. RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice |
| 0 | -- | 0 | Xianliang Liu, Jiawei Luo, Xinyan Wang, Yang Zhang, Junjie Chen. Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization |
| 0 | -- | 0 | Le Yang, Runpu Chen, Steve Goodison, Yijun Sun. A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer |
| 0 | -- | 0 | Fu Liu, Zhimiao Zhao, Yun Liu. PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network |
| 0 | -- | 0 | Shunying Liu, Lingfei Li, Yi Liang, Yang Tan, Xiaoyu Wang, Yanhai Feng, Nian Chen, Xia Lei. Novel genetic insight for psoriasis: integrative genome-wide analyses in 863 080 individuals and proteome-wide Mendelian randomization |
| 0 | -- | 0 | Yves Gaetan Nana Teukam, Federico Zipoli, Teodoro Laino, Emanuele Criscuolo, Francesca Grisoni, Matteo Manica. Integrating genetic algorithms and language models for enhanced enzyme design |
| 0 | -- | 0 | Jammi Prasanthi Sirasani, Cory Gardner, Gihwan Jung, Hyunju Lee, Tae-Hyuk Ahn. Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives |
| 0 | -- | 0 | Mianyan Li, Thomas Hall, David E. MacHugh, Liang Chen, Dorian Garrick, Lixian Wang, Fuping Zhao. KPRR: a novel machine learning approach for effectively capturing nonadditive effects in genomic prediction |
| 0 | -- | 0 | Xintian Xu, Rui Li, Ouyang Mo, Kai Liu, Justin Li, Pei Hao. Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline |
| 0 | -- | 0 | Junning Feng, Yong Liang, Tianwei Yu. ADM: adaptive graph diffusion for meta-dimension reduction |
| 0 | -- | 0 | Chelsea Chen Yuge, Ee Soon Hang, Madasamy Ravi Nadar Mamtha, Shashikant Vishwakarma, Sijia Wang, Cheng Wang, Nguyen-Quoc-Khanh Le. RNA-ModX: a multilabel prediction and interpretation framework for RNA modifications |
| 0 | -- | 0 | You Wu, Pengfei Xu, Liyuan Wang, Shuai Liu, Yingnan Hou, Hui Lu, Peng Hu, Xiaofei Li, Xiang Yu. scGO: interpretable deep neural network for cell status annotation and disease diagnosis |
| 0 | -- | 0 | Xiaotao Shen, Songjie Chen, Liang Liang, Monika Avina, Hanyah Zackriah, Laura Jelliffe-Pawlowski, Larry Rand, Michael P. Snyder. Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy |
| 0 | -- | 0 | Geyan Ye, Xibao Cai, Houtim Lai, Xing Wang 0007, Junhong Huang, Longyue Wang, Wei Liu 0005, Xiangxiang Zeng. DrugAssist: a large language model for molecule optimization |
| 0 | -- | 0 | Ivan Ferrari, Federica De Grossi, Giancarlo Lai, Stefania Oliveto, Giorgia Deroma, Stefano Biffo, Nicola Manfrini. CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs |
| 0 | -- | 0 | Peng Liu, Yuchen Pan, Hung-Ching Chang, Wenjia Wang, Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George C. Tseng, Liza Konnikova, Silvia Liu. Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating |
| 0 | -- | 0 | Luciano I Zablocki, Leandro A Bugnon, Matias Gerard, Leandro E. Di Persia, Georgina Stegmayer, Diego H. Milone. Comprehensive benchmarking of large language models for RNA secondary structure prediction |
| 0 | -- | 0 | Xiangfei Zhou, Hao Wu. scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data |
| 0 | -- | 0 | Shilong Wang, Hai Cui, Yanchen Qu, Yijia Zhang. Multi-source biological knowledge-guided hypergraph spatiotemporal subnetwork embedding for protein complex identification |
| 0 | -- | 0 | Sangmin Seo, Hwanhee Kim, Jieun Lee, Seungyeon Choi, Sanghyun Park. Exploring the potential of compound-protein complex structure-free models in virtual screening using BlendNet |
| 0 | -- | 0 | Cathal Ormond, Niamh M. Ryan, Mathieu Cap, William Byerley, Aiden P. Corvin, Elizabeth A. Heron. BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees |
| 0 | -- | 0 | Jing Li, Qinglin Mei, Chaoxia Yang, Naibo Zhu, Guojun Li. TransBic: bucket trend-preserving biclustering for finding local and interpretable expression patterns |
| 0 | -- | 0 | Uwaise Ibna Islam, Andre Luiz Campelo dos Santos, Ria Kanjilal, Raquel Assis. Learning genotype-phenotype associations from gaps in multi-species sequence alignments |
| 0 | -- | 0 | Zhenxian Zheng, Yingxuan Ren, Lei Chen 0072, Angel On Ki Wong, Shumin Li, Xian Yu, Tak Wah Lam, Ruibang Luo. Repun: an accurate small variant representation unification method for multiple sequencing platforms |
| 0 | -- | 0 | Genhui Zheng, Dingfeng Wu, Xiuxia Wei, Dongpo Xu, Tiantian Mao, Deyu Yan, Wenhao Han, Xiaoxiao Shang, Zikun Chen, Jingxuan Qiu, Kailin Tang, Zhiwei Cao, Tianyi Qiu. PbsNRs: predict the potential binders and scaffolds for nuclear receptors |
| 0 | -- | 0 | Ruiqian Yao, Lu Sun, Ruifang Gao, Yue-mei, Geng Xue, Dong Yu. PTTM: dissecting the profile of tumor tissue microbiome to reveal microbiota features and associations with host transcriptome |
