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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 21
Volume 21, Number 1, January - February 2024
- Yamane El-Zein
, Mathieu Lemay, Kévin Huguenin:
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data. 1-13 - Chao Tu, Denghui Du, Tieyong Zeng, Yu Zhang:
Deep Multi-Dictionary Learning for Survival Prediction With Multi-Zoom Histopathological Whole Slide Images. 14-25 - Jordan Morris, Ashur Rafiev, Graeme M. Bragg, Mark L. Vousden, David B. Thomas, Alex Yakovlev, Andrew D. Brown:
An Event-Driven Approach to Genotype Imputation on a Custom RISC-V Cluster. 26-35 - Souradipto Choudhuri, Keya Sau:
CodonU: A Python Package for Codon Usage Analysis. 36-44 - Shengpeng Yu, Hong Wang, Jing Li, Jun Zhao, Cheng Liang, Yanshen Sun:
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations. 45-56 - Rui Guo, Xu Tian, Hanhe Lin, Stephen J. McKenna, Hong-Dong Li, Fei Guo, Jin Liu:
Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis. 57-68 - Jonas Kristiansen Nøland, Steinar Thorvaldsen:
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model. 69-83 - Wenliang Tang, Zhaohong Deng, Hanwen Zhou, Wei Zhang, Fuping Hu, Kup-Sze Choi, Shitong Wang:
MVDINET: A Novel Multi-Level Enzyme Function Predictor With Multi-View Deep Interactive Learning. 84-94 - Shujie Dong, Yuansheng Liu, Yongshun Gong, Xiangjun Dong, Xiangxiang Zeng:
scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data. 95-105 - Nicolò Rossi, Nicola Gigante, Nicola Vitacolonna, Carla Piazza:
Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE. 106-119 - Dandan Li, Zhen Xiao, Han Sun, Xingpeng Jiang, Weizhong Zhao, Xianjun Shen:
Prediction of Drug-Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding. 120-128 - Changyong Yu, Yuhai Zhao, Chu Zhao, Jianyu Jin, Keming Mao, Guoren Wang:
MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping. 129-142 - Wei Wang, MengXue Yu, Bin Sun, Juntao Li, Dong Liu, Hongjun Zhang, Xianfang Wang, Yun Zhou:
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction. 143-154 - Rituparna Sinha, Rajat Kumar Pal, Rajat K. De:
ENLIGHTENMENT: A Scalable Annotated Database of Genomics and NGS-Based Nucleotide Level Profiles. 155-168 - Eric J. Barnett, Daniel G. Onete, Asif Salekin, Stephen V. Faraone:
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance. 169-177 - Yuerui Liu, Yongquan Jiang, Fan Zhang, Yan Yang:
A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction. 178-187 - Junchang Xin, Mingcan Wang, Luxuan Qu, Qi Chen, Weiyiqi Wang, Zhiqiong Wang:
BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction. 188-199 - Pengcheng Zeng, Zhixiang Lin:
scICML: Information-Theoretic Co-Clustering-Based Multi-View Learning for the Integrative Analysis of Single-Cell Multi-Omics Data. 200-207 - Bindi M. Nagda, Van Minh Nguyen, Ryan T. White:
promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences. 208-214
Volume 21, Number 2, March - April 2024
- Fernando Cruz, João Capela, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. 215-226 - Hao Zhang, Jiao Jiao, Tianheng Zhao, Enshuang Zhao, Lanhui Li, Guihua Li, Borui Zhang, Qing-Ming Qin:
GERWR: Identifying the Key Pathogenicity- Associated sRNAs of Magnaporthe Oryzae Infection in Rice Based on Graph Embedding and Random Walk With Restart. 227-239 - Daniel Manu, Jingjing Yao, Wuji Liu, Xiang Sun:
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery. 240-253 - Zhao-Qi Hu, Yuan-Mao Hung, Li-Han Chen, Liang-Chuan Lai, Min-Hsiung Pan, Eric Y. Chuang, Mong-Hsun Tsai:
NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. 254-264 - Sichen Jin, Yijia Zhang, Huimin Yu, Mingyu Lu:
SADR: Self-Supervised Graph Learning With Adaptive Denoising for Drug Repositioning. 265-277 - Alina F. Leuchtenberger, Arndt von Haeseler:
Learning From an Artificial Neural Network in Phylogenetics. 278-288 - Wenjing Wang, Pengyong Han, Zhengwei Li, Ru Nie, Kangwei Wang, Lei Wang, Hongmei Liao:
LMGATCDA: Graph Neural Network With Labeling Trick for Predicting circRNA-Disease Associations. 289-300 - Tiantian Li, Haitao Jiang, Binhai Zhu, Lusheng Wang, Daming Zhu:
Flanked Block-Interchange Distance on Strings. 301-311
Volume 21, Number 3, May - June 2024
- João Paulo Pereira Zanetti, Lucas Peres Oliveira, João Meidanis, Leonid Chindelevitch:
Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance. 316-327 - Nan Sheng, Xuping Xie, Yan Wang, Lan Huang, Shuangquan Zhang, Ling Gao, Hao Wang:
A Survey of Deep Learning for Detecting miRNA- Disease Associations: Databases, Computational Methods, Challenges, and Future Directions. 328-347 - Tara Newman, Hiu Fung Kevin Chang, Hosna Jabbari:
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots. 348-359 - Juan Wang, Zhen-Chang Wang, Shasha Yuan, Chun-Hou Zheng, Jin-Xing Liu, Junliang Shang:
A Clustering Method for Single-Cell RNA-Seq Data Based on Automatic Weighting Penalty and Low-Rank Representation. 360-371 - Xiaohui Yang, Ye-Tong Wang, Ming-Hui Wu, Fan Li, Cheng-Long Zhou, Li-Jun Yang, Chen Zheng, Yong Li, Zhi Li, Si-Yi Guo, Chun-Peng Song:
SLPA-Net: A Real-Time Recognition Network for Intelligent Stomata Localization and Phenotypic Analysis. 372-382 - Shan Zhang, Yuan Zhou, Pei Geng, Qing Lu:
Functional Neural Networks for High-Dimensional Genetic Data Analysis. 383-393 - Cheng Yan, Guihua Duan:
PMDAGS: Predicting miRNA-Disease Associations With Graph Nonlinear Diffusion Convolution Network and Similarities. 394-404 - Sheena K. S., Madhu S. Nair:
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression. 405-415 - Wei Wang, Zhenxi Sun, Dong Liu, Hongjun Zhang, Juntao Li, Xian-Fang Wang, Yun Zhou:
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling. 416-427 - Sunyong Yoo, Myeonghyeon Jeong, Subhin Seomun, Kiseong Kim, Youngmahn Han:
Interpretable Prediction of SARS-CoV-2 Epitope-Specific TCR Recognition Using a Pre-Trained Protein Language Model. 428-438 - Pallavi M. Shanthappa, Neeraj Verma, Anu George, Pawan K. Dhar, Prashanth Athri:
Computational Prediction of Potential Vaccine Candidates From tRNA Encoded peptides (tREP) Using a Bioinformatic Workflow and Molecular Dynamics Validations. 439-449 - Arnav Solanki, James L. Cornette, Julia Udell, George Vasmatzis, Marc D. Riedel:
Evasive Spike Variants Elucidate the Preservation of T Cell Immune Response to the SARS-CoV-2 Omicron Variant. 450-460 - Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen:
Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. 461-471 - Minglie Li, Shusen Zhou, Tong Liu, Chanjuan Liu, Mujun Zang, Qingjun Wang:
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants. 472-479 - Ke Ma, Jiawei Li, Mengyuan Zhao, Ibrahim Zamit, Bin Lin, Fei Guo, Jijun Tang:
PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection. 480-491 - Weiling Li, Raunaq Malhotra, Steven H. Wu, Manjari Jha, Allen G. Rodrigo, Mary Poss, Raj Acharya:
ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data. 492-500 - Gabriel Cardona, Joan Carles Pons, Gerard Ribas, Tomás Martínez Coronado:
