Explanipedia

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups Open

Sungwon Jeon, Hansol Choi, Yeonsu Jeon, Whan-Hyuk Choi, Hyunjoo Choi , et al. · 2024

Background Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome–wide association …

Comparative analysis of repeat content in plant genomes, large and small Open

Joris Argentin, Dan Bolser, Paul Kersey, Paul Flicek · 2023

The DNA Features pipeline is the analysis pipeline at EMBL-EBI that annotates repeat elements, including transposable elements. With Ensembl’s goal to stay at the cutting edge of genome annotation, we proved that this pipeline needed an up…

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups Open

Sungwon Jeon, Hansol Choi, Yeonsu Jeon, Whan-Hyuk Choi, Hyunjoo Choi , et al. · 2022

We present 4,157 whole-genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest whole genomic resource of Koreans. Korea4K provides 45,537,252 variants and encompasses most of the common and rare variants in Ko…

LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads Open

Hui-Su Kim, Asta Blažytė, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim , et al. · 2022

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly, constructed using 57× nanopore long reads and polished using 47× short paired-end reads. We util…

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates Open

Sungwon Jeon, Asta Blažytė, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon , et al. · 2021

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates. Open

Sungwon Jeon, Asta Blažytė, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon , et al. · 2021

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potenti…

The Lithuanian reference genome LT1 - a human<i>de novo</i>genome assembly with short and long read sequence and Hi-C data Open

Hui-Su Kim, Asta Blažytė, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim , et al. · 2021

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 47× of short paired-end reads. We also uti…

Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing Open

Hak‐Min Kim, Sungwon Jeon, Oksung Chung, Je Hoon Jun, Hui-Su Kim , et al. · 2021

Background DNBSEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI using DNA nanoball and combinatorial probe anchor synthesis technologies to generate short reads at a very large scale—up to 60 human genomes per d…

Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling Open

Yeonsu Jeon, Sungwon Jeon, Asta Blažytė, Yeo Jin Kim, Jasmin Junseo Lee , et al. · 2021

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016…

Ethnicity-dependent allele frequencies are correlated with COVID-19 case fatality rate Open

Sungwon Jeon, Asta Blažytė, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon , et al. · 2020

Coronavirus disease (COVID-19), caused by SARS-CoV-2, has a higher case fatality rate (CFR) in European ethnic groups than in others, especially East Asians. One explanation to this phenomenon might be TMPRSS2, a key processing enzyme esse…

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research Open

Marcela K. Tello‐Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei , et al. · 2020

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open acces…

Efficient mutation screening for cervical cancers from circulating tumor DNA in blood Open

Sun‐Young Lee, Dong‐Kyu Chae, Sung-Hun Lee, Yohan Lim, Jahyun An , et al. · 2020

Ethnicity-dependent allele frequencies are correlated with COVID-19 case fatality rate Open

Sungwon Jeon, Asta Blažytė, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon , et al. · 2020

Coronavirus disease (COVID-19), caused by SARS-CoV-2, has a higher case fatality rate (CFR) in European ethnic groups than in others, especially East Asians. One explanation to this phenomenon might be TMPRSS2, a key processing enzyme esse…

Korean Genome Project: 1094 Korean personal genomes with clinical information Open

Sungwon Jeon, Youngjune Bhak, Yeonsong Choi, Yeonsu Jeon, Seunghoon Kim , et al. · 2020

The initial phase of the Korean Genome Project (Korea1K) releases 1094 whole genomes, along with data of 79 clinical traits.

Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing Open

Hak‐Min Kim, Sungwon Jeon, Oksung Chung, Je Hoon Jun, Hui-Su Kim , et al. · 2020

Background MGISEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI utilizing DNA nanoball and combinatorial probe anchor synthesis technologies for generating short reads at a very large scale – up to 60 human geno…

Decoding a highly mixed Kazakh genome Open

Madina Seidualy, Asta Blažytė, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon , et al. · 2020

Additional file 1 of Efficient mutation screening for cervical cancers from circulating tumor DNA in blood Open

Sun-Young Lee, Dong‐Kyu Chae, Sung-Hun Lee, Yohan Lim, Jahyun An , et al. · 2020

Additional file 1: Supplementary Table 1. The list of genetic variants at baseline.

Ensembl Genomes 2020—enabling non-vertebrate genomic research Open

Kevin Howe, Bruno Contreras‐Moreira, Nishadi De Silva, G. Maslen, Wasiu Akanni , et al. · 2019

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.e…

Gramene 2018: unifying comparative genomics and pathway resources for plant research Open

Marcela K. Tello‐Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell , et al. · 2017

This FAIRsharing record describes: Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of…

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species Open

Paul Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu , et al. · 2017

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). To…

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Open

Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao‐Qi Zhang, Roberto A. Barrero , et al. · 2017

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations Open

Bernardo Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil , et al. · 2017

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have gener…

A chromosome conformation capture ordered sequence of the barley genome Open

Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven Twardziok , et al. · 2017

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations Open

Bernardo Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil , et al. · 2016

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have gener…

Navigating the research data life cycle Open

Philippa C. Griffin, R. Appels, Dieter Bulach, Kevin J. Dudley, Gabriel Keeble‐Gagnère , et al. · 2016

transPLANT Resources for Triticeae Genomic Data Open

M. Spannagl, Michaël Alaux, Matthias Lange, Dan Bolser, Kai Christian Bader , et al. · 2015

The genome sequences of many important Triticeae species, including bread wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploi…

Ensembl Genomes 2016: more genomes, more complexity Open

Paul Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt , et al. · 2015

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.e…

Gramene 2016: comparative plant genomics and pathway resources Open

Marcela K. Tello‐Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson , et al. · 2015

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archi…

Tools and data services registry: a community effort to document bioinformatics resources Open

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza , et al. · 2015

This FAIRsharing record describes: bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.

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