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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
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Algorithms for Computational Biology: Sixth Edition. 1 - Thien Le
Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. 2-15 - Sridevi Maharaj
Common Neighbors Extension of the Sticky Model for PPI Networks Evaluated by Global and Local Graphlet Similarity. 16-26 - Peng Xiao
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
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
Cross-Domain Classification Model With Knowledge Utilization Maximization for Recognition of Epileptic EEG Signals. 53-61 - Chenxi Huang
A Deep Segmentation Network of Multi-Scale Feature Fusion Based on Attention Mechanism for IVOCT Lumen Contour. 62-69 - Pengjiang Qian
Transforming UTE-mDixon MR Abdomen-Pelvis Images Into CT by Jointly Leveraging Prior Knowledge and Partial Supervision. 70-82 - Rishav Singh
Imbalanced Breast Cancer Classification Using Transfer Learning. 83-93 - Xiang Yu
ResNet-SCDA-50 for Breast Abnormality Classification. 94-102 - Jintai Chen
A Transfer Learning Based Super-Resolution Microscopy for Biopsy Slice Images: The Joint Methods Perspective. 103-113 - Yong Jin
Learning Transferable Driven and Drone Assisted Sustainable and Robust Regional Disease Surveillance for Smart Healthcare. 114-125 - Hansaim Lim
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
An Ultra-Fast and Parallelizable Algorithm for Finding $k$k-Mismatch Shortest Unique Substrings. 138-148 - Pawel Tabaszewski, Pawel Górecki
Consensus of All Solutions for Intractable Phylogenetic Tree Inference. 149-161 - Srilakshmi Pattabiraman
Profile Hidden Markov Models Are Not Identifiable. 162-172 - Jiaqi Guan
A Method for Generating Synthetic Electronic Medical Record Text. 173-182 - Ruiqi Qin
An Ontology-Independent Representation Learning for Similar Disease Detection Based on Multi-Layer Similarity Network. 183-193 - Wei Long, Tiange Li, Yang Yang
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
GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF. 205-215 - Bo Yang
Integrating Multi-Omic Data With Deep Subspace Fusion Clustering for Cancer Subtype Prediction. 216-226 - Lei Du
Multi-Task Sparse Canonical Correlation Analysis with Application to Multi-Modal Brain Imaging Genetics. 227-239 - Jianliang Gao
Protein2Vec: Aligning Multiple PPI Networks with Representation Learning. 240-249 - Cameron T. Chalk
Composable Rate-Independent Computation in Continuous Chemical Reaction Networks. 250-260 - Sara-Jane Dunn
Formal Analysis of Network Motifs Links Structure to Function in Biological Programs. 261-271 - Pavol Bokes
MicroRNA Based Feedforward Control of Intrinsic Gene Expression Noise. 272-282 - Keenan Breik
Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks. 283-295 - Min Zeng
A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information. 296-305 - Quanhua Mu
CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. 306-311 - Limin Li
Cross-species Data Classification by Domain Adaptation via Discriminative Heterogeneous Maximum Mean Discrepancy. 312-324 - Yubo Wang, Yijie Ding
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
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
Analysis of Subtelomeric REXTAL Assemblies Using QUAST. 365-372 - Yue Zhao
Deep Pathway Analysis V2.0: A Pathway Analysis Framework Incorporating Multi-Dimensional Omics Data. 373-385 - Daniel W. Schultz
Parallel Methods for Finding $k$k-Mismatch Shortest Unique Substrings Using GPU. 386-395
Volume 18, Number 2, March - April 2021
- Titinunt Kitrungrotsakul
A Cascade of 2.5D CNN and Bidirectional CLSTM Network for Mitotic Cell Detection in 4D Microscopy Image. 396-404 - Wen Zhang
A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations. 405-415 - Biing-Feng Wang
A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees. 416-430 - Yunpei Xu, Hong-Dong Li, Yi Pan
