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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 18
Volume 18, Number 1, January - February 2021
- Carlos Martín-Vide, Miguel A. Vega-Rodríguez
:
Algorithms for Computational Biology: Sixth Edition. 1
- Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, Tandy J. Warnow:
Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. 2-15 - Sridevi Maharaj, Taotao Qian, Zarin Ohiba, Wayne B. Hayes:
Common Neighbors Extension of the Sticky Model for PPI Networks Evaluated by Global and Local Graphlet Similarity. 16-26 - Peng Xiao, Xingyu Cai, Sanguthevar Rajasekaran:
EMS3: An Improved Algorithm for Finding Edit-Distance Based Motifs. 27-37 - Liu Liu, Reza Zare, Shuihua Wang:
Guest Editorial: Transfer Learning Methods Used in Medical Imaging and Health Informatics. 38-39 - Yizhang Jiang, Xiaoqing Gu, Dongrui Wu, Wenlong Hang, Jing Xue, Shi Qiu, Chin-Teng Lin:
A Novel Negative-Transfer-Resistant Fuzzy Clustering Model With a Shared Cross-Domain Transfer Latent Space and its Application to Brain CT Image Segmentation. 40-52 - Kaijian Xia, Tongguang Ni, Hongsheng Yin, Bo Chen:
Cross-Domain Classification Model With Knowledge Utilization Maximization for Recognition of Epileptic EEG Signals. 53-61 - Chenxi Huang, Yisha Lan, Gaowei Xu, Xiaojun Zhai, Jipeng Wu, Fan Lin, Nianyin Zeng, Qingqi Hong, E. Y. K. Ng, Yonghong Peng, Fei Chen, Guokai Zhang:
A Deep Segmentation Network of Multi-Scale Feature Fusion Based on Attention Mechanism for IVOCT Lumen Contour. 62-69 - Pengjiang Qian, Jiamin Zheng, Qiankun Zheng, Yuan Liu, Tingyu Wang, Rose Al Helo, Atallah Baydoun, Norbert Avril, Rodney J. Ellis, Harry Friel, Melanie S. Traughber, Ajit Devaraj, Bryan J. Traughber, Raymond F. Muzic Jr.:
Transforming UTE-mDixon MR Abdomen-Pelvis Images Into CT by Jointly Leveraging Prior Knowledge and Partial Supervision. 70-82 - Rishav Singh, Tanveer Ahmed, Abhinav Kumar, Amit Kumar Singh, Anil Kumar Pandey, Sanjay Kumar Singh:
Imbalanced Breast Cancer Classification Using Transfer Learning. 83-93 - Xiang Yu, Cheng Kang, David S. Guttery, Seifedine Nimer Kadry, Yang Chen, Yu-Dong Zhang:
ResNet-SCDA-50 for Breast Abnormality Classification. 94-102 - Jintai Chen, Haochao Ying, Xuechen Liu, Jingjing Gu, Ruiwei Feng, Tingting Chen, Honghao Gao, Jian Wu:
A Transfer Learning Based Super-Resolution Microscopy for Biopsy Slice Images: The Joint Methods Perspective. 103-113 - Yong Jin, Zhenjiang Qian, Shengrong Gong, Weiyong Yang:
Learning Transferable Driven and Drone Assisted Sustainable and Robust Regional Disease Surveillance for Smart Healthcare. 114-125 - Hansaim Lim, Lei Xie:
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. 126-137 - Daniel R. Allen, Sharma V. Thankachan, Bojian Xu:
An Ultra-Fast and Parallelizable Algorithm for Finding $k$k-Mismatch Shortest Unique Substrings. 138-148 - Pawel Tabaszewski, Pawel Górecki, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein:
Consensus of All Solutions for Intractable Phylogenetic Tree Inference. 149-161 - Srilakshmi Pattabiraman, Tandy J. Warnow:
Profile Hidden Markov Models Are Not Identifiable. 162-172 - Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang:
A Method for Generating Synthetic Electronic Medical Record Text. 173-182 - Ruiqi Qin, Lei Duan, Huiru Zheng, Jesse Li-Ling, Kaiwen Song, Yidan Zhang:
An Ontology-Independent Representation Learning for Similar Disease Detection Based on Multi-Layer Similarity Network. 183-193 - Wei Long, Tiange Li, Yang Yang, Hong-Bin Shen:
FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks. 194-204 - Suyang Dai, Yuxia Ding, Zihan Zhang, Wenxuan Zuo, Xiaodi Huang, Shanfeng Zhu:
GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF. 205-215 - Bo Yang, Yupei Zhang, Shanmin Pang, Xuequn Shang, Xueqing Zhao, Minghui Han:
Integrating Multi-Omic Data With Deep Subspace Fusion Clustering for Cancer Subtype Prediction. 216-226 - Lei Du, Kefei Liu, Xiaohui Yao, Shannon L. Risacher, Junwei Han, Andrew J. Saykin, Lei Guo, Li Shen:
Multi-Task Sparse Canonical Correlation Analysis with Application to Multi-Modal Brain Imaging Genetics. 227-239 - Jianliang Gao, Ling Tian, Tengfei Lv, Jianxin Wang, Bo Song, Xiaohua Hu:
Protein2Vec: Aligning Multiple PPI Networks with Representation Learning. 240-249 - Cameron T. Chalk, Niels Kornerup, Wyatt Reeves, David Soloveichik:
Composable Rate-Independent Computation in Continuous Chemical Reaction Networks. 250-260 - Sara-Jane Dunn, Hillel Kugler, Boyan Yordanov:
Formal Analysis of Network Motifs Links Structure to Function in Biological Programs. 261-271 - Pavol Bokes, Michal Hojcka, Abhyudai Singh:
MicroRNA Based Feedforward Control of Intrinsic Gene Expression Noise. 272-282 - Keenan Breik, Cameron T. Chalk, David Doty, David Haley, David Soloveichik:
Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. 283-295 - Min Zeng, Min Li, Zhihui Fei, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang:
A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information. 296-305 - Quanhua Mu, Jiguang Wang:
CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. 306-311 - Limin Li, Menglan Cai:
Cross-species Data Classification by Domain Adaptation via Discriminative Heterogeneous Maximum Mean Discrepancy. 312-324 - Yubo Wang, Yijie Ding, Jijun Tang, Yu Dai, Fei Guo:
CrystalM: A Multi-View Fusion Approach for Protein Crystallization Prediction. 325-335 - Haixia Shang, Zhi-Ping Liu:
Prioritizing Type 2 Diabetes Genes by Weighted PageRank on Bilayer Heterogeneous Networks. 336-346 - Ruiqing Zheng, Min Li, Xiang Chen, Siyu Zhao, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. 347-354 - Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang:
An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. 355-364 - Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman:
Analysis of Subtelomeric REXTAL Assemblies Using QUAST. 365-372 - Yue Zhao, Dong-Guk Shin:
Deep Pathway Analysis V2.0: A Pathway Analysis Framework Incorporating Multi-Dimensional Omics Data. 373-385 - Daniel W. Schultz, Bojian Xu:
Parallel Methods for Finding $k$k-Mismatch Shortest Unique Substrings Using GPU. 386-395
Volume 18, Number 2, March - April 2021
- Titinunt Kitrungrotsakul, Xian-Hua Han, Yutaro Iwamoto, Satoko Takemoto, Hideo Yokota, Sari Ipponjima, Tomomi Nemoto, Wei Xiong, Yen-Wei Chen:
A Cascade of 2.5D CNN and Bidirectional CLSTM Network for Mitotic Cell Detection in 4D Microscopy Image. 396-404 - Wen Zhang, Zhishuai Li, Wenzheng Guo, Weitai Yang, Feng Huang:
A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations. 405-415 - Biing-Feng Wang, Krister M. Swenson:
A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees. 416-430 - Yunpei Xu, Hong-Dong Li, Yi Pan, Feng Luo, Fang-Xiang Wu, Jianxin Wang:
A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering. 431-442 - Sahar Araghi, Thanh Nguyen:
A Hybrid Supervised Approach to Human Population Identification Using Genomics Data. 443-454 - Hsin-Hung Chou, Ching-Tien Hsu, Li-Hsuan Chen, Yue-Cheng Lin, Sun-Yuan Hsieh:
A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model. 455-462 - Huimin Luo, Jianxin Wang, Cheng Yan, Min Li, Fang-Xiang Wu, Yi Pan:
A Novel Drug Repositioning Approach Based on Collaborative Metric Learning. 463-471 - Seyedeh Shaghayegh Sadeghi, Mohammad Reza Keyvanpour:
An Analytical Review of Computational Drug Repurposing. 472-488 - Anupam Banerjee, Kuntal Pal, Pralay Mitra:
An Evolutionary Profile Guided Greedy Parallel Replica-Exchange Monte Carlo Search Algorithm for Rapid Convergence in Protein Design. 489-499 - Wanrong Gu, Ziye Zhang, Xianfen Xie, Yichen He:
An Improved Muti-Task Learning Algorithm for Analyzing Cancer Survival Data. 500-511 - Kevin Chow, Aisharjya Sarkar, Rasha Elhesha, Pietro Cinaglia, Ahmet Ay, Tamer Kahveci:
ANCA: Alignment-Based Network Construction Algorithm. 512-524 - Miguel González, Cristina Gutiérrez, Rodrigo Martínez:
Bayesian Inference in Y-Linked Two-Sex Branching Processes with Mutations: ABC Approach. 525-538 - Xiguo Yuan, Jiaao Yu, Jianing Xi, Liying Yang, Junliang Shang, Zhe Li, Junbo Duan:
CNV_IFTV: An Isolation Forest and Total Variation-Based Detection of CNVs from Short-Read Sequencing Data. 539-549 - Sourav Biswas, Sumanta Ray, Sanghamitra Bandyopadhyay:
Colored Network Motif Analysis by Dynamic Programming Approach: An Application in Host Pathogen Interaction Network. 550-561 - Jacob C. Kimmel, Andrew S. Brack, Wallace F. Marshall:
Deep Convolutional and Recurrent Neural Networks for Cell Motility Discrimination and Prediction. 562-574 - Min Li, Yake Wang, Ruiqing Zheng, Xinghua Shi, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. 575-582 - Jingrong Zhang, Zihao Wang, Zhiyong Liu, Fa Zhang:
Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI. 583-595 - Muhammad Awais, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou:
iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition. 596-610 - Cheng Yan, Guihua Duan, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
MCHMDA: Predicting Microbe-Disease Associations Based on Similarities and Low-Rank Matrix Completion. 611-620 - Cheng Peng, Xinyu Wu, Wen Yuan, Xinran Zhang, Yu Zhang, Ying Li:
MGRFE: Multilayer Recursive Feature Elimination Based on an Embedded Genetic Algorithm for Cancer Classification. 621-632 - Alexandre Gondeau, Zahia Aouabed, Mohamed Hijri, Pedro R. Peres-Neto, Vladimir Makarenkov:
Object Weighting: A New Clustering Approach to Deal with Outliers and Cluster Overlap in Computational Biology. 633-643 - Alireza Karbalayghareh, Xiaoning Qian, Edward R. Dougherty:
Optimal Bayesian Transfer Learning for Count Data. 644-655 - Andrés F. López-Lopera, Nicolas Durrande, Mauricio A. Álvarez:
Physically-Inspired Gaussian Process Models for Post-Transcriptional Regulation in Drosophila. 656-666 - Qinhu Zhang, Zhen Shen, De-Shuang Huang:
Predicting in-vitro Transcription Factor Binding Sites Using DNA Sequence + Shape. 667-676 - Jingxuan Qiu, Tianyi Qiu, Qingli Dong, Dongpo Xu, Xiang Wang, Qi Zhang, Jing Pan, Qing Liu:
Predicting the Antigenic Relationship of Foot-and-Mouth Disease Virus for Vaccine Selection Through a Computational Model. 677-685 - Chen Zhang, Yanrui Ding:
Probing the Relation Between Community Evolution in Dynamic Residue Interaction Networks and Xylanase Thermostability. 686-696 - Gui-Jun Zhang, Tengyu Xie, Xiao-Gen Zhou, Liu-Jing Wang, Jun Hu:
Protein Structure Prediction Using Population-Based Algorithm Guided by Information Entropy. 697-707 - Saikat Biswas, Pabitra Mitra, Krothapalli Sreenivasa Rao:
Relation Prediction of Co-Morbid Diseases Using Knowledge Graph Completion. 708-717 - Xiaona Song, Mi Wang, Shuai Song, Choon Ki Ahn:
Sampled-Data State Estimation of Reaction Diffusion Genetic Regulatory Networks via Space-Dividing Approaches. 718-730 - Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, Jake Y. Chen, Zechen Chong:
Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. 731-744 - Md Ekramul Hossain, Arif Khan, Mohammad Ali Moni, Shahadat Uddin:
Use of Electronic Health Data for Disease Prediction: A Comprehensive Literature Review. 745-758 - Pratik Singh, Gayadhar Pradhan:
A New ECG Denoising Framework Using Generative Adversarial Network. 759-764 - Md Anisur Rahman, Li-Minn Ang, Kah Phooi Seng:
Data Convexity and Parameter Independent Clustering for Biomedical Datasets. 765-772 - Weiyang Chen, Weiwei Li:
Definition and Usage of Texture Feature for Biological Sequence. 773-776 - Sambriddhi Mainali, Fredy A. Colorado, Max H. Garzon:
Foretelling the Phenotype of a Genomic Sequence. 777-783 - Linyu Wang, Shaoge Zheng, Hao Zhang, Zhiyang Qiu, Xiaodan Zhong, Haiming Liu, Yuanning Liu:
ncRFP: A Novel end-to-end Method for Non-Coding RNAs Family Prediction Based on Deep Learning. 784-789 - Aman Chawla, Salvatore D. Morgera, Arthur Snider:
On Axon Interaction and Its Role in Neurological Networks. 790-796 - Jia Zhu, Zetao Zheng, Min Yang, Gabriel Pui Cheong Fung, Changqin Huang:
Protein Complexes Detection Based on Semi-Supervised Network Embedding Model. 797-803 - Robert Penchovsky, Nikolet Pavlova, Dimitrios Kaloudas:
RSwitch: A Novel Bioinformatics Database on Riboswitches as Antibacterial Drug Targets. 804-808
Volume 18, Number 3, May - June 2021
- Da Yan, Sharma V. Thankachan, Jake Y. Chen:
Guest Editorial for Selected Papers From BIOKDD 2019. 809-810 - Vineet K. Raghu, Xiaoyu Ge, Arun Balajiee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis:
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. 811-822 - Tianwen Jiang, Qingkai Zeng, Tong Zhao, Bing Qin, Ting Liu, Nitesh V. Chawla, Meng Jiang:
Biomedical Knowledge Graphs Construction From Conditional Statements. 823-835 - Jithin K. Sreedharan, Krzysztof Turowski, Wojciech Szpankowski:
Revisiting Parameter Estimation in Biological Networks: Influence of Symmetries. 836-849 - Ke Yan, Zhiwei Ji, Qun Jin, Qing-Guo Wang:
Guest Editorial: Machine Learning for AI-Enhanced Healthcare and Medical Services: New Development and Promising Solution. 850-851 - Sheng Lian, Lei Li, Guiren Lian, Xiao Xiao, Zhiming Luo, Shaozi Li:
A Global and Local Enhanced Residual U-Net for Accurate Retinal Vessel Segmentation. 852-862 - Huijuan Lu, Huiyun Gao, Minchao Ye, Xiuhui Wang:
A Hybrid Ensemble Algorithm Combining AdaBoost and Genetic Algorithm for Cancer Classification with Gene Expression Data. 863-870 - Xiaodan Yan, Baojiang Cui, Yang Xu, Peilin Shi, Ziqi Wang:
A Method of Information Protection for Collaborative Deep Learning under GAN Model Attack. 871-881 - Qingchen Zhang, Changchuan Bai, Laurence T. Yang, Zhikui Chen, Peng Li, Hang Yu:
A Unified Smart Chinese Medicine Framework for Healthcare and Medical Services. 882-890 - Dehua Chen, Meihua Huang, Weimin Li:
Knowledge-Powered Deep Breast Tumor Classification With Multiple Medical Reports. 891-901 - Yiyuan Chen, Yufeng Wang, Liang Cao, Qun Jin:
CCFS: A Confidence-Based Cost-Effective Feature Selection Scheme for Healthcare Data Classification. 902-911 - Xiaokang Zhou, Yue Li, Wei Liang:
CNN-RNN Based Intelligent Recommendation for Online Medical Pre-Diagnosis Support. 912-921 - Lu Yan, Weihong Huang, Liming Wang, Song Feng, Yonghong Peng, Jie Peng:
Data-Enabled Digestive Medicine: A New Big Data Analytics Platform. 922-931 - Mauricio Guevara-Souza, Edgar E. Vallejo, Karol Estrada:
Detecting Clustered Independent Rare Variant Associations Using Genetic Algorithms. 932-939 - Yongjin Zhou, Weijian Huang, Pei Dong, Yong Xia, Shanshan Wang:
D-UNet: A Dimension-Fusion U Shape Network for Chronic Stroke Lesion Segmentation. 940-950 - Yaqi Wang, Lingling Sun, Qun Jin:
Enhanced Diagnosis of Pneumothorax with an Improved Real-Time Augmentation for Imbalanced Chest X-rays Data Based on DCNN. 951-962 - Xiuhui Wang, Shiling Feng, Wei Qi Yan:
Human Gait Recognition Based on Self-Adaptive Hidden Markov Model. 963-972 - Jayanta Kumar Pal, Shubhra Sankar Ray, Sankar K. Pal:
Identifying Drug Resistant miRNAs Using Entropy Based Ranking. 973-984 - Bing Wang, Changqing Mei, Yuanyuan Wang, Yuming Zhou, Mu-Tian Cheng, Chunhou Zheng, Lei Wang, Jun Zhang, Peng Chen, Yan Xiong:
Imbalance Data Processing Strategy for Protein Interaction Sites Prediction. 985-994 - Xiran Jiang, Jiaxin Li, Yangyang Kan, Tao Yu, Shijie Chang, Xianzheng Sha, Hairong Zheng, Yahong Luo, Shanshan Wang:
MRI Based Radiomics Approach With Deep Learning for Prediction of Vessel Invasion in Early-Stage Cervical Cancer. 995-1002 - Cheng Li, Jingxu Xu, Qiegen Liu, Yongjin Zhou, Lisha Mou, Zuhui Pu, Yong Xia, Hairong Zheng, Shanshan Wang:
Multi-View Mammographic Density Classification by Dilated and Attention-Guided Residual Learning. 1003-1013 - Ali Cakmak, M. Hasan Celik:
Personalized Metabolic Analysis of Diseases. 1014-1025 - Wenyan Wang, Yuming Zhou, Mu-Tian Cheng, Yan Wang, Chun-Hou Zheng, Yan Xiong, Peng Chen, Zhiwei Ji, Bing Wang:
Potential Pathogenic Genes Prioritization Based on Protein Domain Interaction Network Analysis. 1026-1034 - Souad Bouasker, Wissem Inoubli, Sadok Ben Yahia, Gayo Diallo:
Pregnancy Associated Breast Cancer Gene Expressions : New Insights on Their Regulation Based on Rare Correlated Patterns. 1035-1048 - Jiechen Li, Haochen Zhao, Zhanwei Xuan, Jingwen Yu, Xiang Feng, Bo Liao, Lei Wang:
A Novel Approach for Potential Human LncRNA-Disease Association Prediction Based on Local Random Walk. 1049-1059 - Min Liu, Yalan Liu, Weili Qian, Yaonan Wang:
DeepSeed Local Graph Matching for Densely Packed Cells Tracking. 1060-1069 - Zhen Zhang, Junwei Luo, Juan Shang, Min Li, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy. 1070-1081 - Tingting Yu, Jianxing Liu, Qingshuang Zeng, Ligang Wu:
Dissipativity-Based Filtering for Switched Genetic Regulatory Networks with Stochastic Disturbances and Time-Varying Delays. 1082-1092 - Ying An, Nengjun Huang, Xianlai Chen, Fang-Xiang Wu, Jianxin Wang:
High-Risk Prediction of Cardiovascular Diseases via Attention-Based Deep Neural Networks. 1093-1105 - Qingfeng Chen, Dehuan Lai, Wei Lan, Ximin Wu, Baoshan Chen, Jin Liu, Yi-Ping Phoebe Chen, Jianxin Wang:
ILDMSF: Inferring Associations Between Long Non-Coding RNA and Disease Based on Multi-Similarity Fusion. 1106-1112 - Xiangmin Ji, Lei Wang, Liyan Hua, Xueying Wang, Pengyue Zhang, Aditi Shendre, Weixing Feng, Jin Li, Lang Li:
Improved Adverse Drug Event Prediction Through Information Component Guided Pharmacological Network Model (IC-PNM). 1113-1121