| 0 | -- | 0 | Luca Cattelani, Vittorio Fortino. Dual-stage optimizer for systematic overestimation adjustment applied to multi-objective genetic algorithms for biomarker selection |
| 0 | -- | 0 | Junxi Xie, Xiaopeng Jin, Hang Wei, Saisai Sun, Yumeng Liu. IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning |
| 0 | -- | 0 | Chunying Wang, Di Zhang, Yuexin Ma, Yonghao Zhao, Ping Liu, Xiang Li. WheatGP, a genomic prediction method based on CNN and LSTM |
| 0 | -- | 0 | Yang Yang, Zixuan Zheng, Yuyang Xu, Huifang Wei, Wenying Yan. BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction |
| 0 | -- | 0 | Shuhe Liu, Zhen Wei, Daniel F. Carr, John Moraros. Deciphering the genetic interplay between depression and dysmenorrhea: a Mendelian randomization study |
| 0 | -- | 0 | Xikang Feng, Miaozhe Huo, He Li, Yongze Yang, Yuepeng Jiang, Liang He, Shuai Cheng Li. A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions |
| 0 | -- | 0 | Alida Zárate, Lorena Díaz-González, Blanca Taboada. VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification |
| 0 | -- | 0 | Alfred Ultsch, Jörn Lötsch. Augmenting small biomedical datasets using generative AI methods based on self-organizing neural networks |
| 0 | -- | 0 | Gang Wen, Limin Li. Federated transfer learning with differential privacy for multi-omics survival analysis |
| 0 | -- | 0 | Shuailin Xue, Fangfang Zhu, Jinyu Chen, Wenwen Min. Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN |
| 0 | -- | 0 | Zexuan Wang, Qipeng Zhan, Shu Yang, Shizhuo Mu, Jiong Chen, Sumita Garai, Patryk Orzechowski, Joost B. Wagenaar, Li Shen 0001. QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics |
| 0 | -- | 0 | Zheyu Ding, Rong Wei, Jianing Xia, Yonghao Mu, Jiahuan Wang, Yingying Lin. Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review |
| 0 | -- | 0 | Marco Antônio M. Pretti, Gustavo Fioravanti Vieira, Mariana Boroni, Martín H. Bonamino. Unveiling cross-reactivity: implications for immune response modulation in cancer |
| 0 | -- | 0 | Siwei Wu, Chaoyi Yin, Yuezhu Wang, Huiyan Sun. Identifying cancer prognosis genes through causal learning |
| 0 | -- | 0 | Jin Zhang, Yan Yang, Muheng Shang, Lei Guo, Daoqiang Zhang, Lei Du. Mutual-assistance learning for trustworthy biomarker discovery and disease prediction |
| 0 | -- | 0 | Rui Niu, Jingwei Wang, Yanli Li, Jiren Zhou, Yang Guo, Xuequn Shang 0001. Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition |
| 0 | -- | 0 | Hai Cui, Meiyu Duan, Haijia Bi, Xiaobo Li 0007, Xiaodi Hou, Yi-Jia Zhang 0001. Heterogeneous graph contrastive learning with gradient balance for drug repositioning |
| 0 | -- | 0 | Yuqi Miao, Huang Xu, Shuang Wang. PartIES: a disease subtyping framework with Partition-level Integration using diffusion-Enhanced Similarities from multi-omics Data |
| 0 | -- | 0 | Jiachen Chen, Joanne M. Murabito, Kathryn L. Lunetta. ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks |
| 0 | -- | 0 | Hui Li, Lu Meng, Hongke Wang, Liang Cui, Heyu Sheng, Peiyan Zhao, Shuo Hong, Xinhua Du, Shi Yan, Yun Xing, Shicheng Feng, Yan Zhang, Huan Fang, Jing Bai, Yan Liu, Shaowei Lan, Tao Liu, Yanfang Guan, Xuefeng Xia, Xin Yi, Ying Cheng. Precise identification of somatic and germline variants in the absence of matched normal samples |
| 0 | -- | 0 | Yushuang He, Feng Zhou, Jiaxing Bai, Yichun Gao, Xiaobing Huang, Ying Wang. ViTax: adaptive hierarchical viral taxonomy classification with a taxonomy belief tree on a foundation model |
| 0 | -- | 0 | Ruogu Wang, Yunlong Feng, Alex M. Valm. A framework of multi-view machine learning for biological spectral unmixing of fluorophores with overlapping excitation and emission spectra |
| 0 | -- | 0 | Cheng Han, Shanshan Fu, Miaomiao Chen, Yujie Gou, Dan Liu, Chi Zhang, Xinhe Huang, Leming Xiao, Miaoying Zhao, Jiayi Zhang, Qiang Xiao, Di Peng, Yu Xue 0001. GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites |
| 0 | -- | 0 | Xiaoyi Li, Kangli Zhu, Ying Zhen. A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning |
| 0 | -- | 0 | Yiwen Yang, Chengming Zhang 0003, Zhaonan Liu, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen, Wu Wei. MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics |
| 0 | -- | 0 | Haicheng Li, Junhua Niu, Yalan Sheng, Yifan Liu, Shan Gao. SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data |
| 0 | -- | 0 | Yuxuan Pang, Chunxuan Wang, Yao-zhong Zhang, Zhuo Wang, Seiya Imoto, Tzong-Yi Lee. STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics |
| 0 | -- | 0 | Cui-Xiang Lin, Hong-Dong Li, Jianxin Wang 0001. LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes |
| 0 | -- | 0 | Si Zheng 0001, Yaowen Gu, Yuzhen Gu, Yelin Zhao, Liang Li, Min Wang, Rui Jiang 0001, Xia Yu, Ting Chen, Jiao Li 0001. Machine learning-enabled virtual screening indicates the anti-tuberculosis activity of aldoxorubicin and quarfloxin with verification by molecular docking, molecular dynamics simulations, and biological evaluations |
| 0 | -- | 0 | Lijun Cai, Guanyu Yue, Yifan Chen, Li Wang 0145, Xiaojun Yao, Quan Zou 0001, Xiangzheng Fu, Dong-Sheng Cao 0001. ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction |
| 0 | -- | 0 | Xin Ma, Lijing Lin, Qian Zhao, Mudassar Iqbal. TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data |
| 0 | -- | 0 | Qinglong Zhang, Liping Kang, Haoran Yang, Fei Liu, Xiaohui Wu. Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA |
| 0 | -- | 0 | Harvard Wai Hann Hui, Wei Xin Chan, Wilson Wen Bin Goh. Assessing the impact of batch effect associated missing values on downstream analysis in high-throughput biomedical data |
| 0 | -- | 0 | Yi Zhang, Jindi Huang, Xinze Li, Wenqi Sun, Nana Zhang, Jiquan Zhang, Tiegen Chen, Ling Wang. Self-awareness of retrosynthesis via chemically inspired contrastive learning for reinforced molecule generation |
| 0 | -- | 0 | Nandhini Rajagopal, Udit Choudhary, Kenny Tsang, Kyle P. Martin, Murat Karadag, Hsin-Ting Chen, Na-Young Kwon, Joseph Mozdzierz, Alexander M. Horspool, Li Li, Peter M. Tessier, Michael S. Marlow, Andrew E. Nixon, Sandeep Kumar. Deep learning-based design and experimental validation of a medicine-like human antibody library |
| 0 | -- | 0 | Giuseppe Defazio, Marco Antonio Tangaro, Graziano Pesole, Bruno Fosso. kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes |
| 0 | -- | 0 | Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Siyuan Li 0002, Zihan Liu, Zhen Lei 0001, Ju-Sheng Zheng, Stan Z. Li. FGeneBERT: function-driven pre-trained gene language model for metagenomics |
| 0 | -- | 0 | Bo Wang, Yahui Long, Yuting Bai, Jiawei Luo 0001, Chee-Keong Kwoh 0001. STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution |
| 0 | -- | 0 | Liguo Ye, Cheng Ye, Pengtao Li, Yu Wang, Wenbin Ma. Inferring the genetic relationships between unsupervised deep learning-derived imaging phenotypes and glioblastoma through multi-omics approaches |
| 0 | -- | 0 | Yueer Li, Chen Peng, Fei Chi, Zinuo Huang, Mengyi Yuan, Xin Zhou, Chao Jiang. The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees |
| 0 | -- | 0 | Lingsheng Cai, Xiuli Ma, Jianzhu Ma. Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks |
| 0 | -- | 0 | . Correction to: Unveiling cross-reactivity: implications for immune response modulation in cancer |
| 0 | -- | 0 | Jiaojiao Guan, Yongxin Ji, Cheng Peng, Wei Zou, Xubo Tang, Jiayu Shang, Yanni Sun. GOPhage: protein function annotation for bacteriophages by integrating the genomic context |
| 0 | -- | 0 | Pengcheng Yang, Youngwoo Lee, Daniel B. Szymanski, Jun Xie. Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions |
| 0 | -- | 0 | Jinyu Chen, Wenwen Min. sTPLS: identifying common and specific correlated patterns under multiple biological conditions |
| 0 | -- | 0 | Mengya Liu, Zhan-Li Sun, Zhigang Zeng, Kin-Man Lam 0001. N6-methyladenine sites |
| 0 | -- | 0 | Wenjie Sun, Daphne van Ginneken, Leïla Perié. scMitoMut for calling mitochondrial lineage-related mutations in single cells |
| 0 | -- | 0 | Marin Volaric, Nevenka Mestrovic, Evelin Despot-Slade. SatXplor - a comprehensive pipeline for satellite DNA analyses in complex genome assemblies |
| 0 | -- | 0 | George Assaf, Fei Liu 0006, Monika Heiner. Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets |
| 0 | -- | 0 | Shijie Luo, Ming Zhu, Liquan Lin, Jiajing Xie, Shihao Lin, Ying Chen, Jiali Zhu, Jialiang Huang. DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile |
| 0 | -- | 0 | Olivier Cinquin. Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics |
| 0 | -- | 0 | Tingpeng Yang, Yonghong He, Yu Wang. Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences |
| 0 | -- | 0 | Sara Cuvertino, Terence Garner, Evgenii Martirosian, Bridgious Walusimbi, Susan J. Kimber, Siddharth Banka, Adam Stevens. Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome |
| 0 | -- | 0 | Elena Domínguez Romero, Stanislav Mazurenko, Martin Scheringer, Vítor A. P. Martins dos Santos, Chris T. A. Evelo, Mihail Anton, John M. Hancock, Anze Zupanic, María Suárez-Diez. Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models |
| 0 | -- | 0 | Kaiyuan Yang 0009, Jiabei Cheng, Shenghao Cao, Xiaoyong Pan, Hong-bin Shen, Ye Yuan. Predicting transcriptional changes induced by molecules with MiTCP |
| 0 | -- | 0 | Cheng Tan 0012, Yijie Zhang, Zhangyang Gao, Hanqun Cao, Siyuan Li 0002, Siqi Ma, Mathieu Blanchette, Stan Z. Li. R3Design: deep tertiary structure-based RNA sequence design and beyond |