Comparison of Orchard Networks Using Their Extended $\mu$μ-Representation. 501-507 - Alejandro Valdés-Jiménez, Miguel Reyes-Parada, Gabriel Núñez-Vivanco, Daniel Jiménez-González:
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns. 508-515
Volume 21, Number 5, September - October 2024
- Zhipeng Cai, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 1141-1142 - Junwen Duan, Shuyue Liu, Xincheng Liao, Feng Gong, Hailin Yue, Jianxin Wang:
Chinese EMR Named Entity Recognition Using Fused Label Relations Based on Machine Reading Comprehension Framework. 1143-1153 - Zeqian Li, Yi-Jia Zhang, Peixuan Zhou:
Temporal Protein Complex Identification Based on Dynamic Heterogeneous Protein Information Network Representation Learning. 1154-1164 - Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen:
Guest Editorial Selected Papers From BIOKDD 2022. 1165-1167 - Farhan Tanvir, Khaled Mohammed Saifuddin, Muhammad Ifte Khairul Islam, Esra Akbas:
DDI Prediction With Heterogeneous Information Network - Meta-Path Based Approach. 1168-1179 - Shaina Raza, Chen Ding:
Improving Clinical Decision Making With a Two-Stage Recommender System. 1180-1190 - Cunmei Ji, Ning Yu, Yu-Tian Wang, Jiancheng Ni, Chun-Hou Zheng:
SGLMDA: A Subgraph Learning-Based Method for miRNA-Disease Association Prediction. 1191-1201 - Junwen Duan, Huai Guo, Han Jiang, Fei Guo, Jian-xin Wang:
Boundary-Aware Dual Biaffine Model for Sequential Sentence Classification in Biomedical Documents. 1202-1210 - Yen-Che Hsiao, Abhishek Dutta:
Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives. 1211-1230 - Qingsong Wang, Ruiquan Ge, Changmiao Wang, Ahmed Elazab, Qiming Fang, Renfeng Zhang:
TDFFM: Transformer and Deep Forest Fusion Model for Predicting Coronavirus 3C-Like Protease Cleavage Sites. 1231-1241 - Ana León Palacio, Alberto García S., José Fabián Reyes Román, Mireia Costa, Oscar Pastor:
The Delfos Platform: A Conceptual Model-Based Solution for the Enhancement of Precision Medicine. 1242-1253 - Changfeng Cai, Jianghui Li, Yuanling Xia, Weihua Li:
FluPMT: Prediction of Predominant Strains of Influenza A Viruses via Multi-Task Learning. 1254-1263 - Sumona Biswas, Shovan Barma:
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images. 1264-1273 - Wenya Yang, Sai Zou, Hongfeng Gao, Lei Wang, Wei Ni:
A Novel Method for Targeted Identification of Essential Proteins by Integrating Chemical Reaction Optimization and Naive Bayes Model. 1274-1286 - Sen Yang, Peng Cheng, Yang Liu, Dawei Feng, Shengqi Wang:
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer. 1287-1298 - Xiaoya Chong, Howard Leung, Qing Li, Jianhua Yao, Niyun Zhou:
Deep Spatio-Temporal Network for Low-SNR Cryo-EM Movie Frame Enhancement. 1299-1310 - Yin Guo, Yanni Xiao, Limin Li:
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples. 1311-1321 - Seyed Hamid Hosseini, Mahdi Imani:
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks. 1322-1334 - Huan Wang, Ziwen Cui, Yinguang Yang, Baijing Wang, Lida Zhu, Wen Zhang:
A Network Enhancement Method to Identify Spurious Drug-Drug Interactions. 1335-1347 - Ying Liang, Xiya You, Ze-Qun Zhang, Shi Qiu, Suhui Li, Lianlian Fu:
MGFmiRNAloc: Predicting miRNA Subcellular Localization Using Molecular Graph Feature and Convolutional Block Attention Module. 1348-1357 - Ruiquan Ge, Yixiao Xia, Minchao Jiang, Gangyong Jia, Xiaoyang Jing, Ye Li, Yunpeng Cai:
