Annually, through InCoB recognizes deserving students or researchers alike for their best paper and poster submission and travel fellowship. Through special event, APBioNet rewards their deserving ExCo and members in Lifelong Service Awards and Meritorious Service Awards. Generally, this special awards are upon recommendation by ExCo members.

InCoB Best Paper/Poster

2023:

Tong Si, Zackary Hopkins, John Yanev, Jie Hou and Haijun Gong
sc-fGAIN: An f-divergence-based Generative Adversarial Imputation Method for scRNA-sq Data Analysis

 

Omer Alkhnbashi, Sven Hauns and Rolf Backofen
Deepdefense: Automatic annotation and classification of immune systems in prokaryotes using Deep Learning

2020:

Hao Jia, Sung-Joon Park, Kenta Nakai
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.

Akila Surendran, C. Forbes Dewey, Jr., Boon Chuan Low, Lisa Tucker-Kellogg
A computational model of mutual antagonism in the mechano-signaling network of RhoA and nitric oxide.

Amish Kumar, Gitanjali Yadav
Shared ancestry of core-histone subunits and non-histone plant proteins containing the histone fold motif (hfm).

Yueh-Hua Tu, Hsueh-Fen Juan, Hsuan-Cheng Huang
Identification of cell states using super-enhancer RNA.

Ling Wan, Justin Song, Virginia He, Yongqun He
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis.

2017:

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.

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

2016:

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.

2015:

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
Privacy-preserving search for chemical compound databases.

InCoB Travel Fellowship

2023:

Bhavika Berwal
Nela Pragathi Sneha
Anuja Jain
Aparna Anandan
Yamuna Annadurai
Navya Tyagi
Halimat Atanda
Achala Shenali Fernando Vitharanage
Namrata Bhattacharya

2019:

Debangana Chakravorty
Abhirupa Ghosh
Sudipto Bhattacharjee
Hendrick Gao Min Lim
Taiyun Kim
Yue Cao
Jacob Bradford

2018:

Shuhaila binti Mat Sharani
Chong Li Chuin
Ashish Kumar Agrahari
Nikita Poddar
Bharati Pandey
Rakesh Trivedi
Tan Hui Ming
Jaamuna A/P Gnanaserkhar
Shakti Darsshini A/P Kamalanathan

2017:

Fatemeh Abbasi
Huaming Chen
Yuansheng Liu
Lim Wan Ching
Herty Liany
Joel Low Zi-Bin
Xin Wang
Li Liu
KyoungYeul Lee
Nikhil Pathak
Truong Cong Doan
Shaogui Wu
Koh Ling Li

2016:

Snehal Dilip Karpe
Ting-wen Chen
Vaishali Parag Waman
K.Praveen Kumar
Ruban Durairaj. D
Onkar Singh
Neha Bhardwaj
Abhishek Subramanian
Chaowang Lan

2015:

Ugur Sezerman
Tan Swan
Renhua Song
Jingren
Garima Singh
Ching Yee Lau
Chieh Hua Lin
Chia Chun Chiu
Cheng Sheng Zhu