A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering. 431-442 - Sahar Araghi
A Hybrid Supervised Approach to Human Population Identification Using Genomics Data. 443-454 - Hsin-Hung Chou
A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model. 455-462 - Huimin Luo, Jianxin Wang
A Novel Drug Repositioning Approach Based on Collaborative Metric Learning. 463-471 - Seyedeh Shaghayegh Sadeghi
An Analytical Review of Computational Drug Repurposing. 472-488 - Anupam Banerjee
An Evolutionary Profile Guided Greedy Parallel Replica-Exchange Monte Carlo Search Algorithm for Rapid Convergence in Protein Design. 489-499 - Wanrong Gu
An Improved Muti-Task Learning Algorithm for Analyzing Cancer Survival Data. 500-511 - Kevin Chow, Aisharjya Sarkar
ANCA: Alignment-Based Network Construction Algorithm. 512-524 - Miguel González
Bayesian Inference in Y-Linked Two-Sex Branching Processes with Mutations: ABC Approach. 525-538 - Xiguo Yuan
CNV_IFTV: An Isolation Forest and Total Variation-Based Detection of CNVs from Short-Read Sequencing Data. 539-549 - Sourav Biswas
Colored Network Motif Analysis by Dynamic Programming Approach: An Application in Host Pathogen Interaction Network. 550-561 - Jacob C. Kimmel
Deep Convolutional and Recurrent Neural Networks for Cell Motility Discrimination and Prediction. 562-574 - Min Li
DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. 575-582 - Jingrong Zhang
Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI. 583-595 - Muhammad Awais
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
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
Object Weighting: A New Clustering Approach to Deal with Outliers and Cluster Overlap in Computational Biology. 633-643 - Alireza Karbalayghareh
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
Predicting in-vitro Transcription Factor Binding Sites Using DNA Sequence + Shape. 667-676 - Jingxuan Qiu
Predicting the Antigenic Relationship of Foot-and-Mouth Disease Virus for Vaccine Selection Through a Computational Model. 677-685 - Chen Zhang
Probing the Relation Between Community Evolution in Dynamic Residue Interaction Networks and Xylanase Thermostability. 686-696 - Gui-Jun Zhang
Protein Structure Prediction Using Population-Based Algorithm Guided by Information Entropy. 697-707 - Saikat Biswas
Relation Prediction of Co-Morbid Diseases Using Knowledge Graph Completion. 708-717 - Xiaona Song
Sampled-Data State Estimation of Reaction Diffusion Genetic Regulatory Networks via Space-Dividing Approaches. 718-730 - Guimu Guo
Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. 731-744 - Md Ekramul Hossain
Use of Electronic Health Data for Disease Prediction: A Comprehensive Literature Review. 745-758 - Pratik Singh
A New ECG Denoising Framework Using Generative Adversarial Network. 759-764 - Md Anisur Rahman
Data Convexity and Parameter Independent Clustering for Biomedical Datasets. 765-772 - Weiyang Chen
Definition and Usage of Texture Feature for Biological Sequence. 773-776 - Sambriddhi Mainali
Foretelling the Phenotype of a Genomic Sequence. 777-783 - Linyu Wang
ncRFP: A Novel end-to-end Method for Non-Coding RNAs Family Prediction Based on Deep Learning. 784-789 - Aman Chawla
On Axon Interaction and Its Role in Neurological Networks. 790-796 - Jia Zhu
Protein Complexes Detection Based on Semi-Supervised Network Embedding Model. 797-803 - Robert Penchovsky
RSwitch: A Novel Bioinformatics Database on Riboswitches as Antibacterial Drug Targets. 804-808
Volume 18, Number 3, May - June 2021
- Da Yan
Guest Editorial for Selected Papers From BIOKDD 2019. 809-810 - Vineet K. Raghu
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. 811-822 - Tianwen Jiang
Biomedical Knowledge Graphs Construction From Conditional Statements. 823-835 - Jithin K. Sreedharan
Revisiting Parameter Estimation in Biological Networks: Influence of Symmetries. 836-849 - Ke Yan
Guest Editorial: Machine Learning for AI-Enhanced Healthcare and Medical Services: New Development and Promising Solution. 850-851 - Sheng Lian
