APBC2020

The 18th Asia Pacific Bioinformatics Conference

Postponed to 18th (Tue) - 20th (Thu) August, 2020 (final) | Samjung Hotel, Seoul, Korea
Gangnam district Night view of Seoul K-pop band Twice Apgujeong Rodeo Street

Conference Program

Day 1: Aug. 18th, 2020
09:00 - 09:30 Registration
Hall Adonis Geranium
Tutorial Tutorial 1 (link) Tutorial 2 (link)
9:30 - 12:00 AI and Network Bioinformatics for Multi-omics Data Analysis
Sun Kim (Seoul National University), Inuk Jung (Kyunpook National University)
Scalable single cell RNA-seq analysis on the cloud
Joshua Ho , Xiunan Fang, Gordon Qian (University of Hong Kong)
12:00 - 13:00 Lunch(Adonis)
13:00 - 13:10 Opening Remarks (Adonis)
Parallel Session Protein Informatics I Single cell analysis
13:10 - 13:35 Twadn: An efficient alignment algorithm based on time warping for pairwise dynamic networks
Jialu Hu, Yuanke Zhong, Junhao He and Xuequn Shang
Effective single-cell clustering through ensemble feature selection and similarity measurements
Hyundoo Jeong and Navadon Khunlertgit
13:35 - 14:00 TNFPred: Identifying tumor necrosis factors using hybrid features based on word embeddings
Trinh-Trung-Duong Nguyen, Yu-Yen Ou, Nguyen-Quoc-Khanh Le, Quang-Thai Ho and Dinh-Van Phan
I-Impute: a self-consistent strategy to impute single cell RNA sequencing data
Xikang Feng, Lingxi Chen, Zishuai Wang and Shuai Cheng Li
14:00 - 14:25 Explicit Representation of Protein Activity States Significantly Improves Causal Discovery of Protein Phosphorylation Networks
Jinling Liu, Xiaojun Ma, Greg Cooper and Xinghua Lu
EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes
Xiaoyang Chen, Shengquan Chen and Rui Jiang
14:25 - 14:50 ClusterM: A scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks
Yijie Wang, Hyundoo Jeong, Byung-Jun Yoon and Xiaoning Qian
Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation
Ah-Jung Jeon and Greg Tucker-Kellogg
14:50 - 15:10 Coffe Break (Rosemary)
Parallel Session Protein Informatics II Drug Development and Analysis
15:10 - 15:35 Model-based clustering for flow and mass cytometry data with clinical information
Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura
hERG-Att: Self-Attention-Based Deep Neural Network for Predicting hERG Blockers
Hyunho Kim and Hojung Nam
15:35 - 16:00 Stage-specific Protein-domain Mutational Profile of Invasive Ductal Breast Cancer
Ting Yu, Kwok Pui Choi, Ee Sin Chen and Louxin Zhang
A learning-based framework for drug-target interaction prediction based on feature representation learning and deep neural network
Jiajie Peng, Jingyi Li and Xuequn Shang
16:00 - 16:25 Computationally Identifying Hot Spots in Protein-DNA Binding Interfaces Using an Ensemble Approach
Yuliang Pan, Jihong Guan and Shuigeng Zhou
NEDD: a network embedding based method for predicting drug-disease associations
Renyi Zhou, Zhangli Lu, Huimin Luo, Min Zeng and Min Li
16:25 - 16:50 Prediction of hot spots in protein–DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting
Li Ke, Zhang Sijia and Xia Junfeng
DBCSMOTE: a clustering-based oversampling technique for data imbalance in warfarin dose prediction
Yanyun Tao, Yuzhen Zhang and Bin Jiang
16:50 - 17:10 Coffe Break(Rosemary)
17:10 - 18:10 Keynote Speech (Adonis)
Title: TBA
Sang Yup Lee (KAIST)
Session Chair: TBA
18:10 - 18:30 Poster Session(Rosemary)



