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Results: 2254
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)...
The Role of Long-Alkyl-Group Spacers in Glycolated Copolymers for High-Performance Organic Electrochemical Transistors.
Ellasia Tan, Jingwan Kim, Katherine Stewart, Charalampos Pitsalidis, Sooncheol Kwon, Nicholas Siemons, Jehan Kim, Yifei Jiang, Jarvist M Frost, Drew Pearce, James E Tyrrell, Jenny Nelson, Roisin M Owens, Yun-Hi Kim, Ji-Seon Kim
May 27, 2022
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
Efficient iterative Hi-C scaffolder based on N-best neighbors
Abstract: Background: Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most...
Multiomics data integration to reveal chromatin remodeling and reorganization induced by gene mutational synergy.
Recurrent gene mutations often cooperate in a predefined stepwise and synergistic manner to alter global transcription, through directly or indirectly remodeling epigenetic landscape on linear and three-dimensional (3D) scales....
Efficient iterative Hi-C scaffolder based on N-best neighbors.
BACKGROUND: Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic...
Efficient iterative Hi-C scaffolder based on N-best neighbors.
BACKGROUND: Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic...
Comparison of Hi-C results using in-solution versus in-nucleus ligation.
Takashi Nagano, Csilla Várnai, Stefan Schoenfelder, Biola-Maria Javierre, Steven W Wingett, Peter Fraser
Jul 15, 2019
BACKGROUND: Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ...
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.
Roland Jäger, Gabriele Migliorini, Marc Henrion, Radhika Kandaswamy, Helen E Speedy, Andreas Heindl, Nicola Whiffin, Maria J Carnicer, Laura Broome, Nicola Dryden, Takashi Nagano, Stefan Schoenfelder, Martin Enge, Yinyin Yuan, Jussi Taipale, Peter Fraser, Olivia Fletcher, Richard S Houlston
Jul 15, 2019
Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide...
Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy
Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow...
HiCUP
Steven Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews
Jul 15, 2019
HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified...
GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.
Borbala Mifsud, Inigo Martincorena, Elodie Darbo, Robert Sugar, Stefan Schoenfelder, Peter Fraser, Nicholas M Luscombe
Jul 15, 2019
Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult...
Application of ferroelectric materials for improving output power of energy harvesters.
In terms of advances in technology, especially electronic devices for human use, there are needs for miniaturization, low power, and flexibility. However, there are problems that can be caused by these changes in terms of...
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Takashi Nagano, Yaniv Lubling, Tim J Stevens, Stefan Schoenfelder, Eitan Yaffe, Wendy Dean, Ernest D Laue, Amos Tanay, Peter Fraser
Jul 15, 2019
Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture (3C) assess contacts for...
Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.
David Lando, Srinjan Basu, Tim J Stevens, Andy Riddell, Kai J Wohlfahrt, Yang Cao, Wayne Boucher, Martin Leeb, Liam P Atkinson, Steven F Lee, Brian Hendrich, Dave Klenerman, Ernest D Laue
Feb 28, 2018
Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types...
CHiCAGO
Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne, Peter Fraser, Mikhail Spivakov
Jul 15, 2019
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of...
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.
Minjun Yang, Mattias Vesterlund, Ioannis Siavelis, Larissa H Moura-Castro, Anders Castor, Thoas Fioretos, Rozbeh Jafari, Henrik Lilljebjörn, Duncan T Odom, Linda Olsson, Naveen Ravi, Eleanor L Woodward, Louise Harewood, Janne Lehtiö, Kajsa Paulsson
Jun 20, 2019
Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic...
Adolescent Aneuploidy CCCTC-Binding Factor Cell Cycle Proteins Child Child Preschool Chromatin Chromosomal Proteins Non-Histone Chromosome Aberrations Core Binding Factor Alpha 2 Subunit Female Gene Dosage Gene Expression Profiling Gene Expression Regulation Leukemic Genome Human Genome-Wide Association Study Humans Infant Infant Newborn Male Precursor Cell Lymphoblastic Leukemia-Lymphoma Proteogenomics Proteome Proto-Oncogene Proteins c-ets Repressor Proteins Sequence Analysis RNA Transcription Genetic
Top-down, bottom-up, or both? Toward an integrative perspective on operations strategy formation
Operations strategy is formed via complex processes that transpire in multiple directions at multiple organizational levels. While most previous studies focus on the “macro-level” process of strategy formation from the dominant...
Mitochondrial ROS-derived PTEN oxidation activates PI3K pathway for mTOR-induced myogenic autophagy.
Jin-Hwan Kim, Tae Gyu Choi, Seolhui Park, Hyeong Rok Yun, Ngoc Ngo Yen Nguyen, Yong Hwa Jo, Miran Jang, Jieun Kim, Joungmok Kim, Insug Kang, Joohun Ha, Michael P Murphy, Dean G Tang, Sung Soo Kim
Nov 21, 2018
Animals Apoptosis Autophagy Autophagy-Related Protein-1 Homolog Cell Differentiation Cell Line Mice Mitochondria Organophosphorus Compounds PTEN Phosphohydrolase Phosphatidylinositol 3-Kinases Phosphorylation Proto-Oncogene Proteins c-akt RNA Interference RNA Small Interfering Reactive Oxygen Species Signal Transduction Sirolimus Superoxide Dismutase TOR Serine-Threonine Kinases Ubiquinone
Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C.
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
Jul 15, 2019
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms...
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.
Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours
Louise Harewood, Kamal Kishore, Matthew D Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V. P Collins, Peter Fraser
Jun 28, 2017
Abstract
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and...
Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours
L Harewood, K Kishore, MD Eldridge, S Wingett, D Pearson, S Schoenfelder, VP Collins, P Fraser
Aug 10, 2017
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome...
Anaplastic astrocytoma Cancer chromosome conformation capture Chromosome rearrangement Copy number variation Glioblastoma Hi-C Tumour Chromosome Aberrations Chromosome Breakpoints Chromosome Inversion DNA Copy Number Variations Humans In Situ Hybridization Fluorescence Neoplasms Translocation Genetic
Culture creation and change
This review presents comprehensive analyses of extant research on culture creation and change. We use the framework of culture creation and change (Kim & Toh, 2019), which consists of three unique perspectives, to understand...
A novel cell culture model for studying differentiation and apoptosis in the mouse mammary gland.
BACKGROUND: This paper describes the derivation and characterization of a novel, conditionally immortal mammary epithelial cell line named KIM-2. These cells were derived from mid-pregnant mammary glands of a mouse harbouring...
Animals Antigens Viral Tumor Apoptosis Biomarkers Breast Caseins Cell Culture Techniques Cell Differentiation Cell Line Transformed Epithelium Female Gene Dosage Genetic Vectors Lactoglobulins Mice Mice Transgenic Milk Proteins Pregnancy Promoter Regions Genetic Recombinant Proteins Signal Transduction Simian virus 40 Transcriptional Activation
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