A Global and Local Enhanced Residual U-Net for Accurate Retinal Vessel Segmentation. 852-862 - Huijuan Lu, Huiyun Gao, Minchao Ye
A Hybrid Ensemble Algorithm Combining AdaBoost and Genetic Algorithm for Cancer Classification with Gene Expression Data. 863-870 - Xiaodan Yan
A Method of Information Protection for Collaborative Deep Learning under GAN Model Attack. 871-881 - Qingchen Zhang
A Unified Smart Chinese Medicine Framework for Healthcare and Medical Services. 882-890 - Dehua Chen, Meihua Huang
Knowledge-Powered Deep Breast Tumor Classification With Multiple Medical Reports. 891-901 - Yiyuan Chen, Yufeng Wang
CCFS: A Confidence-Based Cost-Effective Feature Selection Scheme for Healthcare Data Classification. 902-911 - Xiaokang Zhou
CNN-RNN Based Intelligent Recommendation for Online Medical Pre-Diagnosis Support. 912-921 - Lu Yan, Weihong Huang
Data-Enabled Digestive Medicine: A New Big Data Analytics Platform. 922-931 - Mauricio Guevara-Souza
Detecting Clustered Independent Rare Variant Associations Using Genetic Algorithms. 932-939 - Yongjin Zhou
D-UNet: A Dimension-Fusion U Shape Network for Chronic Stroke Lesion Segmentation. 940-950 - Yaqi Wang
Enhanced Diagnosis of Pneumothorax with an Improved Real-Time Augmentation for Imbalanced Chest X-rays Data Based on DCNN. 951-962 - Xiuhui Wang
Human Gait Recognition Based on Self-Adaptive Hidden Markov Model. 963-972 - Jayanta Kumar Pal
Identifying Drug Resistant miRNAs Using Entropy Based Ranking. 973-984 - Bing Wang
Imbalance Data Processing Strategy for Protein Interaction Sites Prediction. 985-994 - Xiran Jiang
MRI Based Radiomics Approach With Deep Learning for Prediction of Vessel Invasion in Early-Stage Cervical Cancer. 995-1002 - Cheng Li
Multi-View Mammographic Density Classification by Dilated and Attention-Guided Residual Learning. 1003-1013 - Ali Cakmak
Personalized Metabolic Analysis of Diseases. 1014-1025 - Wenyan Wang, Yuming Zhou, Mu-Tian Cheng, Yan Wang, Chun-Hou Zheng
Potential Pathogenic Genes Prioritization Based on Protein Domain Interaction Network Analysis. 1026-1034 - Souad Bouasker
Pregnancy Associated Breast Cancer Gene Expressions : New Insights on Their Regulation Based on Rare Correlated Patterns. 1035-1048 - Jiechen Li
A Novel Approach for Potential Human LncRNA-Disease Association Prediction Based on Local Random Walk. 1049-1059 - Min Liu
DeepSeed Local Graph Matching for Densely Packed Cells Tracking. 1060-1069 - Zhen Zhang, Junwei Luo
Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy. 1070-1081 - Tingting Yu
Dissipativity-Based Filtering for Switched Genetic Regulatory Networks with Stochastic Disturbances and Time-Varying Delays. 1082-1092 - Ying An
High-Risk Prediction of Cardiovascular Diseases via Attention-Based Deep Neural Networks. 1093-1105 - Qingfeng Chen
ILDMSF: Inferring Associations Between Long Non-Coding RNA and Disease Based on Multi-Similarity Fusion. 1106-1112 - Xiangmin Ji
Improved Adverse Drug Event Prediction Through Information Component Guided Pharmacological Network Model (IC-PNM). 1113-1121 - Meng-Meng Yin
LWPCMF: Logistic Weighted Profile-Based Collaborative Matrix Factorization for Predicting MiRNA-Disease Associations. 1122-1129 - Sune S. Nielsen
Machine Learning to Support the Presentation of Complex Pathway Graphs. 1130-1141 - Farzeen Munir
MILAMP: Multiple Instance Prediction of Amyloid Proteins. 1142-1150 - Michael R. Schwob
Modeling Cell Communication with Time-Dependent Signaling Hypergraphs. 1151-1163 - Füsun Er
Predicting the Prognosis of MCI Patients Using Longitudinal MRI Data. 1164-1173 - Sangseon Lee
Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands. 1174-1183 - Ang Bian, Xiaoyi Jiang
Resolving Colliding Larvae by Fitting ASM to Random Walker-Based Pre-Segmentations. 1184-1194 - Md. Rafiqul Islam, Md. Shahidul Islam
RNA Secondary Structure Prediction with Pseudoknots Using Chemical Reaction Optimization Algorithm. 1195-1207 - Serhan Yilmaz
SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS. 1208-1216 - Jun Zhou
Synthesis of the Dynamical Properties of Feedback Loops in Bio-Pathways. 1217-1226
Volume 18, Number 4, July - August 2021
- Dong-Qing Wei
Editorial: Computational Genomics and Molecular Medicine for Emerging COVID-19. 1227-1229 - Chunmei Cui
AGTR2, One Possible Novel Key Gene for the Entry of SARS-CoV-2 Into Human Cells. 1230-1233 - Yadunath Pathak
Deep Bidirectional Classification Model for COVID-19 Disease Infected Patients. 1234-1241 - Jin-Xiong Lv
Detection of Phenotype-Related Mutations of COVID-19 via the Whole Genomic Data. 1242-1249 - Ming Xiao
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV. 1250-1261 - Chandrabose Selvaraj
High-Throughput Screening and Quantum Mechanics for Identifying Potent Inhibitors Against Mac1 Domain of SARS-CoV-2 Nsp3. 1262-1270 - Broto Chakrabarty
Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics. 1271-1280 - Elmeri M. Jokinen
Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents. 1281-1289 - Deshan Zhou
LUNAR : Drug Screening for Novel Coronavirus Based on Representation Learning Graph Convolutional Network. 1290-1298 - Aman Chandra Kaushik, Aamir Mehmood
CoronaPep: An Anti-Coronavirus Peptide Generation Tool. 1299-1304 - Zhimiao Yu, Jiarui Lu, Yuan Jin, Yang Yang
KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information. 1305-1314 - ShanShan Hu
A Convolutional Neural Network System to Discriminate Drug-Target Interactions. 1315-1324 - Enze Liu
A Fast and Furious Bayesian Network and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks. 1325-1335 - Hector Carrillo-Cabada
A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes. 1336-1349 - Aiying Zhang
A Latent Gaussian Copula Model for Mixed Data Analysis in Brain Imaging Genetics. 1350-1360 - Ulavappa B. Angadi
A Novel Way of Comparing Protein 3D Structure Using Graph Partitioning Approach. 1361-1368 - Liguang Wang
AFSBN: A Method of Artificial Fish Swarm Optimizing Bayesian Network for Epistasis Detection. 1369-1383 - Ziying Yang, Guoxian Yu
CDPath: Cooperative Driver Pathways Discovery Using Integer Linear Programming and Markov Clustering. 1384-1395 - Bing Nan Li
Celiac Disease Detection From Videocapsule Endoscopy Images Using Strip Principal Component Analysis. 1396-1404 - Yan Ge
Cell Mechanics Based Computational Classification of Red Blood Cells Via Machine Intelligence Applied to Morpho-Rheological Markers. 1405-1415 - Wenju Zhang
ChimST: An Efficient Spectral Library Search Tool for Peptide Identification from Chimeric Spectra in Data-Dependent Acquisition. 1416-1425 - Sidharth Maheshwari
CORAL: Verification-Aware OpenCL Based Read Mapper for Heterogeneous Systems. 1426-1438 - Yingwen Zhao, Jun Wang
Cross-Species Protein Function Prediction with Asynchronous-Random Walk. 1439-1450 - Jun Zhang, Qingcai Chen
DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory. 1451-1463 - Shaoliang Peng
Discriminant Projection Shared Dictionary Learning for Classification of Tumors Using Gene Expression Data. 1464-1473 - Furkan Ozden, Metin Can Siper
DORMAN: Database of Reconstructed MetAbolic Networks. 1474-1480 - Yue Hu
DSTPCA: Double-Sparse Constrained Tensor Principal Component Analysis Method for Feature Selection. 1481-1491 - Xingyu Liao
EPGA-SC : A Framework for de novo Assembly of Single-Cell Sequencing Reads. 1492-1503 - Afsaneh Javadi, Faezeh Keighobadi, Vahab Nekoukar
Finite-Set Model Predictive Control of Melanoma Cancer Treatment Using Signaling Pathway Inhibitor of Cancer Stem Cell. 1504-1511 - Chao Wang
GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing. 1512-1523 - Gaurav Sharma
Hybrid Machine Learning Models for Predicting Types of Human T-cell Lymphotropic Virus. 1524-1534 - Methun Kamruzzaman
Hyppo-X: A Scalable Exploratory Framework for Analyzing Complex Phenomics Data. 1535-1548 - Meiling Wang
Identify Consistent Cross-Modality Imaging Genetic Patterns via Discriminant Sparse Canonical Correlation Analysis. 1549-1561 - Pingjian Ding
