APBC2021: The 19th Asia Pacific Bioinformatics Conference

Conference Program

February 3,2021(wednesday)

Time*

Event

8:00-9:00

Registration

9:00-9:10

Opening Remarks

9:10-10:00

Moderator : Dr. Sunny Sun (Institute of Molecular Medicine, NCKU)

Keynote 1
The role of artificial intelligence in rare disease research
Dr. Fumihiko Matsuda
(Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Japan)

10:00-10:10

Coffee Break

10:10-12:10

Session 1: Population genetics & evolutionary genomics

Moderator : Dr. Chao-Li Huang (Institute of Tropical Plant Sciences and Microbiology, NCKU)

10:10	A Common Methodological Phylogenomics Framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones Filippo Utro (IBM Research, United States)
10:25	Correlating Twitter Sentiments with COVID-19: A Tale of Three North American Cities Andrew Fisher (Lakehead University, Canada)
10:40	Identifying health related occupations of Twitter Users through word embedding and deep neural networks Gautam Srivastava (Brandon University, Canada)
10:55	Alternative splicing plays key roles in response to stress across different stages of fighting in the fish Betta splendens Vu Trieu-Duc (Kitasato University, Japan)
11:10	Identification of fish species through tRNA-based primer design Tun-Wen Pai (National Taipei University of Technology, Taiwan)
11:25	Maximum Parsimony Reconciliation in the DTLOR Model Ran Libeskind-Hadas (Harvey Mudd College, USA)
11:40	Development and validation of an expanded targeted sequencing panel for noninvasive prenatal diagnosis of sporadic skeletal dysplasia Yen An Tang (National Cheng Kung University, Taiwan)

12:10-13:00

Lunch Seminar
A Platform for Heterogeneous Bioinformatics Workflows: Unprecedented Innovation to Tackle the Challenges of Large-Scale Genomics
Atgenomix

13:00-15:00

Session 2: Sequencing technologies and genome analysis

Moderator : Dr. Yen An Tang (Institute of Molecular Medicine, NCKU)

13:00	A tool for analyzing and visualizing ribosome profiling data at the isoform level Joseph T. Tseng (National Cheng Kung University, Taiwan)
13:15	SCYN: Single cell CNV profiling method using dynamic programming Xikang Feng (Northwestern Polytechnical University, China)
13:30	Genome-wide identification of associations between enhancer and alternative splicing in human and mouse Huai-Kuang Tsai (Institute of Information Science, Academia Sinica, Taiwan)
13:45	XGBCDA: A multiple heterogeneous networks-based method for predicting circRNA-disease associations Shensi Yuan (Xinjiang University, China)
14:00	CircVIS: A platform for circRNA visual presentation Kuei-Yang Hsiao (National Chung Hsing University, Taiwan)
14:15	Efficient Assembly Consensus Algorithms for Divergent Contig Sets Annie Chateau (Montpellier University, France)
14:30	Inferring gene regulatory network from single-cell transcriptomic data by integrating multiple prior networks Yanglan Gan (Donghua University, China)

15:00-15:10

Coffee Break

15:10-17:10

Session 3: Epigenetics & RNA Analysis

Moderator : Dr. Tsung-lin Liu (Department of Biotechnology and Bioindustry Sciences, NCKU)

15:10	Deep neural network models for cell type prediction based on single-cell Hi-C data Bing Zhou (Northwest A&F University , China)
15:25	Velo-Predictor: An Ensemble Learning Pipeline for RNA Velocity Prediction Xin Wang (Shanghaitech University, China)
15:40	Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states Jia-Hsin Huang (National Institute for Basic Biology, Japan)
15:55	Stratification of lncRNA modulation networks in breast cancer Wen-Hsuan Yu (National Taiwan University, Taiwan)
16:10	Gene Expression Analysis of Combined RNA-seq Experiments Using a Receiver Operating Characteristic Calibrated Procedure Shuen-Lin Jeng (National Cheng Kung University, Taiwan)
16:25	MultiSourcCFS:Inferring circRNA functional similarity based on?multiple data sources Liang Shu (Central South University, China)
16:40	An extensive examination of discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters using machine learning based approaches Nguyen Trinh Trung Duong (Yuan Ze University, Taiwan)

