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Best Paper Awards of BMC Track of InCoB 2017

ID	Authors, Title	Decision	Awards
35	Haiyong Zheng, Ruchen Wang, Zhibin Yu, Nan Wang, Zhaorui Gu and Bing Zheng. Automatic plankton image classification combining multiple view features via multiple kernel learning	BMC Bioinformatics Supplement	Gold
54	Ari Hardianto, Muhammad Yusuf, Fei Liu and Shoba Ranganathan. Exploration of charge states of balanol analogues acting as ATP mimics in kinases	BMC Bioinformatics Supplement	Gold
64	Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen and Chin Lung Lu. R3D-BLAST2: an improved search tool for similar RNA 3D substructures	BMC Bioinformatics Supplement	Gold
130	Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang and Xuequn Shang. Identifying term relations cross different gene ontology categories	BMC Bioinformatics Supplement	Silver
12	Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li and Wen Zhang. 16sPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on 16S Metagenomic Sequencing	BMC Bioinformatics Supplement	Bronze
50	Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu and Jinn-Moon Yang. Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection	BMC Bioinformatics Supplement	Bronze
111	Kyoungyeul Lee, Minho Lee and Dongsup Kim. Utilizing Random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server	BMC Bioinformatics Supplement	Bronze
116	Yahui Sun, Chenkai Ma and Saman Halgamuge. The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways	BMC Bioinformatics Supplement	Bronze
17	Yu-Wei Wu. ezTree: an automated pipeline for identifying marker genes and inferring phylogenetic relationships for uncultivated prokaryotic draft genomes	BMC Genomics Supplement	Gold
65	Wan Ching Lim and Asif M. Khan. Mapping T-cell epitopes in the ebolavirus proteome	BMC Genomics Supplement	Gold
67	Yaowei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Wu Zhong, Xuan Li, Chen Chen and Pei Hao. A survey on cellular RNA editing activity in response to Candida albicans infections	BMC Genomics Supplement	Gold
81	Yingying Cao, Ruiyuan Cao, Yaowei Huang, Hongxia Zhou, Yuanhua Liu, Xuan Li, Wu Zhong and Pei Hao. A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza A viruses	BMC Genomics Supplement	Gold
61	Kun Chen, Li Liu, Xiaotuo Zhang, Yuanyuan Yuan, Shuchao Ren, Junqiang Guo, Qingyi Wang, Peiran Liao, Shipeng Li, Xiuming Cui, Yong-Fang Li and Yun Zheng. Phased secondary small interfering RNAs in Panax notoginseng	BMC Genomics Supplement	Silver
14	Guo Weifeng, Zhang Shaowu, Shi Qianqian, Zhang Chengming, Zeng Tao and Chen Luonan. A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification	BMC Genomics Supplement	Bronze
52	Yuko Makita, Mika Kawashima, Nyok Sean Lau, Minami Matsui and Ahmad Sofiman Othman. Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches	BMC Genomics Supplement	Bronze
66	Asif M. Khan, Yongli Hu, Olivo Miotto, Natascha M. Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan and J. Thomas August. Analysis of Viral Diversity for Vaccine Target Discovery	BMC Medical Genomics Supplement	Gold
2	Y-H. Taguchi. Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases	BMC Medical Genomics Supplement	Silver
97	Jonathan Dayton and Stephen Piccolo. Classifying cancer genome aberrations by their mutually exclusive effects on transcription	BMC Medical Genomics Supplement	Bronze
23	Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng and Lei Shi. A linear programming computational framework integrates phosphor-proteomics and prior knowledge to predict drug efficacy	BMC Systems Biology Supplement	Gold
75	Lichun Ma and Jie Zheng. A Polynomial Based Model for Cell Fate Prediction in Human Diseases	BMC Systems Biology Supplement	Gold
79	Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee. Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas	BMC Systems Biology Supplement	Gold
46	Ying Xu, Jiaogen Zhou, Shuigeng Zhou and Jihong Guan. CPredictor3.0: Effectively detecting protein complexes from PPI networks with expression data and functional annotations	BMC Systems Biology Supplement	Silver
