Accepted Papers


Number Authors Titles
5 Jiangyong Wei, Tianshou Zhou and Tianhai Tian SCOUT: A new algorithm for the inference of pseudo-time trajectory using single-cell data
9 Audrey Legendre, Eric Angel and Fariza Tahi RCPred: RNA Complex Prediction as a constrained maximum weight clique problem
18 Petronela Buiga, Ari Elson, Lydia Tabernero and Jean-Marc Schwartz Modelling the role of dual specificity phosphatases in Herceptin resistant breast cancer cell lines
19 Xiujuan Lei, Ming Fang, Ling Guo and Fang-Xiang Wu Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks
20 Pawel Gorecki, Oliver Eulenstein and Jerzy Tiuryn The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost
21 Melissa Grueter, Kalani Duran, Ramya Ramalingam and Ran Libeskind-Hadas Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model
23 Hongzhe Guo, Yilei Fu, Yan Gao, Junyi Li, Yadong Wang and Bo Liu deGSM: memory scalable construction of large scale de Bruijn Graph
24 Qi Tian, Jianxiao Zou, Shicai Fan, Jianxiong Tang, Yuan Fang and Zhongli Yu MRCNN: A deep learning model for regression of genome-wide DNA methylation
25 Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri and Jun Sese reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses for a robust RNA reactivity classification
26 Kishan K C, Rui Li, Feng Cui and Anne Haake GNE: A deep learning framework for gene network inference by aggregating biological information
29 Qijin Yin, Mengmeng Wu, Hairong Lv and Rui Jiang DeepHistone: a deep learning approach to predicting histone modifications
30 Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu and Laxmi Parida Signal Enrichment of Metagenome Sequencing Reads using Topological Data Analysis
31 Wenting Liu and Jagath Rajapakse Fusing Gene Expression and Transitive Protein-Protein Interaction for Gene Regulatory Networks
33 Xiaoying Li, Yaping Lin, Changlong Gu and Jialiang Yang FCMDAP: Using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs
34 Hansheng Xue, Xuequn Shang and Jiajie Peng Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO
38 Yuanyu He, Yaping Lin and Tuanfei Zhu A class imbalance-aware Relief algorithm for the classification of tumors using microarray gene expression data
41 Guangsheng Wu, Juan Liu and Xiang Yue Prediction of drug-disease associations based on ensemble meta paths and singular value decomposition
46 Ran Li, Xiangrui Zeng, Stephanie Siegmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv and Min Xu Automatic Localization and Identification of Mitochondria in Cellular Electron Cryo-Tomography using Faster-RCNN
49 Nayang Shan, Zuoheng Wang and Lin Hou Identification of trans-eQTLs using mediation analysis with multiple mediators
53 Bipasa Biswas and Yinglei Lai A Distance-type Measure Approach to the Analysis of Copy Number Variation in DNA Sequencing Data
54 Nan Du, Jiao Chen and Yanni Sun Improving the sensitivity of detecting long read overlaps using grouped short k-mer matches
56 Jiaying You, Pingzhao Hu and Robert McLeod Predicting Drug-Target Interaction Network Using Deep Learning Model
62 Inkyung Jung, Hyunwoong Kim, Dongchan Yang and Jayoung Ryu A new class of super-enhancers associated with fast recovery of 3D chromatin loops
67 Xiaoxin Ye and Joshua Ho Ultrafast clustering of single-cell flow cytometry data using FlowGrid
73 Yasuo Tabei, Masaaki Kotera, Ryusuke Sawada and Yoshihiro Yamanishi Network-based characterization of drug-protein interaction signatures with a space-efficient approach
79 Jingli Wu, Qirong Cai, Jinyan Wang and Yuanxiu Liao Identifying Mutated Driver Pathways in Cancer by Integrating Multi-Omics Data
80 Ko Abe, Masaaki Hirayama, Kinji Ohno and Teppei Shimamura ENIGMA: An Enterotype-Like Unigram Mixture Model for Microbial Association Analysis
84 Shaokun An, Lin Wan and Liang Ma TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data
86 Kui Hua and Xuegong Zhang Estimating the Total Genome Length of a Metagenomic Sample Using K-mers
