Bioinformatics Research and Applications

Description

This book constitutes the proceedings of the 14th International Conference on Bioinformatics Research and Applications, ISBRA 2018, held in Beijing, China, in June 2018. The 24 full and 10 short papers presented in this volume were carefully reviewed and selected from a total of 138 submissions. They were organized in topical sections named: network analysis and modelling; genomic data analysis; cancer data analysis; structure and interaction; HPC and CryoEM; machine and deep learning; data analysis and methodology; analysis and visualization tools; and RNA-Seq data analysis. Front Matter ....Pages I-XXII Front Matter ....Pages 1-1 Prediction of Drug Response with a Topology Based Dual-Layer Network Model (Suyun Huang, Xing-Ming Zhao)....Pages 3-12 GRTR: Drug-Disease Association Prediction Based on Graph Regularized Transductive Regression on Heterogeneous Network (Qiao Zhu, Jiawei Luo, Pingjian Ding, Qiu Xiao)....Pages 13-25 An Improved Particle Swarm Optimization with Dynamic Scale-Free Network for Detecting Multi-omics Features (Huiyu Li, Sheng-Jun Li, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng)....Pages 26-37 PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks (Siyu Zhao, Ruiqing Zheng, Xiang Chen, Yaohang Li, Fang-Xiang Wu, Min Li)....Pages 38-48 Front Matter ....Pages 49-49 Bounds on Identification of Genome Evolution Pacemakers (Sagi Snir)....Pages 51-62 REXTAL: Regional Extension of Assemblies Using Linked-Reads (Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman)....Pages 63-78 A Scalable Reference-Free Metagenomic Binning Pipeline (Terry Ma, Xin Xing)....Pages 79-83 Front Matter ....Pages 85-85 The Review of the Major Entropy Methods and Applications in Biomedical Signal Research (Guangdi Liu, Yuan Xia, Chuanwei Yang, Le Zhang)....Pages 87-100 Inferring Dysregulated Pathways of Driving Cancer Subtypes Through Multi-omics Integration (Kai Shi, Lin Gao, Bingbo Wang)....Pages 101-112 An Extension of Deep Pathway Analysis: A Pathway Route Analysis Framework Incorporating Multi-dimensional Cancer Genomics Data (Yue Zhao)....Pages 113-124 Hierarchical Similarity Network Fusion for Discovering Cancer Subtypes (Shuhui Liu, Xuequn Shang)....Pages 125-136 Front Matter ....Pages 137-137 Sprites2: Detection of Deletions Based on an Accurate Alignment Strategy (Zhen Zhang, Jianxin Wang, Junwei Luo, Juan Shang, Min Li, Fang-Xiang Wu et al.)....Pages 139-150 KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk (Canshang Deng, Qingfeng Chen, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang et al.)....Pages 151-162 XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting (Lei Deng, Zuojin Dong, Hui Liu)....Pages 163-173 A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations (Alexander Churkin, Danny Barash)....Pages 174-178 Screening of Sonic Hedgehog (Shh) Inhibitors in the Hedgehog Signaling Pathway from Traditional Chinese Medicine (TCM) Database Through Structure-Based Pharmacophore Design (Ilmi Fadhilah Rizki, Mochammad Arfin Fardiansyah Nasution, Syafrida Siregar, Mega Maulina Ekawati, Usman Sumo Friend Tambunan)....Pages 179-184 Novel Inhibitors of T315I Mutant BCR-ABL1 Tyrosine Kinase for Chronic Myeloid Leukemia Disease Through Fragment-Based Drug Design (Satya Anindita, Atika Marnolia, Hersal Hermana Putra, Muhammad Chandra Haikal, Usman Sumo Friend Tambunan)....Pages 185-190 Front Matter ....Pages 191-191 On k-Mismatch Shortest Unique Substring Queries Using GPU (Daniel W. Schultz, Bojian Xu)....Pages 193-204 Memory-Efficient and Stabilizing Management System and Parallel Methods for RELION Using CUDA and MPI (Jingrong Zhang, Zihao Wang, Yu Chen, Zhiyong Liu, Fa Zhang)....Pages 205-216 GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps (Albert Ng, Adedayo Odesile, Dong Si)....Pages 217-226 A Fast Genome Sequence Aligner Based on Minimal Perfect Hash Algorithm Realized with FPGA Based Heterogeneous Computing Platform (Ke Huang, Shubo Yang, Zhaojian Luo, Ke Yang, Menghan Chen, Guopeng Wei et al.)....Pages 227-232 A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps (Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer et al.)....Pages 233-238 Front Matter ....Pages 239-239 Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning (Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang)....Pages 241-252 A Deep Learning Method for Prediction of Benign Epilepsy with Centrotemporal Spikes (Ming Yan, Ling Liu, Sihan Chen, Yi Pan)....Pages 253-258 LSTM Recurrent Neural Networks for Influenza Trends Prediction (Liyuan Liu, Meng Han, Yiyun Zhou, Yan Wang)....Pages 259-264 Predicting Gene-Disease Associations with Manifold Learning (Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu)....Pages 265-271 Front Matter ....Pages 273-273 On Approaching the One-Sided Exemplar Adjacency Number Problem (Letu Qingge, Killian Smith, Sean Jungst, Binhai Zhu)....Pages 275-286 Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences (Xiaofeng Fu, Yiqun Xiao, Yang Yang)....Pages 287-298 Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data (Sagi Snir, Ben Yohay)....Pages 299-313 Predicting Opioid Epidemic by Using Twitter Data (Yubao Wu, Pavel Skums, Alex Zelikovsky, David Campo Rendon, Xueting Liao)....Pages 314-318 Front Matter ....Pages 319-319 Cluster Matching Distance for Rooted Phylogenetic Trees (Jucheol Moon, Oliver Eulenstein)....Pages 321-332 Front Matter ....Pages 333-333 Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA-seq Data (Krzysztof Gogolewski, Maciej Sykulski, Neo Christopher Chung, Anna Gambin)....Pages 335-346 Locality Sensitive Imputation for Single-Cell RNA-Seq Data (Marmar Moussa, Ion I. Măndoiu)....Pages 347-360 Back Matter ....Pages 361-362