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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 20
Volume 20, Number 1, January - February 2023
- Qiaoming Liu
, Xudong Zhao, Guohua Wang:
A Clustering Ensemble Method for Cell Type Detection by Multiobjective Particle Optimization. 1-14 - Kun Liu, Hong-Dong Li, Yaohang Li, Jun Wang, Jianxin Wang:
A Comparison of Topologically Associating Domain Callers Based on Hi-C Data. 15-29 - Jan Klosa, Noah Simon, Volkmar Liebscher, Dörte Wittenburg:
A Fitted Sparse-Group Lasso for Genome-Based Evaluations. 30-38 - Chengzhuan Yang, Lincong Fang, Qian Yu, Hui Wei:
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification. 39-51 - Feng Zhou, Meng-Meng Yin, Jing-Xiu Zhao, Junliang Shang, Jin-Xing Liu:
A Method Based On Dual-Network Information Fusion to Predict MiRNA-Disease Associations. 52-60 - Qiang Yu, Xiao Zhang, Yana Hu, Shengpin Chen, Liying Yang:
A Method for Predicting DNA Motif Length Based On Deep Learning. 61-73 - Weixian Huang, Kaiwen Tan, Ziye Zhang, Jinlong Hu, Shoubin Dong:
A Review of Fusion Methods for Omics and Imaging Data. 74-93 - Ashish Ranjan, Archana Tiwari, Akshay Deepak:
A Sub-Sequence Based Approach to Protein Function Prediction via Multi-Attention Based Multi-Aspect Network. 94-105 - Jun Bai, Chuantao Yin, Jianfei Zhang, Yanmeng Wang, Yi Dong, Wenge Rong, Zhang Xiong:
Adversarial Knowledge Distillation Based Biomedical Factoid Question Answering. 106-118 - Katrin Sophie Bohnsack, Marika Kaden, Julia Abel, Thomas Villmann:
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective. 119-135 - Steffy Maria Joseph, P. S. Sathidevi:
An Automated cDNA Microarray Image Analysis for the Determination of Gene Expression Ratios. 136-150 - Sahar Iravani, Tim O. F. Conrad:
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data. 151-161 - Kanchan Jha, Sriparna Saha:
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions. 162-173 - Shankarachary Ragi, Md Hafizur Rahman, Jamison Duckworth, Kalimuthu Jawaharraj, Parvathi Chundi, Venkataramana Gadhamshetty:
Artificial Intelligence-Driven Image Analysis of Bacterial Cells and Biofilms. 174-184 - Hao Zhang, Chuanxu Yan, Yewei Xia, Jihong Guan, Shuigeng Zhou:
Causal Gene Identification Using Non-Linear Regression-Based Independence Tests. 185-195 - Naser Anjum, Raian Latif Nabil, Rakibul Islam Rafi, Md. Shamsuzzoha Bayzid, Mohammad Saifur Rahman:
CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets. 196-205 - Tuan D. Pham:
Classification of Caenorhabditis Elegans Locomotion Behaviors With Eigenfeature-Enhanced Long Short-Term Memory Networks. 206-216 - Ichcha Manipur, Maurizio Giordano, Marina Piccirillo, Seetharaman Parashuraman, Lucia Maddalena:
Community Detection in Protein-Protein Interaction Networks and Applications. 217-237 - Rizwan Qureshi, Bin Zou, Tanvir Alam, Jia Wu, Victor H. F. Lee, Hong Yan:
Computational Methods for the Analysis and Prediction of EGFR-Mutated Lung Cancer Drug Resistance: Recent Advances in Drug Design, Challenges and Future Prospects. 238-255 - Jingbo Yang, Denan Zhang, Yiyang Cai, Kexin Yu, Mingming Li, Lei Liu, Xiujie Chen:
Computational Prediction of Drug Phenotypic Effects Based on Substructure-Phenotype Associations. 256-265 - Wook Lee, Seokwoo Lee, Kyungsook Han:
Constructing a Cancer Patient-Specific Network Based on Second-Order Partial Correlations of Gene Expression and DNA Methylation. 266-276 - Zhi-Hao Liu, Cunmei Ji, Jian-Cheng Ni, Yu-Tian Wang, Li-Juan Qiao, Chun-Hou Zheng:
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association. 277-284 - Yang Hua, Xiaoning Song, Zhenhua Feng, Xiaojun Wu, Josef Kittler, Dong-Jun Yu:
CPInformer for Efficient and Robust Compound-Protein Interaction Prediction. 285-296 - Kailong Li, Lijun Quan, Yelu Jiang, Yan Li, Yiting Zhou, Tingfang Wu, Qiang Lyu:
ctP2ISP: Protein-Protein Interaction Sites Prediction Using Convolution and Transformer With Data Augmentation. 297-306 - Xiuquan Du, Jiajia Hu:
Deep Multi-Label Joint Learning for RNA and DNA-Binding Proteins Prediction. 307-320 - Xiaohui Yang, Zijun Xi, Jie-Ping Li, Xin-Lei Feng, Xiao-Hong Zhu, Si-Yi Guo, Chun-Peng Song:
Deep Transfer Learning-Based Multi-Object Detection for Plant Stomata Phenotypic Traits Intelligent Recognition. 321-329 - Onur Can Uner, Halil Ibrahim Kuru, Ramazan Gokberk Cinbis, Öznur Tastan, A. Ercüment Çiçek:
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction. 330-339 - Zimo Huang, Jun Wang, Zhongmin Yan, Lin Wan, Maozu Guo:
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data. 340-351 - Jinghang Lin, Xiaoran Tong, Chenxi Li, Qing Lu:
Expectile Neural Networks for Genetic Data Analysis of Complex Diseases. 352-359 - Lucia Williams, Alexandru I. Tomescu, Brendan Mumey:
Flow Decomposition With Subpath Constraints. 360-370 - Huadong Wang, Jianhui Sun, Mengya Liu, Chun-Hou Zheng, Junfeng Xia, Na Cheng:
frDSM: An Ensemble Predictor With Effective Feature Representation for Deleterious Synonymous Mutation in Human Genome. 371-377 - Cheng-Hong Yang, Hsiu-Chen Huang, Ming-Feng Hou, Li-Yeh Chuang, Yu-Da Lin:
Fuzzy-Based Multiobjective Multifactor Dimensionality Reduction for Epistasis Analysis. 378-387 - Jianwei Li, Duanyang Wang, Zhenwu Yang, Ming Liu:
HEGANLDA: A Computational Model for Predicting Potential Lncrna-Disease Associations Based On Multiple Heterogeneous Networks. 388-398 - Qie Liu, Junhao Li, Mingyu Dong, Min Liu, Yi Chai:
Identification of Gene Regulatory Networks Using Variational Bayesian Inference in the Presence of Missing Data. 399-409 - Ashwin Lahorkar, Hrushikesh Bhosale, Aamod Sane, Vigneshwar Ramakrishnan, Valadi K. Jayaraman:
Identification of Phase Separating Proteins With Distributed Reduced Alphabet Representations of Sequences. 410-420 - Jiazhou Chen, Guoqiang Han, Aodan Xu, Tatsuya Akutsu, Hongmin Cai:
Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model. 421-431 - Ning Wang, Jun Zhang, Bin Liu:
iDRBP-EL: Identifying DNA- and RNA- Binding Proteins Based on Hierarchical Ensemble Learning. 432-441 - Antonio R. Paiva, Giovanni Pilloni:
Inferring Microbial Biomass Yield and Cell Weight Using Probabilistic Macrochemical Modeling. 442-454 - Huanhuan Wang, Xiang Wu:
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies. 455-464 - Yingyi Liu, Hong-Dong Li, Yunpei Xu, Yi-Wei Liu, Xiaoqing Peng, Jianxin Wang:
IsoCell: An Approach to Enhance Single Cell Clustering by Integrating Isoform-Level Expression Through Orthogonal Projection. 465-475 - Zhaowu Lu, Jun Wang, Rui Mao, Minhua Lu, Jun Shi:
Jointly Composite Feature Learning and Autism Spectrum Disorder Classification Using Deep Multi-Output Takagi-Sugeno-Kang Fuzzy Inference Systems. 476-488 - Yi Sun, Jian Wang, Hongfei Lin, Yijia Zhang, Zhihao Yang:
Knowledge Guided Attention and Graph Convolutional Networks for Chemical-Disease Relation Extraction. 489-499 - Yijie Ding, Wenying He, Jijun Tang, Quan Zou, Fei Guo:
Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via $L_{2,1/2}$L2,1/2-Matrix Norm. 500-511 - Xingze Wang, Guoxian Yu, Zhongmin Yan, Lin Wan, Wei Wang, Lizhen Cui:
Lung Cancer Subtype Diagnosis by Fusing Image-Genomics Data and Hybrid Deep Networks. 512-523 - Mengmeng Kuang, Yong Zhang, Tak Wah Lam, Hing-Fung Ting:
MLProbs: A Data-Centric Pipeline for Better Multiple Sequence Alignment. 524-533 - Jin-Xing Liu, Meng-Meng Yin, Ying-Lian Gao, Junliang Shang, Chun-Hou Zheng:
MSF-LRR: Multi-Similarity Information Fusion Through Low-Rank Representation to Predict Disease-Associated Microbes. 534-543 - Xiaofeng Shi, Cheng Liang, Hong Wang:
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification. 544-556 - Diego de S. Lima, Luiz J. A. Amichi, Maria A. Fernandez, Ademir Aparecido Constantino, Flávio A. V. Seixas:
NCYPred: A Bidirectional LSTM Network With Attention for Y RNA and Short Non-Coding RNA Classification. 557-565 - Wenming Wu, Xiaoke Ma:
Network-Based Structural Learning Nonnegative Matrix Factorization Algorithm for Clustering of scRNA-Seq Data. 566-575 - Chunjiang Yu, Xin Qi, Wenying Yan, Wentao Wu, Bairong Shen:
Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. 576-585 - Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu:
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction. 586-594 - Zhaoying Chai, Han Jin, Shenghui Shi, Siyan Zhan, Lin Zhuo, Yu Yang, Qi Lian:
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition. 595-605 - Tzu-Hsuan Wu, Peng-Chan Lin, Hsin-Hung Chou, Meng-Ru Shen, Sun-Yuan Hsieh:
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies. 606-615 - Ying He, Qinhu Zhang, Siguo Wang, Zhanheng Chen, Zhen Cui, Zhen-Hao Guo, De-Shuang Huang:
Predicting the Sequence Specificities of DNA-Binding Proteins by DNA Fine-Tuned Language Model With Decaying Learning Rates. 616-624 - Mukunthan Tharmakulasingam, Brian Gardner, Roberto La Ragione, Anil Fernando:
Rectified Classifier Chains for Prediction of Antibiotic Resistance From Multi-Labelled Data With Missing Labels. 625-636 - Ye Li, Fanhui Kong, Hui Cui, Fan Wang, Chunquan Li, Jiquan Ma:
SENIES: DNA Shape Enhanced Two-Layer Deep Learning Predictor for the Identification of Enhancers and Their Strength. 637-645 - Dhananjay Kimothi, Pravesh Biyani, James M. Hogan, Melissa J. Davis:
Sequence Representations and Their Utility for Predicting Protein-Protein Interactions. 646-657 - Jiazhou Chen, Wentao Rong, Guihua Tao, Hongmin Cai:
Similarity Fusion via Exploiting High Order Proximity for Cancer Subtyping. 658-667 - Vishal Rana, Eli Chien, Jianhao Peng, Olgica Milenkovic:
Small-Sample Estimation of the Mutational Support and Distribution of SARS-CoV-2. 668-682 - Romica Kerketta, M. Frank Erasmus, Bridget S. Wilson, Ádám M. Halász, Jeremy S. Edwards:
Spatial Stochastic Model of the Pre-B Cell Receptor. 683-693 - Hongxiao Wang, Hao Zheng, Danny Z. Chen:
TANGO: A GO-Term Embedding Based Method for Protein Semantic Similarity Prediction. 694-706 - Cui Su, Jun Pang:
Target Control of Asynchronous Boolean Networks. 707-719 - Evgenia Chunikhina, Paul Logan, Yevgeniy Kovchegov, Anatoly Yambartsev, Debashis Mondal, Andrey Morgun:
The C-SHIFT Algorithm for Normalizing Covariances. 720-730 - Xinxing Yang, Genke Yang, Jian Chu:
The Neural Metric Factorization for Computational Drug Repositioning. 731-741 - Nikhila T. Suresh, Vimina E. R., Krishnakumar U.:
Topology Driven Analysis of Protein - Protein Interactome for Prioritizing Key Comorbid Genes via Sub Graph Based Average Path Length Centrality. 742-751 - Manisha Saini, Seba Susan:
VGGIN-Net: Deep Transfer Network for Imbalanced Breast Cancer Dataset. 752-762 - Qiaoliang Liu, Fu Liu, Yan Miao, Jiaxue He, Tian Dong, Tao Hou, Yun Liu:
Virsearcher: Identifying Bacteriophages from Metagenomes by Combining Convolutional Neural Network and Gene Information. 763-774 - Hajin Jeon, Jeongmin Bae, Hyerin Kim, Min-Soo Kim:
VPrimer: A Method of Designing and Updating Primer and Probe With High Variant Coverage for RNA Virus Detection. 775-784 - Yixiong Liang, Zhihua Yin, Haotian Liu, Hailong Zeng, Jianxin Wang, Jianfeng Liu, Nanying Che:
Weakly Supervised Deep Nuclei Segmentation With Sparsely Annotated Bounding Boxes for DNA Image Cytometry. 785-795 - Turki M. Sobahy, Olaa A. Motwalli, Meshari Alazmi:
AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants. 796-801 - Hemanth Kari, Surya Manikhanta Sowri Bandi, Aditya Kumar, Venkata Rajesh Yella:
DeePromClass: Delineator for Eukaryotic Core Promoters Employing Deep Neural Networks. 802-807
Volume 20, Number 2, March - April 2023
- Isabel González-Crespo, Antonio Gómez-Caamaño, Óscar López Pouso, John D. Fenwick, Juan Pardo-Montero:
A Biomathematical Model of Tumor Response to Radioimmunotherapy With αPDL1 and αCTLA4. 808-821 - Xiong Li, Yangkai Lin, Chengwang Xie, Zejun Li, Min Chen, Peng Wang, Juan Zhou:
A Clustering Method Unifying Cell-Type Recognition and Subtype Identification for Tumor Heterogeneity Analysis. 822-832 - Min Li, Wenbo Shi, Fuhao Zhang, Min Zeng, Yaohang Li:
A Deep Learning Framework for Predicting Protein Functions With Co-Occurrence of GO Terms. 833-842 - Xiaoqing Peng, Wenjin Zhang, Wanxin Cui, Binrong Ding, Qingtong Lyu, Jianxin Wang:
ADmeth: A Manually Curated Database for the Differential Methylation in Alzheimer's Disease. 843-851 - Qichang Zhao, Guihua Duan, Mengyun Yang, Zhongjian Cheng, Yaohang Li, Jianxin Wang:
AttentionDTA: Drug-Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism. 852-863 - Jiasheng Si, Liu Sun, Deyu Zhou, Jie Ren, Lin Li:
Biomedical Argument Mining Based on Sequential Multi-Task Learning. 864-874 - Mahdieh Ghasemi, Maseud Rahgozar, Kaveh Kavousi:
Complex Disease Genes Identification Using a Heterogeneous Network Embedding Approach. 875-882 - Dong Jun Jee, Yixin Kong, Hyonho Chun:
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data. 883-893 - Volkan Altuntas:
Diffusion Alignment Coefficient (DAC): A Novel Similarity Metric for Protein-Protein Interaction Network. 894-903 - Mobeen Ur Rehman, Hilal Tayara, Kil To Chong:
DL-m6A: Identification of N6-Methyladenosine Sites in Mammals Using Deep Learning Based on Different Encoding Schemes. 904-911 - Zhong-Ze Yu, Chunxiang Peng, Jun Liu, Biao Zhang, Xiao-Gen Zhou, Gui-Jun Zhang:
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance. 912-922 - Xin Huang, Benzhe Su, Chenbo Zhu, Xinyu He, Xiaohui Lin:
Dynamic Network Construction for Identifying Early Warning Signals Based On a Data-Driven Approach: Early Diagnosis Biomarker Discovery for Gastric Cancer. 923-931 - Xuan Lin, Zhe Quan, Zhi-Jie Wang, Yan Guo, Xiangxiang Zeng, Philip S. Yu:
Effectively Identifying Compound-Protein Interaction Using Graph Neural Representation. 932-943 - Yongxian Fan, Guicong Sun, Xiaoyong Pan:
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites. 944-954 - Shamima Rashid, Suresh Sundaram, Chee Keong Kwoh:
Empirical Study of Protein Feature Representation on Deep Belief Networks Trained With Small Data for Secondary Structure Prediction. 955-966 - Chao Wang, Quan Zou, Ying Ju, Hua Shi:
Enhancer-FRL: Improved and Robust Identification of Enhancers and Their Activities Using Feature Representation Learning. 967-975 - Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Zhongfei Zhang, Wen Zhang:
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks. 976-985 - Yang Shen, Jinlin Zhu, Zhaohong Deng, Wenwei Lu, Hongchao Wang:
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics. 986-998 - Leandro E. Di Persia, Tiago Lopez, Agustin Arce, Diego H. Milone, Georgina Stegmayer:
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data. 999-1008 - Filippo Castiglione, Christine Nardini, Elia Onofri, Marco Pedicini, Paolo Tieri:
Explainable Drug Repurposing Approach From Biased Random Walks. 1009-1019 - Tri Minh Nguyen, Thomas P. Quinn, Thin Nguyen, Truyen Tran:
Explaining Black Box Drug Target Prediction Through Model Agnostic Counterfactual Samples. 1020-1029 - Chunyan Tang, Cheng Zhong, Mian Wang, Fengfeng Zhou:
FMGNN: A Method to Predict Compound-Protein Interaction With Pharmacophore Features and Physicochemical Properties of Amino Acids. 1030-1040 - Jiwen Liu, Zhufang Kuang, Lei Deng:
GCNPCA: miRNA-Disease Associations Prediction Algorithm Based on Graph Convolutional Neural Networks. 1041-1052 - Zhen Tian, Haichuan Fang, Zhixia Teng, Yangdong Ye:
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes. 1053-1064 - Thang Chu, Thuy Trang Nguyen, Bui Duong Hai, Quang Huy Nguyen, Tuan Nguyen:
Graph Transformer for Drug Response Prediction. 1065-1072 - Bryan Herrera-Romero, Diego Almeida-Galárraga, Graciela M. Salum, Fernando Villalba-Meneses, Marco Esteban Gudiño-Gomezjurado:
GUSignal: An Informatics Tool to Analyze Glucuronidase Gene Expression in Arabidopsis Thaliana Roots. 1073-1080 - Junwei Sun, Haoping Ji, Yingcong Wang, Yanfeng Wang:
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement. 1081-1091 - Vicky Zheng, Ahmet Erdem Sariyüce, Jaroslaw Zola:
Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices. 1092-1103 - Yasin Görmez, Zafer Aydin:
IGPRED-MultiTask: A Deep Learning Model to Predict Protein Secondary Structure, Torsion Angles and Solvent Accessibility. 1104-1113 - Yongping Du, Jingya Yan, Yuxuan Lu, Yiliang Zhao, Xingnan Jin:
Improving Biomedical Question Answering by Data Augmentation and Model Weighting. 1114-1124 - S. Sujamol, Vimina E. R., Krishnakumar U.:
Improving miRNA Disease Association Prediction Accuracy Using Integrated Similarity Information and Deep Autoencoders. 1125-1136 - Xueli Song, Rongpeng Li, Kaiming Wang, Yuntong Bai, Yuzhu Xiao, Yu-Ping Wang:
Joint Sparse Collaborative Regression on Imaging Genetics Study of Schizophrenia. 1137-1146 - Changzhi Jiang, Minli Tang, Shuting Jin, Wei Huang, Xiangrong Liu:
KGNMDA: A Knowledge Graph Neural Network Method for Predicting Microbe-Disease Associations. 1147-1155 - Xianyu Zhu, Jinjiang Li, Runchang Jia, Bin Liu, Zhuohan Yao, Aihong Yuan, Yingqiu Huo, Haixi Zhang:
LAD-Net: A Novel Light Weight Model for Early Apple Leaf Pests and Diseases Classification. 1156-1169 - Xiaoke Ma, Wei Zhao, Wenming Wu:
Layer-Specific Modules Detection in Cancer Multi-Layer Networks. 1170-1179 - Zhengsen Pan, Shusen Zhou, Hailin Zou, Chanjuan Liu, Mujun Zang, Tong Liu, Qingjun Wang:
MCNN: Multiple Convolutional Neural Networks for RNA-Protein Binding Sites Prediction. 1180-1187 - Ashish Ranjan,