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

Volume 17, Issue 6

1832 -- 1834Da Yan 0001, Xin Gao 0001, Samah J. Fodeh, Jake Y. Chen. Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018
1835 -- 1845Michael Sokolovsky, Francisco Guerrero, Sarun Paisarnsrisomsuk, Carolina Ruiz, Sergio A. Alvarez. Deep Learning for Automated Feature Discovery and Classification of Sleep Stages
1846 -- 1857Matthew B. A. McDermott, Jennifer Wang, Wen-Ning Zhao, Steven Sheridan, Peter Szolovits, Isaac S. Kohane, Stephen J. Haggarty, Roy H. Perlis. Deep Learning Benchmarks on L1000 Gene Expression Data
1858 -- 1870Jingyi Zheng, Fushing Hsieh, Linqiang Ge. A Data-Driven Approach to Predict and Classify Epileptic Seizures from Brain-Wide Calcium Imaging Video Data
1871 -- 1882Hongming Xu, SunHo Park, Tae-Hyun Hwang. Computerized Classification of Prostate Cancer Gleason Scores from Whole Slide Images
1883 -- 1894Shreyasi Pathak, Jorit van Rossen, Onno Vijlbrief, Jeroen Geerdink, Christin Seifert, Maurice van Keulen. Post-Structuring Radiology Reports of Breast Cancer Patients for Clinical Quality Assurance
1895 -- 1906Enrique Noriega-Atala, Paul Douglas Hein, Shraddha Satish Thumsi, Zechy Wong, Xia Wang, Sean M. Hendryx, Clayton T. Morrison. Extracting Inter-Sentence Relations for Associating Biological Context with Events in Biomedical Texts
1907 -- 1917Jonathon A. Gibbs, Michael P. Pound, Andrew P. French, Darren M. Wells, Erik H. Murchie, Tony P. Pridmore. Active Vision and Surface Reconstruction for 3D Plant Shoot Modelling
1918 -- 1931Xiaoyang Jing, Qiwen Dong, Daocheng Hong, Ruqian Lu. Amino Acid Encoding Methods for Protein Sequences: A Comprehensive Review and Assessment
1932 -- 1945Soumya Paul, Cui Su, Jun Pang 0001, Andrzej Mizera. An Efficient Approach Towards the Source-Target Control of Boolean Networks
1946 -- 1954Letu Qingge, Killian Smith, Sean Jungst, Baihui Wang, Qing Yang 0003, Binhai Zhu. Approaching the One-Sided Exemplar Adjacency Number Problem
1955 -- 1965Mohammad Bozlul Karim, Ming Huang 0002, Naoaki Ono, Shigehiko Kanaya, Md. Altaf-Ul-Amin. BiClusO: A Novel Biclustering Approach and Its Application to Species-VOC Relational Data
1966 -- 1980Guang-Hui Liu, Bei-Wei Zhang, Gang Qian, Bin Wang 0041, Bo Mao, Isabelle Bichindaritz. Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks
1981 -- 1993Nicola Paoletti, Kin Sum Liu, hongkai Chen, Scott A. Smolka, Shan Lin. Data-Driven Robust Control for a Closed-Loop Artificial Pancreas
1994 -- 2004Jian Liu, Qiuru Liu, Lei Zhang, Shuhui Su, Yongzhuang Liu. Enabling Massive XML-Based Biological Data Management in HBase
2005 -- 2016Pratik Dutta, Sriparna Saha 0001, Saraansh Chopra, Varnika Miglani. Ensembling of Gene Clusters Utilizing Deep Learning and Protein-Protein Interaction Information
2017 -- 2028Lun Hu, Pengwei Hu, Xin Luo 0001, Xiaohui Yuan, Zhu-Hong You. Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites
2029 -- 2039Xinyi Yu, Wenge Rong, Jingshuang Liu, Deyu Zhou, Yuanxin Ouyang, Zhang Xiong. LSTM-Based End-to-End Framework for Biomedical Event Extraction
2040 -- 2052Ehsan Kazemi 0001, Matthias Grossglauser. MPGM: Scalable and Accurate Multiple Network Alignment
2053 -- 2061Wei Zhang 0079, Jia Xu 0002, Xiufen Zou. Predicting Essential Proteins by Integrating Network Topology, Subcellular Localization Information, Gene Expression Profile and GO Annotation Data
2062 -- 2073Zengyou He, Can Zhao, Hao Liang, Bo Xu 0008, Quan Zou 0001. Protein Complexes Identification with Family-Wise Error Rate Control
2074 -- 2085Midusha Shrestha, Truong X. Tran, Bidhan Bhattarai, Marc L. Pusey, Ramazan S. Aygün. Schema Matching and Data Integration with Consistent Naming on Protein Crystallization Screens
2086 -- 2097Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W. H. Wong. Semiglobal Sequence Alignment with Gaps Using GPU
2098 -- 2106Shun-ichi Azuma, Toshimitsu Kure, Toshiharu Sugie. Structural Bistability Analysis of Flower-Shaped and Chain-Shaped Boolean Networks
2107 -- 2118John A. Rhodes. Topological Metrizations of Trees, and New Quartet Methods of Tree Inference