20	Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi and Tzong Yi Lee. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions	BMC Systems Biology Supplement	Bronze
48	Daniel Trejo Banos, Mohamed Elati and Pauline Trébulle. Integrating transcriptional activity in genome-scale models of metabolism	BMC Systems Biology Supplement	Bronze
60	Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob White, Hanry Yu and Lisa Tucker-Kellogg. Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model	BMC Systems Biology Supplement	Bronze
86	Maulida Mazaya, Hung-Cuong Trinh and Yung-Keun Kwon. Construction and analysis of gene-gene dynamics influence networks based on a Boolean model	BMC Systems Biology Supplement	Bronze
90	Truong Cong Doan and Yung-Keun Kwon. Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks	BMC Systems Biology Supplement	Bronze
98	Qingping Liu, Jiahao Wang, Yan Zhu and Yongqun He. Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism	BMC Systems Biology Supplement	Bronze
125	Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang and Tzong Yi Lee. MDD-Carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs	BMC Systems Biology Supplement	Bronze

Provisionally Accepted Papers by InCoB 2017

BMC Track
ID	Title	Authors
2	Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases	Y-H. Taguchi
3	Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction	Yosvany López, Alok Sharma, Abdollah Dehzangi, Sunil Pranit Lal, Ghazaleh Taherzadeh, Abdul Sattar and Tatsuhiko Tsunoda
4	Hadamard Kernel SVM: Applications for Breast Cancer Outcome Predictions	Hao Jiang, Wai-Ki Ching, Wai-Shun Cheung, Wenpin Hou and Hong Yin
5	An improved discriminative filter bank selection approach for motor imagery EEG signal classification using mutual information	Shiu Kumar, Alok Sharma and Tatsuhiko Tsunoda
8	InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk	Liang Cheng, Yue Jiang, Hong Ju, Jie Sun, Meng Zhou, Yang Hu and Jiajie Peng
9	CORNAS: Coverage-dependent RNA-Seq analysis of gene expression data without biological replicates	Joel Low, Tsung Fei Khang and Martti Tammi
12	16sPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on 16S Metagenomic Sequencing	Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li and Wen Zhang
14	A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification	Guo Weifeng, Zhang Shaowu, Shi Qianqian, Zhang Chengming, Zeng Tao and Chen Luonan
16	PGAP-X: Extension on pan-genome analysis pipeline	Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu and Jingfa Xiao
17	ezTree: an automated pipeline for identifying marker genes and inferring phylogenetic relationships for uncultivated prokaryotic draft genomes	Yu-Wei Wu
19	Identification of prognostic signature in cancer based on DNA methylation interaction network	Weilin Hu and Xionghui Zhou
20	Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions	Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi and Tzong Yi Lee
21	Detecting Causal Gene Regulations from Short Time-series Data Based on Prediction of Topologically Equivalent Attractors	Ben-Gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu and Luonan Chen
23	A linear programming computational framework integrates phosphor-proteomics and prior knowledge to predict drug efficacy	Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng and Lei Shi
24	Constraint-based Perturbation Analysis with Cluster Newton Method : A Case Study of Personalized Parameter Estimations with Irinotecan Whole-Body Physiologically Based Pharmacokinetic Model	Shun Asami, Daisuke Kiga and Akihiko Konagaya
28	Refine Gene Functional Similarity Network Based on Interaction Networks	Maozu Guo and Zhen Tian
30	Divisive Hierarchical Maximum Likelihood Clustering	Alok Sharma, Yosvany Lopez and Tatsuhiko Tsunoda
31	Subtype identification from heterogeneous TCGA datasets on a genomic scale by multi-view clustering with enhanced consensus	Menglan Cai and Limin Li
35	Automatic plankton image classification combining multiple view features via multiple kernel learning	Haiyong Zheng, Ruchen Wang, Zhibin Yu, Nan Wang, Zhaorui Gu and Bing Zheng
37	Automated classification and characterization of the mitotic spindle following knockdown of a mitosis-related protein	Matloob Khushi, Imraan Dean, Erdahl Teber, Megan Chircop, Jonathan Arthur and Neftali Flores-Rodriguez