Day 2: Aug. 19th, 2020
09:00 - 09:30 Registration
Hall Adonis Geranium
09:30 - 10:30 Keynote Speech (Adonis)
"Gene network reconstruction using single cell transcriptomic data reveals condition specific regulators"
Kyoung Jae Won (Copenhagen, BRIC)
Session Chair: TBA
10:30 - 10:45 Coffe Break(Rosemary)
Parallel Session Cancer informatics I Sequence analysis I
10:45 - 11:10 A Graph-Based Multi-Sample Test for Identifying Pathways Associated with Cancer Progression
Qingyang Zhang, Ghadeer Mahdi and Hao Chen
DCHap: A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data
Yanbo Li and Yu Lin
11:10 - 11:35 Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme
Yujie You, Yujie Chen, Wanjing Lei, Tingting Li, Ming Xiao, Huiru Zheng and Le Zhang
A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model
Jiaqi Liu, Jiayin Wang, Daocheng Dai, Xuanping Zhang, Zhongmeng Zhao, Xin Lai, Xiaoyan Zhu, Juan Wang and Zhimin Li
11:35 - 12:00 Pan-cancer analysis of differential DNA methylation patterns
Mai Shi, Stephen Kwok-Wing Tsui, Hao Wu and Ying-Ying Wei
GPU Acceleration of Darwin Read Overlapper for de Novo Assembly of Long DNA Reads
Nauman Ahmed, Tong Dong, Koen Bertels and Zaid Al-Ars
12:00 - 13:30 Lunch(Adonis)
Parallel Session Cancer Informatics II Sequence analysis II
13:30 - 13:55 Genomic amplification of chromosome 20q13.33 is the earliest biomarker for the development of sporadic colorectal carcinoma
H. Sunny Sun, Vo-Minh-Hoang Bui, Clément Mettling and Jonathan Jou
Sequence-based projection neighborhood non-negative matrix factorization for virus-human protein interaction prediction
Yingjun Ma, Piao Zou, Tingting He and Xingpeng Jiang
13:55 - 14:20 Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening
Laura Moody, Hong Chen and Yuan-Xiang Pan
SETE: Sequence-based ensemble learning approach for TCR epitope binding prediction
Yao Tong, Tian Zheng, Xuanping Zhang and Jiayin Wang
14:20 - 14:45 Improving Lung Cancer Risk Stratification Leveraging Whole Transcriptome RNA Sequencing and Machine Learning across Multiple Cohorts
Yoonha Choi, Jing Huang and Jianghan Qu
Fully automated web-based tool identifying regulatory hotspots
Ju Hun Choi, Taegun Kim, Junghyun Jung and Jong Wha J Joo
14:45 - 15:10 A new approach to deriving prognostic gene pairs from cancer patient-specific gene correlation networks
Byungkyu Park, Wook Lee and Kyungsook Han
Optimizing Performance of GATK Workflows Using Apache Arrow In-Memory Data Framework
Tanveer Ahmad
15:10 - 15:30 Coffe Break(Rosemary)
Parallel Session RNA analysis
16:00 - 16:25 Predicting Novel CircRNA-Disease Associations Based on Random Walk and Logistic Regression Model
Yulian Ding, Bolin Chen, Xiujuan Lei, Bo Liao and Fangxiang Wu
16:25 - 16:50 MicroRNA-disease association prediction by matrix tri-factorization
Huiran Li, Yin Guo, Menglan Cai and Limin Li
16:50 - 17:15 Inferring LncRNA-disease Associations Based On Graph Autoencoder Matrix Completion
Wei Lan, Ximin Wu, Qingfeng Chen, Wei Peng, Jin Liu and Jianxin Wang
17:15 - 17:40 Predicting miRNA-disease associations using a hybrid feature representation in the heterogeneous network
Minghui Liu, Jingyi Yang, Jiacheng Wang and Lei Deng
18:00~ Banquet(Geranium)