2119 -- 2130Gui-jun Zhang, Xiao-Qi Wang, Lai-Fa Ma, Liu-Jing Wang, Jun Hu, Xiao-gen Zhou. Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction
2131 -- 2140Adeola Ogunleye, Qing-Guo Wang. XGBoost Model for Chronic Kidney Disease Diagnosis
2141 -- 2147Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, María Rodríguez Martínez. FPGA Accelerated Analysis of Boolean Gene Regulatory Networks
2148 -- 2154Ming Xiao, Xiangyu Yang, Jun Yu, Le Zhang 0004. CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study
2155 -- 2161Manuela Petti, Daniele Bizzarri, Antonella Verrienti, Rosa Falcone, Lorenzo Farina. Connectivity Significance for Disease Gene Prioritization in an Expanding Universe
2162 -- 2169Le Ou-Yang, Xiao-fei Zhang, Xiaohua Hu, Hong Yan 0001. Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model
2170 -- 2175Yadong Dong, Yongqi Sun, Chao Qin, Weiguo Zhu. EPMDA: Edge Perturbation Based Method for miRNA-Disease Association Prediction
2176 -- 2182Yixin Wang, Md. Noor-A.-Rahim, Jingyun Zhang, Erry Gunawan, Yong Liang Guan 0001, Chueh-Loo Poh. Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage
2183 -- 2188Rajkumar Chakraborty, Yasha Hasija. Predicting MicroRNA Sequence Using CNN and LSTM Stacked in Seq2Seq Architecture
2189 -- 2195Michael Schmidt, Kay Hamacher, Felix Reinhardt, Thea S. Lotz, Florian Groher, Beatrix Suess, Sven Jager. SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures
2196 -- 0Jong Ho Jhee, Sunjoo Bang, Dong-Gi Lee, Hyunjung Shin. Corrections to "Comorbidity Scoring With Causal Disease Networks"
2197 -- 0Jin Zhao 0005, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu. Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads"

Volume 17, Issue 5

1474 -- 1475De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha. Guest Editorial for Special Section on the 14th International Conference on Intelligent Computing (ICIC)
1476 -- 1482Wook Lee, Kyungsook Han. Constructive Prediction of Potential RNA Aptamers for a Protein Target
1483 -- 1492Zhen Shen, Su-Ping Deng, De-Shuang Huang. Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature
1493 -- 1503Huiqiang Jia, Haichao Wei, Daming Zhu, Jingjing Ma, Hai Yang, Ruizhi Wang, Xianzhong Feng. PASA: Identifying More Credible Structural Variants of Hedou12
1504 -- 1515Jian Liu, Zhi Qu, Mo Yang, Jialiang Sun, Shuhui Su, Lei Zhang. Jointly Integrating VCF-Based Variants and OWL-Based Biomedical Ontologies in MongoDB
1516 -- 1524Pengwei Hu, Yu-An Huang, Keith C. C. Chan, Zhu-Hong You. Learning Multimodal Networks From Heterogeneous Data for Prediction of lncRNA-miRNA Interactions
1525 -- 1534Xiaoli Lin, Xiaolong Zhang 0002, Xin Xu 0007. Efficient Classification of Hot Spots and Hub Protein Interfaces by Recursive Feature Elimination and Gradient Boosting
1535 -- 1545Jade Hind, Paulo Lisboa, Abir Jaafar Hussain, Dhiya Al-Jumeily. A Novel Approach to Detecting Epistasis using Random Sampling Regularisation
1546 -- 1554Jianqiang Li 0001, Xiaofeng Shi, Zhu-Hong You, Hai-Cheng Yi, Zhuangzhuang Chen, Qiuzhen Lin, Min Fang. Using Weighted Extreme Learning Machine Combined With Scale-Invariant Feature Transform to Predict Protein-Protein Interactions From Protein Evolutionary Information
1555 -- 1562Maryam S. Daneshpour, Hossein Mahjub, Hamid Pezeshk, Mehdi Sadeghi. A Network-Based Comparison Between Molecular Apocrine Breast Cancer Tumor and Basal and Luminal Tumors by Joint Graphical Lasso
1563 -- 1572Qian Guo, Tianhong Pan, Shan Chen, Xiaobo Zou, Dorothy Yu Huang. A Novel Edge Effect Detection Method for Real-Time Cellular Analyzer Using Functional Principal Component Analysis
1573 -- 1581Nirmala Sharma, Harish Sharma, Ajay Sharma. An Effective Solution for Large Scale Single Machine Total Weighted Tardiness Problem using Lunar Cycle Inspired Artificial Bee Colony Algorithm
1582 -- 1594Aisharjya Sarkar, Yilmaz Atay, Alana Lorraine Erickson, Ivan Arisi, Cesare Saltini, Tamer Kahveci. An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer
1595 -- 1604Cheng Yan, Guihua Duan, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang 0001. BRWMDA: Predicting Microbe-Disease Associations Based on Similarities and Bi-Random Walk on Disease and Microbe Networks