43	Predicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression	Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Yu-Xi Long and Siu-Ming Yiu
45	A computational model to predict the best orange-derived adjuvants in vaccination strategies against Human Papillomavirus	Marzio Pennisi, Giulia Russo, Silvia Ravalli and Francesco Pappalardo
46	CPredictor3.0: Effectively detecting protein complexes from PPI networks with expression data and functional annotations	Ying Xu, Jiaogen Zhou, Shuigeng Zhou and Jihong Guan
48	Integrating transcriptional activity in genome-scale models of metabolism	Daniel Trejo Banos, Mohamed Elati and Pauline Trébulle
49	MultiDCoX: Multi-factor Analysis of Differential Co-expression	Herty Liany, Jagath Rajapakse and R. Krishna Murthy Karuturi
50	Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection	Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu and Jinn-Moon Yang
52	Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches	Yuko Makita, Mika Kawashima, Nyok Sean Lau, Minami Matsui and Ahmad Sofiman Othman
54	Exploration of charged states of balanol analogues acting as ATP mimics in kinases	Ari Hardianto, Muhammad Yusuf, Fei Liu and Shoba Ranganathan
60	Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model	Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob White, Hanry Yu and Lisa Tucker-Kellogg
61	Phased secondary small interfering RNAs in Panax notoginseng	Kun Chen, Li Liu, Xiaotuo Zhang, Yuanyuan Yuan, Shuchao Ren, Junqiang Guo, Qingyi Wang, Peiran Liao, Shipeng Li, Xiuming Cui, Yong-Fang Li and Yun Zheng
63	GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service.	Yiqi Wang, Gen Li, Mark Ma, Fazhong He, Zhuo Song, Wei Zhang and Chengkun Wu
64	R3D-BLAST2: an improved search tool for similar RNA 3D substructures	Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen and Chin Lung Lu
65	Mapping T-cell epitopes in the ebolavirus proteome	Wan Ching Lim and Asif M. Khan
66	Analysis of Viral Diversity for Vaccine Target Discovery	Asif M. Khan, Yongli Hu, Olivo Miotto, Natascha M. Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan and J. Thomas August
67	A survey on cellular RNA editing activity in response to Candida albicans infections	Yaowei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Wu Zhong, Xuan Li, Chen Chen and Pei Hao
71	Biclustering of human tissue-specific circular RNAs reveals potential circRNA biomarkers	Yu-Chen Liu, Yu-Jung Chiu, Jian-Rong Li, Chuan-Hu Sun, Chun-Chi Liu and Hsien-Da Huang
75	A Polynomial Based Model for Cell Fate Prediction in Human Diseases	Lichun Ma and Jie Zheng
79	Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas	Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee
81	A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza A viruses	Yingying Cao, Ruiyuan Cao, Yaowei Huang, Hongxia Zhou, Yuanhua Liu, Xuan Li, Wu Zhong and Pei Hao
86	Construction and analysis of gene-gene dynamics influence networks based on a Boolean model	Maulida Mazaya, Hung-Cuong Trinh and Yung-Keun Kwon
88	GTZ: a fast compression and cloud transmission tool optimized for FASTQ files	Yuting Xing, Gen Li, Zhenguo Wang, Bolun Feng, Zhuo Song and Chengkun Wu
89	Dependency-based long short term memory network for drug-drug interaction extraction	Wei Wang, Xi Yang, Canqun Yang, Xiao-Wei Guo, Xiang Zhang and Chengkun Wu
90	Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks	Truong Cong Doan and Yung-Keun Kwon
97	Classifying cancer genome aberrations by their mutually exclusive effects on transcription	Jonathan Dayton and Stephen Piccolo
98	Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism	Qingping Liu, Jiahao Wang, Yan Zhu and Yongqun He
103	A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction	Lei Deng, Chao Fan and Zhiwen Zeng
110	Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes	Naoki Osato
111	Utilizing Random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server	Kyoungyeul Lee, Minho Lee and Dongsup Kim
112	CoMet: A workflow using contig coverage and composition for binning a metagenomic sample with high precision	Damayanthi Herath, Sen-Lin Tang, Kshitij Tandon, David Ackland and Saman Halgamuge