Inferring Synergistic Drug Combinations Based on Symmetric Meta-Path in a Novel Heterogeneous Network. 1562-1571 - Lei Deng
LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction. 1572-1581 - Ling Huang
oComm: Overlapping Community Detection in Multi-View Brain Network. 1582-1595 - Konstantinos Pliakos
Predicting Drug-Target Interactions With Multi-Label Classification and Label Partitioning. 1596-1607 - Saptarshi Pyne
Rapid Reconstruction of Time-varying Gene Regulatory Networks with Limited Main Memory. 1608-1619 - Tianshu Feng
Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets. 1620-1631 - Ting Xu, Le Ou-Yang
Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression. 1632-1642
Volume 18, Number 5, September - October 2021
- Kaijian Xia, Yizhang Jiang, Yudong Zhang
Guest Editorial: Advanced Machine-Learning Methods for Brain-Machine Interfacing or Brain-Computer Interfacing. 1643-1644 - Xiaotong Gu, Zehong Cao
EEG-Based Brain-Computer Interfaces (BCIs): A Survey of Recent Studies on Signal Sensing Technologies and Computational Intelligence Approaches and Their Applications. 1645-1666 - Yuanpeng Zhang
Epilepsy Signal Recognition Using Online Transfer TSK Fuzzy Classifier Underlying Classification Error and Joint Distribution Consensus Regularization. 1667-1678 - Xiaoqing Gu
A Hierarchical Discriminative Sparse Representation Classifier for EEG Signal Detection. 1679-1687 - Zhihan Lv
Advanced Machine-Learning Methods for Brain-Computer Interfacing. 1688-1698 - Bo Lin
A Multi-Scale Activity Transition Network for Data Translation in EEG Signals Decoding. 1699-1709 - Shuaiqi Liu
Subject-Independent Emotion Recognition of EEG Signals Based on Dynamic Empirical Convolutional Neural Network. 1710-1721 - Chenxi Huang
Predicting Human Intention-Behavior Through EEG Signal Analysis Using Multi-Scale CNN. 1722-1729 - De-Shuang Huang
Guest Editorial for Special Section on the 15th International Conference on Intelligent Computing (ICIC). 1730-1732 - Kai Zheng
MISSIM: An Incremental Learning-Based Model With Applications to the Prediction of miRNA-Disease Association. 1733-1742 - Qinhu Zhang
Predicting TF-DNA Binding Motifs from ChIP-seq Datasets Using the Bag-Based Classifier Combined With a Multi-Fold Learning Scheme. 1743-1751 - Hongjie Wu
Empirical Potential Energy Function Toward ab Initio Folding G Protein-Coupled Receptors. 1752-1762 - Yue Liu, Shu-Lin Wang
DMFMDA: Prediction of Microbe-Disease Associations Based on Deep Matrix Factorization Using Bayesian Personalized Ranking. 1763-1772 - Xinguo Lu
frDriver: A Functional Region Driver Identification for Protein Sequence. 1773-1783 - Jiang Xie
Prediction of Essential Genes in Comparison States Using Machine Learning. 1784-1792 - Qinhu Zhang
Multi-Scale Capsule Network for Predicting DNA-Protein Binding Sites. 1793-1800 - Menglu Li
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. 1801-1810 - Xiguo Yuan
A Local Outlier Factor-Based Detection of Copy Number Variations From NGS Data. 1811-1820 - Hai-Hui Huang
A Novel Cox Proportional Hazards Model for High-Dimensional Genomic Data in Cancer Prognosis. 1821-1830 - Jinhao Zhang, Zehua Zhang, Lianrong Pu, Jijun Tang, Fei Guo
AIEpred: An Ensemble Predictive Model of Classifier Chain to Identify Anti-Inflammatory Peptides. 1831-1840 - Ying Qian
Alignment-Free Sequence Comparison With Multiple k Values. 1841-1849 - Benlian Xu
An Automated Cell Tracking Approach With Multi-Bernoulli Filtering and Ant Colony Labor Division. 1850-1863 - Gautam Kumar, Rajnish Kumar, Manoj Kumar Pal, Nilotpal Pramanik, Tapobrata Lahiri
APT: An Automated Probe Tracker From Gene Expression Data. 1864-1874 - Yue Zhang, Chunfang Zheng, Sindeed Islam, Yong-Min Kim
Branching Out to Speciation in a Model of Fractionation: The Malvaceae. 1875-1884 - Atefeh Ghasemnejad, Samira Bazmara, Mahsa Shadmani, Kamran Pooshang Bagheri
Designing a New Multi-Epitope Pertussis Vaccine with Highly Population Coverage Based on a Novel Sequence and Structural Filtration Algorithm. 1885-1892 - Xiguo Yuan
ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference. 1893-1901 - Chetna Kumari
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques. 1902-1913 - Jiaojiao Chen
Few-Shot Breast Cancer Metastases Classification via Unsupervised Cell Ranking. 1914-1923 - Belal Medhat
FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for DNA-Sequences. 1924-1936 - Cangzhi Jia
Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. 1937-1945 - Hang Wei
iLncRNAdis-FB: Identify lncRNA-Disease Associations by Fusing Biological Feature Blocks Through Deep Neural Network. 1946-1957 - Veronica Suaste Morales, Sheridan K. Houghten
Lossy Compression of Quality Values in Sequencing Data. 1958-1969 - Shahid Iqbal, Zahid Halim
Orienting Conflicted Graph Edges Using Genetic Algorithms to Discover Pathways in Protein-Protein Interaction Networks. 1970-1985 - Yijie Ding
Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation. 1986-1995 - Da Zhang
Protein Family Classification from Scratch: A CNN Based Deep Learning Approach. 1996-2007 - Ke Yan
Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores. 2008-2016 - Hong Wei
RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility. 2017-2022 - Kuan-Hao Chao
RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow. 2023-2031 - Lauren Spirko-Burns
Supervised Dimension Reduction for Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards. 2032-2044 - Muhammad Aizaz Akmal, Waqar Hussain
Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. 2045-2056
Volume 18, Number 6, November - December 2021
- Aidong Zhang
EIC Farewell and New EIC Introduction. 2057 - Srinivas Aluru
Editorial: From the New Editor-in-Chief. 2058 - Carlos Martín-Vide
Algorithms for Computational Biology: Seventh Edition. 2059-2060 - Tathagata Debnath
Fast Optimal Circular Clustering and Applications on Round Genomes. 2061-2071 - Shaoheng Liang
Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data. 2072-2079 - Andre Rodrigues Oliveira
Sorting Permutations by Intergenic Operations. 2080-2093 - Gabriel Siqueira
Heuristics for Genome Rearrangement Distance With Replicated Genes. 2094-2108 - Nickolas Steinauer
Computational Modeling of Gene-Specific Transcriptional Repression, Activation and Chromatin Interactions in Leukemogenesis by LASSO-Regularized Logistic Regression. 2109-2122 - Louxin Zhang
Guest Editorial for the 17th Asia Pacific Bioinformatics Conference. 2123-2124 - Pawel Górecki
The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost. 2125-2135 - Melissa Grueter, Kalani Duran
Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model. 2136-2143 - Haoxing Du, Yi Sheng Ong, Marina Knittel, Ross Mawhorter, Nuo Liu, Gianluca Gross, Reiko Tojo, Ran Libeskind-Hadas
Multiple Optimal Reconciliations Under the Duplication-Loss-Coalescence Model. 2144-2156 - Hongzhe Guo
deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph. 2157-2166 - Cui Su
Towards Optimal Decomposition of Boolean Networks. 2167-2176 - Tom Hartmann
Sorting Signed Permutations by Inverse Tandem Duplication Random Losses. 2177-2188 - Nguyen-Quoc-Khanh Le
Prediction of FMN Binding Sites in Electron Transport Chains Based on 2-D CNN and PSSM Profiles. 2189-2197 - Ozan Firat Özgül
A Convolutional Deep Clustering Framework for Gene Expression Time Series. 2198-2207 - Fuhao Zhang, Hong Song, Min Zeng
A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information. 2208-2217 - Zilu Wang
A Memristive Circuit Implementation of Eyes State Detection in Fatigue Driving Based on Biological Long Short-Term Memory Rule. 2218-2229 - Pablo Nascimento da Silva
A Novel Feature Selection Method for Uncertain Features: An Application to the Prediction of Pro-/Anti-Longevity Genes. 2230-2238 - Dong Li
Active Module Identification From Multilayer Weighted Gene Co-Expression Networks: A Continuous Optimization Approach. 2239-2248 - Qiong Fang
An Effective Biclustering-Based Framework for Identifying Cell Subpopulations From scRNA-seq Data. 2249-2260 - Junyi Chen