1605 -- 1612Chen Peng, Yang Zheng, De-Shuang Huang. Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes
1613 -- 1624Pourya Naderi Yeganeh, M. Taghi Mostafavi. Causal Disturbance Analysis: A Novel Graph Centrality Based Method for Pathway Enrichment Analysis
1625 -- 1638Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport
1639 -- 1647Xiangxiang Zeng, Yinglai Lin, Yuying He, Linyuan Lü, Xiaoping Min, Alfonso Rodríguez-Patón. Deep Collaborative Filtering for Prediction of Disease Genes
1648 -- 1659Ashish Ranjan, Md. Shah Fahad, David Fernández-Baca, Akshay Deepak, Sudhakar Tripathi. Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences
1660 -- 1670Sunil Datt Sharma, Sanjeev Narayan Sharma, Rajiv Saxena. Identification of Short Exons Disunited by a Short Intron in Eukaryotic DNA Regions
1671 -- 1681Min Wang, Ting-Zhu Huang, Jian Fang 0001, Vince D. Calhoun, Yu-Ping Wang 0002. Integration of Imaging (epi)Genomics Data for the Study of Schizophrenia Using Group Sparse Joint Nonnegative Matrix Factorization
1682 -- 1690Lan Zhao, Hong Yan 0001. MCNF: A Novel Method for Cancer Subtyping by Integrating Multi-Omics and Clinical Data
1691 -- 1702Matthieu Pichené, Sucheendra K. Palaniappan, Eric Fabre, Blaise Genest. Modeling Variability in Populations of Cells Using Approximated Multivariate Distributions
1703 -- 1713Yuan Zhang, Haihong Liu, Zhouhong Li, Zhonghua Miao, Jin Zhou. Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation
1714 -- 1720Sijia Wu, Xiaoming Wu, Jie Tian, Xiaobo Zhou, Liyu Huang. PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses
1721 -- 1728Laiyi Fu, Qinke Peng, Ling Chai. Predicting DNA Methylation States with Hybrid Information Based Deep-Learning Model
1729 -- 1740Sushmita Paul, Madhumita Madhumita. 3: Computational Method for Identification of miRNA-mRNA Regulatory Modules in Cervical Cancer
1741 -- 1750Zhen Shen, Su-Ping Deng, De-Shuang Huang. RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks
1751 -- 1761Saad Raza, Ghulam Abbas, Syed Sikander Azam. Screening Pipeline for Flavivirus Based Inhibitors for Zika Virus NS1
1762 -- 1772Keisuke Kawano, Satoshi Koide, Chie Imamura. Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation
1773 -- 1784Xiangtao Li, Ka Chun Wong. Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering
1785 -- 1796Dongjin Choi, Lee Sael. SNeCT: Scalable Network Constrained Tucker Decomposition for Multi-Platform Data Profiling
1797 -- 1809Ali Ahmed Al-Matouq, Taous-Meriem Laleg-Kirati, Carlo Novara, Ivana Rabbone, Tyrone Vincent. Sparse Reconstruction of Glucose Fluxes Using Continuous Glucose Monitors
1810 -- 1821Bahar Tercan, Aybar C. Acar. The Use of Informed Priors in Biclustering of Gene Expression with the Hierarchical Dirichlet Process
1822 -- 1831Milana Grbic, Aleksandar Kartelj, Savka Jankovic, Dragan Matic, Vladimir Filipovic. Variable Neighborhood Search for Partitioning Sparse Biological Networks into the Maximum Edge-Weighted $k$k-Plexes

Volume 17, Issue 4

1093 -- 1104Jose M. Herruzo, Sonia González-Navarro, Pablo Ibáñez-Marín, Víctor Viñals Yúfera, Jesús Alastruey-Benedé, Oscar G. Plata. Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor
1105 -- 1114Arghavan Bahadorinejad, Mahdi Imani, Ulisses M. Braga-Neto. Adaptive Particle Filtering for Fault Detection in Partially-Observed Boolean Dynamical Systems
1115 -- 1124Hannes Klarner, Frederike Heinitz, Sarah Nee, Heike Siebert. Basins of Attraction, Commitment Sets, and Phenotypes of Boolean Networks
1125 -- 1133Hasindu Gamaarachchi, Arash Bayat, Bruno Gaëta, Sri Parameswaran. Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling
1134 -- 1140Michael Youmans, John Christian Givhan Spainhour, Peng Qiu. Classification of Antibacterial Peptides Using Long Short-Term Memory Recurrent Neural Networks
1141 -- 1153Xiguo Yuan, Jun Bai, Junying Zhang, Liying Yang, Junbo Duan, Yaoyao Li, Meihong Gao. CONDEL: Detecting Copy Number Variation and Genotyping Deletion Zygosity from Single Tumor Samples Using Sequence Data
1154 -- 1173Hussain A. Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita. (Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices
1174 -- 1186Michael Taynnan Barros, Subhrakanti Dey. Feed-Forward and Feedback Control in Astrocytes for Ca$^{2+}$2+-Based Molecular Communications Nanonetworks
1187 -- 1197Fuyan Hu, Yuxuan Zhou, Qing Wang, Zhiyuan Yang, Yu Shi, Qingjia Chi. Gene Expression Classification of Lung Adenocarcinoma into Molecular Subtypes
1198 -- 1210Venkateshwarlu Y. Gudur, Amit Acharyya. Hardware-Software Codesign Based Accelerated and Reconfigurable Methodology for String Matching in Computational Bioinformatics Applications
1211 -- 1221Guoyi Zhao, Li Guo 0012, Yong Zhang, Lixin Gao 0001, Li-Jun Ma. Identifying TF Binding Motifs from a Partial Set of Target Genes and its Application to Regulatory Network Inference
1222 -- 1230Niko Yasui, Chrysafis Vogiatzis, Ruriko Yoshida, Kenji Fukumizu. imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming
1231 -- 1240Zhimin Deng, Xinan Zhang, Tianhai Tian. Inference of Model Parameters Using Particle Filter Algorithm and Copula Distributions
1241 -- 1252Haluk Damgacioglu, Emrah Celik, Nurcin Celik. Intra-Cluster Distance Minimization in DNA Methylation Analysis Using an Advanced Tabu-Based Iterative $k$k-Medoids Clustering Algorithm (T-CLUST)
1253 -- 1261Yingxia Sun, Xuan Wang, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng 0001, Xiujuan Lei. Introducing Heuristic Information Into Ant Colony Optimization Algorithm for Identifying Epistasis
1262 -- 1275Xiaohui Yang, Li Tian, Yunmei Chen, Lijun Yang, Shuang Xu, Wenming Wu. Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition
1276 -- 1289Norman, Christopher Rodriguez, Pradeep Chowriappa, Sumeet Dua. Local Similarity Matrix for Cysteine Disulfide Connectivity Prediction from Protein Sequences
1290 -- 1302Aparajita Khan, Pradipta Maji. Low-Rank Joint Subspace Construction for Cancer Subtype Discovery
1303 -- 1316Abhinandan Khan, Goutam Saha 0002, Rajat Kumar Pal. Modified Half-System Based Method for Reverse Engineering of Gene Regulatory Networks
1317 -- 1328Alexandre V. Fassio, Lucianna Helene Santos, Sabrina de Azevedo Silveira, Rafaela S. Ferreira, Raquel Cardoso de Melo Minardi. nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale
1329 -- 1340Xiao-ying Liu, Sai Wang, Hai Zhang 0001, Hui Zhang 0032, Ziyi Yang, Yong Liang 0001. Novel Regularization Method for Biomarker Selection and Cancer Classification
1341 -- 1351Jiawei Luo, Yahui Long. NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity
1352 -- 1363Chao Lan, Sai Nivedita Chandrasekaran, Jun Huan. On the Unreported-Profile-is-Negative Assumption for Predictive Cheminformatics
1364 -- 1371Poulami Majumder, Partha Pratim Ray, Sujay Ghosh, Subrata Kumar Dey. Potential Effect of Tobacco Consumption through Smoking and Chewing Tobacco on IL1beta Protein Expression in Chronic Periodontitis Patients: In Silico Molecular Docking Study
1372 -- 1382Abdollah Amirkhani, Mojtaba Kolahdoozi, Chen Wang, Lukasz A. Kurgan. Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps
1383 -- 1393Jiyun Zhou, Qin Lu 0001, Ruifeng Xu, Lin Gui 0003, Hongpeng Wang. Prediction of TF-Binding Site by Inclusion of Higher Order Position Dependencies
1394 -- 1405Wei Shao 0005, Sheng-Jun Huang, Mingxia Liu, Daoqiang Zhang. Querying Representative and Informative Super-Pixels for Filament Segmentation in Bioimages
1406 -- 1418Volkan Altuntas, Murat Gök, Tamer Kahveci. Stability Analysis of Biological Networks' Diffusion State
1419 -- 1429Jun Hu, Xiaogen Zhou, Yi-Heng Zhu, Dong-jun Yu, Gui-jun Zhang. TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning
1430 -- 1439Wenbo Wang, Junlin Wang, Dong Xu 0002, Yi Shang. Two New Heuristic Methods for Protein Model Quality Assessment
1440 -- 1450Liana Amaya Moreno, Maryam Omidi, Marcus Wurlitzer, Bérengère Luthringer, Heike Helmholz, Hartmut Schlüter, Regine Willumeit-Römer, Armin Fügenschuh. Understanding Protein Networks Using Vester's Sensitivity Model
1451 -- 1458Gaoshi Li, Min Li 0007, Jianxin Wang, Yaohang Li, Yi Pan 0001. United Neighborhood Closeness Centrality and Orthology for Predicting Essential Proteins
