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IEEE/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