Accepted Papers

• Pavithra Balasubramanian, Anand Balupuri and Seung Joo Cho. Receptor-guided 3D-QSAR studies, Molecular Dynamics Simulation and Free energy calculations of Btk kinase inhibitors.


• Wilson Wen Bin Goh and Limsoon Wong. Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- A case study in clinical proteomics


• Xiao-Fei Zhang, Le Ou-Yang and Hong Yan. Node-based differential network analysis in genomics


• Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung and Jung Kyoon Choi. Prediction of Recurrent Regulatory Mutations in Noncoding Cancer Genomes


• Zhang Chuanchao, Liu Juan, Shi Qianqian, Zeng Tao and Chen Luonan. Comparative network stratification analysis for identifying functional interpretable network biomarkers


• Yi Liu, Weiping Sun, Baozhen Shan and Kaizhong Zhang. DISC: Disulfide Linkage Characterization from Tandem Mass Spectra


• Weiyun Ma, Dmitriy Smirnov and Ran Libeskind-Hadas. DTL Reconciliation Repair


• Xiao Dong Feng. Entrapment sequences method for evaluation of database search engines and quality control methods in shotgun proteomics


• Shuhao Sun, Fima Klebaner and Tianhai Tian. Inbreeding Depression in Large Populations with Polygenic Traits


• Qin Xin, Jianping Wu and Ke Xu. A novel wearable device for continuous, non-invasion blood pressure measurement


• Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian and Byung-Jun Yoon. Optimal hybrid sequencing and assembly: feasibility conditions for accurate genome reconstruction and cost minimization strategy


• Daesik Choi, Byungkyu Park, Hanju Chae, Wook Lee and Kyungsook Han. Predicting protein-binding regions in RNA using nucleotide profiles and compositions


• Yuchao Xia, Yun Liu, Minghua Deng and Ruibin Xi. Pysim-sv: a package for simulating structural variation data with GC-biases


• Wei-Sheng Tien, Jun-Hong Chen and Kun-Pin Wu. SheddomeDB: the ectodomain shedding database for membrane-bound shed markers


• Min Li, Xiaodong Yan, Junwei Luo, Fangxiang Wu, Yi Pan and Jianxin Wang. PECC: correcting contigs based on paired-end read distribution


• Jing Ren, Jiangning Song, John Ellis and Jinyan Li. Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences


• Shuai An, Jun Wang and Jinmao Wei. Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection


• Jarno Alanko, Djamal Belazzougui, Fabio Cunial and Veli Mäkinen. A framework for space-efficient read clustering in metagenomic samples


• Junpeng Zhang, Thuc Le, Lin Liu and Jiuyong Li. Identifying miRNA sponge modules using biclustering and regulatory scores


• Xiaoke Ma, Liang Yu, Peizhuo Wang and Xiaofei Yang. Subtype specic and common DNA methylation patterns of long non-coding RNAs in breast cancer


• Vicky Chen, John Paisley and Xinghua Lu. Revealing Common Disease Mechanisms Shared by Tumors of Different Tissues of Origin through Semantic Representation of Genomic Alterations and Topic Modeling


• Nan Jiang, Wenge Rong, Yifan Nie, Yikang Shen and Zhang Xiong. Negative Sampling with Multi-Layer Perceptron for Biological Event Trigger Identification


• Lei Sun, Jun Wang and Jinmao Wei. Feature Selection Based on AUC and Variable Complementarity


• Agnieszka Mykowiecka, Pawel Szczesny and Pawel Gorecki. Inferring gene-species assignments in the presence of horizontal gene transfer


• Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo and Sun Kim. Construction of Condition-specific Pathway Interaction Network by Computing Shortest Paths on Weighted PPI


• Dong Li, Zhisong Pan, Guyu Hu, Zexuan Zhu and Shan He. Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme


• Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf and Matthias Bernt. Genome Rearrangement with ILP


• Manuel Lafond, Cedric Chauve, Nadia El-Mabrouk and Aïda Ouangraoua. Gene Tree Construction and Correction using SuperTree and Reconciliation


• Weiqi Chen, Jing Liu and Shan He. Identification of active modules in Protein Protein Interaction networks: an integrated multi-objective approach


