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MetaBase--the wiki-database of biological databases.
Dan M Bolser, Pierre-Yves Chibon, Nicolas Palopoli, Sungsam Gong, Daniel Jacob, Victoria Dominguez Del Angel, Dan Swan, Sebastian Bassi, Virginia González, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J Provart, Dave Clements, Daniel P Renfro, Daeui Bhak, Jong Bhak
Apr 16, 2019
Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the...
Decoding a highly mixed Kazakh genome.
Madina Seidualy, Asta Blazyte, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon, Jungeun Kim, Anders Eriksson, Dan Bolser, Changhan Yoon, Andrea Manica, Semin Lee, Jong Bhak
Feb 18, 2021
We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a...
Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates.
Sungwon Jeon, Asta Blazyte, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon, Youngjune Bhak, Dan Bolser, Andrea Manica, Eun-Seok Shin, Yun Sung Cho, Byung Chul Kim, Namhee Ryoo, Hansol Choi, Jong Bhak
Oct 31, 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....
allele frequency case fatality rate TMPRSS2 covid-19 SARS-CoV-2 Humans Serine Endopeptidases Mortality Gene Frequency Polymorphism Single Nucleotide Models Molecular Asian Continental Ancestry Group European Continental Ancestry Group Republic of Korea covid-19
Published by: Molecules and cells
Decoding a highly mixed Kazakh genome
Madina Seidualy, Asta Blazyte, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon, Jungeun Kim, Anders Eriksson, Dan Bolser, Changhan Yoon, Andrea Manica, Semin Lee, Jong Bhak
Jun 06, 2020
Abstract: We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis...
Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates.
Sungwon Jeon, Asta Blazyte, Changhan Yoon, Hyojung Ryu, Yeonsu Jeon, Youngjune Bhak, Dan Bolser, Andrea Manica, Eun-Seok Shin, Yun Sung Cho, Byung Chul Kim, Namhee Ryoo, Hansol Choi, Jong Bhak
Nov 09, 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....
Welfare Genome Project
Yeonsu Jeon, Sungwon Jeon, Asta Blazyte, Yeo Jin Kim, Jasmin Junseo Lee, Youngjune Bhak, Yun Sung Cho, Yeshin Park, Eui-Kyu Noh, Andrea Manica, Jeremy S. Edwards, Dan Bolser, Sukyeon Kim, Yuji Lee, Changhan Yoon, Semin Lee, Byung Chul Kim, Neung Hwa Park, Jong Bhak
Feb 23, 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...
Welfare Genome Project
Yeonsu Jeon, Sungwon Jeon, Asta Blazyte, Yeo Jin Kim, Jasmin Junseo Lee, Youngjune Bhak, Yun Sung Cho, Yeshin Park, Eui-Kyu Noh, Andrea Manica, Jeremy S Edwards, Dan Bolser, Sukyeon Kim, Yuji Lee, Changhan Yoon, Semin Lee, Byung Chul Kim, Neung Hwa Park, Jong Bhak
Mar 08, 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...
Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago.
Veronika Siska, Eppie Ruth Jones, Sungwon Jeon, Youngjune Bhak, Hak-Min Kim, Yun Sung Cho, Hyunho Kim, Kyusang Lee, Elizaveta Veselovskaya, Tatiana Balueva, Marcos Gallego-Llorente, Michael Hofreiter, Daniel G Bradley, Anders Eriksson, Ron Pinhasi, Jong Bhak, Andrea Manica
Mar 14, 2017
East Asia Russian Far East ancient genetics human population genetics Neolithic Archaeology DNA Mitochondrial Asia Eastern Genome Human Genotype Guanine Nucleotide Exchange Factors Humans Phenotype Polymorphism Single Nucleotide principal component analysis Receptors Ectodysplasin Ubiquitin-Protein Ligases
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information.
Hui-Su Kim, Sungwon Jeon, Changjae Kim, Yeon Kyung Kim, Yun Sung Cho, Jungeun Kim, Asta Blazyte, Andrea Manica, Semin Lee, Jong Bhak
Jan 02, 2020
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information.
Hui-Su Kim, Sungwon Jeon, Changjae Kim, Yeon Kyung Kim, Yun Sung Cho, Jungeun Kim, Asta Blazyte, Andrea Manica, Semin Lee, Jong Bhak
Jan 06, 2020
BACKGROUND:Long DNA reads produced by single-molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short-read DNA fragments. For de novo assembly, Pacific Biosciences (PacBio)...
A protein domain interaction interface database
Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak
Apr 16, 2019
BACKGROUND: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational...
The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.