1459 -- 1473Xin Mou, Hasan M. Jamil. Visual Life Sciences Workflow Design Using Distributed and Heterogeneous Resources

Volume 17, Issue 3

726 -- 727Jie Zheng 0002, Jinyan Li, Yun Zheng. Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018)
728 -- 738Xingyu Liao, Min Li 0007, You Zou, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang. An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data
739 -- 747Shunfang Wang, Zicheng Cao, Mingyuan Li, Yaoting Yue. G-DipC: An Improved Feature Representation Method for Short Sequences to Predict the Type of Cargo in Cell-Penetrating Peptides
748 -- 757Yong Liu 0020, Min Wu 0008, Chenghao Liu, Xiaoli Li 0001, Jie Zheng 0002. 2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization
758 -- 768Junrong Song, Wei Peng, Feng Wang. An Entropy-Based Method for Identifying Mutual Exclusive Driver Genes in Cancer
769 -- 776Jiajie Peng, Linjiao Zhu, Yadong Wang, Jin Chen. Mining Relationships among Multiple Entities in Biological Networks
777 -- 787Heng Yao, Yunjia Shi, Jihong Guan, Shuigeng Zhou. Accurately Detecting Protein Complexes by Graph Embedding and Combining Functions with Interactions
788 -- 795Yuanyuan Ma, Xiaohua Hu, Tingting He, Xingpeng Jiang. Clustering and Integrating of Heterogeneous Microbiome Data by Joint Symmetric Nonnegative Matrix Factorization with Laplacian Regularization
796 -- 803Renjie Tan, Jixuan Wang, Xiaoliang Wu, Liran Juan, Tianjiao Zhang, Rui Ma, Qing Zhan, Tao Wang, Shuilin Jin, Qinghua Jiang, Yadong Wang. ERDS-Exome: A Hybrid Approach for Copy Number Variant Detection from Whole-Exome Sequencing Data
804 -- 816Shaoliang Peng, Xiaoyu Zhang, Wenhe Su, Dong Dong, Yutong Lu, Xiangke Liao, Kai Lu, Canqun Yang, Jie Liu 0002, Weiliang Zhu, Dongqing Wei. High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer
817 -- 827Min Li 0007, Xiangmao Meng, Ruiqing Zheng, Fang-Xiang Wu, Yaohang Li, Yi Pan 0001, Jianxin Wang. Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network
828 -- 840Mohammad Arifur Rahman, Nathan Lapierre, Huzefa Rangwala. Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL)
841 -- 846Lishuang Li, Yuxin Jiang. Integrating Language Model and Reading Control Gate in BLSTM-CRF for Biomedical Named Entity Recognition
847 -- 857Binbin Wu, Min Li 0007, Xingyu Liao, Junwei Luo, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang. MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents
858 -- 867Huiru Zheng, Haiying Wang 0001, Richard J. Dewhurst, Rainer Roehe. Improving the Inference of Co-Occurrence Networks in the Bovine Rumen Microbiome
868 -- 876Fatima Zare, Sardar Ansari, Kayvan Najarian, Sheida Nabavi. Preprocessing Sequence Coverage Data for More Precise Detection of Copy Number Variations
877 -- 886Junwei Luo, Jianxin Wang, Juan Shang, HuiMin Luo, Min Li 0007, Fang-Xiang Wu, Yi Pan 0001. GapReduce: A Gap Filling Algorithm Based on Partitioned Read Sets
887 -- 898Haigen Hu, Qiu Guan, Shengyong Chen, Zhiwei Ji, Yao Lin. Detection and Recognition for Life State of Cell Cancer Using Two-Stage Cascade CNNs
899 -- 905Yuansheng Liu, Chaowang Lan, Michael Blumenstein, Jinyan Li. Bi-Level Error Correction for PacBio Long Reads
906 -- 915Peng Ni, Jianxin Wang, Ping Zhong 0002, Yaohang Li, Fang-Xiang Wu, Yi Pan 0001. Constructing Disease Similarity Networks Based on Disease Module Theory
916 -- 929Zhi-Zhong Chen, Youta Harada, Yuna Nakamura, Lusheng Wang 0001. Faster Exact Computation of rSPR Distance via Better Approximation
930 -- 937Zaobo He, Jiguo Yu, Ji Li 0007, Qilong Han, Guangchun Luo, Yingshu Li. Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data
938 -- 948Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu. IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads
949 -- 958Jingsong Zhang, Jianmei Guo, Ming Zhang, Xiangtian Yu, Xiaoqing Yu, Weifeng Guo, Tao Zeng, Luonan Chen. Efficient Mining Multi-Mers in a Variety of Biological Sequences
959 -- 971Fatima Boukari, Sokratis Makrogiannis. Automated Cell Tracking Using Motion Prediction-Based Matching and Event Handling
972 -- 980Lei Wang, Zhu-Hong You, De-Shuang Huang, Fengfeng Zhou. Combining High Speed ELM Learning with a Deep Convolutional Neural Network Feature Encoding for Predicting Protein-RNA Interactions