February 4,2021(Thursday)

Time*

Event

9:00-9:10

Network preparation

9:10-10:00

Moderator : Dr. Wen-Lian Hsu (Institute of Information Science, Academia Sinica)

Keynote 2
Text Mining for Biomedical Applications
Dr. Sophia Ananiadou
(Computer Science, University of Manchester & National Centre for Text Mining, UK)

10:00-10:10

Coffee Break

10:10-12:10

Session 4: AI applications in biomedicine

Moderator : Dr. Hsueh-Fen Juan (Department of Life Science, NTU)

10:10	Gene Expression Data Classification Using Topology and Machine Learning Models Soham Mukherjee (Purdue University, USA)
10:25	Predicting subcellular location of protein with evolution information and sequence-based deep learning Jijun Tang (University of South Carolina, USA)
10:40	Predicting family physicians based on their practice using machine learning Arunim Garg (Lakehead University, Canada)
10:55	Deep learning and multi-omics approach to predict drug responses in cancer Wang Conghao (Nanynag Technological University, Singapore)
11:10	Pattern recognition of Topology Association Domain using Deep Learning Jia-Ming Chang (National Chengchi University, Taiwan)
11:25	Ensemble learning for predicting ex vivo human placental barrier permeability Chun-Wei Tung (Taipei Medical University, Taiwan)
11:40	GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs Anuradha Wickramarachchi (Australian National University, Australia)

12:10-13:00

Lunch Seminar
Illumina DRAGEN Bio-IT Platform - best-in-class accuracy, speeds and scalability
Genetech Biotech Co., Ltd.

13:00-15:00

Session 5: Bioimaging & Health informatics

Moderator : Dr. Hsuan-Cheng Huang (Institute of BioMedical Informatics, YMU)

13:00	Learning Semi-Supervised Enrichment of Longitudinal Imaging-Genetic Data for Improved Prediction of Cognitive Decline Hoon Seo (Colorado School of Mines, USA)
13:15	Pyramid Focusing Network for mutation prediction and classification in CT images Xukun Zhang (East China Normal University, China)
13:30	A clinical, genetic and image-aided computational model to infer the development of Alzheimer's disease spectrum Fan Zhu (Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , China)
13:45	Inferring miRNA-disease associations using collaborative filtering and resource allocation on a tripartite graph Van Tinh Nguyen (Hanoi University of Industry, Vietnam)
14:00	MitoTox: a comprehensive mitochondrial toxicity database An-Chi Wei (National Taiwan University, Taiwan)
14:15	Resting state functional connectivity analysis during general anesthesia: A high-density EEG study Ling Zou (Changzhou University, China)
14:30	Classification of microRNA Disease Association Based on k-mer Sequence Representation Only Malik Yousef (Zefat Academic College, Israel)

15:00-15:10

Coffee Break

15:10-17:10

Session 6: Data mining

Moderator : Dr. Paul Horton (Department of Computer Science and Information Eng., NCKU)

15:10	Deep GONet: Self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data Victoria Bourgeais (Universite Evry, Universite Paris-Saclay, France)
15:25	The Protein-Protein Interaction Ontology: for Better Representing and Capturing the Biological Context of Protein Interaction Mansheng Li (Beijing Proteome Research Center, China)
15:40	Mining a Stroke Knowledge Graph from literature Xi Yang (Natinal University of Defense Technology, China)
15:55	A Tag Based Joint Extraction Model for Chinese Medical Text XingYu Liu (Beijing University of Aeronautics and Astronautics, China)
16:10	An aggregation method to identify the RNA meta-stable secondary structure and its functionally interpretable structure ensemble Tzu-Hsien Yang (National University of Kaohsiung, Taiwan)
16:25	A Clinical Dataset and Various Baselines for Chromosome Instance Segmentation Runhua Huang (South China Normal University, China)
16:40	CoMI: Consensus Mutual Information for Tissue-specific Gene Signatures Sing-Han Huang (National Chiao Tung University, Taiwan)