Hak-Min Kim, Jessica A Weber, Nayoung Lee, Seung Gu Park, Yun Sung Cho, Youngjune Bhak, Nayun Lee, Yeonsu Jeon, Sungwon Jeon, Victor Luria, Amir Karger, Marc W Kirschner, Ye Jin Jo, Seonock Woo, Kyoungsoon Shin, Oksung Chung, Jae-Chun Ryu, Hyung-Soon Yim, Jung-Hyun Lee, Jeremy S Edwards, Andrea Manica, Jong Bhak, Seungshic Yum
Apr 16, 2019
BACKGROUND: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class...
Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent.
Marcos Gallego Llorente, Eppie Jones, Anders Eriksson, Veronika Siska, KW Arthur, JW Arthur, MC Curtis, Jay Stock, M Coltorti, P Pieruccini, S Stretton, F Brock, T Higham, Y Park, M Hofreiter, DG Bradley, J Bhak, R Pinhasi, Andrea Manica
Dec 04, 2015
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many...
Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.
Soonok Kim, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, JeHoon Jun, HyeJin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee, Jeremy S Edwards, Jessica A Weber, Jo Cook, Sangsoo Kim, Hang Lee, Andrea Manica, Ilbeum Lee, Stephen J O'Brien, Jong Bhak, Joo-Hong Yeo
Aug 16, 2017
BACKGROUND: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent...
Corrigendum
Yun Sung Cho, Hyunho Kim, Hak-Min Kim, Sungwoong Jho, JeHoon Jun, Yong Joo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S Edwards, Semin Lee, Byung Chul Kim, Andrea Manica, Tae-Kwang Oh, George M Church, Jong Bhak
Feb 13, 2019
This corrects the article DOI: 10.1038/ncomms13637.
Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.
Muhammad Ilyas, Jong-Soo Kim, Jesse Cooper, Young-Ah Shin, Hak-Min Kim, Yun Sung Cho, Seungwoo Hwang, Hyunho Kim, Jaewoo Moon, Oksung Chung, JeHoon Jun, Achal Rastogi, Sanghoon Song, Junsu Ko, Andrea Manica, Ziaur Rahman, Tayyab Husnain, Jong Bhak
Sep 29, 2016
BACKGROUND: Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region...
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.
M Aranda, Y Li, YJ Liew, S Baumgarten, O Simakov, MC Wilson, J Piel, H Ashoor, S Bougouffa, VB Bajic, T Ryu, T Ravasi, T Bayer, G Micklem, H Kim, J Bhak, TC LaJeunesse, CR Voolstra
Aug 01, 2018
Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often...
Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent.
M Gallego Llorente, ER Jones, A Eriksson, V Siska, KW Arthur, JW Arthur, MC Curtis, JT Stock, M Coltorti, P Pieruccini, S Stretton, F Brock, T Higham, Y Park, M Hofreiter, DG Bradley, J Bhak, R Pinhasi, A Manica
Aug 09, 2017
An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.
Yun Sung Cho, Hyunho Kim, Hak-Min Kim, Sungwoong Jho, JeHoon Jun, Yong Joo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S Edwards, Semin Lee, Byung Chul Kim, Andrea Manica, Tae-Kwang Oh, George M Church, Jong Bhak
Aug 16, 2017
Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or...
The genetics of an early Neolithic pastoralist from the Zagros, Iran.
M Gallego-Llorente, S Connell, ER Jones, DC Merrett, Y Jeon, A Eriksson, V Siska, C Gamba, C Meiklejohn, R Beyer, S Jeon, YS Cho, M Hofreiter, J Bhak, A Manica, R Pinhasi
Oct 18, 2018
The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an...
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles.
Yun Sung Cho, Je Hoon Jun, Jung A Kim, Hak-Min Kim, Oksung Chung, Seung-Gu Kang, Jin-Young Park, Hwa-Jung Kim, Sunghyun Kim, Hee-Jong Kim, Jin-Ho Jang, Ki-Jeong Na, Jeongho Kim, Seung Gu Park, Hwang-Yeol Lee, Andrea Manica, David P Mindell, Jérôme Fuchs, Jeremy S Edwards, Jessica A Weber, Christopher C Witt, Joo-Hong Yeo, Soonok Kim, Jong Bhak
Sep 18, 2019
BACKGROUND: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. RESULTS: Here, we...
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles
Yun Sung Cho, Je Hoon Jun, Jung A Kim, Hak-Min Kim, Oksung Chung, Seung-Gu Kang, Jin-Young Park, Hwa-Jung Kim, Sunghyun Kim, Hee-Jong Kim, Jin-Ho Jang, Ki-Jeong Na, Jeongho Kim, Seung Gu Park, Hwang-Yeol Lee, Andrea Manica, David P. Mindell, Jérôme Fuchs, Jeremy S. Edwards, Jessica A. Weber, Christopher C. Witt, Joo-Hong Yeo, Soonok Kim, Jong Bhak
Aug 28, 2020
Abstract: Background: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results...