981 -- 989Qiwen Kang, Neil Moore, Christopher L. Schardl, Ruriko Yoshida. CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths
990 -- 998Sarawoot Som-In, Warangkhana Kimpan. Enhancing of Particle Swarm Optimization Based Method for Multiple Motifs Detection in DNA Sequences Collections
999 -- 1009Somayeh Bakhteh, Alireza Ghaffari Hadigheh, Nader Chaparzadeh. Identification of Minimum Set of Master Regulatory Genes in Gene Regulatory Networks
1010 -- 1018Haswanth Vundavilli, Aniruddha Datta, Chao Sima, Jianping Hua, Rosana Lopes, Michael L. Bittner. In Silico Design and Experimental Validation of Combination Therapy for Pancreatic Cancer
1019 -- 1031Ping Xuan, Tonghui Shen, Xiao Wang, Tiangang Zhang, Weixiong Zhang. Inferring Disease-Associated microRNAs in Heterogeneous Networks with Node Attributes
1032 -- 1041Hui Jiang, Jianxin Wang, Min Li 0007, Wei Lan, Fang-Xiang Wu, Yi Pan 0001. miRTRS: A Recommendation Algorithm for Predicting miRNA Targets
1042 -- 1055Ayan Chaudhury, John L. Barron. Plant Species Identification from Occluded Leaf Images
1056 -- 1067Mustafa Alshawaqfeh, Ahmad Al Kawam, Erchin Serpedin, Aniruddha Datta. Robust Recurrent CNV Detection in the Presence of Inter-Subject Variability
1068 -- 1081Gui-jun Zhang, Lai-Fa Ma, Xiao-Qi Wang, Xiaogen Zhou. Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction
1082 -- 1091Xiguo Yuan, Meihong Gao, Jun Bai, Junbo Duan. SVSR: A Program to Simulate Structural Variations and Generate Sequencing Reads for Multiple Platforms
1092 -- 0Paola Lecca, Angela Re. Correction to "A Reaction-Based Model of the State Space of Chemical Reaction Systems Enables Efficient Simulations"

Volume 17, Issue 2

366 -- 375Ziwei Chen, Xiangqi Bai, Liang Ma, Xiawei Wang, Xiuqin Liu, Yuting Liu, Luonan Chen, Lin Wan. A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data
376 -- 389Lihua Zhang, Shihua Zhang. Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data
390 -- 401Feng Li, Lin Gao, Bingbo Wang. Detection of Driver Modules with Rarely Mutated Genes in Cancers
402 -- 410Hao Jiang 0009, Yushan Qiu, Wenpin Hou, Xiaoqing Cheng, Man Yi Yim, Wai-Ki Ching. Drug Side-Effect Profiles Prediction: From Empirical to Structural Risk Minimization
411 -- 421Zhan-Ying Feng, Yong Wang. ELF: Extract Landmark Features By Optimizing Topology Maintenance, Redundancy, and Specificity
422 -- 434Jianing Xi, Ao Li, Minghui Wang. HetRCNA: A Novel Method to Identify Recurrent Copy Number Alternations from Heterogeneous Tumor Samples Based on Matrix Decomposition Framework
435 -- 448Ye Liu, Michael K. Ng, Stephen Wu 0001. Multi-Domain Networks Association for Biological Data Using Block Signed Graph Clustering
449 -- 458Jifan Shi, Juan Zhao, Xiaoping Liu 0002, Luonan Chen, Tiejun Li. Quantifying Direct Dependencies in Biological Networks by Multiscale Association Analysis
459 -- 468Rajan Kapoor, Aniruddha Datta, Chao Sima, Jianping Hua, Rosana Lopes, Michael L. Bittner. A Gaussian Mixture-Model Exploiting Pathway Knowledge for Dissecting Cancer Heterogeneity
469 -- 482Paola Lecca, Angela Re. A Reaction-Based Model of the State Space of Chemical Reaction Systems Enables Efficient Simulations
483 -- 494Kaspar Riesen, Miquel Ferrer, Horst Bunke. Approximate Graph Edit Distance in Quadratic Time
495 -- 505Xiujuan Lei, Xiaoqin Yang, Fang-Xiang Wu. Artificial Fish Swarm Optimization Based Method to Identify Essential Proteins
506 -- 515Rishika Sen, Somnath Tagore, Rajat K. De. ASAPP: Architectural Similarity-Based Automated Pathway Prediction System and Its Application in Host-Pathogen Interactions
516 -- 525Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng 0002. Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network
526 -- 535Hossein Yazdani, Leo L. Cheng, David C. Christiani, Azam Yazdani. Bounded Fuzzy Possibilistic Method Reveals Information about Lung Cancer through Analysis of Metabolomics
536 -- 546Yujie Li, Heng Huang, Hanbo Chen, Tianming Liu. Deep Neural Networks for In Situ Hybridization Grid Completion and Clustering
