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@article{DBLP:journals/tcbb/BarnettOSF24,
author = {Eric J. Barnett and
Daniel G. Onete and
Asif Salekin and
Stephen V. Faraone},
title = {Genomic Machine Learning Meta-regression: Insights on Associations
of Study Features With Reported Model Performance},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {169--177},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3343808},
doi = {10.1109/TCBB.2023.3343808},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/BarnettOSF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ChoudhuriS24,
author = {Souradipto Choudhuri and
Keya Sau},
title = {CodonU: {A} Python Package for Codon Usage Analysis},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {36--44},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3335823},
doi = {10.1109/TCBB.2023.3335823},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/ChoudhuriS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CruzCFRD24,
author = {Fernando Cruz and
Jo{\~{a}}o Capela and
Eug{\'{e}}nio C. Ferreira and
Miguel Rocha and
Oscar D{\'{\i}}as},
title = {BioISO: An Objective-Oriented Application for Assisting the Curation
of Genome-Scale Metabolic Models},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {215--226},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3339972},
doi = {10.1109/TCBB.2023.3339972},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CruzCFRD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/DongLGDZ24,
author = {Shujie Dong and
Yuansheng Liu and
Yongshun Gong and
Xiangjun Dong and
Xiangxiang Zeng},
title = {scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for
Single-Cell RNA-Seq Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {95--105},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3337231},
doi = {10.1109/TCBB.2023.3337231},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/DongLGDZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ElZeinLH24,
author = {Yamane El{-}Zein and
Mathieu Lemay and
K{\'{e}}vin Huguenin},
title = {PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees
on Biomedical Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {1--13},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3286274},
doi = {10.1109/TCBB.2023.3286274},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/ElZeinLH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/GuoTLMLGL24,
author = {Rui Guo and
Xu Tian and
Hanhe Lin and
Stephen J. McKenna and
Hong{-}Dong Li and
Fei Guo and
Jin Liu},
title = {Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative
Disease Diagnosis},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {57--68},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3335369},
doi = {10.1109/TCBB.2023.3335369},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/GuoTLMLGL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/HuHCLPCT24,
author = {Zhao{-}Qi Hu and
Yuan{-}Mao Hung and
Li{-}Han Chen and
Liang{-}Chuan Lai and
Min{-}Hsiung Pan and
Eric Y. Chuang and
Mong{-}Hsun Tsai},
title = {{NURECON:} {A} Novel Online System for Determining Nutrition Requirements
Based on Microbial Composition},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {254--264},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3349572},
doi = {10.1109/TCBB.2024.3349572},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/HuHCLPCT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/JinZYL24,
author = {Sichen Jin and
Yijia Zhang and
Huimin Yu and
Mingyu Lu},
title = {{SADR:} Self-Supervised Graph Learning With Adaptive Denoising for
Drug Repositioning},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {265--277},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3351079},
doi = {10.1109/TCBB.2024.3351079},
timestamp = {Mon, 06 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/JinZYL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LeuchtenbergerH24,
author = {Alina F. Leuchtenberger and
Arndt von Haeseler},
title = {Learning From an Artificial Neural Network in Phylogenetics},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {278--288},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3352268},
doi = {10.1109/TCBB.2024.3352268},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LeuchtenbergerH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiJZWZ24,
author = {Tiantian Li and
Haitao Jiang and
Binhai Zhu and
Lusheng Wang and
Daming Zhu},
title = {Flanked Block-Interchange Distance on Strings},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {301--311},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3351440},
doi = {10.1109/TCBB.2024.3351440},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LiJZWZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiXSJZS24,
author = {Dandan Li and
Zhen Xiao and
Han Sun and
Xingpeng Jiang and
Weizhong Zhao and
Xianjun Shen},
title = {Prediction of Drug-Disease Associations Based on Multi-Kernel Deep
Learning Method in Heterogeneous Graph Embedding},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {120--128},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3339189},
doi = {10.1109/TCBB.2023.3339189},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/LiXSJZS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiuJZY24,
author = {Yuerui Liu and
Yongquan Jiang and
Fan Zhang and
Yan Yang},
title = {A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {178--187},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3345647},
doi = {10.1109/TCBB.2023.3345647},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/LiuJZY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ManuYLS24,
author = {Daniel Manu and
Jingjing Yao and
Wuji Liu and
Xiang Sun},
title = {GraphGANFed: {A} Federated Generative Framework for Graph-Structured
Molecules Towards Efficient Drug Discovery},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {240--253},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3349990},
doi = {10.1109/TCBB.2024.3349990},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ManuYLS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/MorrisRBVTYB24,
author = {Jordan Morris and
Ashur Rafiev and
Graeme M. Bragg and
Mark L. Vousden and
David B. Thomas and
Alex Yakovlev and
Andrew D. Brown},
title = {An Event-Driven Approach to Genotype Imputation on a Custom {RISC-V}
Cluster},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {26--35},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3328714},
doi = {10.1109/TCBB.2023.3328714},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/MorrisRBVTYB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/NagdaNW24,
