Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

Volume 20, Issue 3

1626 -- 1627Carlos Martín-Vide, Miguel A. Vega-Rodríguez. Algorithms for Computational Biology: Eighth Edition
1628 -- 1640Alexsandro Oliveira Alexandrino, Klairton Lima Brito, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias. Reversal and Indel Distance With Intergenic Region Information
1641 -- 1653Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias. Genome Rearrangement Distance With a Flexible Intergenic Regions Aspect
1654 -- 1666Kaari Landry, Aivee Teodocio, Manuel Lafond, Olivier Tremblay Savard. Defining Phylogenetic Network Distances Using Cherry Operations
1667 -- 1678Chenqi Mou, Wenwen Ju. Sparse Triangular Decomposition for Computing Equilibria of Biological Dynamic Systems Based on Chordal Graphs
1679 -- 1690David Schaller 0001, Manuela Geiß, Marc Hellmuth, Peter F. Stadler. Best Match Graphs With Binary Trees
1691 -- 1699Yin Yao, Martin C. Frith. Improved DNA-Versus-Protein Homology Search for Protein Fossils
1700 -- 1712Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow. Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem
1713 -- 1724Kaitao Wu, Lexiang Wang, Bo Liu 0023, Yang Liu 0039, Yadong Wang, Junyi Li. PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction
1725 -- 1736Alejandro F. Villaverde, Elba Raimúndez-Álvarez, Jan Hasenauer, Julio R. Banga. Assessment of Prediction Uncertainty Quantification Methods in Systems Biology
1737 -- 1745Jinmiao Song, Shengwei Tian, Long Yu, Qimeng Yang, Yuanxu Wang, Qiguo Dai, Xiaodong Duan. ISLMI: Predicting lncRNA-miRNA Interactions Based on Information Injection and Second-Order Graph Convolution Network
1746 -- 1760Yan Kang, Haining Wang, Bin Pu, Liu Tao, Jianguo Chen, Philip S. Yu. A Hybrid Two-Stage Teaching-Learning-Based Optimization Algorithm for Feature Selection in Bioinformatics
1761 -- 1773Pranab Das, Yogita Thakran, S. R. Ngamwal Anal, Vipin Pal, Anju Yadav. BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs
1774 -- 1782Wen-Yu Xi, Feng Zhou, Ying-Lian Gao, Jin-Xing Liu, Chun-Hou Zheng 0001. LDCMFC: Predicting Long Non-Coding RNA and Disease Association Using Collaborative Matrix Factorization Based on Correntropy
1783 -- 1794Ramkishore Bhattacharyya. Bidirectional Association Discovery Leads to Precise Identification of Lung Cancer Biomarkers and Genome Taxa Class
1795 -- 1806Vianney Kengne Tchendji, Franklin Ingrid Kamga Youmbi, Clémentin Tayou Djamégni, Jerry Lacmou Zeutouo. A Parallel Tiled and Sparsified Four-Russians Algorithm for Nussinov's RNA Folding
1807 -- 1816Jie Xu, Guanxue Yang, Guohai Liu, Hui Liu 0010. Inferring Gene Regulatory Networks via Ensemble Path Consistency Algorithm Based on Conditional Mutual Information
1817 -- 1828Pradeep Kumar Das, Biswajeet Sahoo, Sukadev Meher. An Efficient Detection and Classification of Acute Leukemia Using Transfer Learning and Orthogonal Softmax Layer-Based Model
1829 -- 1841Marcelo Rodrigues de Holanda Maia, Alexandre Plastino 0001, Alex Alves Freitas, João Pedro de Magalhães. Interpretable Ensembles of Classifiers for Uncertain Data With Bioinformatics Applications
1842 -- 1853Shutao Chen, Lin Zhang 0015, Xiangzhi Chen, Hui Liu 0024. FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data
1854 -- 1863Hui Yu 0011, Kangkang Li, Jianyu Shi. DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction
1864 -- 1875Jun Bai, Chuantao Yin, Zimeng Wu, Jianfei Zhang, Yanmeng Wang, Guanyi Jia, Wenge Rong, Zhang Xiong 0001. Improving Biomedical ReQA With Consistent NLI-Transfer and Post-Whitening