114	Novel human microbe-disease association prediction using network consistency projection	Zhi-Chao Jiang and De-Shuang Huang
116	The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways	Yahui Sun, Chenkai Ma and Saman Halgamuge
119	Differential responses of innate immunity triggered by different subtypes of influenza A viruses in human and avian hosts	Yingying Cao, Yaowei Huang, Ke Xu, Yuanhua Liu, Ye Xu, Pei Hao, Wu Zhong and Xuan Li
123	Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using Random Forest	Xin Wang, Peijie Lin and Joshua Ho
125	MDD-Carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs	Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang and Tzong Yi Lee
130	Identifying term relations cross different gene ontology categories	Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang and Xuequn Shang
132	CNN-BLPred: A Convolutional Neural Network based predictor for β-Lactamases (BL) and their classes	Clarence White, Hamid Ismail, Hiroto Saigo and Dukka Kc
139	2D-EM Clustering Approach for High-Dimensional Data	Alok Sharma, Piotr J. Kamola and Tatsuhiko Tsunoda
TCBB Track
ID	Title	Authors
51	Bi-level error correction for PacBio long reads	Yuansheng Liu, Chaowang Lan, Michael Blumenstein and Jinyan Li
84	Detection and Recognition for Life State of Cell Cancer Using Two-Stage Cascade CNNs	Haigen Hu, Qiu Guan, Shengyong Chen, Zhiwei Ji and Yao Lin
101	GapReduce: a gap filling algorithm based on partitioned read sets	Junwei Luo, Jianxin Wang, Juan Shang, Huimin Luo, Min Li, Fangxiang Wu and Yi Pan
JBCB Track
ID	Title	Authors
6	MPTM: A TOOL FOR MINING PROTEIN POST-TRANSLATIONAL MODIFICATIONS FROM LITERATURE	Dongdong Sun, Minghui Wang and Ao Li
105	Bone Marrow Cavity Segmentation using Graph-cuts with Wavelet-Based Texture Feature	Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Masaru Ishii and Hideo Matsuda
129	Comparison of different approaches for identifying subnetworks in metabolic networks	Abolfazl Rezvan and Changiz Eslahchi
PeerJ Track
ID	Title	Authors
93	Automated Classification of Tropical Shrub Species: A Hybrid of Leaf Shape and Machine Learning Approach	Siow Wee Chang, Miraemiliana Murat, Arpah A., Hwa Jen Yap and Kien Thai Yong
Bioinformatics Track
ID	Title	Authors
107	Search for overlapping subgraphs to detect multiple epitopes from an antigen	Shaogui Wu, Jin Xie, Jiawen Jiang, Wencui Li, Fei Luo and Liang Zhao

Provisionally Accepted Posters by InCoB 2017

ID	Title	Authors
53	A Comparison Study for Supervised Machine Learning Models in Cancer Classification	Huaming Chen, Hong Zhao, Lei Wang, Jiangning Song and Jun Shen
62	High performance computing for accelerating a next-generation sequencing-based clinical pathogen identification pipeline	Haoran Ma, Tin Wee Tan and Kenneth Hon Kim Ban
135	Rapid Cluster Analysis of Wound Microbiota	Timothy Chappell, Shlomo Geva, James M Hogan, Flavia Huygens, Wayne Kelly and Dimitri Perrin
141	A New Semantic Disease-Disease Similarity Based on the Environment Information and Disease-related Genes	Fatemeh Abbasi and Changiz Eslahchi
142	MOROKOSHI: Transcriptome database in Sorghum bicolor and its updates	Yuko Makita, Mika Kawashima, Tomoko Kuriyama, Setsuko Shimada and Minami Matsui
143	Prediction of GPCR-G Protein Coupling Specificity Based on Transmembrane Topologies	Riku Ashida and Yasuhito Inoue
151	Identification of deregulated transcription factors involved in subtypes of cancers	Magali Champion, Julien Chiquet, Pierre Neuvial, Mohamed Elati and Etienne Birmele
154	Transfer-of-training framework to find similarity and classify protein complexes	Shruti Gupta, Manisha Kalsan, Dana Mary Varghese, Ajay Arya, Ajay Kumar Verma and Shandar Ahmad
155	Infectious Disease Modelling and Surveillance through Unstructured Twitter Data for understanding location specific Toxicological Trends	Saurabh Sugha and Dr Shandar Ahmad
160	Sequence evolution of the methicillin resistant mecA gene	Ling Li Koh, Charisma Nair Murali, Mohammad Asif Khan and Swee Hua Erin Lim
161	BioCarian: An Engine for Searching Biological Databases	Nazar Zaki and Chandana Tennakoon
163	TimeXNet: Prediction and analysis of cellular response pathways	Phit Ling Tan, Ashwini Patil and Kenta Nakai