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

APBC Online Conference - Day I (Aug. 18th, 2020)

09:00-09:20 Offline Registration
09:20-09:30 Opening Remarks
09:30-10:10 Keynote Speech
Systems metabolic engineering for sustainability and good health
Sang Yup Lee (KAIST)
Session 1 Phylogenetics and Evolutionary Biology (Session chair: Chungoo Park)
10:10-10:20 Exact Median-tree Inference for Unrooted Reconciliation Costs
Pawel Gorecki, Alexey Markin and Oliver Eulenstein
10:20-10:30 A Generalized Robinson-Foulds Distance for Labeled Trees
Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond and Gabriela Lobinska
10:30-10:40 Minimizing Genomic Duplication Episodes
Jarosław Paszek, Jerzy Tiuryn and Pawel Gorecki
10:40-10:50 Computing the distribution of the Robinson-Foulds distance
Maryam Hayati and Leonid Chindelevitch
10:50-11:00 Summary and Q&A
Session Chair
Session 2 RNA Analysis (Session chair: Daehyun Baek)
11:00-11:10 Predicting Novel CircRNA-Disease Associations Based on Random Walk and Logistic Regression Model
Yulian Ding, Bolin Chen, Xiujuan Lei, Bo Liao and Fangxiang Wu
11:10-11:20 MicroRNA-disease association prediction by matrix tri-factorization
Huiran Li, Yin Guo, Menglan Cai and Limin Li
11:20-11:30 Inferring LncRNA-disease Associations Based On Graph Autoencoder Matrix Completion
Wei Lan, Ximin Wu, Qingfeng Chen, Wei Peng, Jin Liu and Jianxin Wang
11:30-11:40 Predicting miRNA-disease associations using a hybrid feature representation in the heterogeneous network
Minghui Liu, Jingyi Yang, Jiacheng Wang and Lei Deng
11:40-11:50 Summary and Q&A
Session Chair

Break (12:00-13:00, Lunch at offline conference)

Session 3 Sequence Analysis I (Session chair: Murim Choi)
13:00-13:10 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
13:10-13:20 Hierarchical structured Component Analysis for Microbiome Data Using Taxonomy Assignments
Nayeon Kang, Sun Ah Kim and Taesung Park
13:20-13:30 MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
Benjamin Albrecht, Caner Bagci and Daniel Huson
13:30-13:40 DCHap: A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data
Yanbo Li and Yu Lin
13:40-13:50 GPU Acceleration of Darwin Read Overlapper for de Novo Assembly of Long DNA Reads
Nauman Ahmed, Tong Dong, Koen Bertels and Zaid Al-Ars
13:50-14:00 Summary and Q&A
Session Chair
Session 4 Sequence Analysis II (Session chair: Murim Choi)
14:10-14:20 SETE: Sequence-based ensemble learning approach for TCR epitope binding prediction
Yao Tong, Tian Zheng, Xuanping Zhang and Jiayin Wang
14:20-14:30 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
14:30-14:40 Optimizing Performance of GATK Workflows Using Apache Arrow In-Memory Data Framework
Tanveer Ahmad
14:40-14:50 Fully automated web-based tool identifying regulatory hotspots
Ju Hun Choi, Taegun Kim, Junghyun Jung and Jong Wha J Joo
14:50-15:00 DeepMutation: A Hybrid Deep Neural Network for Accurate Variant Pathogenicity Prediction
Hongfei Cui, Shaoming Song, Rui Jiang and Mingxin Gan
15:00-15:10 Summary and Q&A
Session Chair

Break (15:10-15:30, Coffee break at offline conference)

Session 5 Cancer Informatics I (Session chair: Kwoneel Kim)
15:30-15:40 A Graph-Based Multi-Sample Test for Identifying Pathways Associated with Cancer Progression
Qingyang Zhang, Ghadeer Mahdi and Hao Chen
15:40-15:50 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
15:50-16:00 Pan-cancer analysis of differential DNA methylation patterns
Mai Shi, Stephen Kwok-Wing Tsui, Hao Wu and Ying-Ying Wei
16:00-16:10 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
16:10-16:20 Summary and Q&A
Session Chair
Session 6 Cancer Informatics II (Session chair: Kwoneel Kim)
16:20-16:30 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
16:30-16:40 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
16:40-16:50 Improving Lung Cancer Risk Stratification Leveraging Whole Transcriptome RNA Sequencing and Machine Learning across Multiple Cohorts
Yoonha Choi, Jing Huang and Jianghan Qu
16:50-17:00 A new approach to deriving prognostic gene pairs from cancer patient-specific gene correlation networks
Byungkyu Park, Wook Lee and Kyungsook Han
17:00-17:10 Summary and Q&A
Session Chair

