List of Accepted Papers

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paper#	Author/Title
5	Junhee Seok, Weihong Xu, Ronald Davis and Wenzhong Xiao. RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays ◆Abstract
6	Kazuhiro Maeda and Hiroyuki Kurata. Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity ◆Abstract
9	Wenbao Yu and Taesung Park. AucPR: An AUC-based approach using penalized regression for disease prediction with high-dimensiona omics datal ◆Abstract
12	Daniel Tabas-Madrid, Ander Muniategui, Ignacio Sánchez-Caballero, Dannys Martinez-Herrera, Carlos Oscar S. Sorzano, Angel Rubio and Alberto Pascual-Montano. Improving miRNA-mRNA Interaction Predictions ◆Abstract
15	Wei-Sheng Wu, Mei-Huei Jhu and Fu-Jou Lai. Identifying cooperative transcription factors in yeast using multiple data sources ◆Abstract
18	Tun-Wen Pai. Identification of conserved and polymorphic STRs for personal genomes ◆Abstract
19	Kamal Taha, Paul Yoo and Sami Muhaidat. Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction ◆Abstract
21	Lujia Chen, Chunhui Cai, Vicky Chen and Xinghua Lu. Trans-species learning of cellular signaling systems with bimodal deep belief networks ◆Abstract
22	Masaaki Kotera, Yosuke Nishimura, Zen-Ichi Nakagawa, Ai Muto, Yuki Moriya, Shinobu Okamoto, Shuichi Kawashima, Toshiaki Katayama, Toshiaki Tokimatsu, Minoru Kanehisa and Susumu Goto. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB Enzyme List ◆Abstract
23	Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki and Daron Standley. Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation ◆Abstract
29	Chern Han Yong, Osamu Maruyama and Limsoon Wong. Discovery of Small Protein Complexes from PPI Networks ◆Abstract
30	Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata and Masao Nagasaki. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads ◆Abstract
31	Kansuporn Sriyudthsak, Yuji Sawada, Yukako Chiba, Yui Yamashita, Shigehiko Kanaya, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito, Ebernard O. Voit, Fumihide Shiraishi and Masami Yokota Hirai. U–system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network ◆Abstract
34	Idoia Ochoa, Mikel Hernaez and Tsachy Weissman. Aligned Genomic Data Compression via Improved Modeling ◆Abstract
39	Xiaolei Wang, Hiroyuki Kuwahara and Xin Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels ◆Abstract
51	Bingqing Lin, Li-Feng Zhang and Xin Chen. LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data ◆Abstract
55	Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar and Iana Pyrogova. An $O(m \log m)$-time algorithm for detecting superbubbles ◆Abstract
56	Yutaka Ueno, Shuntaro Ito and Akihiko Konagaya. IMPLEMENTING A MODELING SOFTWARE FOR ANIMATED PROTEIN-COMPLEX INTERACTIONS USING A PHYSICS SIMULATION LIBRARY ◆Abstract
58	Che Lin, Chin-Nan Lin, Yu-Chao Wang, Fang-Yu Liu, Yu-Wen Chien, Yung-Jun Chuang, Chung-Yu Lan, Wen-Ping Hsieh and Bor-Sen Chen. Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection ◆Abstract
66	Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim and Doheon Lee. SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data ◆Abstract
67	So Kobiki and Osamu Maruyama. ReSAPP: Predicting overlapping protein complexes by merging multiple sampled partitions of proteins ◆Abstract
69	Ryota Mori, Michiaki Hamada and Kiyoshi Asai. Efficient calculation of exact probability distributions of integer features on RNA secondary structures ◆Abstract
70	Junfang Chen, Pavlo Lutsik, Ruslan Akulenko, Jörn Walter and Volkhard Helms. AKSmooth: Human colon methylome profiling using low-coverage bisulfite sequencing data ◆Abstract
71	Pawel Badnarz and Bartek Wilczynski. Supervised learning method for predicting chromatin boundary associated insulator elements ◆Abstract
76	Dan He. IPED2: Inheritance Path based Pedigree Reconstruction Algorithm for Complicated Pedigrees ◆Abstract
77	Ho-Sik Seok, Taemin Song, Sek Won Kong and Kyu-Baek Hwang. An Efficient Search Algorithm for Finding Genomic-range Overlaps Based on the Maximum Range Length ◆Abstract
81	Jung-Hsien Chiang and Jiun-Huang Ju. Discovering novel protein-protein interactions by measuring the protein semantic similarity from biomedical literature ◆Abstract
82	Chih-Yuan Hsu, Tsu-Chun Yu, Ling-Jiun Lin, Rei-Hsing Hu and Bor-Sen Chen. Systematic Approach to Escherichia coli Cell Population Control using a Genetic Lysis Circuit ◆Abstract
86	Alexandros Manolakos, Idoia Ochoa, Kartik Venkat, Andrea Goldsmth and Olivier Gevaert. CaMoDi: A new method for fast Cancer Module Discovery ◆Abstract
87	Broto Chakrabarty and Nita Parekh. PRIGSA: Protein Repeat Identification by Graph Spectral Analysis ◆Abstract
88	Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang and Jin Chen. An Integrative Approach for Measuring Semantic Similarities using Gene Ontology ◆Abstract
90	Yi-Yu Hsu and Hung-Yu Kao. Curatable Named-entity Recognition using Semantic Relations ◆Abstract
91	Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz and Christina Boucher. HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly ◆Abstract
92	Wei-Sheng Wu, Ming-Liang Wei, Chia-Ming Yeh and Tien-Hao Chang. A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae ◆Abstract
94	Michal Wozniak, Jerzy Tiuryn and Limsoon Wong. GWAMAR: Genome-wide assessment of mutations associated with drug resistance in bacteria ◆Abstract

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