February 5,2021(Friday)

Time*

Event

9:00-9:10

Network preparation

9:10-10:00

Moderator : Dr. Shaw-Jenq Tsai (Department of Physiology, NCKU)

Keynote 3
Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression
Dr.Yu-Ju Chen
(Institute of Chemistry, Academia Sinica, Taiwan)

10:00-10:10

Coffee Break

10:10-12:10

Session 7: Network biology & Drug Development

Moderator : Dr. Yu-Fan Liu (Department of Biomedical Science, CSMU)

10:10	DeepSIRT: A Deep Neural Network for Identification of Sirtuin Targets and their Subcellular Localizations Yu-Yen Ou (Yuan Ze University, Taiwan)
10:25	Pharmacophore anchor models of ATAT1 to discover potential inhibitors and lead optimization Nung-Yu Hsu (National Chiao-Tung University, Taiwan)
10:40	SPP-CPI: Predicting Compound–Protein Interactions Based on Neural Networks Xuelian Li (East China Normal University, China)
10:55	Estimation of important binding sites in compounds that interact with proteins Kouhei Tachibana (Kobe University, Japan)
11:10	Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach: assessment of solidity on diverse set of preparations Xue Zhu (Huazhong University of Science and Technology, China)
11:25	Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction Shuai Lu (Zhengzhou University, China)
11:40	GRAde: a long-read sequencing approach to efficiently identify the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid remediable aldosteronism Chia-Lang Hsu (National Taiwan University Hospital, Taiwan)

12:10-13:00

Lunch Seminar
全球疫情帶來的醫藥產業新秩序—數據為王、有「它」就強！
VtR Incorporated

13:00-15:00

Session 8: Cancer Genomics and informatics

Moderator : Dr. Liang-Yi Hung (Department of Biotechnology and Bioindustry Sciences, NCKU)

13:00	LCMD: Lung Cancer Metabolome Database Hsin-Yi Wu (National Taiwan University, Taiwan)
13:15	Modular signature of long non-coding RNA association networks as a prognostic biomarker in lung cancer Albert Li (National Taiwan University, Taiwan)
13:30	A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients Ka-Lok Ng (Asia University, Taiwan)
13:45	Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways Po-Wen Wang (National Chiao Tung University, Taiwan)
14:00	MD-UNET: Multi-input Dilated U-shape Neural Network for Segmenta-tion of Bladder Cancer Ruiquan Ge (Hangzhou Dianzi University, China)
14:15	Identification of novel miRNA signature for estimating survival time in patients with head and neck squamous cell carcinomas Shinn-Ying Ho (National Chiao Tung University, Taiwan)
14:30	Constructing lncRNA-miRNA-mRNA networks specific to individual cancer patients and finding prognostic biomarkers Kyungsook Han (Inha University, Korea)

15:00-15:10

Coffee Break

15:10-17:10

Session 9: Multi-omics analysis

Moderator : Dr. Tsung Ming Chen (Department and of Graduate Institute of Aquaculture, NKUST)

15:10	Integrated OMICs approach for the group 1 protease mite-allergen of house dust mite Dermatophagoides microceras Yu-Fan Liu (Chung Shan Medical University, Taiwan)
15:25	Shaking the β-bulges Alexandre G. de Brevern (INSERM, France)
15:40	A New Family of Similarity Measures for Scoring Confidence of Protein Interactions using Gene Ontology Madhusudan Paul (Visva-Bharati , India)
15:55	Evaluation validation of a qPCR curve analysis method and conventional approaches Yashu Zhang (The Ocean University of China, China)
16:10	MultiTrans: a novel algorithm for transcriptome assembly through mixed integer linear programming Jin Zhao (Shandong University, China)
16:25	CirPred, the first structure modelling and linker design system for circularly-permuted proteins Wei-Cheng Lo (National Chiao Tung University, Taiwan)
16:40	METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs Zhenmiao Zhang (Hong Kong Baptist University, Hong Kong)

17:10-17:20

Closing Remark

* Taiwan Standard Time: GMT+8