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ORCID14th ISBRA 2018: Beijing, China
- Fa Zhang, Zhipeng Cai, Pavel Skums, Shihua Zhang:
Bioinformatics Research and Applications - 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. Lecture Notes in Computer Science 10847, Springer 2018, ISBN 978-3-319-94967-3
Network Analysis and Modelling
- Suyun Huang, Xing-Ming Zhao:
Prediction of Drug Response with a Topology Based Dual-Layer Network Model. 3-12 - Qiao Zhu, Jiawei Luo, Pingjian Ding, Qiu Xiao:
GRTR: Drug-Disease Association Prediction Based on Graph Regularized Transductive Regression on Heterogeneous Network. 13-25 - Huiyu Li, Shengjun Li, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng:
An Improved Particle Swarm Optimization with Dynamic Scale-Free Network for Detecting Multi-omics Features. 26-37 - Siyu Zhao, Ruiqing Zheng, Xiang Chen, Yaohang Li, Fang-Xiang Wu
, Min Li:
PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks. 38-48
Genomic Data Analysis
- Sagi Snir:
Bounds on Identification of Genome Evolution Pacemakers. 51-62 - Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman:
REXTAL: Regional Extension of Assemblies Using Linked-Reads. 63-78 - Terry Ma, Xin Xing:
A Scalable Reference-Free Metagenomic Binning Pipeline. 79-83
Cancer Data Analysis
- Guangdi Liu, Yuan Xia, Chuanwei Yang, Le Zhang:
The Review of the Major Entropy Methods and Applications in Biomedical Signal Research. 87-100 - Kai Shi, Lin Gao, Bingbo Wang:
Inferring Dysregulated Pathways of Driving Cancer Subtypes Through Multi-omics Integration. 101-112 - Yue Zhao:
An Extension of Deep Pathway Analysis: A Pathway Route Analysis Framework Incorporating Multi-dimensional Cancer Genomics Data. 113-124 - Shuhui Liu, Xuequn Shang:
Hierarchical Similarity Network Fusion for Discovering Cancer Subtypes. 125-136
Structure and Interaction
- Zhen Zhang, Jianxin Wang, Junwei Luo, Juan Shang, Min Li, Fang-Xiang Wu, Yi Pan:
Sprites2: Detection of Deletions Based on an Accurate Alignment Strategy. 139-150 - Canshang Deng, Qingfeng Chen, Zhixian Liu, Ruiqing Zheng, Jin Liu, Jianxin Wang, Wei Lan:
KSIBW: Predicting Kinase-Substrate Interactions Based on Bi-random Walk. 151-162 - Lei Deng, Zuojin Dong, Hui Liu:
XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting. 163-173 - Alexander Churkin, Danny Barash:
A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations. 174-178 - Ilmi Fadhilah Rizki, Mochammad Arfin Fardiansyah Nasution, Syafrida Siregar, Mega Maulina Ekawati, Usman Sumo Friend Tambunan:
Screening of Sonic Hedgehog (Shh) Inhibitors in the Hedgehog Signaling Pathway from Traditional Chinese Medicine (TCM) Database Through Structure-Based Pharmacophore Design. 179-184 - Satya Anindita, Atika Marnolia, Hersal Hermana Putra, Muhammad Chandra Haikal, Usman Sumo Friend Tambunan:
Novel Inhibitors of T315I Mutant BCR-ABL1 Tyrosine Kinase for Chronic Myeloid Leukemia Disease Through Fragment-Based Drug Design. 185-190
HPC and CryoEM
- Daniel W. Schultz, Bojian Xu:
On k-Mismatch Shortest Unique Substring Queries Using GPU. 193-204 - Jingrong Zhang, Zihao Wang, Yu Chen, Zhiyong Liu, Fa Zhang:
Memory-Efficient and Stabilizing Management System and Parallel Methods for RELION Using CUDA and MPI. 205-216 - Albert Ng, Adedayo Odesile, Dong Si:
GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps. 217-226 - Ke Huang, Shubo Yang, Zhaojian Luo, Ke Yang, Menghan Chen, Guopeng Wei, Jian Huang:
A Fast Genome Sequence Aligner Based on Minimal Perfect Hash Algorithm Realized with FPGA Based Heterogeneous Computing Platform. 227-232 - Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer, Jing He:
A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps. 233-238
Machine and Deep Learning
- Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang:
Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. 241-252 - Ming Yan, Ling Liu, Sihan Chen, Yi Pan:
A Deep Learning Method for Prediction of Benign Epilepsy with Centrotemporal Spikes. 253-258 - Liyuan Liu, Meng Han, Yiyun Zhou, Yan Wang:
LSTM Recurrent Neural Networks for Influenza Trends Prediction. 259-264 - Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu:
Predicting Gene-Disease Associations with Manifold Learning. 265-271
Data Analysis and Methodology
- Letu Qingge, Killian Smith, Sean Jungst, Binhai Zhu:
On Approaching the One-Sided Exemplar Adjacency Number Problem. 275-286 - Xiaofeng Fu, Yiqun Xiao, Yang Yang:
Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences. 287-298 - Sagi Snir, Ben Yohay:
Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data. 299-313 - Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao:
Predicting Opioid Epidemic by Using Twitter Data. 314-318
Analysis and Visualization Tools
- Jucheol Moon, Oliver Eulenstein:
Cluster Matching Distance for Rooted Phylogenetic Trees. 321-332
RNA-Seq Data Analysis
- Krzysztof Gogolewski, Maciej Sykulski, Neo Christopher Chung, Anna Gambin:
Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA-seq Data. 335-346 - Marmar Moussa, Ion I. Mandoiu:
Locality Sensitive Imputation for Single-Cell RNA-Seq Data. 347-360
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