author = {Bindi M. Nagda and
Van Minh Nguyen and
Ryan T. White},
title = {promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting
{DNA} Promoter Sequences},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {208--214},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3339597},
doi = {10.1109/TCBB.2023.3339597},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/NagdaNW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/NolandT24,
author = {Jonas Kristiansen N{\o}land and
Steinar Thorvaldsen},
title = {The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher
Mutation Model},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {69--83},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3336850},
doi = {10.1109/TCBB.2023.3336850},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/NolandT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/RossiGVP24,
author = {Nicol{\`{o}} Rossi and
Nicola Gigante and
Nicola Vitacolonna and
Carla Piazza},
title = {Inferring Markov Chains to Describe Convergent Tumor Evolution With
{CIMICE}},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {106--119},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3337258},
doi = {10.1109/TCBB.2023.3337258},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/RossiGVP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SinhaPD24,
author = {Rituparna Sinha and
Rajat Kumar Pal and
Rajat K. De},
title = {{ENLIGHTENMENT:} {A} Scalable Annotated Database of Genomics and NGS-Based
Nucleotide Level Profiles},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {155--168},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3340067},
doi = {10.1109/TCBB.2023.3340067},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/SinhaPD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TangDZZHCW24,
author = {Wenliang Tang and
Zhaohong Deng and
Hanwen Zhou and
Wei Zhang and
Fuping Hu and
Kup{-}Sze Choi and
Shitong Wang},
title = {{MVDINET:} {A} Novel Multi-Level Enzyme Function Predictor With Multi-View
Deep Interactive Learning},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {84--94},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3337158},
doi = {10.1109/TCBB.2023.3337158},
timestamp = {Sat, 23 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/TangDZZHCW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TuDZZ24,
author = {Chao Tu and
Denghui Du and
Tieyong Zeng and
Yu Zhang},
title = {Deep Multi-Dictionary Learning for Survival Prediction With Multi-Zoom
Histopathological Whole Slide Images},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {14--25},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3321593},
doi = {10.1109/TCBB.2023.3321593},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/TuDZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/WangHLNWWL24,
author = {Wenjing Wang and
Pengyong Han and
Zhengwei Li and
Ru Nie and
Kangwei Wang and
Lei Wang and
Hongmei Liao},
title = {{LMGATCDA:} Graph Neural Network With Labeling Trick for Predicting
circRNA-Disease Associations},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {289--300},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2024.3355093},
doi = {10.1109/TCBB.2024.3355093},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/WangHLNWWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/WangYSLLZWZ24,
author = {Wei Wang and
MengXue Yu and
Bin Sun and
Juntao Li and
Dong Liu and
Hongjun Zhang and
Xianfang Wang and
Yun Zhou},
title = {{SMGCN:} Multiple Similarity and Multiple Kernel Fusion Based Graph
Convolutional Neural Network for Drug-Target Interactions Prediction},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {143--154},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3339645},
doi = {10.1109/TCBB.2023.3339645},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/WangYSLLZWZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/XinWQCWW24,
author = {Junchang Xin and
Mingcan Wang and
Luxuan Qu and
Qi Chen and
Weiyiqi Wang and
Zhiqiong Wang},
title = {{BIC-LP:} {A} Hybrid Higher-Order Dynamic Bayesian Network Score Function
for Gene Regulatory Network Reconstruction},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {188--199},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3345317},
doi = {10.1109/TCBB.2023.3345317},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/XinWQCWW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/YuWLZLS24,
author = {Shengpeng Yu and
Hong Wang and
Jing Li and
Jun Zhao and
Cheng Liang and
Yanshen Sun},
title = {A Multi-Relational Graph Encoder Network for Fine-Grained Prediction
of MiRNA-Disease Associations},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {45--56},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3335007},
doi = {10.1109/TCBB.2023.3335007},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/YuWLZLS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/YuZZJMW24,
author = {Changyong Yu and
Yuhai Zhao and
Chu Zhao and
Jianyu Jin and
Keming Mao and
Guoren Wang},
title = {MiniDBG: {A} Novel and Minimal De Bruijn Graph for Read Mapping},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {129--142},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3340251},
doi = {10.1109/TCBB.2023.3340251},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/YuZZJMW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ZengL24,
author = {Pengcheng Zeng and
Zhixiang Lin},
title = {scICML: Information-Theoretic Co-Clustering-Based Multi-View Learning
for the Integrative Analysis of Single-Cell Multi-Omics Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {1},
pages = {200--207},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3305989},
doi = {10.1109/TCBB.2023.3305989},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/ZengL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ZhangJZZLLZQ24,
author = {Hao Zhang and
Jiao Jiao and
Tianheng Zhao and
Enshuang Zhao and
Lanhui Li and
Guihua Li and
Borui Zhang and
Qing{-}Ming Qin},
title = {{GERWR:} Identifying the Key Pathogenicity- Associated sRNAs of Magnaporthe
Oryzae Infection in Rice Based on Graph Embedding and Random Walk
With Restart},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {21},
number = {2},
pages = {227--239},
year = {2024},
url = {https://doi.org/10.1109/TCBB.2023.3348080},
doi = {10.1109/TCBB.2023.3348080},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ZhangJZZLLZQ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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