Ari Hardianto, Muhammad Yusuf, Fei Liu and Shoba Ranganathan.

Exploration of charge states of balanol analogues acting as ATP mimics in kinases

Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen and Chin Lung Lu.

R3D-BLAST2: an improved search tool for similar RNA 3D substructures

Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang
and Xuequn Shang.

Identifying term relations cross different gene ontology categories

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

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

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

Yahui Sun, Chenkai Ma and Saman Halgamuge.

The node-weighted Steiner tree approach to identify elements of cancer-related
signaling pathways

Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang
and Xuequn Shang.

Identifying term relations cross different gene ontology categories

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

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

Yu-Wei Wu.

ezTree: an automated pipeline for identifying marker genes and inferring
phylogenetic relationships for uncultivated prokaryotic draft genomes

Wan Ching Lim and Asif M. Khan.

Mapping T-cell epitopes in the ebolavirus proteome

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

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

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

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

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

Y-H. Taguchi

Tensor decomposition-based unsupervised feature extraction identifies candidate
genes that induce post-traumatic stress disorder-mediated heart diseases

Jonathan Dayton and Stephen Piccolo

Classifying cancer genome aberrations by their mutually exclusive effects on
Transcription

Lichun Ma and Jie Zheng

A Polynomial Based Model for Cell Fate Prediction in Human Diseases

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

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

Ying Xu, Jiaogen Zhou, Shuigeng Zhou and Jihong Guan

CPredictor3.0: Effectively detecting protein complexes from PPI networks with
expression data and functional annotations

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

Daniel Trejo Banos, Mohamed Elati and Pauline Trébulle.

Integrating transcriptional activity in genome-scale models of metabolism

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

Maulida Mazaya, Hung-Cuong Trinh and Yung-Keun Kwon.

Construction and analysis of gene-gene dynamics influence networks based on a
Boolean model

Truong Cong Doan and Yung-Keun Kwon.

Investigation on changes of modularity and robustness by edge-removal
mutations in signaling networks

Qingping Liu, Jiahao Wang, Yan Zhu and Yongqun He.

Ontology-based systematic representation and analysis of traditional Chinese
drugs against rheumatism

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.

Ali Ezzat, Min Wu, Xiaoli Li and Chee Keong Kwoh

Drug-­target interaction prediction via class imbalance­-aware ensemble learning

Mei Hou, Feng Tian, Shuai Jiang, Lei Kong, Dechang Yang and Ge Gao

LocExpress: a web server for efficiently estimating expression of novel transcripts

Kopal Joshi, Sukriti Goyal, Sonam Grover, Salma Jamal, Aditi Singh, Pawan Dhar and Abhinav Grover

Novel group­-based QSAR and combinatorial design of CK-­1δ inhibitors as neuroprotective agents

Wilson Wen Bin Goh

Fuzzy-­FishNET: A highly reproducible protein complex­-based approach for feature selection in comparative proteomics

Minsu Lee and Hyungjune Lee

DMirNet: Inferring direct microRNA-­mRNA association networks

Jayapriya J and Michael Arock

GPU based Hybrid Bioinspired Algorithm for Aligning Multiple Sequences

Vaishali Waman, Pandurang Kolekar, Mukund Ramatirthakar, Mohan Kale and Urmila Kulkarni­-Kale

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

Chia-Chun Chiu and Wei-Sheng Wu.

Investigation of microRNAs in mouse macrophage responses to lipoposaccharide-stimulation by combining gene expression with microRNA-target information

Chalini Wijetunge, Isaam Saeed, Berin Boughton, Ute Roessner and Saman Halgamuge.

A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model

Chieh-Hua Lin, Yu-Bin Wang, Shu-Hwa Chen, Chao Agnes Hsiung and Chung-Yen Lin.

Precise Genotyping and Recombination Detection of Enterovirus

Karen Ryall, Jihye Kim, Peter Klauck, Jimin Shin, Minjae Yoo, Anastasia Ionkina, Todd Pitts, John Tentler, Jennifer Diamond, Gail Eckhardt, Lynn Heasley, Jaewoo Kang and Aik Choon Tan.

An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer

Lars R. Olsen, Christian Simon, Ulrich Johan Kudahl, Frederik Otzen Bagger, Ole Winther, Ellis L Reinherz, Guang Lan Zhang and Vladimir Brusic

A computational method for identification of viral vaccine targets from protein regions of conserved HLA binding

Yung-Hao Wong, Chia-Chou Wu, Hsien-Yong Lai, Bo-Ren Jheng, Hsing-Yu Weng, Tzu-Hao Chang and Bor-Sen Chen.

Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data

Luke Vandewater, Vladimir Brusic, William Wilson, Lance Macaulay and Ping Zhang.

An Adaptive Genetic Algorithm for Selection of Blood-based Biomarkers for Prediction of Alzheimer’s Disease Progression

Fu-Jou Lai, Hong-Tsun Chang and Wei-Sheng Wu.

PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast

Duleepa Jayasundara, Isaam Saeed, Bill C. Chang, Sen-Lin Tang and Saman K. Halgamuge.

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

Lee Kien Leow, Li-Lee Chew, Ving Ching Chong and Sarinder Kaur Dhillon.

Automated identification of copepods using digital image processing and artificial neural network

Kouichi Kimura and Asako Koike.

Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data

Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka and Kiyoshi Asai.

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