Volume 20 Supplement 2

Selected articles from the 17th Asia Pacific Bioinformatics Conference (APBC 2019): genomics

Research

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.

Wuhan, China14-16 January 2019

Edited by, David Sankoff, Guoliang Li, Louxin Zhang, Yi-Ping Phoebe Chen, Shaoliang Peng and Hong-Yu Zhang.

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MRCNN: a deep learning model for regression of genome-wide DNA methylation

Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence th...

Authors: Qi Tian, Jianxiao Zou, Jianxiong Tang, Yuan Fang, Zhongli Yu and Shicai Fan

Citation: BMC Genomics 2019 20(Suppl 2):192

Content type: Research Published on: 4 April 2019
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DeepHistone: a deep learning approach to predicting histone modifications

Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage....

Authors: Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv and Rui Jiang

Citation: BMC Genomics 2019 20(Suppl 2):193

Content type: Research Published on: 4 April 2019
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Signal enrichment with strain-level resolution in metagenomes using topological data analysis

A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of ...

Authors: Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu and Laxmi Parida

Citation: BMC Genomics 2019 20(Suppl 2):194

Content type: Research Published on: 4 April 2019
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A distance-type measure approach to the analysis of copy number variation in DNA sequencing data

The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years....

Authors: Bipasa Biswas and Yinglei Lai

Citation: BMC Genomics 2019 20(Suppl 2):195

Content type: Research Published on: 4 April 2019
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Improving the sensitivity of long read overlap detection using grouped short k-mer matches

Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio seq...

Authors: Nan Du, Jiao Chen and Yanni Sun

Citation: BMC Genomics 2019 20(Suppl 2):190

Content type: Research Published on: 4 April 2019
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ENIGMA: an enterotype-like unigram mixture model for microbial association analysis

One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial comm...

Authors: Ko Abe, Masaaki Hirayama, Kinji Ohno and Teppei Shimamura

Citation: BMC Genomics 2019 20(Suppl 2):191

Content type: Research Published on: 4 April 2019
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TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection an...

Authors: Shaokun An, Liang Ma and Lin Wan

Citation: BMC Genomics 2019 20(Suppl 2):224

Content type: Research Published on: 4 April 2019
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Estimating the total genome length of a metagenomic sample using k-mers

Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the componen...

Authors: Kui Hua and Xuegong Zhang

Citation: BMC Genomics 2019 20(Suppl 2):183

Content type: Research Published on: 4 April 2019
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GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optim...

Authors: Shanshan Ren, Nauman Ahmed, Koen Bertels and Zaid Al-Ars

Citation: BMC Genomics 2019 20(Suppl 2):184

Content type: Research Published on: 4 April 2019
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Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis

Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence p...

Authors: Dongmei Ai, Xiaoxin Li, Hongfei Pan, Jiamin Chen, Jacob A. Cram and Li C. Xia

Citation: BMC Genomics 2019 20(Suppl 2):185

Content type: Research Published on: 4 April 2019
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Large-scale 3D chromatin reconstruction from chromosomal contacts

Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible i...

Authors: Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng and Shuaicheng Li

Citation: BMC Genomics 2019 20(Suppl 2):186

Content type: Research Published on: 4 April 2019
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Meta-network: optimized species-species network analysis for microbial communities

The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data min...

Authors: Pengshuo Yang, Shaojun Yu, Lin Cheng and Kang Ning

Citation: BMC Genomics 2019 20(Suppl 2):187

Content type: Research Published on: 4 April 2019
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Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues

Epigenome is highly dynamic during the early stages of embryonic development. Epigenetic modifications provide the necessary regulation for lineage specification and enable the maintenance of cellular identity...

Authors: Xia Zhang, Yanglan Gan, Guobing Zou, Jihong Guan and Shuigeng Zhou

Citation: BMC Genomics 2019 20(Suppl 2):221

Content type: Research Published on: 4 April 2019
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A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side

Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNP...

Authors: Sungjoon Park, Minsu Kim, Seokjun Seo, Seungwan Hong, Kyoohyung Han, Keewoo Lee, Jung Hee Cheon and Sun Kim

Citation: BMC Genomics 2019 20(Suppl 2):188

Content type: Research Published on: 4 April 2019
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Microbiota in the apical root canal system of tooth with apical periodontitis

Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as w...

Authors: Wenhao Qian, Ting Ma, Mao Ye, Zhiyao Li, Yuanhua Liu and Pei Hao

Citation: BMC Genomics 2019 20(Suppl 2):189

Content type: Research Published on: 4 April 2019
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Selected articles from the 17th Asia Pacific Bioinformatics Conference (APBC 2019): genomics

Research

MRCNN: a deep learning model for regression of genome-wide DNA methylation

DeepHistone: a deep learning approach to predicting histone modifications

Signal enrichment with strain-level resolution in metagenomes using topological data analysis

A distance-type measure approach to the analysis of copy number variation in DNA sequencing data

Improving the sensitivity of long read overlap detection using grouped short k-mer matches

ENIGMA: an enterotype-like unigram mixture model for microbial association analysis

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

Estimating the total genome length of a metagenomic sample using k-mers

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis

Large-scale 3D chromatin reconstruction from chromosomal contacts

Meta-network: optimized species-species network analysis for microbial communities

Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side

Microbiota in the apical root canal system of tooth with apical periodontitis

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