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Bioinformatics Research and Applications

14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings

  • Fa Zhang
  • Zhipeng Cai
  • Pavel Skums
  • Shihua Zhang
Conference proceedings ISBRA 2018

Part of the Lecture Notes in Computer Science book series (LNCS, volume 10847)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 10847)

Table of contents

  1. Front Matter
    Pages I-XXII
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  2. Network Analysis and Modelling

    1. Front Matter
      Pages 1-1
      PDF
    2. Prediction of Drug Response with a Topology Based Dual-Layer Network Model
      Suyun Huang, Xing-Ming Zhao
      Pages 3-12
    3. 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
    4. 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
    5. 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

  3. Genomic Data Analysis

    1. Front Matter
      Pages 49-49
      PDF
    2. Bounds on Identification of Genome Evolution Pacemakers
      Sagi Snir
      Pages 51-62
    3. REXTAL: Regional Extension of Assemblies Using Linked-Reads
      Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman
      Pages 63-78
    4. A Scalable Reference-Free Metagenomic Binning Pipeline
      Terry Ma, Xin Xing
      Pages 79-83

  4. Cancer Data Analysis

    1. Front Matter
      Pages 85-85
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    2. The Review of the Major Entropy Methods and Applications in Biomedical Signal Research
      Guangdi Liu, Yuan Xia, Chuanwei Yang, Le Zhang
      Pages 87-100
    3. Inferring Dysregulated Pathways of Driving Cancer Subtypes Through Multi-omics Integration
      Kai Shi, Lin Gao, Bingbo Wang
      Pages 101-112
    4. An Extension of Deep Pathway Analysis: A Pathway Route Analysis Framework Incorporating Multi-dimensional Cancer Genomics Data
      Yue Zhao
      Pages 113-124
    5. Hierarchical Similarity Network Fusion for Discovering Cancer Subtypes
      Shuhui Liu, Xuequn Shang
      Pages 125-136

  5. Structure and Interaction

    1. Front Matter
      Pages 137-137
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    2. 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
    3. 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
    4. XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting
      Lei Deng, Zuojin Dong, Hui Liu
      Pages 163-173
    5. 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
    6. 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
    7. 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

  6. HPC and CryoEM

    1. Front Matter
      Pages 191-191
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    2. On k-Mismatch Shortest Unique Substring Queries Using GPU
      Daniel W. Schultz, Bojian Xu
      Pages 193-204
    3. 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
    4. GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps
      Albert Ng, Adedayo Odesile, Dong Si
      Pages 217-226
    5. 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
    6. 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

  7. Machine and Deep Learning

    1. Front Matter
      Pages 239-239
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    2. 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
    3. A Deep Learning Method for Prediction of Benign Epilepsy with Centrotemporal Spikes
      Ming Yan, Ling Liu, Sihan Chen, Yi Pan
      Pages 253-258
    4. LSTM Recurrent Neural Networks for Influenza Trends Prediction
      Liyuan Liu, Meng Han, Yiyun Zhou, Yan Wang
      Pages 259-264
    5. Predicting Gene-Disease Associations with Manifold Learning
      Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu
      Pages 265-271

  8. Data Analysis and Methodology

    1. Front Matter
      Pages 273-273
      PDF
    2. On Approaching the One-Sided Exemplar Adjacency Number Problem
      Letu Qingge, Killian Smith, Sean Jungst, Binhai Zhu
      Pages 275-286
    3. Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences
      Xiaofeng Fu, Yiqun Xiao, Yang Yang
      Pages 287-298
    4. Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data
      Sagi Snir, Ben Yohay
      Pages 299-313
    5. Predicting Opioid Epidemic by Using Twitter Data
      Yubao Wu, Pavel Skums, Alex Zelikovsky, David Campo Rendon, Xueting Liao
      Pages 314-318

  9. Analysis and Visualization Tools

    1. Front Matter
      Pages 319-319
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    2. Cluster Matching Distance for Rooted Phylogenetic Trees
      Jucheol Moon, Oliver Eulenstein
      Pages 321-332

  10. RNA-Seq Data Analysis

    1. Front Matter
      Pages 333-333
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    2. 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
    3. Locality Sensitive Imputation for Single-Cell RNA-Seq Data
      Marmar Moussa, Ion I. Măndoiu
      Pages 347-360
  11. Back Matter
    Pages 361-362
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About these proceedings

Introduction

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.

Keywords

artificial intelligence bioinformatics cross-validation CUDA genes gpu parallel algorithms parallel processing systems problem solving processors semantics Support Vector Machines (SVM) biomedical databases biomolecular imaging comparative genomics gene expression analysis structural biology molecular modeling

Editors and affiliations

  • Fa Zhang
    • 1
  • Zhipeng Cai
    • 2
  • Pavel Skums
    • 3
  • Shihua Zhang
    • 4
  1. 1.Chinese Academy of SciencesBeijingChina
  2. 2.Georgia State UniversityAtlantaUSA
  3. 3.Georgia State UniversityAtlantaUSA
  4. 4.Chinese Academy of SciencesBeijingChina

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-319-94968-0
  • Copyright Information Springer International Publishing AG, part of Springer Nature 2018
  • Publisher Name Springer, Cham
  • eBook Packages Computer Science
  • Print ISBN 978-3-319-94967-3
  • Online ISBN 978-3-319-94968-0
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site
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