547 -- 557Abazar Arabameri, Davud Asemani, Pegah Teymourpour. Detection of Colorectal Carcinoma Based on Microbiota Analysis Using Generalized Regression Neural Networks and Nonlinear Feature Selection
558 -- 565Shengping Yang, Mitchell S. Wachtel, Jiangrong Wu. DFseq: Distribution-Free Method to Detect Differential Gene Expression for RNA-Sequencing Data
566 -- 586Hussain A. Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita. Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools
587 -- 598Hang Wang, Jianing Xi, Minghui Wang, Ao Li. Dual-Layer Strengthened Collaborative Topic Regression Modeling for Predicting Drug Sensitivity
599 -- 607Lishuang Li, Yang Liu, Meiyue Qin. Extracting Biomedical Events with Parallel Multi-Pooling Convolutional Neural Networks
608 -- 622Aydin Saribudak, Adarsha A. Subick, Na Hyun Kim, Joshua A. Rutta, M. Ümit Uyar. Gene Expressions, Hippocampal Volume Loss, and MMSE Scores in Computation of Progression and Pharmacologic Therapy Effects for Alzheimer's Disease
623 -- 634Qiu Xiao, Jiawei Luo, Cheng Liang, Guanghui Li 0003, Jie Cai, Pingjian Ding, Ying Liu 0027. Identifying lncRNA and mRNA Co-Expression Modules from Matched Expression Data in Ovarian Cancer
635 -- 646Ali Karimnezhad, David R. Bickel. Incorporating Prior Knowledge about Genetic Variants into the Analysis of Genetic Association Data: An Empirical Bayes Approach
647 -- 656Rongrong Zhang, Ming Hu, Yu Zhu, Zhaohui S. Qin, Ke Deng, Jun S. Liu. Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model
657 -- 667Zhen Cao, Shihua Zhang. Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks
668 -- 678Paul Fergus, Casimiro Aday Curbelo Montañez, Basma Abdulaimma, Paulo Lisboa, Carl Chalmers, Beth Pineles. Utilizing Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women
679 -- 689Qinhu Zhang, Lin Zhu 0008, Wenzheng Bao, De-Shuang Huang. Weakly-Supervised Convolutional Neural Network Architecture for Predicting Protein-DNA Binding
690 -- 703Saurav Mallik, Sanghamitra Bandyopadhyay. WeCoMXP: Weighted Connectivity Measure Integrating Co-Methylation, Co-Expression and Protein-Protein Interactions for Gene-Module Detection
704 -- 711Samah J. Fodeh, Taihua Li, Haya Jarad, Basmah Safdar. Classification of Patients with Coronary Microvascular Dysfunction
712 -- 718Rui Yuan, Le Ou-Yang, Xiaohua Hu, Xiao-fei Zhang. Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate $t$t-Distribution
719 -- 725E. Onur Karakaslar, Baris Coskun, Hassiba Outilaft, Izzie-Jacques Namer, A. Ercument Cicek. Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery

Volume 17, Issue 1

1 -- 0Carlos Martín-Vide, Miguel A. Vega-Rodríguez. Algorithms for Computational Biology: Fifth Edition
2 -- 13Klairton Lima Brito, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias. Heuristics for the Reversal and Transposition Distance Problem
14 -- 26Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation
27 -- 36Atsuko Miyawaki-Kuwakado, Soichiro Komori, Fumihide Shiraishi. A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models
37 -- 46Ranjan Kumar Maji, Sunirmal Khatua, Zhumur Ghosh. A Supervised Ensemble Approach for Sensitive microRNA Target Prediction
47 -- 55Mehmet Kocak, Khyobeni Mozhui. An Application of the Bayesian Periodicity Test to Identify Diurnal Rhythm Genes in the Brain
56 -- 70Syed Sazzad Ahmed, Swarup Roy, Jugal Kalita. Assessing the Effectiveness of Causality Inference Methods for Gene Regulatory Networks
71 -- 81Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang. Class Balanced Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions
82 -- 90Jing wei Tan, Siow-Wee Chang, Sameem Abdul Kareem, Hwa Jen Yap, Kien-Thai Yong. Deep Learning for Plant Species Classification Using Leaf Vein Morphometric
91 -- 101Yangqin Feng, Lei Zhang 0005, Juan Mo. Deep Manifold Preserving Autoencoder for Classifying Breast Cancer Histopathological Images
102 -- 109Mahnaz Habibi, Pegah Khosravi. Disruption of Protein Complexes from Weighted Complex Networks
110 -- 123Yicheng He, Junfeng Liu, Xia Ning. Drug Selection via Joint Push and Learning to Rank