HybAVPnet: A Novel Hybrid Network Architecture for Antiviral Peptides Prediction. 1358-1365 - Xubin Wang, Yunhe Wang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li:
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner. 1366-1379 - Xiaowen Hu, Ying Jiang, Lei Deng:
Exploring ncRNA-Drug Sensitivity Associations via Graph Contrastive Learning. 1380-1389 - Sankar Mondal, Pradipta Maji:
Multi-Task Learning and Sparse Discriminant Canonical Correlation Analysis for Identification of Diagnosis-Specific Genotype-Phenotype Association. 1390-1402 - Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning. 1403-1412 - Wei Lan, Chunling Li, Qingfeng Chen, Ning Yu, Yi Pan, Yu Zheng, Yi-Ping Phoebe Chen:
LGCDA: Predicting CircRNA-Disease Association Based on Fusion of Local and Global Features. 1413-1422 - Mingshuai Chen, Quan Zou, Ren Qi, Yijie Ding:
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites. 1423-1435 - Razan Alkhanbouli, Amira Al-Aamri, Maher Maalouf, Kamal Taha, Andreas Henschel, Dirar Homouz:
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics. 1436-1444 - Pengli Lu, Yuehao Wang:
RDGAN: Prediction of circRNA-Disease Associations via Resistance Distance and Graph Attention Network. 1445-1457 - Lingling Zhao, Yan Zhu, Naifeng Wen, Chunyu Wang, Junjie Wang, Yongfeng Yuan:
Drug-Target Binding Affinity Prediction in a Continuous Latent Space Using Variational Autoencoders. 1458-1467 - Muhao Xu, Zhenfeng Zhu, Yawei Zhao, Kunlun He, Qinghua Huang, Yao Zhao:
RedCDR: Dual Relation Distillation for Cancer Drug Response Prediction. 1468-1479 - Hang Gao, Wenjun Shen, Rui Li, Cheng Liu, Si Wu:
Collaborative Structure-Preserved Missing Data Imputation for Single-Cell RNA-Seq Clustering. 1480-1491 - Zile Wang, Hai-Yun Wang, Jianping Zhao, Junfeng Xia, Chun-Hou Zheng:
scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data. 1492-1503 - Mohammad Alali, Mahdi Imani:
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks. 1504-1517 - Yanan Zhang, Xiangzhi Bai:
Geometry-Augmented Molecular Representation Learning for Property Prediction. 1518-1528 - Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes. 1529-1541 - Qiang Yu, Yana Hu, Xinnan Hu, Jingfen Lan, Yang Guo:
An Efficient Exact Algorithm for Planted Motif Search on Large DNA Sequence Datasets. 1542-1551 - Huaxin Pang, Shikui Wei, Zhuoran Du, Yufeng Zhao, Shengxing Cai, Yao Zhao:
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction. 1552-1564 - Longxin Zhang, Wenliang Zeng, Jingsheng Chen, Jianguo Chen, Keqin Li:
ParaCPI: A Parallel Graph Convolutional Network for Compound-Protein Interaction Prediction. 1565-1578 - Maotao Liu, Yifan Yang, Qun Liu, Li Liu, Guoyin Wang:
A Knowledge-Driven Self-Supervised Approach for Molecular Generation. 1579-1590 - Xiaoxiao Sun, Paul Sajda:
Circular Clustering With Polar Coordinate Reconstruction. 1591-1600
Volume 21, Number 6, November - December 2024
- Su Datt Lam, Wai Keat Yam, Yi-Ping Phoebe Chen:
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference. 1601-1603 - Lin Zhu, Xin Kang, Chunhe Li, Jie Zheng:
TMELand: An End-to-End Pipeline for Quantification and Visualization of Waddington's Epigenetic Landscape Based on Gene Regulatory Network. 1604-1612 - Chenglin Yu, Shu Zhang, Muheng Shang, Lei Guo, Junwei Han, Lei Du:
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics. 1613-1622 - Ryota Ido, Shengjuan Cao, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
