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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 - E. 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,