124 -- 135Jiyun Zhou, Qin Lu 0001, Ruifeng Xu, Lin Gui 0003, Hongpeng Wang. EL_LSTM: Prediction of DNA-Binding Residue from Protein Sequence by Combining Long Short-Term Memory and Ensemble Learning
136 -- 148Tony Pan, Rahul Nihalani, Srinivas Aluru. Fast de Bruijn Graph Compaction in Distributed Memory Environments
149 -- 157Michal Marczyk, Roman Jaksik, Andrzej Polanski, Joanna Polanska. GaMRed - Adaptive Filtering of High-Throughput Biological Data
158 -- 164Joan Carles Pons, Céline Scornavacca, Gabriel Cardona. kk LGT Networks
165 -- 176Jiulun Cai, Hongmin Cai, Jiazhou Chen, Xi Yang. Identifying "Many-to-Many" Relationships between Gene-Expression Data and Drug-Response Data via Sparse Binary Matching
177 -- 188Xingyu Liao, Min Li 0007, Junwei Luo, You Zou, Fang-Xiang Wu, Yi Pan 0001, Feng Luo, Jianxin Wang. Improving de novo Assembly Based on Read Classification
189 -- 197Tianyi Zhang, Minghui Wang, Jianing Xi, Ao Li. LPGNMF: Predicting Long Non-Coding RNA and Protein Interaction Using Graph Regularized Nonnegative Matrix Factorization
198 -- 206Patricia Carvajal López, Fernando D. Von Borstel, Amada Torres, Gabriella Rustici, Joaquín Gutiérrez, Eduardo Romero Vivas. Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection
207 -- 219Sudipta Acharya, Sriparna Saha 0001, Prasanna Pradhan. Multi-Factored Gene-Gene Proximity Measures Exploiting Biological Knowledge Extracted from Gene Ontology: Application in Gene Clustering
220 -- 225Tao Li, Xiankai Zhang, Feng Luo, Fang-Xiang Wu, Jianxin Wang. MultiMotifMaker: A Multi-Thread Tool for Identifying DNA Methylation Motifs from Pacbio Reads
226 -- 237Xiangtao Li, Shixiong Zhang, Ka Chun Wong. Nature-Inspired Multiobjective Epistasis Elucidation from Genome-Wide Association Studies
238 -- 249Guoxian Yu, Keyao Wang, Guangyuan Fu, Maozu Guo, Jun Wang 0035. NMFGO: Gene Function Prediction via Nonnegative Matrix Factorization with Gene Ontology
250 -- 263Ali Foroughi Pour, Lori A. Dalton. Optimal Bayesian Filtering for Biomarker Discovery: Performance and Robustness
264 -- 277Sepideh Mazrouee, Wei Wang 0010. PolyCluster: Minimum Fragment Disagreement Clustering for Polyploid Phasing
278 -- 291Saptarshi Pyne, Alok Ranjan Kumar, Ashish Anand. Rapid Reconstruction of Time-Varying Gene Regulatory Networks
292 -- 301Ramón A. Delgado, Zhiyong Chen 0001, Richard H. Middleton. Stepwise Tikhonov Regularisation: Application to the Prediction of HIV-1 Drug Resistance
302 -- 315Kieran Alden, Jason Cosgrove, Mark Coles, Jon Timmis. Using Emulation to Engineer and Understand Simulations of Biological Systems
316 -- 320Dor Ganor, Ron Y. Pinter, Meirav Zehavi. A Note on GRegNetSim: A Tool for the Discrete Simulation and Analysis of Genetic Regulatory Networks
321 -- 326Chu Pan, Jiawei Luo, Jiao Zhang 0003, Xin Li. BiModule: Biclique Modularity Strategy for Identifying Transcription Factor and microRNA Co-Regulatory Modules
327 -- 333Ka Chun Wong, Shankai Yan, Qiuzhen Lin, Xiangtao Li, Chengbin Peng. Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors
334 -- 338Arash Bayat, Nandan P. Deshpande, Marc R. Wilkins, Sri Parameswaran. Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach
339 -- 346Jianxiao Liu, Jianbing Yan, Zonglin Tian, Yingjie Xiao, Haijun Liu, Songlin Hao, Xiaolong Zhang, Chaoyang Wang, Jianchao Sun, Huan Yu. Gene Regulatory Relationship Mining Using Improved Three-Phase Dependency Analysis Approach
347 -- 353Firat Ismailoglu, Rachel Cavill, Evgueni N. Smirnov, Shuang Zhou 0001, Pieter Collins, Ralf Peeters. Heterogeneous Domain Adaptation for IHC Classification of Breast Cancer Subtypes
354 -- 357Efraín Pinzón-Reyes, William Armando Alvarez, Paola Rondón-Villarreal, Hernán Guillermo Hernández. Softepigen: Primers Design Web-Based Tool for MS-HRM Technique
358 -- 364Nataliya Sokolovska, Olga Permiakova, Sofia K. Forslund, Jean-Daniel Zucker. Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines
365 -- 0Shailima Rampogu, Seok-Ju Park, Keun-Woo Lee, Ayoung Baek, Rohit Bavi, Minky Son, Guang Ping Cao, Raj Kumar, Chanin Park, Amir Zeb, Rabia Mukthar Rana. Correction to "Identification of Novel Scaffolds with Dual Role as Antiepileptic and Anti-Breast Cancer"