Categorical Matrix Completion With Active Learning for High-Throughput Screening. 2261-2270 - Oyetunji E. Ogundijo
Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption. 2271-2280 - Shaoxun Yuan
Classification of Mild Cognitive Impairment With Multimodal Data Using Both Labeled and Unlabeled Samples. 2281-2290 - Anne-Marie Lyne
Comparing Phylogenetic Approaches to Reconstructing Cell Lineage From Microsatellites With Missing Data. 2291-2301 - Guillermo Blanco
Computational Approach to the Systematic Prediction of Glycolytic Abilities: Looking Into Human Microbiota. 2302-2313 - Eyla Willing, Jens Stoye
Computing the Inversion-Indel Distance. 2314-2326 - Junzhong Ji
Convolutional Neural Network With Graphical Lasso to Extract Sparse Topological Features for Brain Disease Classification. 2327-2338 - Annalisa Occhipinti
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism. 2339-2352 - Min Zeng
DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations. 2353-2363 - Nelson R. C. Monteiro
Drug-Target Interaction Prediction: End-to-End Deep Learning Approach. 2364-2374 - Chuan-Yuan Wang
Dual Hyper-Graph Regularized Supervised NMF for Selecting Differentially Expressed Genes and Tumor Classification. 2375-2383 - Hanif Yaghoobi
EBST: An Evolutionary Multi-Objective Optimization Based Tool for Discovering Potential Biomarkers in Ovarian Cancer. 2384-2393 - Hongwei Huo
Efficient Compression and Indexing for Highly Repetitive DNA Sequence Collections. 2394-2408 - Sanjay S. Bankapur
Enhanced Protein Structural Class Prediction Using Effective Feature Modeling and Ensemble of Classifiers. 2409-2419 - Zhiyuan Zhu
Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors. 2420-2430 - Yunhe Wang
Evolving Multiobjective Cancer Subtype Diagnosis From Cancer Gene Expression Data. 2431-2444 - Xiangtao Li
Evolving Transcriptomic Profiles From Single-Cell RNA-Seq Data Using Nature-Inspired Multiobjective Optimization. 2445-2458 - Yu-Hao Ke, Jen-Wei Huang
Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps. 2459-2470 - Javier Pérez-Rodríguez
Floating Search Methodology for Combining Classification Models for Site Recognition in DNA Sequences. 2471-2482 - Xingyi Li, Ju Xiang
FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers. 2483-2491 - Payal Gaggar
Genome-Scale Identification, in Silico Characterization and Interaction Study Between Wheat SNARE and NPSN Gene Families Involved in Vesicular Transport. 2492-2501 - Hao Li
Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model. 2502-2513 - Kai Shi
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. 2514-2525 - Hilal Tayara
Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning. 2526-2534 - Jiawei Luo
Incorporating Clinical, Chemical and Biological Information for Predicting Small Molecule-microRNA Associations Based on Non-Negative Matrix Factorization. 2535-2545 - Hai-Cheng Yi
Learning Representation of Molecules in Association Network for Predicting Intermolecular Associations. 2546-2554 - Jie Xing
Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets. 2555-2565 - Antara Pal
Manipulating Extracellular Matrix Organizations and Parameters to Control Local Cancer Invasion. 2566-2576 - Xiaowei Zhao
MHRWR: Prediction of lncRNA-Disease Associations Based on Multiple Heterogeneous Networks. 2577-2585 - Beiji Zou, Yulan Dai
Multi-Label Classification Scheme Based on Local Regression for Retinal Vessel Segmentation. 2586-2597 - Lijia Ma
Multi-Neighborhood Learning for Global Alignment in Biological Networks. 2598-2611 - Surama Biswas
Multi-objective Simulated Annealing Variants to Infer Gene Regulatory Network: A Comparative Study. 2612-2623 - Jie Yang, Song He
NegStacking: Drug-Target Interaction Prediction Based on Ensemble Learning and Logistic Regression. 2624-2634 - Pascal Schlosser
Netboost: Boosting-Supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease. 2635-2648 - Nadia S. Taou, Michael A. Lones