87 Shanshan Ren, Nauman Ahmed, Koen Bertels and Zaid Al-Ars GPU Accelerated Sequence Alignment with Traceback for GATK HaplotypeCaller
88 Ziying Yang, Guoxian Yu, Maozu Guo and Jun Wang CDPath: Cooperative driver pathways discovery using integer linear programming and Markov clustering
89 Cui Su, Jun Pang and Soumya Paul Towards Optimal Decomposition of Boolean Networks
100 Lunfei Liu, Wenting Liu, Yuxin Zheng, Jisu Chen, Jiong Zhou, Huatuo Dai, Suiqing Cai, Jianjun Liu, Min Zheng and Yunqing Ren Anti-TNF-α Treatment-related Pathways and Biomarkers Revealed by Transcriptome Analysis in Chinese Psoriasis Patients
104 Haoxing Du, Yi Sheng Ong, Marina Knittel, Ross Mawhorter, Ivy Liu, Gianluca Gross, Reiko Tojo, Ran Libeskind-Hadas and Yi-Chieh Wu Multiple Optimal Reconciliations under the Duplication-Loss-Coalescence Model
108 Safa Jammali, Jean-David Aguilar, Esaie Kuitche Kamela and Aïda Ouangraoua SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
109 Dongmei Ai, Xiaoxin Li, Hongfei Pan and Li Xia Extending Liquid Association to Explore Mediated Co-varying Dynamics in Marine Microbial Community
113 Yue Zhang, Chunfang Zheng, Sindeed Islam, Yong-Min Kim and David Sankoff Branching out to Speciation with a Birth-and-Death Model of Fractionation: the Malvaceae
117 Tom Hartmann, Max Bannach and Martin Middendorf Sorting Signed Permutations by Inverse Tandem Duplication Random Losses
124 Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng and Shuaicheng Li Large-Scale 3D Chromatin Reconstruction From Chromosomal Contacts
126 Kang Ning and Pengshuo Yang Meta-Network: Optimized species-species network analysis for microbial communities
127 Yangjing Gan, Yi Rong, Fei Huang, Lun Hu, Xiaohan Yu, Pengfei Duan, Shengwu Xiong, Haiping Liu, Jing Peng and Yuan Xiaohui Automatic Hierarchy Classification in Venation Networks using Directional Morphological Filtering for Hierarchical Structure Traits Extraction
129 Zhang Xia, Gan Yanglan, Zou Guobing, Guan Jihong and Zhou Shuigeng Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues
130 Zhijie Ni, Xiao Zheng and Xiufen Zou scLRTD : A novel low rank tensor decomposition method for single-cell RNA-sequencing data imputing
134 Binh P. Nguyen and Nguyen-Quoc-Khanh Le Prediction of FMN Binding Sites in Electron Transport Chain based on 2-D CNN and PSSM Profiles
139 Djordje Djordjevic, Joshua Tang, Yun Xin Chen, Shu Lun Shannon Kwan, Raymond Ling, Gordon Qian, Chelsea Woo, Samuel Ellis and Joshua Ho Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus
140 Dongbo Bu, Chao Wang, Haicang Zhang, Shiwei Sun, Yi Wei and Wei-Mou Zheng Constructing optimal energy functions for protein structure prediction using reverse Monte Carlo sampling
141 Sungjoon Park, Minsu Kim, Seokjun Seo, Seungwan Hong, Kyoohyung Han, Keewoo Lee, Jung Hee Cheon and Sun Kim A Secure SNP Panel Scheme using Homomorphically Encrypted K-mers without SNP Calling on the User Side
143 Pritha Dutta, Lichun Ma, Yusuf Ali, Peter M.A. Sloot and Jie Zheng Boolean Network Modeling of β-cell Apoptosis and Insulin Resistance in Type 2 Diabetes Mellitus
145 Dongbo Bu, Jingwei Zhang, Shiwei Sun, Yaojun Wang, Chuncui Huang, Yan Li, Jinyu Zhou, Hui Wang and Fusong Ju De Novo glycan structural identification from mass spectra using tree merging strategy
146 Shiquan Sun, Yabo Chen, Yang Liu and Xuequn Shang A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
148 Yangyang Hao, Quan-Yang Duh, Richard Kloos, Joshua Babiarz, R. Mack Harrell, S. Thomas Traweek, Su Yeon Kim, Grazyna Fedorowicz, P. Sean Walsh, Peter Sadow, Jing Huang and Giulia Kennedy Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms
149 Quan Chen and Jun Zhu Detecting Virus-specific Effects on Post-infection Temporal Gene Expression
150 Wenhao Qian, Ting Ma, Mao Ye, Zhiyao Li, Yuanhua Liu and Pei Hao Microbiota in the Apical Root Canal System of Tooth with Apical Perodontitis