Day 3: Aug. 20th, 2020
09:00 - 09:30 Registration
Hall Adonis Geranium
09:30 - 10:30 Keynote Speech (Adonis)
Presentation title: Accelerating Drug Discovery with an AI-Based Virtual Human System CODA
Doheon Lee (KAIST)
Session Chair: TBA
10:30 - 10:45 Coffe Break(Rosemary)
Parallel Session Multi-omics analysis Deep Learning
10:45 - 11:10 Integrated metabolomics and transcriptomics study of traditional herb AstragalusmembranaceusBge.var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients
Xueting Wu, Xuetong Li, Wei Wang, Yuanhong Shan, Cuiting Wang, Mulan Zhu, Qiong La, Yang Zhong, Ye Xu, Peng Nan and Xuan Li
A Scalable Embedding based Neural Network Method for Discovering Knowledge from Biomedical Literature
Shengtian Sang, Xiaoxia Liu, Xiaoyu Chen and Di Zhao
11:10 - 11:35 Multi-omics profiling reveals microRNA-mediated insulin signaling networks
Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng and Hsien-Da Huang
DeepMutation: A Hybrid Deep Neural Network for Accurate Variant Pathogenicity Prediction
Hongfei Cui, Shaoming Song, Rui Jiang and Mingxin Gan
11:35 - 12:00 A consensus multi-view multi-objective gene selection approach for improved sample classification
Sudipta Acharya, Laizhong Cui and Yi Pan
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication
Tzong-Yi Lee, Kai-Yao Huang, Cheng-Hsiang Chuang and Tzu-Hao Chang
12:00 - 13:00 Lunch (Adonis)
Parallel Session Biomedical Image analysis Phylogenetics and Evolutionary Biology
13:00 - 13:25 CIR-Net: Automatic Classification of Human Chromosome based on Inception-ResNet Architecture
Chengchuang Lin, Gansen Zhao, Zhirong Yang, Aihua Yin, Xinming Wang, Li Guo, Hanbiao Chen, Lei Zhao, Tianxing Wang, Bichao Ding, Xiongwen Pang, Ma Zhaohui and Qiren Chen
Exact Median-tree Inference for Unrooted Reconciliation Costs
Pawel Gorecki, Alexey Markin and Oliver Eulenstein
13:25 - 13:50 Spark-based parallel calculation of 3D Fourier shell correlation for macromolecule structure local resolution estimation
Yongchun Lu, Xiangrui Zeng, Xinhui Tian, Xiao Shi, Hui Wang, Xiaohui Zheng, Xiaodong Liu, Xiaofang Zhao, Xin Gao and Min Xu
A Generalized Robinson-Foulds Distance for Labeled Trees
Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond and Gabriela Lobinska
13:50 - 14:15 Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan
Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park and Dokyoon Kim
Minimizing Genomic Duplication Episodes
Jarosław Paszek, Jerzy Tiuryn and Pawel Gorecki
14:15 - 14:40
Computing the distribution of the Robinson-Foulds distance
Maryam Hayati and Leonid Chindelevitch
15:40 - 16:00 Coffe Break(Rosemary)
Parallel Session Metagenome and Microbiome Information Extraction
16:00 - 16:25 Evaluation of experimental protocols for shotgun whole-genome metagenomic discovery of antibiotic resistant genes
Ken Hung-On Yu, Xiunan Fang, Haobin Yao, Bond Ng, Tak Kwan Leung, Ling-Ling Wang, Chi Ho Lin, Agnes Sze Wah Chan, Wai Keung Leung, Suet Yi Leung and Joshua Wing Kei Ho
Biomedical document triage using a hierarchical attention-based capsule network
Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and Yijia Zhang
16:25 - 16:50 Hierarchical structured Component Analysis for Microbiome Data Using Taxonomy Assignments
Sun Ah Kim and Taesung Park
Identifying Pre-outbreak Signals of Hand, Foot and Mouth Disease Based on Landscape Dynamic Network Marker
Yongjun Li, Xuhang Zhang, Rong Xie, Yucong Pan, Rui Liu and Pei Chen
16:50 - 17:15 MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
Benjamin Albrecht, Caner Bagci and Daniel Huson
protein2vec: Predicting Protein-Protein Interactions Based on LSTM
Man Zhu, Jiongmin Zhang and Ying Qian
17:15-17:30 Award Ceremony
17:30-17:40 Closing Remarks