• Shifu Chen, Tanxiao Huang, Yanqing Zhou, Mingyan Xu and Jia Gu. AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for Fastq Data


• Shuqin Zhang, Limin Li and Michael Kwok-Po Ng. Drug-target Interaction Prediction by Integrating Multiview Network Data


• Sangseob Leem and Taesung Park. An empirical fuzzy multifactor dimensionality reduction method for detecting gene-gene interactions


• Ming Gao, Xiangke Liao, Chengkun Wu, Wenqiang Yu and Shaoliang Peng. P-Hint-Hunt: A Deep Parallelized Whole Genome DNA Methylation Detection Tool


• Yang Yang, Ning Huang, Luning Hao and Wei Kong. A clustering-based approach for the identification of microRNA combinatorial biomarkers


• Ipputa Tada, Yasuhiro Tanizawa and Masanori Arita. Visualization of consensus genome structure without using a reference genome


• Bingxin Lu, Louxin Zhang and Hon Wai Leong. A Program to Compute the Soft Robinson–Foulds Distance between Phylogenetic Networks


• Debolina Goswami, Sukriti Goyal, Salma Jamal, Ritu Jain, Divya Wahi and Abhinav Grover. GQSAR Modeling and Combinatorial library generation of 4-phenylquinazoline-2-carboxamide derivatives as Antiproliferative Agents in Human Glioblastoma Tumors


• Dimitris Papamichail, Angela Huang, Edward Kennedy, Jan-Lucas Ott, Andrew Miller and Georgios Papamichail. Live Phylogeny with Polytomies: Finding the Most Compact Parsimonious Trees


• Andrzej Mizera, Jun Pang and Qixia Yuan. Reviving the two-state Markov chain approach


• Chandana Tennakoon and Wing-Kin Sung. BATVI: Fast, Sensitive and Accurate Detection of Virus Integrations


• Vikas Bansal. A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments


• Monika Balvočiūtė and Daniel Huson. SILVA, RDP, Greengenes, NCBI and OTT --- How do these taxonomies compare?


• Qiao Liu and Rui Jiang. A sequence-based method to predict the impact of regulatory variants using random forest


• Yue Zhang, Chunfang Zheng and David Sankoff. Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation


• Jie Zhang, Zhigen Zhao, Kai Zhang and Zhi Wei. A Feature Sampling Strategy for Analysis of High Dimensional Genomic Data


• Yu-Chen Liu and Hsien-Da Huang. Plant miRNAs found in human circulating sys-tem provide evidences of cross kingdom RNAi


• Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu and Tzong Yi Lee. Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features


• Jarosław Paszek and Pawel Gorecki. Efficient Algorithms for Genomic Duplication Models


• Zhentang Li, Yi Wang and Fei Wang. Fuwa: a decision-tree-based fast variant caller for next-generation sequencing data


• Wei-Hsiang Kung, Ching-Fang Yu, Andy Chi-Lung Lee, Chi-Dung Yang, Fang-Hsin Chen and Hsien-Da Huang. Gene Expression Profiling of Tumor Associated Macrophage after Exposure to Single Dose Irradiaiotn


• Hui-Hui Hsu, Li-Jen Chang and Jinn-Moon Yang. An integrated approach with new strategies for QSAR models and lead optimization


• Mengge Zhang, Lianping Yang, Jie Ren, Nathan Ahlgren, Jed Fuhrman and Fengzhu Sun. Prediction of virus-host infectious association by supervised learning methods


• Lun Hu, Xiaohui Yuan, Pengwei Hu and Keith C. C. Chan. Parallel Identification of Variable-length Patterns for Large-scale Prediction of Protein-protein Interactions Using MapReduce


• Yinglei Lai. A statistical method for the conservative adjustment of false discovery rate (q-value)


• Hai'E Gong, Haicang Zhang, Chao Wang, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu and Jianwei Zhu. Improving prediction of burial state of residues by exploiting correlation among residues


• Zhanzhan Cheng, Kai Huang, Shuigeng Zhou, Hui Liu, Yang Wang and Jihong Guan. Selecting High-Quality Negative Samples for Effectively Predicting Protein-RNA Interactions