| 0 | -- | 0 | Xizi Luo, Amadeus Song Yi Chi, Andre Huikai Lin, Tze Jet Ong, Limsoon Wong, Chowdhury Rafeed Rahman. Benchmarking recent computational tools for DNA-binding protein identification |
| 0 | -- | 0 | Yiwen Wei, Tianyi Qiu, Yisi Ai, Yuxi Zhang, Junting Xie, Dong Zhang, Xiaochuan Luo, Xiulan Sun, Xin Wang, Jingxuan Qiu. Advances of computational methods enhance the development of multi-epitope vaccines |
| 0 | -- | 0 | Yiyang Zhu, Wenying Chen, Kexuan Zhu, Yuxin Liu, Shuiping Huang, Ping Zeng. Polygenic prediction for underrepresented populations through transfer learning by utilizing genetic similarity shared with European populations |
| 0 | -- | 0 | Ankang Wei, Huanghan Zhan, Zhen Xiao, Weizhong Zhao, Xingpeng Jiang. A novel framework for phage-host prediction via logical probability theory and network sparsification |
| 0 | -- | 0 | Sushmita Basu, Jing Yu, Daisuke Kihara, Lukasz A. Kurgan. Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences |
| 0 | -- | 0 | Chen M. Chen, Rosemary Yu. A multi-step completion process model of cell plasticity |
| 0 | -- | 0 | Jin Han, Haohong Zhang, Kang Ning. Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment |
| 0 | -- | 0 | James Strudwick, Laura-Jayne Gardiner, Kate Denning-James, Niina Haiminen, Ashley Evans, Jennifer Kelly, Matthew Madgwick, Filippo Utro, Ed Seabolt, Christopher Gibson, Bharat Bedi, Daniel Clayton, Ciaron Howell, Laxmi Parida, Anna Paola Carrieri. AutoXAI4Omics: an automated explainable AI tool for omics and tabular data |
| 0 | -- | 0 | Baiming Zou, James G. Xenakis, Meisheng Xiao, Apoena Aguiar Ribeiro, Kimon Divaris, Di Wu, Fei Zou. A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction |
| 0 | -- | 0 | Andrea Lomagno, Ishak Yusuf, Gabriele Tosadori, Dario Bonanomi, Pietro Luigi Mauri, Dario Di Silvestre. CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditions |
| 0 | -- | 0 | Xiaoqing Ru, Shulin Zhao, Quan Zou, Lifeng Xu. Identify potential drug candidates within a high-quality compound search space |
| 0 | -- | 0 | Xinyi Mou, Haoyu Du, Guanghua Qiao, Jing Li. Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data |
| 0 | -- | 0 | Qiaolin Lu, Jiayuan Ding, Lingxiao Li, Yi Chang 0001. Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways |
| 0 | -- | 0 | QiQi Lu, Zhixian Liu, Xiaosheng Wang. Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP |
| 0 | -- | 0 | Leandro Murgas, Gianluca Pollastri, Erick Riquelme, Mauricio Sáez, Alberto J. M. Martin. Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states |
| 0 | -- | 0 | Yizhen Wang, Li Cheng 0007, Yanyun Zhang, Yujia Cao, Daniyal M. Al-Ghazzawi. DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks |
| 0 | -- | 0 | Hao Yuan, Parker Hicks, Mansooreh Ahmadian, Kayla A. Johnson, Lydia Valtadoros, Arjun Krishnan. Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata |
| 0 | -- | 0 | Nana Jin, Chuanchuan Nan, Wanyang Li, Peijing Lin, Yu Xin, Jun Wang, Yuelong Chen, Yuanhao Wang, Kaijiang Yu, Changsong Wang, Chunbo Chen, Qingshan Geng, Lixin Cheng. PAGE-based transfer learning from single-cell to bulk sequencing enhances model generalization for sepsis diagnosis |
| 0 | -- | 0 | Zhilong Liu, Hai Lin, Xiang Li, Hao Xue, Yuer Lu, Fei Xu, Jianwei Shuai. The network structural entropy for single-cell RNA sequencing data during skin aging |
| 0 | -- | 0 | Yixuan Wang, Yanfang Guan, Xin Lai, Yuqian Liu, Zhili Chang, Xiaonan Wang, Quan Wang, Jingjing Liu, Jian Zhao, Shuanying Yang, Jiayin Wang, Xiaofeng Song. THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data |
| 0 | -- | 0 | Lin Yuan 0001, Shengguo Sun, Yufeng Jiang, Qinhu Zhang, Lan Ye, Chun-Hou Zheng 0001, De-Shuang Huang. scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning |
| 0 | -- | 0 | Fengyue Zhang, Xuqi Zhao, Jinrui Wei, Lichuan Wu. PathSynergy: a deep learning model for predicting drug synergy in liver cancer |
| 0 | -- | 0 | Donghan Wang, Xu Dong, Xueyou Zhang, Lihong Hu. GADIFF: a transferable graph attention diffusion model for generating molecular conformations |
| 0 | -- | 0 | Xin Ma, Lijing Lin, Qian Zhao, Mudassar Iqbal. TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data |
| 0 | -- | 0 | Hao Lu, Mostafa Rezapour, Haseebullah Baha, Muhammad Khalid Khan Niazi, Aarthi Narayanan, Metin Nafi Gürcan. P-value computation |
| 0 | -- | 0 | Juho Pelto, Kari Auranen, Janne V. Kujala, Leo Lahti. Elementary methods provide more replicable results in microbial differential abundance analysis |
| 0 | -- | 0 | Jiancheng Zhong, Zhiwei Zou, Jie Qiu, Shaokai Wang. ScFold: a GNN-based model for efficient inverse folding of short-chain proteins via spatial reduction |
| 0 | -- | 0 | Yi Zhang 0044, Yin Wang, Xinyuan Liu, Xi Feng. CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data |