Optimising Boolean Synthetic Regulatory Networks to Control Cell States. 2649-2658 - Koyel Mandal
POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data. 2659-2670 - Ping Xuan
Prediction of Drug-Target Interactions Based on Network Representation Learning and Ensemble Learning. 2671-2681 - Ke Yan
Protein Fold Recognition Based on Auto-Weighted Multi-View Graph Embedding Learning Model. 2682-2691 - Xiguo Yuan
STIC: Predicting Single Nucleotide Variants and Tumor Purity in Cancer Genome. 2692-2701 - Sara Montagna
The Impact of Self-Loops on Boolean Networks Attractor Landscape and Implications for Cell Differentiation Modelling. 2702-2713 - Yushan Qiu
Unsupervised Learning Framework With Multidimensional Scaling in Predicting Epithelial-Mesenchymal Transitions. 2714-2723 - Jiunn-Liang Lin
Using Convolutional Neural Networks to Measure the Physiological Age of Caenorhabditis elegans. 2724-2732 - Shiming Wang
WMMDCA: Prediction of Drug Responses by Weight-Based Modular Mapping in Cancer Cell Lines. 2733-2740 - Getulio Pereira, Preetam Ghosh
A Bridging Centrality Plugin for GEPHI and a Case Study for Mycobacterium Tuberculosis H37Rv. 2741-2746 - Victor Luncasu, Madalina Raschip
A Graph-Based Approach for the DNA Word Design Problem. 2747-2752 - Hongmei Jiao, Qikun Shen
Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems. 2753-2758 - Davide Chicco
An Enhanced Random Forests Approach to Predict Heart Failure From Small Imbalanced Gene Expression Data. 2759-2765 - Maxim A. Sikolenko
Barapost: Binning of Nucleotide Sequences According to Taxonomic Annotation. 2766-2767 - Yan Zheng, Hao Wang, Yijie Ding
CEPZ: A Novel Predictor for Identification of DNase I Hypersensitive Sites. 2768-2774 - Ying Song
Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. 2775-2780 - Fan Lu, Yilong Lin, Chongbin Yuan, Xiao-Fei Zhang
EnTSSR: A Weighted Ensemble Learning Method to Impute Single-Cell RNA Sequencing Data. 2781-2787 - Yan Liu
Essential Protein Recognition via Community Significance. 2788-2794 - Noorul Amin
FexRNA: Exploratory Data Analysis and Feature Selection of Non-Coding RNA. 2795-2801 - Eric Chen
GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies. 2802-2808 - Yinuo Lyu
iEnhancer-KL: A Novel Two-Layer Predictor for Identifying Enhancers by Position Specific of Nucleotide Composition. 2809-2815 - Gabriel Vilallonga
In Silico Laboratory Experiments Using Statistical Model Checking: A New Model of the Palytoxin-Induced Pump Channel as Case Study. 2816-2822 - Nathan Davidov, Amanda Hernandez, Justin Jian, Patrick McKenna, K. A. Medlin, Roadra Mojumder, Megan Owen, Andrew Quijano, Amanda Rodriguez, Katherine St. John, Katherine Thai, Meliza Uraga:
Maximum Covering Subtrees for Phylogenetic Networks. 2823-2827 - Philippe Pognonec, Axel Gustovic
Mitotic Index Determination on Live Cells From Label-Free Acquired Quantitative Phase Images Using a Supervised Autoencoder. 2828-2834 - Hovakim Grabski
Molecular Simulations and Markov State Modeling Reveal Inactive Form of Quorum Sensing Regulator SdiA of Escherichia Coli. 2835-2840 - Thin Nguyen
PAN: Personalized Annotation-Based Networks for the Prediction of Breast Cancer Relapse. 2841-2847 - Amelia Villegas-Morcillo
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks. 2848-2854 - Marta Casanellas
SAQ: Semi-Algebraic Quartet Reconstruction. 2855-2861 - Chia-Yen Lee
SNP Data Science for Classification of Bipolar Disorder I and Bipolar Disorder II. 2862-2869 - Andre Rodrigues Oliveira
Sorting Signed Permutations by Intergenic Reversals. 2870-2876 - Sergi Maicas
Spatial Distribution of Antibiotic-Producing Bacteria in Urban Areas. A Case Study in València (Spain). 2877-2883 - Jiaan Dai, Fengchao Yu
Understanding the Limit of Open Search in the Identification of Peptides With Post-translational Modifications - A Simulation-Based Study. 2884-2890 - Yesen Sun
WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data. 2891-2897
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