1876 -- 1889Xiangbin Lin, Weizhuang Kong, Jianxiu Li, Xuexiao Shao, Changting Jiang, Ruilan Yu, Xiaowei Li 0005, Bin Hu 0001. Aberrant Static and Dynamic Functional Brain Network in Depression Based on EEG Source Localization
1890 -- 1904Prasun Chandra Tripathi, Soumen Bag 0001. An Attention-Guided CNN Framework for Segmentation and Grading of Glioma Using 3D MRI Scans
1905 -- 1916Shuhui Liu, Yupei Zhang, Xuequn Shang. GLassonet: Identifying Discriminative Gene Sets Among Molecular Subtypes of Breast Cancer
1917 -- 1925Hegang Chen, Yuyin Lu, Yuedong Yang, Yanghui Rao. A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information
1926 -- 1934Shengli Zhang, Yuanyuan Jing. PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit
1935 -- 1942Minghua Zhao, Min Yuan, Yaning Yang, Steven X. Xu 0001. CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network
1943 -- 1952Qichang Zhao, Guihua Duan, Haochen Zhao, Kai Zheng, Yaohang Li, Jianxin Wang 0001. GIFDTI: Prediction of Drug-Target Interactions Based on Global Molecular and Intermolecular Interaction Representation Learning
1953 -- 1962Qi Dang, Yong Liang 0001, Dong Ou-Yang, Rui Miao, Caijin Ling, Xiao-Ying Liu 0001, Shengli Xie. Improved Computational Drug-Repositioning by Self-Paced Non-Negative Matrix Tri-Factorization
1963 -- 1970Haoyuan Shi, Haisong Feng, Zhenxiao Lu, Wei Xue, Congshan Yang, Zhenyu Yue. GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network
1971 -- 1982Carlos Sequeiros, Irene Otero-Muras, Carlos Vázquez 0002, Julio R. Banga. Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems
1983 -- 1994Arnab Kumar Mondal, Indu Joshi, Pravendra Singh, Prathosh AP. Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations
1995 -- 2006Aranka Steyaert, Pieter Audenaert, Jan Fostier. Improved Node and Arc Multiplicity Estimation in De Bruijn Graphs Using Approximate Inference in Conditional Random Fields
2007 -- 2015Xiaolin Wang, Hongli Gao, Ren Qi, Ruiqing Zheng, Xin Gao 0001, Bin Yu 0007. scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means
2016 -- 2028Liangliang Tian, Haixi Zhang, Bin Liu 0023, Jiaqi Zhang, Nannan Duan, Aihong Yuan, Yingqiu Huo. VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection
2029 -- 2040Shima Shafiee, Abdolhossein Fathi, Ghazaleh Taherzadeh. SPPPred: Sequence-Based Protein-Peptide Binding Residue Prediction Using Genetic Programming and Ensemble Learning
2041 -- 2049Alejandro Fernández-Fraga, Jorge González-Domínguez, Juan Touriño. ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters
2050 -- 2063Xiaowei Gao, Yan Wang, Weimin Hou, Zaiyi Liu, Xiaoke Ma. Multi-View Clustering for Integration of Gene Expression and Methylation Data With Tensor Decomposition and Self-Representation Learning
2064 -- 2077Erhun Giray Tuncay, Riza Cenk Erdur, Tim Conrad 0001. Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA
2078 -- 2088Tanzila Islam, Chyon Hae Kim, Hiroyoshi Iwata, Hiroyuki Shimono, Akio Kimura. DeepCGP: A Deep Learning Method to Compress Genome-Wide Polymorphisms for Predicting Phenotype of Rice
2089 -- 2100Yelu Jiang, Lijun Quan, Kailong Li, Yan Li, Yiting Zhou, Tingfang Wu, Qiang Lyu. DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations
2101 -- 2111Peng Chen, Jian Wang 0021, Hongfei Lin, Yijia Zhang 0001, Zhihao Yang. Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension
2112 -- 2121Asmita Tripathi, Rajkrishna Mondal, Tapobrata Lahiri, Deepak Chaurasiya, Manoj Kumar Pal. TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction
2122 -- 2135Md. Inzamam-Ul-Hossain, Md. Rafiqul Islam. Identification of Essential Protein Using Chemical Reaction Optimization and Machine Learning Technique
2136 -- 2146Yulian Ding, Xiujuan Lei, Bo Liao, Fang-Xiang Wu. Biomarker Identification via a Factorization Machine-Based Neural Network With Binary Pairwise Encoding
2147 -- 2158Yixin Wang, Md. Noor-A-Rahim, Erry Gunawan, Yong Liang Guan 0001, Chueh-Loo Poh. Modelling, Characterization of Data-Dependent and Process-Dependent Errors in DNA Data Storage
2159 -- 2169Yiran Huang, Yongjin Bin, Pingfan Zeng, Wei Lan, Cheng Zhong. NetPro: Neighborhood Interaction-Based Drug Repositioning via Label Propagation
2170 -- 2176Leyla Nazari, Zahra Zinati. Gene Expression Classification for Biomarker Identification in Maize Subjected to Various Biotic Stresses
2177 -- 2189Necla Nisa Soylu, Emre Sefer. BERT2OME: Prediction of 2′-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT
2190 -- 2199Changkun Jiang, Weipeng Lv, Jianqiang Li 0001. Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE
2200 -- 2209Chang Sun, Rong Tang, Jipeng Huang, Jin-Mao Wei 0001, Jian Liu. A Deep Neural Network-Based Co-Coding Method to Predict Drug-Protein Interactions by Analyzing the Feature Consistency Between Drugs and Proteins
2210 -- 2222Aman Sinha, Bo-Cheng Lai, Jhih-Yong Mai. A Bin-Based Indexing for Scalable Range Join on Genomic Data
2223 -- 2232Wei Wang 0166, Bin Sun, MengXue Yu, Shiyu Wu, Dong Liu 0008, Hongjun Zhang, Yun Zhou. GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network
2233 -- 2241LinLin Du, Rui Han, Bo Liu 0023, Yadong Wang, Junyi Li. ScCCL: Single-Cell Data Clustering Based on Self-Supervised Contrastive Learning
2242 -- 2253Vikash Kumar, Akshay Deepak, Ashish Ranjan 0003, Aravind Prakash. Lite-SeqCNN: A Light-Weight Deep CNN Architecture for Protein Function Prediction
2254 -- 2265Yezi He, Xiangtao Chen, Nguyen Hoang Tu, Jiawei Luo 0001. Deep Multi-Constraint Soft Clustering Analysis for Single-Cell RNA-Seq Data via Zero-Inflated Autoencoder Embedding
2266 -- 2277Fan Rao, Minghan Chen, Defu Yang, Bess Morrell, Qianqian Song, Wentao Zhu. scENT for Revealing Gene Clusters From Single-Cell RNA-Seq Data
2278 -- 2290Ekta Shah, Pradipta Maji. Multi-View Kernel Learning for Identification of Disease Genes
2291 -- 2301Richa Dhanuka, Jyoti Prakash Singh, Anushree Tripathi. A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction
2302 -- 2313Ricardo Wandré Dias Pedro, Ana Luiza Silveira Ferreira, Rodolph Vinicius Siqueira Pessoa, Almir Galvão Vieira Bitencourt, Ariane Machado-Lima, Fátima L. S. Nunes. A Stochastic Grammar Approach to Mass Classification in Mammograms
2314 -- 2327Adam Witmer, Rajkumar Theagarajan, Bir Bhanu. Triplet-Net Classification of Contiguous Stem Cell Microscopy Images
2328 -- 2340Zhiming Zhang, Shangce Gao, Zhenyu Lei, RunQun Xiong, Jiujun Cheng. Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure Prediction
2341 -- 2348Hao Zhang, Honglei Song, Xiaoming Xu, Qixin Chang, Mingkai Wang, Yanjie Wei, Zekun Yin, Bertil Schmidt, Weiguo Liu. RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms
2349 -- 2355Momoko Hayamizu, Kazuhisa Makino. Ranking Top-$k$ Trees in Tree-Based Phylogenetic Networks
2356 -- 2361Anushka Mitra, Shibambika Manna, Raima Kundu, Ditipriya Hazra, Amlan Roychowdhury. Brute Force Virtual Drug Screening with Molecular Dynamics Simulation and MM/PBSA to Find Potent Inhibitors of METTL16