| 0 | -- | 0 | Jiajian Luo, Jiye Fu, Zuhong Lu, Jing Tu. Deep learning in integrating spatial transcriptomics with other modalities |
| 0 | -- | 0 | Abdallah Derbalah, Masoud Jamei, Iain Gardner, Armin Sepp. The role of automation in enhancing reproducibility and interoperability of PBPK models |
| 0 | -- | 0 | Wendong Huang, Yaofeng Hu, Lequn Wang, Guangsheng Wu, Chuanchao Zhang, Qianqian Shi. Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity |
| 0 | -- | 0 | Xinglong Wang, Kangjie Xu, Lingling Ma, Ruoxi Sun, Kun Wang, Ruiyan Wang, Junli Zhang, Wenwen Tao, Kai Linghu, Shuyao Yu, Jingwen Zhou. Diffusion model assisted designing self-assembling collagen mimetic peptides as biocompatible materials |
| 0 | -- | 0 | Tong Lu, Wei Guo, Wei Guo, Wangyang Meng, Tianyi Han, Zizhen Guo, Chengqiang Li, Shugeng Gao, Youqiong Ye, Hecheng Li. A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity |
| 0 | -- | 0 | Hongtao Yu, Guojing He, Wei Wang, Senbiao Qin, Yu Wang, Mingze Bai, Kunxian Shu, Dan Pu. A graph neural network approach for accurate prediction of pathogenicity in multi-type variants |
| 0 | -- | 0 | Pawel Dudzic, Bartosz Janusz, Tadeusz Satlawa, Dawid Chomicz, Tomasz Gawlowski, Rafal Grabowski, Przemek Józwiak, Mateusz Tarkowski, Maciej Mycielski, Sonia Wróbel, Konrad Krawczyk. RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database |
| 0 | -- | 0 | Dongping Liu, Dinghao Liu, Kewei Sheng, Zhenyong Cheng, Zixuan Liu, Yanling Qiao, Shangxuan Cai, Yulong Li, Jubo Wang, Hongyang Chen, Chi Hu, Peng Xu, Bin Di, Jun Liao. STNGS: a deep scaffold learning-driven generation and screening framework for discovering potential novel psychoactive substances |
| 0 | -- | 0 | Runqing Wang, Qiguo Dai, Xiaodong Duan, Quan Zou 0001. stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization |
| 0 | -- | 0 | Junhang Cao, Jun Zhang, Qiyuan Yu, Junkai Ji, JianQiang Li, Shan He, Zexuan Zhu. TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model |
| 0 | -- | 0 | Xueshi Yu, Renmin Han, Haitao Jiao, Wenjia Meng. Few-shot classification of Cryo-ET subvolumes with deep Brownian distance covariance |
| 0 | -- | 0 | Tianjiao Zhang, Xiang Zhang, Zhenao Wu, Jixiang Ren, Zhongqian Zhao, Hongfei Zhang, Guohua Wang, Tao Wang 0082. VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network |
| 0 | -- | 0 | Yinhu Li, Guangze Pan, Shuai Wang, Zhengtu Li, Ru Yang, Yiqi Jiang, Yu Chen, Shuaicheng Li 0001, Bairong Shen. Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome |
| 0 | -- | 0 | Xianxiao Zhou, Ling Wu, Minghui Wang, Guojun Wu, Bin Zhang. iDOMO: identification of drug combinations via multi-set operations for treating diseases |
| 0 | -- | 0 | Sara Potente, Diego Boscarino, Dino Paladin, Sergio Marchini, Luca Beltrame, Chiara Romualdi. SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline |
| 0 | -- | 0 | Huan Yang, Minglei Yang, Jiani Chen, Guocong Yao, Quan Zou, Linpei Jia. Multimodal deep learning approaches for precision oncology: a comprehensive review |
| 0 | -- | 0 | Yan-Yu Li, Fengcui Qian, Guo-Rui Zhang, Xue-Cang Li, Li-Wei Zhou, Zheng-Min Yu, Wei Liu, Qiu-Yu Wang, Chunquan Li 0002. FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs |
| 0 | -- | 0 | James Strudwick, Laura-Jayne Gardiner, Kate Denning-James, Niina Haiminen, Ashley Evans, Jennifer Kelly, Matthew Madgwick, Filippo Utro, Ed Seabolt, Christopher Gibson, Bharat Bedi, Daniel Clayton, Ciaron Howell, Laxmi Parida, Anna Paola Carrieri. AutoXAI4Omics: an automated explainable AI tool for omics and tabular data |
| 0 | -- | 0 | Long Xu, Qiang Yang 0015, Weihe Dong, Xiaokun Li, Kuanquan Wang, Suyu Dong, Xianyu Zhang, Tiansong Yang, Gongning Luo, Xingyu Liao, Xin Gao 0001, Guohua Wang. Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy |
| 0 | -- | 0 | Ornit Nahman, Timothy J. Few-Cooper, Shai S. Shen-Orr. Cell-specific priors rescue differential gene expression in spatial spot-based technologies |
| 0 | -- | 0 | Steffen Klamt, Jürgen Zanghellini, Axel von Kamp. Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine |
| 0 | -- | 0 | Peng-Hsuan Li, Yih-Yun Sun, Hsueh-Fen Juan, Chien-Yu Chen 0001, Huai-Kuang Tsai, Jia-Hsin Huang. A large language model framework for literature-based disease-gene association prediction |
| 0 | -- | 0 | Yinhu Li, Guangze Pan, Shuai Wang, Zhengtu Li, Ru Yang, Yiqi Jiang, Yu Chen, Shuaicheng Li 0001, Bairong Shen. Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome |
| 0 | -- | 0 | Yuejun Tan, Linhai Xie, Hong Yang, Qingyuan Zhang, Jinyuan Luo, Yanchun Zhang. BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction |
| 0 | -- | 0 | Shuo Li, Pei Fen Kuan. A systematic evaluation of cell-type-specific differential methylation analysis in bulk tissue |
| 0 | -- | 0 | Yongjie Xu, Zelin Zang, Bozhen Hu, Yue Yuan, Cheng Tan 0012, Jun Xia 0001, Stan Z. Li. Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation |
| 0 | -- | 0 | . Correction to: Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach |
| 0 | -- | 0 | Shan Tharanga, Eyyüb Selim Ünlü, Yongli Hu, Muhammad Farhan Sjaugi, Muhammet A Çelik, Hilal Hekimoglu, Olivo Miotto, Muhammed Miran Öncel, Asif M. Khan. DiMA: sequence diversity dynamics analyser for viruses |
| 0 | -- | 0 | Yunjian Chang, Ligang Wu. CapHLA: a comprehensive tool to predict peptide presentation and binding to HLA class I and class II |
| 0 | -- | 0 | Ying Li 0004, Qifeng Hu, Siyu Han, Rui Wang-Sattler, Wei Du 0002. Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics |
| 0 | -- | 0 | Ankang Wei, Zhen Xiao, Lingling Fu, Weizhong Zhao, Xingpeng Jiang. Predicting phage-host interactions via feature augmentation and regional graph convolution |
| 0 | -- | 0 | Boya Ji, Xiaoqi Wang, Xiang Wang, Liwen Xu, Shaoliang Peng. scDCA: deciphering the dominant cell communication assembly of downstream functional events from single-cell RNA-seq data |
| 0 | -- | 0 | Zheyang Zhang, Ronghan Tang, Ming Zhu, Zhijuan Zhu, Jiali Zhu, Hua Li, Mengsha Tong, Nainong Li, Jialiang Huang. Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia |
| 0 | -- | 0 | Yuanyuan Mo, Juan Liu, Lihua Zhang. Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression |
| 0 | -- | 0 | Junlei Liao, Hongyang Yi, Hao Wang, Sumei Yang, Duanmei Jiang, Xin Huang, Mingxia Zhang, Jiayin Shen, Hongzhou Lu, Yuanling Niu. CDCM: a correlation-dependent connectivity map approach to rapidly screen drugs during outbreaks of infectious diseases |
| 0 | -- | 0 | . Expression of Concern: Bioinformatics in Russia: history and present-day landscape |
| 0 | -- | 0 | Johanna Elena Schmitz, Sven Rahmann. A comprehensive review and evaluation of species richness estimation |
| 0 | -- | 0 | Elissavet Zacharopoulou, Maria D. Paraskevopoulou, Spyros Tastsoglou, Athanasios Alexiou, Anna Karavangeli, Vasileios Pierros, Stefanos Digenis, Galatea Mavromati, Artemis G. Hatzigeorgiou, Dimitra Karagkouni. microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites |
| 0 | -- | 0 | Yinqiao Yan, Xiangyu Luo. BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data |
| 0 | -- | 0 | Isaac Torres, Shufan Zhang, Amanda Bouffier, Michael Skaro, Yue Wu, Lauren Stupp, Jonathan P. Arnold, Y. Anny Chung, Heinz-Bernd Schüttler. MINE: a new way to design genetics experiments for discovery |
| 0 | -- | 0 | Tianyu Liu 0005, Wenxin Long, Zhiyuan Cao, Yuge Wang, Chuan Hua He, Le Zhang, Stephen M. Strittmatter, Hongyu Zhao 0003. CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis |
| 0 | -- | 0 | Xiangnan Xu, Alistair M. Senior, David G. Le Couteur, Victoria C. Cogger, David Raubenheimer, David E. James, Benjamin Parker, Stephen J. Simpson, Samuel Müller 0001, Jean Y. H. Yang. eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions |
| 0 | -- | 0 | Tianjiao Zhang, Xiang Zhang, Zhenao Wu, Jixiang Ren, Zhongqian Zhao, Hongfei Zhang, Guohua Wang, Tao Wang 0082. VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network |
| 0 | -- | 0 | Haoyang Cheng, Zhuoran Liang, Yijin Wu, Jiamin Hu, Bijin Cao, Zekun Liu, Bo Liu, Han Cheng, Ze-Xian Liu. Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets |
| 0 | -- | 0 | Dian Meng, Yu Feng, Kaishen Yuan, Zitong Yu, Qin Cao, Lixin Cheng, Xubin Zheng. scMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics |
| 0 | -- | 0 | Zhen Wang, Yizhen Feng, Qingwen Tian, Ziqi Liu, Pengju Yan, Xiaolin Li. RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models |
| 0 | -- | 0 | Jing Liang, Zhuo Hu, Ying Bi, Han Cheng, Weifeng Guo. Multimodal multiobjective optimization with structural network control principles to optimize personalized drug targets for drug discovery of individual patients |
| 0 | -- | 0 | Cristian Riccio, Max L. Jansen, Felix Thalén, Georgios Koliopanos, Vivian Link, Andreas Ziegler. Assessment of the functionality and usability of open-source rare variant analysis pipelines |
| 0 | -- | 0 | Xiaoyi Li, Kangli Zhu, Ying Zhen. A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning |
| 0 | -- | 0 | Ren Wang, Qiumei Liu, Wenhua You, Huiyu Wang, Yun Chen. A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma |
| 0 | -- | 0 | Kaiwen Zhang, Yuhao Tao, Fei Wang. AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody-antigen interaction prediction |
| 0 | -- | 0 | Yiwen Yang, Chengming Zhang 0003, Zhaonan Liu, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen, Wu Wei. MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics |
| 0 | -- | 0 | Chi Zhang, Yiran Cheng, Kaiwen Feng, Fa Zhang 0001, Renmin Han, Jieqing Feng. UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs |
| 0 | -- | 0 | Lubin Cui, Guiliang Guo, Michael K. Ng, Quan Zou 0001, Yushan Qiu. GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering |
| 0 | -- | 0 | Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-jun Yu, Fang Ge. MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification |
| 0 | -- | 0 | Anqiang Ye, Ji-Yun Zhang, Qian Xu, Hai-Xia Guo, Zhen Liao, Hongtu Cui, DongDong Zhang, Feng-Biao Guo. Carmna: classification and regression models for nitrogenase activity based on a pretrained large protein language model |
| 0 | -- | 0 | Chun Shen Lim, Alexandra K. Gibbon, Anh Thu Tran Nguyen, Gabrielle S. W. Chieng, Chris M. Brown. RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling |
| 0 | -- | 0 | Konstantina Tzavella, Adrián Díaz, Catharina Olsen, Wim F. Vranken. Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep |
| 0 | -- | 0 | Luuk R. Hoegen Dijkhof, Teemu K. E. Rönkkö, Hans C. von Vegesack, Jacob Lenzing, Alexander S. Hauser. Deep learning in GPCR drug discovery: benchmarking the path to accurate peptide binding |
| 0 | -- | 0 | Aoyi Wang, Haoyang Peng, Yingdong Wang, Haoran Zhang, Caiping Cheng, Jinzhong Zhao, Wuxia Zhang, Jianxin Chen, Peng Li 0004. NP-TCMtarget: a network pharmacology platform for exploring mechanisms of action of traditional Chinese medicine |
| 0 | -- | 0 | Yong Liu, Le Zhong, Bin Yan, Zhuobin Chen, Yanjia Yu, Dan Yu, Jing Qin 0004, Junwen Wang. A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks |
| 0 | -- | 0 | Matee Ullah, Shahid Akbar, Ali Raza, Kashif Ahmad Khan, Quan Zou 0001. TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach |
| 0 | -- | 0 | Peng Xia, Wei Wu, Quanzhong Liu, Bin Huang, Min Wu, Zihan Lin, Mengyan Zhu, Miao Yu, Ying Qu, Kening Li, Lingxiang Wu, Ruohan Zhang, Qianghu Wang. SCANER: robust and sensitive identification of malignant cells from the scRNA-seq profiled tumor ecosystem |
| 0 | -- | 0 | Nanhai Jiang, Yang Wu, Steven G. Rozen. Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm |
| 0 | -- | 0 | Tingyu Liu, Qiuhao Chen, Renjie Liu, Yuzhi Sun, Yadong Wang, Yan Zhu, Tianyi Zhao. DMGAT: predicting ncRNA-drug resistance associations based on diffusion map and heterogeneous graph attention network |
| 0 | -- | 0 | Mingguang Shi, Xuefeng Li. Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL |
| 0 | -- | 0 | Xiaolong Zhang, Xianchao Ji, Lingxiang Wang, Lianjiang Chi, Chengtao Li, Shaoqing Wen, Hua Chen. STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data |
| 0 | -- | 0 | Linjie Wang, Huixia Zhang, Bo Yi, Weidong Xie, Kun Yu 0002, Wei Li 0117, Keqin Li, Dazhe Zhao. FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis |
| 0 | -- | 0 | Han Wang, Zilin Ren, Jinghong Sun, Yongbing Chen, Xiaochen Bo, Jiguo Xue, Jingyang Gao, Ming Ni. DeepPFP: a multi-task-aware architecture for protein function prediction |
| 0 | -- | 0 | Sanjana Tule, Gabriel Foley, Mikael Bodén. Do protein language models learn phylogeny? |
| 0 | -- | 0 | Kris Sankaran, Saritha Kodikara, Jingyi Jessica Li, Kim-Anh Lê Cao. Semisynthetic simulation for microbiome data analysis |
| 0 | -- | 0 | Yuxiao Wei, Qi Zhang, Liwei Liu. The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs |
| 0 | -- | 0 | Yutao Zhang, Haocheng Ding, Zhiguang Huo, Li Chen. A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications |
| 0 | -- | 0 | Saurav Chandra Das, Wahia Tasnim, Humayan Kabir Rana, Uzzal Kumar Acharjee, Md. Manowarul Islam, Rabea Khatun. Comprehensive bioinformatics and machine learning analyses for breast cancer staging using TCGA dataset |
| 0 | -- | 0 | Shengjie Liu, Tianwei Yu. Nonlinear embedding and integration of omics data: a fast and tuning-free approach |
| 0 | -- | 0 | Xingyi Li, Jialuo Xu, Junming Li, Jia Gu, Xuequn Shang. Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks |
| 0 | -- | 0 | Qiongyi Zhao, Woo Jun Shim, Yuliangzi Sun, Enakshi Sinniah, Sophie Shen, Mikael Bodén, Nathan J. Palpant. TRIAGE: an R package for regulatory gene analysis |
| 0 | -- | 0 | Yiren Shao, Qi Gao, Liuyang Wang, Dongmei Li, Andrew B. Nixon, Cliburn Chan, Qi-Jing Li, Jichun Xie. B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity |
| 0 | -- | 0 | Kibeom Kim, Juseong Kim, Minwook Kim, Hyewon Lee, Giltae Song. Therapeutic gene target prediction using novel deep hypergraph representation learning |
| 0 | -- | 0 | Mingzhi Yuan, Ao Shen, Yingfan Ma, Jie Du, Bohan An, Manning Wang. ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface |
| 0 | -- | 0 | . Correction to: STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution |
| 0 | -- | 0 | Ashok Kumar, Sonia Chadha, Mradul Sharma, Mukesh Kumar. Deciphering optimal molecular determinants of non-hemolytic, cell-penetrating antimicrobial peptides through bioinformatics and Random Forest |
| 0 | -- | 0 | Yixuan Qiao, Hong Zhou, Yang Liu, Ruixuan Chen, Xiaodong Zhang, Sheng Nie, Fan Fan Hou, Yi Zhao, Xin Xu, Lianhe Zhao. A multi-modal fusion model with enhanced feature representation for chronic kidney disease progression prediction |
| 0 | -- | 0 | Jiachen Chen, Joanne M. Murabito, Kathryn L. Lunetta. ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks |
| 0 | -- | 0 | Lixian Lin, Haoyu Wang, Yuxiao Chen, Yuanyuan Wang, Yujie Xu, Zhenglin Chen, Yuemin Yang, Kunpeng Liu, Xiaokai Ma. STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model |
| 0 | -- | 0 | Cong M. Pham, Timothy J. Rankin, Timothy P. Stinear, Calum J. Walsh, Feargal J. Ryan. TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases |
| 0 | -- | 0 | Tianjiao Zhang, Hao Sun, Zhenao Wu, Zhongqian Zhao, Xingjie Zhao, Hongfei Zhang, Bo Gao, Guohua Wang. GAADE: identification spatially variable genes based on adaptive graph attention network |
| 0 | -- | 0 | Dominik Lux, Katrin Marcus-Alic, Martin Eisenacher, Julian Uszkoreit. ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs |
| 0 | -- | 0 | Guo-Hua Yuan, Jinzhe Li, Zejun Yang, Yao-Qi Chen, Zhonghang Yuan, Tao Chen 0003, Wanli Ouyang, Nanqing Dong, Li Yang. Deep generative model for protein subcellular localization prediction |
| 0 | -- | 0 | . Correction to: BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation |
| 0 | -- | 0 | Raúl Galindo-Hernández, Katya Rodríguez-Vázquez, Edgardo Galán-Vásquez, Carlos Ignacio Hernández Castellanos. Online-adjusted evolutionary biclustering algorithm to identify significant modules in gene expression data |
| 0 | -- | 0 | Ashwin R. Nair, Xingjian Li, Bhupendra Solanki, Souradeep Mukhopadhyay, Ankit Jha, Mostofa Rafid Uddin, Mainak Singha, Biplab Banerjee, Min Xu. Towards molecular structure discovery from cryo-ET density volumes via modelling auxiliary semantic prototypes |
| 0 | -- | 0 | Jordi Martorell-Marugan, Raúl López-Domínguez, Juan Antonio Villatoro-García, Daniel Toro-Domínguez, Marco Chierici, Giuseppe Jurman, Pedro Carmona-Saez. Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics |
| 0 | -- | 0 | . Correction to: Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison |
| 0 | -- | 0 | Upamanyu Ghose, William Sproviero, Laura Winchester, Najaf Amin, Taiyu Zhu, Danielle Newby, Brittany S. Ulm, Angeliki Papathanasiou, Liu Shi, Qiang Liu, Marco Fernandes, Cassandra Adams, Ashwag Albukhari, Majid Almansouri, Hani Choudhry, Cornelia van Duijn, Alejo J. Nevado-Holgado. Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease |
| 0 | -- | 0 | Yunlong Wang, Siyuan Kong, Cong Zhou, Yanfang Wang, Yubo Zhang, Yaping Fang, Guoliang Li 0002. A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles |
| 0 | -- | 0 | Xiaolong Wu, Lehan Zhang, Xiaochu Tong, Yitian Wang, Zimei Zhang, Xiangtai Kong, Shengkun Ni, Xiaomin Luo, Mingyue Zheng, Yun Tang 0001, Xutong Li. miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA |
| 0 | -- | 0 | Gen Li, Sijie Yao, Long Fan. Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types |
| 0 | -- | 0 | Md. Zubbair Malik, Mohammed Dashti, Amit Jangid, Arshad Channanath, Sumi Elsa John, R. K. Brojen Singh, Fahd Al-Mulla, Thangavel Alphonse Thanaraj. Complex p53 dynamics regulated by miR-125b in cellular responses to reactive oxidative stress and DNA damage |
| 0 | -- | 0 | Lan Cao, Wenhao Zhang, Fan Yang, Shengquan Chen, Xiaobing Huang, Feng Zeng, Ying Wang. BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells |
| 0 | -- | 0 | José A. Sánchez-Villanueva, Lia N'guyen, Mathilde Poplineau, Estelle Duprez, Elisabeth Remy, Denis Thieffry. Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy |
| 0 | -- | 0 | Ansar Naseem, Fahad Alturise, Tamim Alkhalifah, Yaser Daanial Khan. ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood-brain barrier peptides |
| 0 | -- | 0 | Zeyin Li, Min Wang, Songge Li, Fangyuan Shi. MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variants |
| 0 | -- | 0 | Meng-Chi Chung, Li-Jen Su, Chien-Lin Chen, Li-Ching Wu. Revealing the antimicrobial potential of traditional Chinese medicine through text mining and molecular computation |
| 0 | -- | 0 | Jiaqi Wang, Ronggang Xi, Yi Wang, Huiyuan Gao, Ming Gao, Xiaozhe Zhang, Lihua Zhang, Yukui Zhang. Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach |
| 0 | -- | 0 | Hong Xia, Boya Ji, Debin Qiao, Shaoliang Peng. CellMsg: graph convolutional networks for ligand-receptor-mediated cell-cell communication analysis |