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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 - Quan Zou, Qi Liu:
Advanced Machine Learning Techniques for Bioinformatics. 1182-1183 - Qinhu Zhang, Lin Zhu, De-Shuang Huang:
High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites. 1184-1192 - Min Li, Zhihui Fei, Min Zeng, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang:
Automated ICD-9 Coding via A Deep Learning Approach. 1193-1202 - Bin Liu, Shumin Li:
ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods. 1203-1210 - Bingqiang Liu, Ling Han, Xiangrong Liu, Jichang Wu, Qin Ma:
Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies. 1211-1218 - Hongyu Liu, Qinmin Vivian Hu, Liang He:
Term-Based Personalization for Feature Selection in Clinical Handover Form Auto-Filling. 1219-1230 - Ran Su, Huichen Wu, Bo Xu, Xiaofeng Liu, Leyi Wei:
Developing a Multi-Dose Computational Model for Drug-Induced Hepatotoxicity Prediction Based on Toxicogenomics Data. 1231-1239 - Liang Yu, Lin Gao:
Human Pathway-Based Disease Network. 1240-1249 - Mahdi Imani, Ulisses M. Braga-Neto:
Control of Gene Regulatory Networks Using Bayesian Inverse Reinforcement Learning. 1250-1261 - Feng-Biao Guo, Xinglai Ji, Jian Huang:
Guest Editorial for Special Section on the 7th National Conference on Bioinformatics and Systems Biology of China. 1262-1263 - Leyi Wei, Pengwei Xing, Gaotao Shi, Zhiliang Ji, Quan Zou:
Fast Prediction of Protein Methylation Sites Using a Sequence-Based Feature Selection Technique. 1264-1273 - Yan Lin, Fa-Zhan Zhang, Kai Xue, Yi-Zhou Gao, Feng-Biao Guo:
Identifying Bacterial Essential Genes Based on a Feature-Integrated Method. 1274-1279 - Yan Shi, Bolun Zhang, Maolin Cai, Weiqing Xu:
Coupling Effect of Double Lungs on a VCV Ventilator with Automatic Secretion Clearance Function. 1280-1287 - Ying Li, Ye He, Siyu Han, Yanchun Liang:
Identification and Functional Inference for Tumor-Associated Long Non-Coding RNA. 1288-1301 - Jun-Ping Zhang, Yi Liu, Wei Sun, Xiao-Yang Zhao, La Ta, Wei-Sheng Guo:
Characteristics of Myosin V Processivity. 1302-1308 - Peng-Mian Feng, Zhenyi Wang, Xiaoyu Yu:
Predicting Antimicrobial Peptides by Using Increment of Diversity with Quadratic Discriminant Analysis Method. 1309-1312 - Guoshi Chai, Min Yu, Lixu Jiang, Yaocong Duan, Jian Huang:
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins. 1313-1315 - Hao Lin, Zhi-Yong Liang, Hua Tang, Wei Chen:
Identifying Sigma70 Promoters with Novel Pseudo Nucleotide Composition. 1316-1321 - Erman Ayday, Muhammad Naveed, Haixu Tang:
GenoPri'17: International Workshop on Genome Privacy and Security. 1322-1323 - Alexander Senf:
End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA. 1324-1327 - Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza, Mickaël Misbach, João Sá Sousa, Sylvain Pradervand, Edoardo Missiaglia, Olivier Michielin, Bryan Ford, Jean-Pierre Hubaux:
MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data. 1328-1341 - Dixie B. Baker, Bartha M. Knoppers, Mark Phillips, David van Enckevort, Petra Kaufmann, Hanns Lochmüller, Domenica Taruscio:
Privacy-Preserving Linkage of Genomic and Clinical Data Sets. 1342-1348 - Jake Weidman, William Aurite, Jens Grossklags:
On Sharing Intentions, and Personal and Interdependent Privacy Considerations for Genetic Data: A Vignette Study. 1349-1361 - Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 1362-1363 - Nina Luhmann, Manuel Lafond, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve:
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. 1364-1373 - Alexey Markin, Oliver Eulenstein:
Efficient Local Search for Euclidean Path-Difference Median Trees. 1374-1385 - Min Li, Peng Ni, Xiaopei Chen, Jianxin Wang, Fang-Xiang Wu, Yi Pan:
Construction of Refined Protein Interaction Network for Predicting Essential Proteins. 1386-1397 - Roman Sergeev, Ivan Kavaliou, Uladzislau V. Sataneuski, Andrei E. Gabrielian, Alex Rosenthal, Michael Tartakovsky, Alexander V. Tuzikov:
Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-Learning Approach. 1398-1408
Volume 16, Number 5, September - October 2019
- Amarda Shehu, Giuseppe Pozzi, Tamer Kahveci:
Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 1409 - Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez:
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. 1410-1423 - Alan M. Cleary, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, Brendan Mumey:
Exploring Frequented Regions in Pan-Genomic Graphs. 1424-1435 - Sunyoung Kwon, Sungroh Yoon:
End-to-End Representation Learning for Chemical-Chemical Interaction Prediction. 1436-1447 - Laraib Malik, Rob Patro:
Rich Chromatin Structure Prediction from Hi-C Data. 1448-1458 - Alexey Markin, Oliver Eulenstein:
Cophenetic Median Trees. 1459-1470 - Lu Zhu, Ralf Hofestädt, Martin Ester:
Tissue-Specific Subcellular Localization Prediction Using Multi-Label Markov Random Fields. 1471-1482 - Thuc Duy Le, Tao Hoang, Jiuyong Li, Lin Liu, Huawen Liu, Shu Hu:
A Fast PC Algorithm for High Dimensional Causal Discovery with Multi-Core PCs. 1483-1495 - Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens:
Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. 1496-1507 - Neda Jahanshad, Joshua Faskowitz, Gennady V. Roshchupkin, Derrek P. Hibar, Boris A. Gutman, Nicholas J. Tustison, Hieab H. H. Adams, Wiro J. Niessen, Meike W. Vernooij, Mohammad Arfan Ikram, Marcel P. Zwiers, Alejandro Arias-Vasquez, Barbara Franke, Jennifer L. Kroll, Benson Mwangi, Jair C. Soares, Alex Ing, Sylvane Desrivières, Gunter Schumann, Narelle K. Hansell, Greig I. de Zubicaray, Katie L. McMahon, Nicholas G. Martin, Margaret J. Wright, Paul M. Thompson:
Multi-Site Meta-Analysis of Morphometry. 1508-1514 - Shokoufeh Mirzaei, Tomer Sidi, Chen Keasar, Silvia Crivelli:
Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning. 1515-1523 - Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi:
Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction. 1524-1536 - Tanay Kumar Saha, Ataur Katebi, Wajdi Dhifli, Mohammad Al Hasan:
Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins Using Frequent Subgraph Mining. 1537-1549 - Marco Frasca, Nicolò Cesa-Bianchi:
Multitask Protein Function Prediction through Task Dissimilarity. 1550-1560 - Jérôme Feret, Heinz Koeppl:
Editorial. 1561 - Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré, Eugenia Oshurko:
Bio-Curation for Cellular Signalling: The KAMI Project. 1562-1573 - Célia Biane, Franck Delaplace:
Causal Reasoning on Boolean Control Networks Based on Abduction: Theory and Application to Cancer Drug Discovery. 1574-1585 - Houssam Abbas, Alëna Rodionova, Konstantinos Mamouras, Ezio Bartocci, Scott A. Smolka, Radu Grosu:
Quantitative Regular Expressions for Arrhythmia Detection. 1586-1597 - Alexander Lück, Pascal Giehr, Karl Nordström, Jörn Walter, Verena Wolf:
Hidden Markov Modelling Reveals Neighborhood Dependence of Dnmt3a and 3b Activity. 1598-1609 - Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, Loïc Paulevé:
Algorithms for the Sequential Reprogramming of Boolean Networks. 1610-1619 - Viacheslav Kapilevich, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka:
Chromatin 3D Reconstruction from Chromosomal Contacts Using a Genetic Algorithm. 1620-1626 - Jong Ho Jhee, Sunjoo Bang, Dong-Gi Lee, Hyunjung Shin:
Comorbidity Scoring with Causal Disease Networks. 1627-1634 - Donghe Li, Wonji Kim, Longfei Wang, Kyong-Ah Yoon, Boyoung Park, Charny Park, Sun-Young Kong, Yongdeuk Hwang, Daehyun Baek, Eun Sook Lee, Sungho Won:
Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data. 1635-1644 - Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada:
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. 1645-1655 - Je-Keun Rhee, Jinseon Yoo, Kyu Ryung Kim, Jeeyoon Kim, Yong-Jae Lee, Byoung Chul Cho, Tae-Min Kim:
Identification of Local Clusters of Mutation Hotspots in Cancer-Related Genes and Their Biological Relevance. 1656-1662 - Shailima Rampogu, Ayoung Baek, Rohit Bavi, Minky Son, Guang Ping Cao, Raj Kumar, Chanin Park, Amir Zeb, Rabia Mukthar Rana, Seok Ju Park, Keun Woo Lee:
Identification of Novel Scaffolds with Dual Role as Antiepileptic and Anti-Breast Cancer. 1663-1674 - Hiroki Sudo, Masanobu Jimbo, Koji Nuida, Kana Shimizu:
Secure Wavelet Matrix: Alphabet-Friendly Privacy-Preserving String Search for Bioinformatics. 1675-1684 - Man-Sun Kim, Dong San Kim, Jeong-Rae Kim:
Stage-Dependent Gene Expression Profiling in Colorectal Cancer. 1685-1692 - SeongRyeol Moon, Curtis Balch, Sungjin Park, Jinhyuk Lee, Jiyong Sung, Seungyoon Nam:
Systematic Inspection of the Clinical Relevance of TP53 Missense Mutations in Gastric Cancer. 1693-1701 - Fanchang Hao, Melvin Zhang, Hon Wai Leong:
A 2-Approximation Scheme for Sorting Signed Permutations by Reversals, Transpositions, Transreversals, and Block-Interchanges. 1702-1711 - Limin Li, Menglan Cai:
Drug Target Prediction by Multi-View Low Rank Embedding. 1712-1721 - Wen-Bin Xie, Hong Yan, Xing-Ming Zhao:
EmDL: Extracting miRNA-Drug Interactions from Literature. 1722-1728 - Yanbo Wang, Quan Liu, Shan Huang, Bo Yuan:
Learning a Structural and Functional Representation for Gene Expressions: To Systematically Dissect Complex Cancer Phenotypes. 1729-1742 - Yishu Wang, Huaying Fang, Dejie Yang, Hongyu Zhao, Minghua Deng:
Network Clustering Analysis Using Mixture Exponential-Family Random Graph Models and Its Application in Genetic Interaction Data. 1743-1752 - Zhenni Zhao, Xinqi Gong:
Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture. 1753-1759 - Xi Yang, Guoqiang Han, Hongmin Cai, Yan Song:
Recovering Hidden Diagonal Structures via Non-Negative Matrix Factorization with Multiple Constraints. 1760-1772
Volume 16, Number 6, November - December 2019
- Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu:
3gClust: Human Protein Cluster Analysis. 1773-1784 - Aida Brankovic, Marjan Hosseini, Luigi Piroddi:
A Distributed Feature Selection Algorithm Based on Distance Correlation with an Application to Microarrays. 1802-1815 - Li Zhang, Ho-Chun Wu, Cheuk Hei Ho, Shing-Chow Chan:
A Multi-Laplacian Prior and Augmented Lagrangian Approach to the Exploratory Analysis of Time-Varying Gene and Transcriptional Regulatory Networks for Gene Microarray Data. 1816-1829 - Toktam Dehghani, Mahmoud Naghibzadeh, Javad Sadri:
Enhancement of Protein β-Sheet Topology Prediction Using Maximum Weight Disjoint Path Cover. 1936-1947 - Ayan Chaudhury, Christopher Ward, Ali Talasaz, Alexander G. Ivanov, Mark Brophy, Bernard Grodzinski, Norman P. A. Hüner, Rajnikant V. Patel, John L. Barron:
Machine Vision System for 3D Plant Phenotyping. 2009-2022 - Ashis Kumer Biswas, Dong-Chul Kim, Mingon Kang, Jean X. Gao:
Robust Inductive Matrix Completion Strategy to Explore Associations Between LincRNAs and Human Disease Phenotypes. 2066-2077 - Aurpan Majumder, Mrityunjay Sarkar, Prolay Sharma:
A Composite Mode Differential Gene Regulatory Architecture based on Temporal Expression Profiles. 1785-1793 - Yujie Feng, Fan Yang, Xichuan Zhou, Yanli Guo, Fang Tang, Fengbo Ren, Jishun Guo, Shuiwang Ji:
A Deep Learning Approach for Targeted Contrast-Enhanced Ultrasound Based Prostate Cancer Detection. 1794-1801 - Anvita Gupta Malhotra, Sudha Singh, Mohit Jha, Khushhali Menaria Pandey:
A Parametric Targetability Evaluation Approach for Vitiligo Proteome Extracted through Integration of Gene Ontologies and Protein Interaction Topologies. 1830-1842 - Juho Timonen, Henrik Mannerström, Harri Lähdesmäki, Jukka Intosalmi:
A Probabilistic Framework for Molecular Network Structure Inference by Means of Mechanistic Modeling. 1843-1854 - Xiaoke Ma, Penggang Sun, Zhong-Yuan Zhang:
An Integrative Framework for Protein Interaction Network and Methylation Data to Discover Epigenetic Modules. 1855-1866 - Claudia Caudai, Emanuele Salerno, Monica Zoppè, Ivan Merelli, Anna Tonazzini:
ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data. 1867-1878 - Huiwei Zhou, Yunlong Yang, Shixian Ning, Zhuang Liu, Chengkun Lang, Yingyu Lin, Degen Huang:
Combining Context and Knowledge Representations for Chemical-Disease Relation Extraction. 1879-1889 - Huimin Luo, Jianxin Wang, Min Li, Junwei Luo, Peng Ni, Kaijie Zhao, Fang-Xiang Wu, Yi Pan:
Computational Drug Repositioning with Random Walk on a Heterogeneous Network. 1890-1900 - Sabrina Stella, Roberto Chignola, Edoardo Milotti:
Dynamical Detection of Boundaries and Cavities in Biophysical Cell-Based Simulations of Growing Tumor Tissues. 1901-1911 - Xingyu Cai, Abdullah-Al Mamun, Sanguthevar Rajasekaran:
Efficient Algorithms for Finding the Closest $l$l-Mers in Biological Data. 1912-1921 - Lun Hu, Xiaohui Yuan, Xing Liu, Shengwu Xiong, Xin Luo:
Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers. 1922-1935 - Xue Jiang, Han Zhang, Zhao Zhang, Xiongwen Quan:
Flexible Non-Negative Matrix Factorization to Unravel Disease-Related Genes. 1948-1957 - Marianna Milano, Pietro Hiram Guzzi, Mario Cannataro:
GLAlign: A Novel Algorithm for Local Network Alignment. 1958-1969 - Amit Paul, Jaya Sil:
Identification of Differentially Expressed Genes to Establish New Biomarker for Cancer Prediction. 1970-1985 - Xiaoke Hao, Xiaohui Yao, Shannon L. Risacher, Andrew J. Saykin, Jintai Yu, Huifu Wang, Lan Tan, Li Shen, Daoqiang Zhang:
Identifying Candidate Genetic Associations with MRI-Derived AD-Related ROI via Tree-Guided Sparse Learning. 1986-1996 - Anjing Fan, Haitao Wang, Hua Xiang, Xiufen Zou:
Inferring Large-Scale Gene Regulatory Networks Using a Randomized Algorithm Based on Singular Value Decomposition. 1997-2008 - Özkan U. Nalbantoglu, Khalid Sayood:
MIMOSA: Algorithms for Microbial Profiling. 2023-2034 - Michail-Antisthenis I. Tsompanas, Andrew Adamatzky, Ioannis Ieropoulos, Neil Phillips, Georgios Ch. Sirakoulis, John Greenman:
Modelling Microbial Fuel Cells Using Lattice Boltzmann Methods. 2035-2045 - Runtao Yang, Chengjin Zhang, Rui Gao, Lina Zhang, Qing Song:
Predicting FAD Interacting Residues with Feature Selection and Comprehensive Sequence Descriptors. 2046-2056 - V. K. Md. Aksam, V. M. Chandrasekaran, Pandurangan Sundaramurthy:
Protein Domain Level Cancer Drug Targets in the Network of MAPK Pathways. 2057-2065 - Benjamin Wingfield, Sonya Coleman, T. M. McGinnity, Anthony J. Bjourson:
Robust Microbial Markers for Non-Invasive Inflammatory Bowel Disease Identification. 2078-2088 - Rahul Kumar Sevakula, Vikas Singh, Nishchal K. Verma, Chandan Kumar, Yan Cui:
Transfer Learning for Molecular Cancer Classification Using Deep Neural Networks. 2089-2100
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