- 2024
- 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 169-177 (2024) - Gabriel Cardona, Joan Carles Pons, Gerard Ribas, Tomás Martínez Coronado:
Comparison of Orchard Networks Using Their Extended $\mu$μ-Representation. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 501-507 (2024) - Souradipto Choudhuri, Keya Sau:
CodonU: A Python Package for Codon Usage Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 36-44 (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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 215-226 (2024) - Shujie Dong, Yuansheng Liu, Yongshun Gong, Xiangjun Dong, Xiangxiang Zeng:
scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 95-105 (2024) - Yamane El-Zein, Mathieu Lemay, Kévin Huguenin:
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 1-13 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 57-68 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 254-264 (2024) - Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen:
Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 461-471 (2024) - Sichen Jin, Yijia Zhang, Huimin Yu, Mingyu Lu:
SADR: Self-Supervised Graph Learning With Adaptive Denoising for Drug Repositioning. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 265-277 (2024) - Alina F. Leuchtenberger, Arndt von Haeseler:
Learning From an Artificial Neural Network in Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 278-288 (2024) - Tiantian Li, Haitao Jiang, Binhai Zhu, Lusheng Wang, Daming Zhu:
Flanked Block-Interchange Distance on Strings. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 301-311 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 492-500 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 120-128 (2024) - Minglie Li, Shusen Zhou, Tong Liu, Chanjuan Liu, Mujun Zang, Qingjun Wang:
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 472-479 (2024) - Yuerui Liu, Yongquan Jiang, Fan Zhang, Yan Yang:
A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 178-187 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 480-491 (2024) - Daniel Manu, Jingjing Yao, Wuji Liu, Xiang Sun:
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 240-253 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 26-35 (2024) - Bindi M. Nagda, Van Minh Nguyen, Ryan T. White:
promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 208-214 (2024) - Tara Newman, Hiu Fung Kevin Chang, Hosna Jabbari:
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 348-359 (2024) - Jonas Kristiansen Nøland, Steinar Thorvaldsen:
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 69-83 (2024) - Nicolò Rossi, Nicola Gigante, Nicola Vitacolonna, Carla Piazza:
Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 106-119 (2024) - Sheena K. S., Madhu S. Nair:
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 405-415 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 439-449 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 328-347 (2024) - Rituparna Sinha, Rajat Kumar Pal, Rajat K. De:
ENLIGHTENMENT: A Scalable Annotated Database of Genomics and NGS-Based Nucleotide Level Profiles. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 155-168 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(3): 450-460 (2024) - 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. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 84-94 (2024) - Chao Tu, Denghui Du, Tieyong Zeng, Yu Zhang:
Deep Multi-Dictionary Learning for Survival Prediction With Multi-Zoom Histopathological Whole Slide Images. IEEE ACM Trans. Comput. Biol. Bioinform. 21(1): 14-25 (2024)