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IEEE/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