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Institution

Ewha Womans University

EducationSeoul, South Korea
About: Ewha Womans University is a education organization based out in Seoul, South Korea. It is known for research contribution in the topics: Population & Cancer. The organization has 13755 authors who have published 25672 publications receiving 595308 citations.


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Journal ArticleDOI
Adam Auton1, Gonçalo R. Abecasis2, David Altshuler3, Richard Durbin4  +514 moreInstitutions (90)
01 Oct 2015-Nature
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

12,661 citations

Journal ArticleDOI
Daniel J. Klionsky1, Kotb Abdelmohsen2, Akihisa Abe3, Joynal Abedin4  +2519 moreInstitutions (695)
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

5,187 citations

Journal ArticleDOI
TL;DR: The first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II) is presented and the detailed structure of a miRNA gene is described, for the first time, by determining the promoter and the terminator of mir‐23a∼27a‐24‐2.
Abstract: MicroRNAs (miRNAs) constitute a large family of noncoding RNAs that function as guide molecules in diverse gene silencing pathways. Current efforts are focused on the regulatory function of miRNAs, while little is known about how these unusual genes themselves are regulated. Here we present the first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II). The primary miRNA transcripts (pri‐miRNAs) contain cap structures as well as poly(A) tails, which are the unique properties of class II gene transcripts. The treatment of human cells with α‐amanitin decreased the level of pri‐miRNAs at a concentration that selectively inhibits pol II activity. Furthermore, chromatin immunoprecipitation analyses show that pol II is physically associated with a miRNA promoter. We also describe, for the first time, the detailed structure of a miRNA gene by determining the promoter and the terminator of mir‐23a∼27a∼24‐2 . These data indicate that pol II is the main, if not the only, RNA polymerase for miRNA gene transcription. Our study offers a basis for understanding the structure and regulation of miRNA genes.

4,304 citations

Journal ArticleDOI
TL;DR: In this paper, first-order changes of wave functions and density with respect to small atomic displacements or infinitesimal homogeneous electric fields within the density-functional theory are studied.
Abstract: Starting from the knowledge of first-order changes of wave functions and density with respect to small atomic displacements or infinitesimal homogeneous electric fields within the density-functional theory, we write the expressions for the diagonal or mixed second-order derivatives of the total energy with respect to these perturbations: dynamical matrices for different wave vectors, Born effective-charge tensors and electronic dielectric permittivity tensors. Interatomic force constants and the phonon-band structure are then obtained by computing the Fourier transform of dynamical matrices on a regular mesh of wave vectors, with an eventual, separate treatment of the long-range dipole-dipole interaction. The same ingredients also allow one to compute the low-frequency response of the crystal to homogeneous electric fields.

2,378 citations

Journal ArticleDOI
Peter H. Sudmant1, Tobias Rausch, Eugene J. Gardner2, Robert E. Handsaker3, Robert E. Handsaker4, Alexej Abyzov5, John Huddleston1, Yan Zhang6, Kai Ye7, Goo Jun8, Goo Jun9, Markus His Yang Fritz, Miriam K. Konkel10, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi11, Francesco Paolo Casale12, Jieming Chen6, Fereydoun Hormozdiari1, Gargi Dayama9, Ken Chen13, Maika Malig1, Mark Chaisson1, Klaudia Walter12, Sascha Meiers, Seva Kashin3, Seva Kashin4, Erik Garrison14, Adam Auton15, Hugo Y. K. Lam, Xinmeng Jasmine Mu6, Xinmeng Jasmine Mu3, Can Alkan16, Danny Antaki17, Taejeong Bae5, Eliza Cerveira, Peter S. Chines18, Zechen Chong13, Laura Clarke12, Elif Dal16, Li Ding7, S. Emery9, Xian Fan13, Madhusudan Gujral17, Fatma Kahveci16, Jeffrey M. Kidd9, Yu Kong15, Eric-Wubbo Lameijer19, Shane A. McCarthy12, Paul Flicek12, Richard A. Gibbs20, Gabor T. Marth14, Christopher E. Mason21, Androniki Menelaou22, Androniki Menelaou23, Donna M. Muzny24, Bradley J. Nelson1, Amina Noor17, Nicholas F. Parrish25, Matthew Pendleton24, Andrew Quitadamo11, Benjamin Raeder, Eric E. Schadt24, Mallory Romanovitch, Andreas Schlattl, Robert Sebra24, Andrey A. Shabalin26, Andreas Untergasser27, Jerilyn A. Walker10, Min Wang20, Fuli Yu20, Chengsheng Zhang, Jing Zhang6, Xiangqun Zheng-Bradley12, Wanding Zhou13, Thomas Zichner, Jonathan Sebat17, Mark A. Batzer10, Steven A. McCarroll3, Steven A. McCarroll4, Ryan E. Mills9, Mark Gerstein6, Ali Bashir24, Oliver Stegle12, Scott E. Devine2, Charles Lee28, Evan E. Eichler1, Jan O. Korbel12 
01 Oct 2015-Nature
TL;DR: In this paper, the authors describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which are constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations.
Abstract: Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

1,971 citations


Authors

Showing all 13863 results

NameH-indexPapersCitations
Yang Yang1642704144071
Mercouri G. Kanatzidis1521854113022
Jongmin Lee1502257134772
Inkyu Park1441767109433
Andrew Ivanov142181297390
Joseph L. Witztum13947274539
Richard J. Johnson13788072201
A. Loginov126112980874
Yang-Kook Sun11778158912
William M. Pardridge11655147861
Edwin K. Silverman11567043901
R. St. Denis11292165326
Shunichi Fukuzumi111125652764
Jonathan L. Sessler11199748758
Juyoung Yoon10843546307
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202361
2022166
20211,868
20201,783
20191,623
20181,607