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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 16
Volume 16, Number 1, January - February 2019
- Yoshihiro Yamanishi, Yasubumi Sakakibara, Yi-Ping Phoebe Chen
:
Guest Editorial for the 16th Asia Pacific Bioinformatics Conference. 1-2
- Kouichi Kimura, Asako Koike:
Parallel Computation of the Burrows-Wheeler Transform of Short Reads Using Prefix Parallelism. 3-13 - Jordan Haack, Eli Zupke, Andrew Ramirez, Yi-Chieh Wu, Ran Libeskind-Hadas:
Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model. 14-22 - Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu, Daniel Valenzuela:
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. 23-30 - Andrzej Mizera, Jun Pang, Hongyang Qu, Qixia Yuan:
Taming Asynchrony for Attractor Detection in Large Boolean Networks. 31-42 - Tiancong Wang, Bin Ma:
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing. 43-51 - Tom Hartmann, Matthias Bernt, Martin Middendorf:
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements. 52-62 - Lei Li, Mukul S. Bansal:
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. 63-76 - Yuhei Nishiyama, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu:
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs. 77-90 - Bairong Shen, Xiaoqian Jiang, Xingming Zhao:
Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare. 91-92 - Md. Nazmus Sadat, Md Momin Al Aziz, Noman Mohammed, Feng Chen, Xiaoqian Jiang, Shuang Wang:
SAFETY: Secure gwAs in Federated Environment through a hYbrid Solution. 93-102 - Chengsheng Mao, Yuan Zhao, Mengxin Sun, Yuan Luo:
Are My EHRs Private Enough? Event-Level Privacy Protection. 103-112 - Yichen Jiang, Jenny Hamer, Chenghong Wang, Xiaoqian Jiang, Miran Kim, Yongsoo Song, Yuhou Xia, Noman Mohammed, Md. Nazmus Sadat, Shuang Wang:
SecureLR: Secure Logistic Regression Model via a Hybrid Cryptographic Protocol. 113-123 - Mengmeng Sun, Tao Ding, Xu-Qing Tang, Keming Yu:
An Efficient Mixed-Model for Screening Differentially Expressed Genes of Breast Cancer Based on LR-RF. 124-130 - Wenliang Zhu, Xiaohe Chen, Yan Wang, Lirong Wang:
Arrhythmia Recognition and Classification Using ECG Morphology and Segment Feature Analysis. 131-138 - Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo:
Natural Language Processing for EHR-Based Computational Phenotyping. 139-153 - Yin-Ying Wang, Chunfeng Cui, Liqun Qi, Hong Yan, Xing-Ming Zhao:
DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets. 154-162 - Dewu Ding, Xiao Sun:
A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of Shewanella. 163-171 - Juan Wang, Jin-Xing Liu, Chun-Hou Zheng, Yaxuan Wang, Xiang-Zhen Kong, Chang-Gang Wen:
A Mixed-Norm Laplacian Regularized Low-Rank Representation Method for Tumor Samples Clustering. 172-182 - Sushmita Paul, Dhanajit Brahma:
An Integrated Approach for Identification of Functionally Similar MicroRNAs in Colorectal Cancer. 183-192 - Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty:
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data. 193-207 - Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu:
Clustering-Based Compression for Population DNA Sequences. 208-221 - Ping Luo, Li-Ping Tian, Jishou Ruan, Fang-Xiang Wu:
Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data. 222-232 - Cheng Yan, Jianxin Wang, Peng Ni, Wei Lan, Fang-Xiang Wu, Yi Pan:
DNRLMF-MDA: Predicting microRNA-Disease Associations Based on Similarities of microRNAs and Diseases. 233-243 - Ronghui Ju, Chenhui Hu, Pan Zhou, Quanzheng Li:
Early Diagnosis of Alzheimer's Disease Based on Resting-State Brain Networks and Deep Learning. 244-257 - Paola Pesantez-Cabrera, Ananth Kalyanaraman:
Efficient Detection of Communities in Biological Bipartite Networks. 258-271 - Xiangtao Li, Ka-Chun Wong:
Elucidating Genome-Wide Protein-RNA Interactions Using Differential Evolution. 272-282 - Xuan Zhang, Quan Zou, Alfonso Rodríguez-Patón, Xiangxiang Zeng:
Meta-Path Methods for Prioritizing Candidate Disease miRNAs. 283-291 - Bin Liu, Junjie Chen, Mingyue Guo, Xiaolong Wang:
Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix. 292-300 - Minghan Chen, Brandon D. Amos, Layne T. Watson, John J. Tyson, Young Cao, Clifford A. Shaffer, Michael W. Trosset, Cihan Oguz, Gisella Kakoti:
Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle. 301-311 - Cheng Liu, Hau-San Wong:
Structured Penalized Logistic Regression for Gene Selection in Gene Expression Data Analysis. 312-321 - Andrés F. López-Lopera, Mauricio A. Álvarez:
Switched Latent Force Models for Reverse-Engineering Transcriptional Regulation in Gene Expression Data. 322-335 - Jiao Zhang, Sam Kwong, Ka-Chun Wong:
ToBio: Global Pathway Similarity Search Based on Topological and Biological Features. 336-349
Volume 16, Number 2, March - April 2019
- Shuigeng Zhou, Yi-Ping Phoebe Chen, Hiroshi Mamitsuka:
Editorial. 350-351 - Xiaojun Chen, Joshua Zhexue Huang, Qingyao Wu, Min Yang:
Subspace Weighting Co-Clustering of Gene Expression Data. 352-364 - Bo Tian, Qiong Duan, Can Zhao, Ben Teng, Zengyou He:
Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data. 365-376 - Bin Xu, Jihong Guan, Yang Wang, Zewei Wang:
Essential Protein Detection by Random Walk on Weighted Protein-Protein Interaction Networks. 377-387 - Weiping Sun, Yi Liu, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang:
An Improved Approach for N-Linked Glycan Structure Identification from HCD MS/MS Spectra. 388-395 - Jingpu Zhang, Zuping Zhang, Zhigang Chen, Lei Deng:
Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference. 396-406 - Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, Lei Deng:
KATZLGO: Large-Scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks. 407-416 - Min Li, Ruiqing Zheng, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. 417-424 - Shaoliang Peng, Yingbo Cui, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao:
A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer. 425-433 - Jie Zhang, Zhigen Zhao, Kai Zhang, Zhi Wei:
A Feature Sampling Strategy for Analysis of High Dimensional Genomic Data. 434-441 - Kefei Liu, Jieping Ye, Yang Yang, Li Shen, Hui Jiang:
A Unified Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq Data. 442-454 - Wei Zhang, Shu-Lin Wang:
An Integrated Framework for Identifying Mutated Driver Pathway and Cancer Progression. 455-464 - Tim Michels, Dimitri Berh, Xiaoyi Jiang:
An RJMCMC-Based Method for Tracking and Resolving Collisions of Drosophila Larvae. 465-474 - Lu Zhang, Qiuping Pan, Yue Wang, Xintao Wu, Xinghua Shi:
Bayesian Network Construction and Genotype-Phenotype Inference Using GWAS Statistics. 475-489 - Koyel Mandal, Rosy Sarmah, Dhruba Kumar Bhattacharyya:
Biomarker Identification for Cancer Disease Using Biclustering Approach: An Empirical Study. 490-509 - Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. 510-523 - Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty:
Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. 524-537 - Huanan Zhang, David Roe, Rui Kuang:
Detecting Population-Differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection. 538-549 - Claudia Caudai, Emanuele Salerno, Monica Zoppè, Anna Tonazzini:
Estimation of the Spatial Chromatin Structure Based on a Multiresolution Bead-Chain Model. 550-559 - Bilal Nizami, Elham Mousavinezhad Sarasia, Mehbub I. K. Momin, Bahareh Honarparvar:
Estrogenic Active Stilbene Derivatives as Anti-Cancer Agents: A DFT and QSAR Study. 560-568 - Biing-Feng Wang, Chih-Yu Li:
Fast Algorithms for Computing Path-Difference Distances. 569-582 - Mathias Foo, Jongrae Kim, Declan G. Bates:
Modelling and Control of Gene Regulatory Networks for Perturbation Mitigation. 583-595 - Son P. Nguyen, Zhaoyu Li, Dong Xu, Yi Shang:
New Deep Learning Methods for Protein Loop Modeling. 596-606 - Yun Niu, Hongmei Wu, Yuwei Wang:
Protein-Protein Interaction Identification Using a Similarity-Constrained Graph Model. 607-616 - Leena Salmela, Alexandru I. Tomescu:
Safely Filling Gaps with Partial Solutions Common to All Solutions. 617-626 - Fernando Lopez-Caamal, Heinrich J. Huber:
Stable IL-$1\beta$1β-Activation in an Inflammasome Signalling Model Depends on Positive and Negative Feedbacks and Tight Regulation of Protein Production. 627-637 - Amir Najafi, Sepehr Janghorbani, Seyed Abolfazl Motahari, Emad Fatemizadeh:
Statistical Association Mapping of Population-Structured Genetic Data. 638-649 - Xiaohui Lin, Xin Huang, Lina Zhou, Weijie Ren, Jun Zeng, Weihong Yao, Xingyuan Wang:
The Robust Classification Model Based on Combinatorial Features. 650-657 - Mingfu Shao, Carl Kingsford:
Theory and A Heuristic for the Minimum Path Flow Decomposition Problem. 658-670 - Florian Kaiser, Dirk Labudde:
Unsupervised Discovery of Geometrically Common Structural Motifs and Long-Range Contacts in Protein 3D Structures. 671-680 - Jiawei Luo, Chu Pan, Gen Xiang, Ying Yin:
A Novel Cluster-Based Computational Method to Identify miRNA Regulatory Modules. 681-687 - Pengyao Ping, Lei Wang, Linai Kuang, Songtao Ye, Muhammad Faisal Buland Iqbal, Tingrui Pei:
A Novel Method for LncRNA-Disease Association Prediction Based on an lncRNA-Disease Association Network. 688-693 - Ruofan Xia, Yu Lin, Jun Zhou, Tieming Geng, Bing Feng, Jijun Tang:
Phylogenetic Reconstruction for Copy-Number Evolution Problems. 694-699 - Warith Eddine Djeddi, Sadok Ben Yahia, Engelbert Mephu Nguifo:
Corrections to "A Novel Computational Approach for Global Alignment for Multiple Biological Networks". 700
Volume 16, Number 3, May - June 2019
- Carlos Martín-Vide, Miguel A. Vega-Rodríguez:
Algorithms for Computational Biology: Third Edition. 701-702 - Syed Ali Ahmed, Saad Mneimneh:
Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-Optimal Solutions. 703-712 - Agnieszka Mykowiecka, Pawel Górecki:
Credibility of Evolutionary Events in Gene Trees. 713-726 - David Sankoff, Chunfang Zheng, Yue Zhang, Joao Meidanis, Eric Lyons, Haibao Tang:
Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. 727-737 - Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot:
Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. 738-748 - De-Shuang Huang, Vitoantonio Bevilacqua, M. Michael Gromiha:
Guest Editorial for Special Section on the 13th International Conference on Intelligent Computing (ICIC). 749-750 - Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng:
A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods. 751-763 - Min Li, Li Tang, Zhongxiang Liao, Junwei Luo, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension. 764-773 - Xiaolong Zhang, Xiaoli Lin, Jiafu Zhao, Qianqian Huang, Xin Xu:
Efficiently Predicting Hot Spots in PPIs by Combining Random Forest and Synthetic Minority Over-Sampling Technique. 774-781 - Lin Yuan, Lehang Guo, Chang-an Yuan, Youhua Zhang, Kyungsook Han, Asoke K. Nandi, Barry Honig, De-Shuang Huang:
Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer. 782-791 - Su-Ping Deng, Wei-Li Guo:
Identifying Key Genes of Liver Cancer by Networking of Multiple Data Sets. 792-800 - Peng Wu, Dong Wang:
Classification of a DNA Microarray for Diagnosing Cancer Using a Complex Network Based Method. 801-808 - Zhu-Hong You, Wenzhun Huang, Shanwen Zhang, Yu-An Huang, Changqing Yu, Li-Ping Li:
An Efficient Ensemble Learning Approach for Predicting Protein-Protein Interactions by Integrating Protein Primary Sequence and Evolutionary Information. 809-817 - Hua Zhong, Mingzhou Song:
A Fast Exact Functional Test for Directional Association and Cancer Biology Applications. 818-826 - Sandip Samaddar, Rituparna Sinha, Rajat K. De:
A Model for Distributed Processing and Analyses of NGS Data under Map-Reduce Paradigm. 827-840 - Dongdong Sun, Minghui Wang, Ao Li:
A Multimodal Deep Neural Network for Human Breast Cancer Prognosis Prediction by Integrating Multi-Dimensional Data. 841-850 - Michiel Van Dyck, Xavier Woot de Trixhe, An Vermeulen, Wim Vanroose:
A Robust Simulator for Physiologically Structured Population Models. 851-864 - Maryam Sharifi, Arta A. Jamshidi, Nazanin Namazi Sarvestani:
An Adaptive Robust Control Strategy in a Cancer Tumor-Immune System Under Uncertainties. 865-873 - Loris Nanni, Sheryl Brahnam, Stefano Ghidoni, Alessandra Lumini:
Bioimage Classification with Handcrafted and Learned Features. 874-885 - Haoyu Cheng, Yong Zhang, Yun Xu:
BitMapper2: A GPU-Accelerated All-Mapper Based on the Sparse q-Gram Index. 886-897 - Pei Wang, Daojie Wang, Jinhu Lu:
Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families. 912-924 - Sven Thiele, Sandra Heise, Wiebke Hessenkemper, Hannes Bongartz, Melissa Fensky, Fred Schaper, Steffen Klamt:
Designing Optimal Experiments to Discriminate Interaction Graph Models. 925-935 - Yi-Yan Zhang, Qin Li, Yi Xin, Wei-Qi Lv:
Differentiating Prostate Cancer from Benign Prostatic Hyperplasia Using PSAD Based on Machine Learning: Single-Center Retrospective Study in China. 936-941 - Dimitrios Kaloudas, Nikolet Pavlova, Robert Penchovsky:
EBWS: Essential Bioinformatics Web Services for Sequence Analyses. 942-953 - Bo Xu, Hongfei Lin, Yuan Lin:
Learning to Refine Expansion Terms for Biomedical Information Retrieval Using Semantic Resources. 954-966 - Tiantian He, Keith C. C. Chan:
Measuring Boundedness for Protein Complex Identification in PPI Networks. 967-979 - Aiguo Wang, Ye Chen, Ning An, Jing Yang, Lian Li, Lili Jiang:
Microarray Missing Value Imputation: A Regularized Local Learning Method. 980-993 - You Song, Siyu Yang, Jinzhi Lei:
ParaCells: A GPU Architecture for Cell-Centered Models in Computational Biology. 994-1006 - Mohammad Nazrul Ishlam Patoary, Carl Tropper, Robert A. McDougal, Zhongwei Lin, William W. Lytton:
Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron. 1007-1019 - Chao Fang, Yi Shang, Dong Xu:
Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks. 1020-1028 - Gregor Urban, Kevin Bache, Duc T. T. Phan, Agua Sobrino, Alexander Shmakov, Stephanie J. Hachey, Christopher C. W. Hughes, Pierre Baldi:
Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images. 1029-1035 - Kumar Saurabh Singh, Bartlomiej J. Troczka, Katherine Beadle, Linda M. Field, T. G. Emyr Davies, Martin S. Williamson, Ralf Nauen, Chris Bass:
Extension of Partial Gene Transcripts by Iterative Mapping of RNA-Seq Raw Reads. 1036-1041 - Jia-Juan Tu, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang:
Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data. 1042-1048
Volume 16, Number 4, July - August 2019
- Aisharjya Sarkar, Yuanfang Ren, Rasha Elhesha, Tamer Kahveci:
A New Algorithm for Counting Independent Motifs in Probabilistic Networks. 1049-1062 - Alexey Markin, Oliver Eulenstein:
Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach. 1063-1076 - Misagh Kordi, Mukul S. Bansal:
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. 1077-1090 - Priyanka Ghosh, Ananth Kalyanaraman:
FastEtch: A Fast Sketch-Based Assembler for Genomes. 1091-1106 - Olivia Choudhury, Ankush Chakrabarty, Scott J. Emrich:
Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation. 1107-1116 - Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru:
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. 1117-1131 - Enrico Siragusa, Niina Haiminen, Filippo Utro, Laxmi Parida:
Linear Time Algorithms to Construct Populations Fitting Multiple Constraint Distributions at Genomic Scales. 1132-1142 - Deeptak Verma, Gevorg Grigoryan, Chris Bailey-Kellogg:
Pareto Optimization of Combinatorial Mutagenesis Libraries. 1143-1153 - Muhibur Rasheed, Nathan Clement, Abhishek Bhowmick, Chandrajit L. Bajaj:
Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling. 1154-1167 - Wenruo Bai, Jeffrey A. Bilmes, William S. Noble:
Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry. 1168-1181