Break (17:10-17:30, Coffe break at offline conference)

17:30-18:30 Tutorial: AI and Network Bioinformatics for Multi-Omics Data Analysis
Sun Kim (SNUH), Inuk Jung (KNU)

APBC Online Conference - Day II (Aug. 19th, 2020)

09:00-09:30 Offline Registration
09:30-10:10 Keynote Speech
Accelerating Drug Discovery with an AI-Based Virtual Human System CODA
Doheon Lee (KAIST)
Session 7 Single Cell analysis (Session chair: Semin Lee)
10:10-10:20 Effective single-cell clustering through ensemble feature selection and similarity measurements
Hyundoo Jeong and Navadon Khunlertgit
10:20-10:30 I-Impute: a self-consistent strategy to impute single cell RNA sequencing data
Xikang Feng, Lingxi Chen, Zishuai Wang and Shuai Cheng Li
10:30-10:40 EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes
Xiaoyang Chen, Shengquan Chen and Rui Jiang
10:40-10:50 Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation
Ah-Jung Jeon and Greg Tucker-Kellogg
10:50-11:00 Summary and Q&A
Session Chair
Session 8 Multi-omics analysis (Session chair: Semin Lee)
11:00-11:10 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
11:10-11:20 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
11:20-11:30 A consensus multi-view multi-objective gene selection approach for improved sample classification
Sudipta Acharya, Laizhong Cui and Yi Pan
11:30-11:40 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
11:40-11:50 Summary and Q&A
Session Chair

Break (12:00-13:00, Lunch at offline conference)

Session 9 Protein Informatics I (Session chair: Dongsup Kim)
13:00-13:10 Twadn: An efficient alignment algorithm based on time warping for pairwise dynamic networks
Jialu Hu, Yuanke Zhong, Junhao He and Xuequn Shang
13:10-13:20 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
13:20-13:30 Explicit Representation of Protein Activity States Significantly Improves Causal Discovery of Protein Phosphorylation Networks
Jinling Liu, Xiaojun Ma, Greg Cooper and Xinghua Lu
13:30-13:40 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
13:40-13:50 protein2vec: Predicting Protein-Protein Interactions Based on LSTM
Man Zhu, Jiongmin Zhang and Ying Qian
13:50-14:00 Summary and Q&A
Session Chair
Session 10 Protein Informatics II (Session chair: Dongsup Kim)
14:10-14:20 Model-based clustering for flow and mass cytometry data with clinical information
Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura
14:20-14:30 Stage-specific Protein-domain Mutational Profile of Invasive Ductal Breast Cancer
Ting Yu, Kwok Pui Choi, Ee Sin Chen and Louxin Zhang
14:30-14:40 Computationally Identifying Hot Spots in Protein-DNA Binding Interfaces Using an Ensemble Approach
Yuliang Pan, Jihong Guan and Shuigeng Zhou
14:40-14:50 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
14:50-15:00 Sequence-based projection neighborhood non-negative matrix factorization for virus-human protein interaction prediction
Yingjun Ma, Piao Zou, Tingting He and Xingpeng Jiang
15:00-15:10 Summary and Q&A
Session Chair

Break (15:10-15:30, Coffee break at offline conference)

Session 11 Drug Development Analysis (Session chair: Hojung Nam)
15:30-15:40 hERG-Att: Self-Attention-Based Deep Neural Network for Predicting hERG Blockers
Hyunho Kim and Hojung Nam
15:40-15:50 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
15:50-16:00 NEDD: a network embedding based method for predicting drug-disease associations
Renyi Zhou, Zhangli Lu, Huimin Luo, Min Zeng and Min Li
16:00-16:10 DBCSMOTE: a clustering-based oversampling technique for data imbalance in warfarin dose prediction
Yanyun Tao, Yuzhen Zhang and Bin Jiang
16:10-16:20 Summary and Q&A
Session Chair
Session 12 Image analysis and Information Extraction (Session chair: Hyunjoo Lee)
16:20-16:30 A Scalable Embedding based Neural Network Method for Discovering Knowledge from Biomedical Literature
Shengtian Sang, Xiaoxia Liu, Xiaoyu Chen and Di Zhao
16:30-16:40 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
16:40-16:50 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
16:50-17:00 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
17:00-17:10 Biomedical document triage using a hierarchical attention-based capsule network
Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and Yijia Zhang
17:10-17:20 Summary and Q&A
Session Chair

Closing Remarks

BIOINFO 2020 - Joint conference with APBC 202 - Day III (Aug. 20th, 2020)

The 16th International Conference on Bioinformatics (APBC/BIOINFO 2020)