A Method for Inferring Polymers Based on Linear Regression and Integer Programming. 1623-1632 - Michael D. Sweeney, Luke Torre-Healy, Virginia L. Ma, Margaret Hall, Lucie Chrastecka, Alisa Yurovsky, Richard A. Moffitt:
FaStaNMF: A Fast and Stable Non-Negative Matrix Factorization for Gene Expression. 1633-1644 - Wenwei Xu, Hao Zhang, Yewei Xia, Yixin Ren, Jihong Guan, Shuigeng Zhou:
Hybrid Causal Feature Selection for Cancer Biomarker Identification From RNA-Seq Data. 1645-1655 - Ümmü Gülsüm Söylemez, Malik Yousef, Zülal Kesmen, Burcu Bakir-Gungor:
Novel Antimicrobial Peptide Design Using Motif Match Score Representation. 1656-1666 - Henry Claussen, Santu Ghosh, Jie Chen:
Exploring Combined Effects of DNA Methylation and Copy Number on Gene Expression With a Two-Stage Approach. 1667-1675 - Jian Zhong, Haochen Zhao, Qichang Zhao, Ruikang Zhou, Lishen Zhang, Fei Guo, Jianxin Wang:
RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site Prediction. 1676-1684 - Wenting Zhao, Gongping Xu, Long Wang, Zhen Cui, Tong Zhang, Jian Yang:
Intra-Inter Graph Representation Learning for Protein-Protein Binding Sites Prediction. 1685-1696 - Yuanfei Dai, Bin Zhang, Shiping Wang:
Distantly Supervised Biomedical Relation Extraction via Negative Learning and Noisy Student Self-Training. 1697-1708 - Vikash Kumar, Akshay Deepak, Ashish Ranjan, Aravind Prakash:
CrossPredGO: A Novel Light-Weight Cross-Modal Multi-Attention Framework for Protein Function Prediction. 1709-1720 - M. Mohamed Divan Masood, D. Manjula, Vijayan Sugumaran:
Transcription Factor Binding Site Prediction Using CnNet Approach. 1721-1730 - Fujin Zhang, Zhangwei Li, Kailong Zhao, Pengxin Zhao, Guijun Zhang:
Prediction of Inter-Residue Multiple Distances and Exploration of Protein Multiple Conformations by Deep Learning. 1731-1739 - Xinyi Qin, Lu Zhang, Min Liu, Guangzhong Liu:
PRFold-TNN: Protein Fold Recognition With an Ensemble Feature Selection Method Using PageRank Algorithm Based on Transformer. 1740-1751 - Chengcheng Zhang, Wei Li, Ming Deng, Yizhang Jiang, Xiaohui Cui, Ping Chen:
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information. 1752-1764 - Weicheng Sun, Chengjuan Ren, Jinsheng Xu, Ping Zhang:
SAGCN: Using Graph Convolutional Network With Subgraph-Aware for circRNA-Drug Sensitivity Identification. 1765-1774 - Jongrae Kim, Woojeong Lee, Kwang-Hyun Cho:
Recursive Self-Composite Approach Toward Structural Understanding of Boolean Networks. 1775-1783 - Khalid Usman, Fangping Wan, Dan Zhao, Jian Peng, Jianyang Zeng:
Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset. 1784-1793 - Zhen Ju, Jingjing Zhang, Xuelei Li, Jintao Meng, Yanjie Wei:
SeedHit: A GPU Friendly Pre-Align Filtering Algorithm. 1794-1802 - Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites. 1803-1815 - Marzieh Emadi, Farsad Zamani Boroujeni, Jamshid Pirgazi:
Improved Fuzzy Cognitive Maps for Gene Regulatory Networks Inference Based on Time Series Data. 1816-1829 - Guangyu Wang, Ying Chu, Qianqian Wang, Limei Zhang, Lishan Qiao, Mingxia Liu:
Graph Convolutional Network With Self-Supervised Learning for Brain Disease Classification. 1830-1841 - Xueqiang Fan, Bing Lin, Jun Hu, Zhongyi Guo:
Ense-i6mA: Identification of DNA N6-Methyladenine Sites Using XGB-RFE Feature Selection and Ensemble Machine Learning. 1842-1854 - Ruriko Yoshida, David Barnhill, Keiji Miura, Daniel K. Howe:
Tropical Density Estimation of Phylogenetic Trees. 1855-1863 - Yong See Foo, Jennifer A. Flegg:
Haplotype Frequency Inference From Pooled Genetic Data With a Latent Multinomial Model. 1864-1873 - Hailin Feng, Chenchen Ke, Quan Zou, Zhechen Zhu, Tongcun Liu:
Prediction of Potential miRNA-Disease Associations Based on a Masked Graph Autoencoder. 1874-1885 - Wentao Zhu, Zhiqiang Du, Ziang Xu, Defu Yang, Minghan Chen, Qianqian Song:
SCRN: Single-Cell Gene Regulatory Network Identification in Alzheimer's Disease. 1886-1896 - Xiuhao Fu, Hao Duan, Xiaofeng Zang, Chunling Liu, Xingfeng Li, Qingchen Zhang, Zilong Zhang, Quan Zou, Feifei Cui:
Hyb_SEnc: An Antituberculosis Peptide Predictor Based on a Hybrid Feature Vector and Stacked Ensemble Learning. 1897-1910 - Fadi Shehadeh, LewisOscar Felix, Markos Kalligeros, Adnan Shehadeh, Beth Burgwyn Fuchs, Frederick M. Ausubel, Paul P. Sotiriadis, Eleftherios Mylonakis:
Machine Learning-Assisted High-Throughput Screening for Anti-MRSA Compounds. 1911-1921 - Vikash Kumar, Akshay Deepak, Ashish Ranjan, Aravind Prakash:
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction. 1922-1933 - Rajesh Kumar Mundotiya, Juhi Priya, Divya Kuwarbi, Teekam Singh:
Enhancing Generalizability in Biomedical Entity Recognition: Self-Attention PCA-CLS Model. 1934-1941 - Aditya Kumar, Deepak Singh:
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction. 1942-1954 - Fernando H. C. Dias, Alexandru I. Tomescu:
Accurate Flow Decomposition via Robust Integer Linear Programming. 1955-1964 - Kamal Taha:
Employing Machine Learning Techniques to Detect Protein Function: A Survey, Experimental, and Empirical Evaluations. 1965-1986 - Changyong Yu, Dekuan Gao, Xu Guo, Haitao Ma, Yuhai Zhao, Guoren Wang:
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph. 1987-1999 - Wenkang Wang, Xiangmao Meng, Ju Xiang, Hayat Dino Bedru, Min Li:
Dopcc: Detecting Overlapping Protein Complexes via Multi-Metrics and Co-Core Attachment Method. 2000-2010 - Zhen Zhang, Zhaohong Deng, Ruibo Li, Wei Zhang, Qiongdan Lou, Kup-Sze Choi, Shitong Wang:
HGLA: Biomolecular Interaction Prediction Based on Mixed High-Order Graph Convolution With Filter Network via LSTM and Channel Attention. 2011-2024 - Qiaozhen Meng, Genlang Chen, Bin Lin, Shixin Zheng, Yulai Lin, Jijun Tang, Fei Guo:
DMAMP: A Deep-Learning Model for Detecting Antimicrobial Peptides and Their Multi-Activities. 2025-2034 - Xiaoli Lin, Zhuang Yin, Xiaolong Zhang, Jing Hu:
KGRLFF: Detecting Drug-Drug Interactions Based on Knowledge Graph Representation Learning and Feature Fusion. 2035-2049 - Siyuan Guo, Jihong Guan, Shuigeng Zhou:
Diffusing on Two Levels and Optimizing for Multiple Properties: A Novel Approach to Generating Molecules With Desirable Properties. 2050-2063 - Xinyu He, Yujie Tang, Bo Yu, Shixin Li, Yonggong Ren:
Joint Extraction of Biomedical Events Based on Dynamic Path Planning Strategy and Hybrid Neural Network. 2064-2075 - Sachin Mathur, Hamid Mattoo, Ziv Bar-Joseph:
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data. 2076-2088 - Jiayi Dong, Jiahao Li, Fei Wang:
Deep Learning in Gene Regulatory Network Inference: A Survey. 2089-2101 - Huiwei Zhou, Wenchu Li, Weihong Yao, Yingyu Lin, Lei Du:
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation. 2102-2112 - Yushan Qiu, Wensheng Chen, Wai-Ki Ching, Hongmin Cai, Hao Jiang, Quan Zou:
AGML: Adaptive Graph-Based Multi-Label Learning for Prediction of RBP and as Event Associations During EMT. 2113-2122 - Qinan Tang, Ying Xiang, Wanling Gao, Liqiang Zhu, Zishu Xu, Yeyun Li, Zhenyu Yue:
TeaTFactor: A Prediction Tool for Tea Plant Transcription Factors Based on BERT. 2123-2132 - Ying Wang, Maoyuan Ma, Yanxin Xie, Qinke Peng, Hongqiang Lyu, Hequan Sun, Laiyi Fu:
KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-Disease Association Prediction. 2133-2144 - Yufei Li, Xiaoyong Ma, Xiangyu Zhou, Penghzhen Cheng, Kai He, Tieliang Gong, Chen Li:
Integrating K+ Entities Into Coreference Resolution on Biomedical Texts. 2145-2155 - Zhijing Li, Liwei Tian, Yiping Jiang, Yucheng Huang:
Relation Extraction in Biomedical Texts: A Cross-Sentence Approach. 2156-2166 - José A. Sáez, José Fernando Vera:
Compact Class-Conditional Attribute Category Clustering: Amino Acid Grouping for Enhanced HIV-1 Protease Cleavage Classification. 2167-2178 - Qingzhou Shi, Kai Zheng, Haoyuan Li, Bo Wang, Xiao Liang, Xinyu Li, Jianxin Wang:
LKLPDA: A Low-Rank Fast Kernel Learning Approach for Predicting piRNA-Disease Associations. 2179-2187 - Vincent Deman, Marine Ciantar, Laurent Naudin, Philippe Castera, Anne-Sophie Beignon:
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems. 2188-2199 - Qi Zhang, Yuxiao Wei, Bo Liao, Liwei Liu, Shengli Zhang:
MMD-DTA: A Multi-Modal Deep Learning Framework for Drug-Target Binding Affinity and Binding Region Prediction. 2200-2211 - Bin Liu, Grigorios Tsoumakas:
Integrating Similarities via Local Interaction Consistency and Optimizing Area Under the Curve Measures via Matrix Factorization for Drug-Target Interaction Prediction. 2212-2225 - Takatora Suzuki, Han Guo, Momoko Hayamizu:
Bridging Between Deviation Indices for Non-Tree-Based Phylogenetic Networks. 2226-2234 - Hao Lu, Zhiqiang Wei, Kun Zhang, Xuze Wang, Liaqat Ali, Hao Liu:
CTsynther: Contrastive Transformer Model for End-to-End Retrosynthesis Prediction. 2235-2245 - Lars Berling, Remco Bouckaert, Alex Gavryushkin:
An Automated Convergence Diagnostic for Phylogenetic MCMC Analyses. 2246-2257 - Chuang Li, Heshi Wang, Yanhua Wen, Rui Yin, Xiangxiang Zeng, Keqin Li:
GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model. 2258-2268 - Yang Hua, Zhenhua Feng, Xiaoning Song, Hui Li, Tianyang Xu, Xiao-Jun Wu, Dong-Jun Yu:
APMG: 3D Molecule Generation Driven by Atomic Chemical Properties. 2269-2279 - Shengwen Tian, Cunmei Ji, Jiancheng Ni, Yutian Wang, Chunhou Zheng:
Using Multi-Encoder Semi-Implicit Graph Variational Autoencoder to Analyze Single-Cell RNA Sequencing Data. 2280-2291 - Juan Wang, Tian-Jing Qiao, Chun-Hou Zheng, Jin-Xing Liu, Junliang Shang:
A New Graph Autoencoder-Based Multi-Level Kernel Subspace Fusion Framework for Single-Cell Type Identification. 2292-2303 - Reza Mazloom, N. Tessa Pierce-Ward, Parul Sharma, Leighton Pritchard, C. Titus Brown, Boris A. Vinatzer, Lenwood S. Heath:
LINgroups as a Robust Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies. 2304-2314 - Ben Xu, Jianping Chen, Yunzhe Wang, Qiming Fu, You Lu:
Reinforced Metapath Optimization in Heterogeneous Information Networks for Drug-Target Interaction Prediction. 2315-2329 - Eleonora Mian, Enrico Petrucci, Cinzia Pizzi, Matteo Comin:
MISSH: Fast Hashing of Multiple Spaced Seeds. 2330-2339 - Runchang Jia, Zhijie He, Cong Wang, Xudong Guo, Fuyi Li:
MetalPrognosis: A Biological Language Model-Based Approach for Disease-Associated Mutations in Metal-Binding Site Prediction. 2340-2348 - Jiashun Wu, Yan Liu, Yiheng Zhu, Dong-Jun Yu:
Improving Antifreeze Proteins Prediction With Protein Language Models and Hybrid Feature Extraction Networks. 2349-2358 - Yuyang Xu, Jingbo Zhou, Haochao Ying, Jintai Chen, Wei Chen, Danny Z. Chen, Jian Wu:
A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction. 2359-2370 - Zhipeng Hu, Gaoshi Li, Xinlong Luo, Wei Peng, Jiafei Liu, Xiaoshu Zhu, Jingli Wu:
Identification of Cancer Driver Genes based on Dynamic Incentive Model. 2371-2381 - Shidi Tang, Ji Ding, Xiangyu Zhu, Zheng Wang, Haitao Zhao, Jiansheng Wu:
Vina-GPU 2.1: Towards Further Optimizing Docking Speed and Precision of AutoDock Vina and Its Derivatives. 2382-2393 - Garud Iyengar, Mitch Perry:
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition. 2394-2405 - Xuena Liang, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng, Juan Wang:
Enhancing Spatial Domain Identification in Spatially Resolved Transcriptomics Using Graph Convolutional Networks With Adaptively Feature-Spatial Balance and Contrastive Learning. 2406-2417 - Haixi Zhang, Jiahui Yang, Chenyan Lv, Xing Wei, Haibin Han, Bin Liu:
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments. 2418-2431 - Luca Cattelani, Arindam Ghosh, Teemu J. Rintala, Vittorio Fortino:
A Comprehensive Evaluation Framework for Benchmarking Multi-Objective Feature Selection in Omics-Based Biomarker Discovery. 2432-2446 - Zhenhao Sun, Meng Wang, Shiqi Wang, Sam Kwong:
LEC-Codec: Learning-Based Genome Data Compression. 2447-2458 - Dengwei Zhao, Jingyuan Zhou, Shikui Tu, Lei Xu:
De Novo Drug Design by Multi-Objective Path Consistency Learning With Beam A* Search. 2459-2470 - Fangfang Su, Chong Teng, Fei Li, Bobo Li, Jun Zhou, Donghong Ji:
Generative Biomedical Event Extraction With Constrained Decoding Strategy. 2471-2484 - Jian Zhong, Haochen Zhao, Qichang Zhao, Jianxin Wang:
A Knowledge Graph-Based Method for Drug-Drug Interaction Prediction With Contrastive Learning. 2485-2495 - Xiangwen Wang, Qiaoying Jin, Li Zou, Xianghong Lin, Yonggang Lu:
Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings. 2496-2509 - Kiefer Andre Bedoya Benites, Wilser Andrés García-Quispes:
RFLP-Inator: Interactive Web Platform for In Silico Simulation and Complementary Tools of the PCR-RFLP Technique. 2510-2517 - Jie Yang, Yapeng Li, Guoyin Wang, Zhong Chen, Di Wu:
An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction. 2518-2530 - Qiao Ning, Yaomiao Zhao, Jun Gao, Chen Chen, Minghao Yin:
Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification. 2531-2542 - Qi Zhu, Aizhen Li, Zheng Zhang, Chuhang Zheng, Junyong Zhao, Jin-Xing Liu, Daoqiang Zhang, Wei Shao:
Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq. 2543-2555 - Keliang Cen, Zheming Xing, Xuan Wang, Yadong Wang, Junyi Li:
circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network. 2556-2567 - Liye Jia, Liancheng Jiang, Junhong Yue, Fang Hao, Yongfei Wu, Xilin Liu:
MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data. 2568-2579 - Siddharth Bhadra-Lobo, Georgy Derevyanko, Guillaume Lamoureux:
Dock2D: Synthetic Data for the Molecular Recognition Problem. 2580-2586 - Desmond S. Lun, Catherine M. Grgicak:
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA. 2587-2591 - Chris Salahub, Jeffrey Uhlmann:
Optimal Structured Matrix Approximation for Robustness to Incomplete Biosequence Data. 2592-2597 - Suzanne W. Dietrich, Wenli Ma, Yian Ding, Karen H. Watanabe, Mary B. Zelinski, James P. Sluka:
MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images. 2598-2603 - Xindi Yu, Shusen Zhou, Mujun Zang, Qingjun Wang, Chanjuan Liu, Tong Liu:
Parallel Convolutional Contrastive Learning Method for Enzyme Function Prediction. 2604-2609
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