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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 17
Volume 17, Number 1, January - February 2020
- Carlos Martín-Vide, Miguel A. Vega-Rodríguez
:
Algorithms for Computational Biology: Fifth Edition. 1 - Klairton Lima Brito, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias:
Heuristics for the Reversal and Transposition Distance Problem. 2-13 - Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, Norbert Zeh:
Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. 14-26 - Atsuko Miyawaki-Kuwakado, Soichiro Komori, Fumihide Shiraishi:
A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models. 27-36 - Ranjan Kumar Maji, Sunirmal Khatua, Zhumur Ghosh:
A Supervised Ensemble Approach for Sensitive microRNA Target Prediction. 37-46 - Mehmet Kocak, Khyobeni Mozhui:
An Application of the Bayesian Periodicity Test to Identify Diurnal Rhythm Genes in the Brain. 47-55 - Syed Sazzad Ahmed, Swarup Roy, Jugal Kalita:
Assessing the Effectiveness of Causality Inference Methods for Gene Regulatory Networks. 56-70 - Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang:
Class Balanced Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions. 71-81 - Jing Wei Tan, Siow-Wee Chang, Sameem Abdul Kareem, Hwa Jen Yap, Kien-Thai Yong:
Deep Learning for Plant Species Classification Using Leaf Vein Morphometric. 82-90 - Yangqin Feng, Lei Zhang, Juan Mo:
Deep Manifold Preserving Autoencoder for Classifying Breast Cancer Histopathological Images. 91-101 - Mahnaz Habibi, Pegah Khosravi:
Disruption of Protein Complexes from Weighted Complex Networks. 102-109 - Yicheng He, Junfeng Liu, Xia Ning:
Drug Selection via Joint Push and Learning to Rank. 110-123 - Jiyun Zhou, Qin Lu, Ruifeng Xu, Lin Gui, Hongpeng Wang:
EL_LSTM: Prediction of DNA-Binding Residue from Protein Sequence by Combining Long Short-Term Memory and Ensemble Learning. 124-135 - Tony Pan, Rahul Nihalani, Srinivas Aluru:
Fast de Bruijn Graph Compaction in Distributed Memory Environments. 136-148 - Michal Marczyk, Roman Jaksik, Andrzej Polanski, Joanna Polanska:
GaMRed - Adaptive Filtering of High-Throughput Biological Data. 149-157 - Joan Carles Pons, Céline Scornavacca, Gabriel Cardona:
Generation of Level-kk LGT Networks. 158-164 - Jiulun Cai, Hongmin Cai, Jiazhou Chen, Xi Yang:
Identifying "Many-to-Many" Relationships between Gene-Expression Data and Drug-Response Data via Sparse Binary Matching. 165-176 - Xingyu Liao, Min Li, Junwei Luo, You Zou, Fang-Xiang Wu, Yi Pan, Feng Luo, Jianxin Wang:
Improving de novo Assembly Based on Read Classification. 177-188 - Tianyi Zhang, Minghui Wang, Jianing Xi, Ao Li:
LPGNMF: Predicting Long Non-Coding RNA and Protein Interaction Using Graph Regularized Nonnegative Matrix Factorization. 189-197 - Patricia 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. 198-206 - Sudipta Acharya, Sriparna Saha, Prasanna Pradhan:
Multi-Factored Gene-Gene Proximity Measures Exploiting Biological Knowledge Extracted from Gene Ontology: Application in Gene Clustering. 207-219 - Tao Li, Xiankai Zhang, Feng Luo, Fang-Xiang Wu, Jianxin Wang:
MultiMotifMaker: A Multi-Thread Tool for Identifying DNA Methylation Motifs from Pacbio Reads. 220-225 - Xiangtao Li, Shixiong Zhang, Ka-Chun Wong:
Nature-Inspired Multiobjective Epistasis Elucidation from Genome-Wide Association Studies. 226-237 - Guoxian Yu, Keyao Wang, Guangyuan Fu, Maozu Guo, Jun Wang:
NMFGO: Gene Function Prediction via Nonnegative Matrix Factorization with Gene Ontology. 238-249 - Ali Foroughi Pour, Lori A. Dalton:
Optimal Bayesian Filtering for Biomarker Discovery: Performance and Robustness. 250-263 - Sepideh Mazrouee, Wei Wang:
PolyCluster: Minimum Fragment Disagreement Clustering for Polyploid Phasing. 264-277 - Saptarshi Pyne, Alok Ranjan Kumar, Ashish Anand:
Rapid Reconstruction of Time-Varying Gene Regulatory Networks. 278-291 - Ramón A. Delgado, Zhiyong Chen, Richard H. Middleton:
Stepwise Tikhonov Regularisation: Application to the Prediction of HIV-1 Drug Resistance. 292-301 - Kieran Alden, Jason Cosgrove, Mark C. Coles, Jon Timmis:
Using Emulation to Engineer and Understand Simulations of Biological Systems. 302-315 - Dor Ganor, Ron Y. Pinter, Meirav Zehavi:
A Note on GRegNetSim: A Tool for the Discrete Simulation and Analysis of Genetic Regulatory Networks. 316-320 - Chu Pan, Jiawei Luo, Jiao Zhang, Xin Li:
BiModule: Biclique Modularity Strategy for Identifying Transcription Factor and microRNA Co-Regulatory Modules. 321-326 - Ka-Chun Wong, Shankai Yan, Qiuzhen Lin, Xiangtao Li, Chengbin Peng:
Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors. 327-333 - Arash Bayat, Nandan P. Deshpande, Marc R. Wilkins, Sri Parameswaran:
Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach. 334-338 - Jianxiao 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. 339-346 - Firat Ismailoglu, Rachel Cavill, Evgueni N. Smirnov, Shuang Zhou, Pieter Collins, Ralf Peeters:
Heterogeneous Domain Adaptation for IHC Classification of Breast Cancer Subtypes. 347-353 - Efraín Pinzón-Reyes, William Armando Alvarez, Paola Rondón-Villarreal, Hernán Guillermo Hernández:
Softepigen: Primers Design Web-Based Tool for MS-HRM Technique. 354-357 - Nataliya Sokolovska, Olga Permiakova, Sofia K. Forslund, Jean-Daniel Zucker:
Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines. 358-364 - Shailima 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". 365
Volume 17, Number 2, March - April 2020
- Ziwei 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. 366-375 - Lihua Zhang, Shihua Zhang:
Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data. 376-389 - Feng Li, Lin Gao, Bingbo Wang:
Detection of Driver Modules with Rarely Mutated Genes in Cancers. 390-401 - Hao Jiang, Yushan Qiu, Wenpin Hou, Xiaoqing Cheng, Man Yi Yim, Wai-Ki Ching:
Drug Side-Effect Profiles Prediction: From Empirical to Structural Risk Minimization. 402-410 - Zhan-Ying Feng, Yong Wang:
ELF: Extract Landmark Features By Optimizing Topology Maintenance, Redundancy, and Specificity. 411-421 - Jianing Xi, Ao Li, Minghui Wang:
HetRCNA: A Novel Method to Identify Recurrent Copy Number Alternations from Heterogeneous Tumor Samples Based on Matrix Decomposition Framework. 422-434 - Ye Liu, Michael K. Ng, Stephen Wu:
Multi-Domain Networks Association for Biological Data Using Block Signed Graph Clustering. 435-448 - Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen, Tiejun Li:
Quantifying Direct Dependencies in Biological Networks by Multiscale Association Analysis. 449-458 - Rajan Kapoor, Aniruddha Datta, Chao Sima, Jianping Hua, Rosana Lopes, Michael L. Bittner:
A Gaussian Mixture-Model Exploiting Pathway Knowledge for Dissecting Cancer Heterogeneity. 459-468 - Paola Lecca, Angela Re:
A Reaction-Based Model of the State Space of Chemical Reaction Systems Enables Efficient Simulations. 469-482 - Kaspar Riesen, Miquel Ferrer, Horst Bunke:
Approximate Graph Edit Distance in Quadratic Time. 483-494 - Xiujuan Lei, Xiaoqin Yang, Fang-Xiang Wu:
Artificial Fish Swarm Optimization Based Method to Identify Essential Proteins. 495-505 - Rishika Sen, Somnath Tagore, Rajat K. De:
ASAPP: Architectural Similarity-Based Automated Pathway Prediction System and Its Application in Host-Pathogen Interactions. 506-515 - Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng:
Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network. 516-525 - Hossein Yazdani, Leo L. Cheng, David C. Christiani, Azam Yazdani:
Bounded Fuzzy Possibilistic Method Reveals Information about Lung Cancer through Analysis of Metabolomics. 526-535 - Yujie Li, Heng Huang, Hanbo Chen, Tianming Liu:
Deep Neural Networks for In Situ Hybridization Grid Completion and Clustering. 536-546 - Abazar Arabameri, Davud Asemani, Pegah Teymourpour:
Detection of Colorectal Carcinoma Based on Microbiota Analysis Using Generalized Regression Neural Networks and Nonlinear Feature Selection. 547-557 - Shengping Yang, Mitchell S. Wachtel, Jiangrong Wu:
DFseq: Distribution-Free Method to Detect Differential Gene Expression for RNA-Sequencing Data. 558-565 - Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita:
Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools. 566-586 - Hang Wang, Jianing Xi, Minghui Wang, Ao Li:
Dual-Layer Strengthened Collaborative Topic Regression Modeling for Predicting Drug Sensitivity. 587-598 - Lishuang Li, Yang Liu, Meiyue Qin:
Extracting Biomedical Events with Parallel Multi-Pooling Convolutional Neural Networks. 599-607 - Aydin 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. 608-622 - Qiu Xiao, Jiawei Luo, Cheng Liang, Guanghui Li, Jie Cai, Pingjian Ding, Ying Liu:
Identifying lncRNA and mRNA Co-Expression Modules from Matched Expression Data in Ovarian Cancer. 623-634 - Ali Karimnezhad, David R. Bickel:
Incorporating Prior Knowledge about Genetic Variants into the Analysis of Genetic Association Data: An Empirical Bayes Approach. 635-646 - Rongrong 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. 647-656 - Zhen Cao, Shihua Zhang:
Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks. 657-667 - Paul 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. 668-678 - Qinhu Zhang, Lin Zhu, Wenzheng Bao, De-Shuang Huang:
Weakly-Supervised Convolutional Neural Network Architecture for Predicting Protein-DNA Binding. 679-689 - Saurav Mallik, Sanghamitra Bandyopadhyay:
WeCoMXP: Weighted Connectivity Measure Integrating Co-Methylation, Co-Expression and Protein-Protein Interactions for Gene-Module Detection. 690-703 - Samah J. Fodeh, Taihua Li, Haya Jarad, Basmah Safdar:
Classification of Patients with Coronary Microvascular Dysfunction. 704-711 - Rui Yuan, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang:
Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate $t$t-Distribution. 712-718 - Emin Onur Karakaslar, Baris Coskun, Hassiba Outilaft, Izzie-Jacques Namer, A. Ercüment Çiçek:
Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery. 719-725
Volume 17, Number 3, May - June 2020
- Jie Zheng, Jinyan Li, Yun Zheng:
Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018). 726-727 - Xingyu Liao, Min Li, You Zou, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data. 728-738 - Shunfang 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. 739-747 - Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng:
SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. 748-757 - Junrong Song, Wei Peng, Feng Wang:
An Entropy-Based Method for Identifying Mutual Exclusive Driver Genes in Cancer. 758-768 - Jiajie Peng, Linjiao Zhu, Yadong Wang, Jin Chen:
Mining Relationships among Multiple Entities in Biological Networks. 769-776 - Heng Yao, Yunjia Shi, Jihong Guan, Shuigeng Zhou:
Accurately Detecting Protein Complexes by Graph Embedding and Combining Functions with Interactions. 777-787 - Yuanyuan Ma, Xiaohua Hu, Tingting He, Xingpeng Jiang:
Clustering and Integrating of Heterogeneous Microbiome Data by Joint Symmetric Nonnegative Matrix Factorization with Laplacian Regularization. 788-795 - Renjie 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. 796-803 - Shaoliang Peng, Xiaoyu Zhang, Wenhe Su, Dong Dong, Yutong Lu, Xiangke Liao, Kai Lu, Canqun Yang, Jie Liu, Weiliang Zhu, Dongqing Wei:
High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer. 804-816 - Min Li, Xiangmao Meng, Ruiqing Zheng, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang:
Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. 817-827 - Mohammad Arifur Rahman, Nathan LaPierre, Huzefa Rangwala:
Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL). 828-840 - Lishuang Li, Yuxin Jiang:
Integrating Language Model and Reading Control Gate in BLSTM-CRF for Biomedical Named Entity Recognition. 841-846 - Binbin Wu, Min Li, Xingyu Liao, Junwei Luo, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents. 847-857 - Huiru Zheng, Haiying Wang, Richard J. Dewhurst, Rainer Roehe:
Improving the Inference of Co-Occurrence Networks in the Bovine Rumen Microbiome. 858-867 - Fatima Zare, Sardar Ansari, Kayvan Najarian, Sheida Nabavi:
Preprocessing Sequence Coverage Data for More Precise Detection of Copy Number Variations. 868-876 - Junwei Luo, Jianxin Wang, Juan Shang, Huimin Luo, Min Li, Fang-Xiang Wu, Yi Pan:
GapReduce: A Gap Filling Algorithm Based on Partitioned Read Sets. 877-886 - Haigen Hu, Qiu Guan, Shengyong Chen, Zhiwei Ji, Yao Lin:
Detection and Recognition for Life State of Cell Cancer Using Two-Stage Cascade CNNs. 887-898 - Yuansheng Liu, Chaowang Lan, Michael Blumenstein, Jinyan Li:
Bi-Level Error Correction for PacBio Long Reads. 899-905 - Peng Ni, Jianxin Wang, Ping Zhong, Yaohang Li, Fang-Xiang Wu, Yi Pan:
Constructing Disease Similarity Networks Based on Disease Module Theory. 906-915 - Zhi-Zhong Chen, Youta Harada, Yuna Nakamura, Lusheng Wang:
Faster Exact Computation of rSPR Distance via Better Approximation. 916-929 - Zaobo He, Jiguo Yu, Ji Li, Qilong Han, Guangchun Luo, Yingshu Li:
Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data. 930-937 - Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu:
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads. 938-948 - Jingsong 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. 949-958 - Fatima Boukari, Sokratis Makrogiannis:
Automated Cell Tracking Using Motion Prediction-Based Matching and Event Handling. 959-971 - Lei 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. 972-980 - Qiwen Kang, Neil Moore, Christopher L. Schardl, Ruriko Yoshida:
CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths. 981-989 - Sarawoot Som-In, Warangkhana Kimpan:
Enhancing of Particle Swarm Optimization Based Method for Multiple Motifs Detection in DNA Sequences Collections. 990-998 - Somayeh Bakhteh, Alireza Ghaffari-Hadigheh, Nader Chaparzadeh:
Identification of Minimum Set of Master Regulatory Genes in Gene Regulatory Networks. 999-1009 - Haswanth Vundavilli, Aniruddha Datta, Chao Sima, Jianping Hua, Rosana Lopes, Michael L. Bittner:
In Silico Design and Experimental Validation of Combination Therapy for Pancreatic Cancer. 1010-1018 - Ping Xuan, Tonghui Shen, Xiao Wang, Tiangang Zhang, Weixiong Zhang:
Inferring Disease-Associated microRNAs in Heterogeneous Networks with Node Attributes. 1019-1031 - Hui Jiang, Jianxin Wang, Min Li, Wei Lan, Fang-Xiang Wu, Yi Pan:
miRTRS: A Recommendation Algorithm for Predicting miRNA Targets. 1032-1041 - Ayan Chaudhury, John L. Barron:
Plant Species Identification from Occluded Leaf Images. 1042-1055 - Mustafa Alshawaqfeh, Ahmad Al Kawam, Erchin Serpedin, Aniruddha Datta:
Robust Recurrent CNV Detection in the Presence of Inter-Subject Variability. 1056-1067 - Gui-Jun Zhang, Lai-Fa Ma, Xiao-Qi Wang, Xiaogen Zhou:
Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction. 1068-1081 - Xiguo Yuan, Meihong Gao, Jun Bai, Junbo Duan:
SVSR: A Program to Simulate Structural Variations and Generate Sequencing Reads for Multiple Platforms. 1082-1091 - Paola Lecca, Angela Re:
Correction to "A Reaction-Based Model of the State Space of Chemical Reaction Systems Enables Efficient Simulations". 1092
Volume 17, Number 4, July - August 2020
- Jose Manuel 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. 1093-1104 - Arghavan Bahadorinejad, Mahdi Imani, Ulisses M. Braga-Neto:
Adaptive Particle Filtering for Fault Detection in Partially-Observed Boolean Dynamical Systems. 1105-1114 - Hannes Klarner, Frederike Heinitz, Sarah Nee, Heike Siebert:
Basins of Attraction, Commitment Sets, and Phenotypes of Boolean Networks. 1115-1124 - Hasindu Gamaarachchi, Arash Bayat, Bruno Gaëta, Sri Parameswaran:
Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling. 1125-1133 - Michael Youmans, John Christian Givhan Spainhour, Peng Qiu:
Classification of Antibacterial Peptides Using Long Short-Term Memory Recurrent Neural Networks. 1134-1140 - Xiguo 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. 1141-1153 - Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita:
(Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices. 1154-1173 - Michael Taynnan Barros, Subhrakanti Dey:
Feed-Forward and Feedback Control in Astrocytes for Ca$^{2+}$2+-Based Molecular Communications Nanonetworks. 1174-1186 - Fuyan Hu, Yuxuan Zhou, Qing Wang, Zhiyuan Yang, Yu Shi, Qingjia Chi:
Gene Expression Classification of Lung Adenocarcinoma into Molecular Subtypes. 1187-1197 - Venkateshwarlu Y. Gudur, Amit Acharyya:
Hardware-Software Codesign Based Accelerated and Reconfigurable Methodology for String Matching in Computational Bioinformatics Applications. 1198-1210 - Guoyi Zhao, Li Guo, Yong Zhang, Lixin Gao, Li-Jun Ma:
Identifying TF Binding Motifs from a Partial Set of Target Genes and its Application to Regulatory Network Inference. 1211-1221 - Niko Yasui, Chrysafis Vogiatzis, Ruriko Yoshida, Kenji Fukumizu:
imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming. 1222-1230 - Zhimin Deng, Xinan Zhang, Tianhai Tian:
Inference of Model Parameters Using Particle Filter Algorithm and Copula Distributions. 1231-1240 - Haluk 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). 1241-1252 - Yingxia Sun, Xuan Wang, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng, Xiujuan Lei:
Introducing Heuristic Information Into Ant Colony Optimization Algorithm for Identifying Epistasis. 1253-1261 - Xiaohui Yang, Li Tian, Yunmei Chen, Lijun Yang, Shuang Xu, Wenming Wu:
Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition. 1262-1275 - Norman "John" Mapes, Christopher Rodriguez, Pradeep Chowriappa, Sumeet Dua:
Local Similarity Matrix for Cysteine Disulfide Connectivity Prediction from Protein Sequences. 1276-1289 - Aparajita Khan, Pradipta Maji:
Low-Rank Joint Subspace Construction for Cancer Subtype Discovery. 1290-1302 - Abhinandan Khan, Goutam Saha, Rajat Kumar Pal:
Modified Half-System Based Method for Reverse Engineering of Gene Regulatory Networks. 1303-1316 - Alexandre V. Fassio, Lucianna Helene Santos, Sabrina de Azevedo Silveira, Rafaela Salgado Ferreira, Raquel Cardoso de Melo Minardi:
nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale. 1317-1328 - Xiao-Ying Liu, Sai Wang, Hai Zhang, Hui Zhang, Ziyi Yang, Yong Liang:
Novel Regularization Method for Biomarker Selection and Cancer Classification. 1329-1340 - Jiawei Luo, Yahui Long:
NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity. 1341-1351 - Chao Lan, Sai Nivedita Chandrasekaran, Jun Huan:
On the Unreported-Profile-is-Negative Assumption for Predictive Cheminformatics. 1352-1363 - Poulami 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. 1364-1371 - Abdollah Amirkhani, Mojtaba Kolahdoozi, Chen Wang, Lukasz A. Kurgan:
Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps. 1372-1382 - Jiyun Zhou, Qin Lu, Ruifeng Xu, Lin Gui, Hongpeng Wang:
Prediction of TF-Binding Site by Inclusion of Higher Order Position Dependencies. 1383-1393 - Wei Shao, Sheng-Jun Huang, Mingxia Liu, Daoqiang Zhang:
Querying Representative and Informative Super-Pixels for Filament Segmentation in Bioimages. 1394-1405 - Volkan Altuntas, Murat Gök, Tamer Kahveci:
Stability Analysis of Biological Networks' Diffusion State. 1406-1418 - Jun 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. 1419-1429 - Wenbo Wang, Junlin Wang, Dong Xu, Yi Shang:
Two New Heuristic Methods for Protein Model Quality Assessment. 1430-1439 - Liana 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. 1440-1450 - Gaoshi Li, Min Li, Jianxin Wang, Yaohang Li, Yi Pan:
United Neighborhood Closeness Centrality and Orthology for Predicting Essential Proteins. 1451-1458 - Xin Mou, Hasan M. Jamil:
Visual Life Sciences Workflow Design Using Distributed and Heterogeneous Resources. 1459-1473
Volume 17, Number 5, September - October 2020
- De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha:
Guest Editorial for Special Section on the 14th International Conference on Intelligent Computing (ICIC). 1474-1475 - Wook Lee, Kyungsook Han:
Constructive Prediction of Potential RNA Aptamers for a Protein Target. 1476-1482 - Zhen Shen, Su-Ping Deng, De-Shuang Huang:
Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature. 1483-1492 - Huiqiang Jia, Haichao Wei, Daming Zhu, Jingjing Ma, Hai Yang, Ruizhi Wang, Xianzhong Feng:
PASA: Identifying More Credible Structural Variants of Hedou12. 1493-1503 - Jian Liu, Zhi Qu, Mo Yang, Jialiang Sun, Shuhui Su, Lei Zhang:
Jointly Integrating VCF-Based Variants and OWL-Based Biomedical Ontologies in MongoDB. 1504-1515 - Pengwei Hu, Yu-An Huang, Keith C. C. Chan, Zhu-Hong You:
Learning Multimodal Networks From Heterogeneous Data for Prediction of lncRNA-miRNA Interactions. 1516-1524 - Xiaoli Lin, Xiaolong Zhang, Xin Xu:
Efficient Classification of Hot Spots and Hub Protein Interfaces by Recursive Feature Elimination and Gradient Boosting. 1525-1534 - Jade Hind, Paulo Lisboa, Abir Jaafar Hussain, Dhiya Al-Jumeily:
A Novel Approach to Detecting Epistasis using Random Sampling Regularisation. 1535-1545 - Jianqiang Li, 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. 1546-1554 - Maryam 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. 1555-1562 - Qian 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. 1563-1572 - Nirmala 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. 1573-1581 - Aisharjya Sarkar, Yilmaz Atay, Alana Lorraine Erickson, Ivan Arisi, Cesare Saltini, Tamer Kahveci:
An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer. 1582-1594 - Cheng Yan, Guihua Duan, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
BRWMDA: Predicting Microbe-Disease Associations Based on Similarities and Bi-Random Walk on Disease and Microbe Networks. 1595-1604 - Chen Peng, Yang Zheng, De-Shuang Huang:
Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes. 1605-1612 - Pourya Naderi Yeganeh, M. Taghi Mostafavi:
Causal Disturbance Analysis: A Novel Graph Centrality Based Method for Pathway Enrichment Analysis. 1613-1624 - Jiri 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. 1625-1638 - Xiangxiang Zeng, Yinglai Lin, Yuying He, Linyuan Lü, Xiaoping Min, Alfonso Rodríguez-Patón:
Deep Collaborative Filtering for Prediction of Disease Genes. 1639-1647 - Ashish Ranjan, Md. Shah Fahad, David Fernández-Baca, Akshay Deepak, Sudhakar Tripathi:
Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences. 1648-1659 - Sunil Datt Sharma, Sanjeev Narayan Sharma, Rajiv Saxena:
Identification of Short Exons Disunited by a Short Intron in Eukaryotic DNA Regions. 1660-1670 - Min Wang, Ting-Zhu Huang, Jian Fang, Vince D. Calhoun, Yu-Ping Wang:
Integration of Imaging (epi)Genomics Data for the Study of Schizophrenia Using Group Sparse Joint Nonnegative Matrix Factorization. 1671-1681 - Lan Zhao, Hong Yan:
MCNF: A Novel Method for Cancer Subtyping by Integrating Multi-Omics and Clinical Data. 1682-1690 - Matthieu Pichené, Sucheendra K. Palaniappan, Eric Fabre, Blaise Genest:
Modeling Variability in Populations of Cells Using Approximated Multivariate Distributions. 1691-1702 - Yuan Zhang, Haihong Liu, Zhouhong Li, Zhonghua Miao, Jin Zhou:
Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation. 1703-1713 - Sijia Wu, Xiaoming Wu, Jie Tian, Xiaobo Zhou, Liyu Huang:
PredictFP2: A New Computational Model to Predict Fusion Peptide Domain in All Retroviruses. 1714-1720 - Laiyi Fu, Qinke Peng, Ling Chai:
Predicting DNA Methylation States with Hybrid Information Based Deep-Learning Model. 1721-1728 - Sushmita Paul, Madhumita:
RFCM3: Computational Method for Identification of miRNA-mRNA Regulatory Modules in Cervical Cancer. 1729-1740 - Zhen Shen, Su-Ping Deng, De-Shuang Huang:
RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks. 1741-1750 - Saad Raza, Ghulam Abbas, Syed Sikander Azam:
Screening Pipeline for Flavivirus Based Inhibitors for Zika Virus NS1. 1751-1761 - Keisuke Kawano, Satoshi Koide, Chie Imamura:
Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation. 1762-1772 - Xiangtao Li, Ka-Chun Wong:
Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering. 1773-1784 - Dongjin Choi, Lee Sael:
SNeCT: Scalable Network Constrained Tucker Decomposition for Multi-Platform Data Profiling. 1785-1796 - Ali Al-Matouq, Taous-Meriem Laleg-Kirati, Carlo Novara, Ivana Rabbone, Tyrone Vincent:
Sparse Reconstruction of Glucose Fluxes Using Continuous Glucose Monitors. 1797-1809 - Bahar Tercan, Aybar C. Acar:
The Use of Informed Priors in Biclustering of Gene Expression with the Hierarchical Dirichlet Process. 1810-1821 - Milana 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. 1822-1831
Volume 17, Number 6, November - December 2020
- Da Yan, Xin Gao, Samah J. Fodeh, Jake Y. Chen:
Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018. 1832-1834 - Michael Sokolovsky, Francisco Guerrero, Sarun Paisarnsrisomsuk, Carolina Ruiz, Sergio A. Alvarez:
Deep Learning for Automated Feature Discovery and Classification of Sleep Stages. 1835-1845 - Matthew 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. 1846-1857 - Jingyi Zheng, Fushing Hsieh, Linqiang Ge:
A Data-Driven Approach to Predict and Classify Epileptic Seizures from Brain-Wide Calcium Imaging Video Data. 1858-1870 - Hongming Xu, Sunho Park, Tae-Hyun Hwang:
Computerized Classification of Prostate Cancer Gleason Scores from Whole Slide Images. 1871-1882 - Shreyasi 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. 1883-1894 - Enrique 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. 1895-1906 - Jonathon 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. 1907-1917 - Xiaoyang Jing, Qiwen Dong, Daocheng Hong, Ruqian Lu:
Amino Acid Encoding Methods for Protein Sequences: A Comprehensive Review and Assessment. 1918-1931 - Soumya Paul, Cui Su, Jun Pang, Andrzej Mizera:
An Efficient Approach Towards the Source-Target Control of Boolean Networks. 1932-1945 - Letu Qingge, Killian Smith, Sean Jungst, Baihui Wang, Qing Yang, Binhai Zhu:
Approaching the One-Sided Exemplar Adjacency Number Problem. 1946-1954 - Mohammad Bozlul Karim, Ming Huang, Naoaki Ono, Shigehiko Kanaya, Md. Altaf-Ul-Amin:
BiClusO: A Novel Biclustering Approach and Its Application to Species-VOC Relational Data. 1955-1965 - Guang-Hui Liu, Bei-Wei Zhang, Gang Qian, Bin Wang, Bo Mao, Isabelle Bichindaritz:
Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks. 1966-1980 - Nicola Paoletti, Kin Sum Liu, Hongkai Chen, Scott A. Smolka, Shan Lin:
Data-Driven Robust Control for a Closed-Loop Artificial Pancreas. 1981-1993 - Jian Liu, Qiuru Liu, Lei Zhang, Shuhui Su, Yongzhuang Liu:
Enabling Massive XML-Based Biological Data Management in HBase. 1994-2004 - Pratik Dutta, Sriparna Saha, Saraansh Chopra, Varnika Miglani:
Ensembling of Gene Clusters Utilizing Deep Learning and Protein-Protein Interaction Information. 2005-2016 - Lun Hu, Pengwei Hu, Xin Luo, Xiaohui Yuan, Zhu-Hong You:
Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites. 2017-2028 - Xinyi Yu, Wenge Rong, Jingshuang Liu, Deyu Zhou, Yuanxin Ouyang, Zhang Xiong:
LSTM-Based End-to-End Framework for Biomedical Event Extraction. 2029-2039 - Ehsan Kazemi, Matthias Grossglauser:
MPGM: Scalable and Accurate Multiple Network Alignment. 2040-2052 - Wei Zhang, Jia Xu, Xiufen Zou:
Predicting Essential Proteins by Integrating Network Topology, Subcellular Localization Information, Gene Expression Profile and GO Annotation Data. 2053-2061 - Zengyou He, Can Zhao, Hao Liang, Bo Xu, Quan Zou:
Protein Complexes Identification with Family-Wise Error Rate Control. 2062-2073 - Midusha Shrestha, Truong X. Tran, Bidhan Bhattarai, Marc L. Pusey, Ramazan S. Aygün:
Schema Matching and Data Integration with Consistent Naming on Protein Crystallization Screens. 2074-2085 - Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W. H. Wong:
Semiglobal Sequence Alignment with Gaps Using GPU. 2086-2097 - Shun-ichi Azuma, Toshimitsu Kure, Toshiharu Sugie:
Structural Bistability Analysis of Flower-Shaped and Chain-Shaped Boolean Networks. 2098-2106 - John A. Rhodes:
Topological Metrizations of Trees, and New Quartet Methods of Tree Inference. 2107-2118 - Gui-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. 2119-2130 - Adeola Ogunleye, Qing-Guo Wang:
XGBoost Model for Chronic Kidney Disease Diagnosis. 2131-2140 - Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, María Rodríguez Martínez:
FPGA Accelerated Analysis of Boolean Gene Regulatory Networks. 2141-2147 - Ming Xiao, Xiangyu Yang, Jun Yu, Le Zhang:
CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study. 2148-2154 - Manuela Petti, Daniele Bizzarri, Antonella Verrienti, Rosa Falcone, Lorenzo Farina:
Connectivity Significance for Disease Gene Prioritization in an Expanding Universe. 2155-2161 - Le Ou-Yang, Xiao-Fei Zhang, Xiaohua Hu, Hong Yan:
Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model. 2162-2169 - Yadong Dong, Yongqi Sun, Chao Qin, Weiguo Zhu:
EPMDA: Edge Perturbation Based Method for miRNA-Disease Association Prediction. 2170-2175 - Yixin Wang, Md. Noor-A-Rahim, Jingyun Zhang, Erry Gunawan, Yong Liang Guan, Chueh-Loo Poh:
Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage. 2176-2182 - Rajkumar Chakraborty, Yasha Hasija:
Predicting MicroRNA Sequence Using CNN and LSTM Stacked in Seq2Seq Architecture. 2183-2188 - Michael Schmidt, Kay Hamacher, Felix Reinhardt, Thea S. Lotz, Florian Groher, Beatrix Suess, Sven Jager:
SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures. 2189-2195 - Jong Ho Jhee, Sunjoo Bang, Dong-Gi Lee, Hyunjung Shin:
Corrections to "Comorbidity Scoring With Causal Disease Networks". 2196 - Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu:
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads". 2197
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