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Results: 78862
BCFtools/csq
MOTIVATION: Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors...
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...
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...
A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning.
Eugenie C Yen, Shane A McCarthy, Juan A Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I Meier, Ian A Warren, Johanna Mappes, Richard Durbin, Chris D Jiggins
Jul 28, 2020
BACKGROUND: Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits...
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...
Twelve years of SAMtools and BCFtools.
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
Apr 19, 2021
BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant...
The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861).
Iliana Bista, Shane A McCarthy, Jonathan Wood, Zemin Ning, H William Detrich Iii, Thomas Desvignes, John Postlethwait, William Chow, Kerstin Howe, James Torrance, Michelle Smith, Karen Oliver, Vertebrate Genomes Project Consortium, Eric A Miska, Richard Durbin
Nov 18, 2020
We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is...
Barriers to a "cyberaware" Scotland?
CYBERSECURITY poses particular challenges to policy, policing and the public. Despite recent shifts in policing and security strategies, online victimisation is a major and growing problem for the Scottish criminal justice...
The prevalence of gestational diabetes mellitus amongst black South African women is a public health concern.
AIMS: This study aimed to determine the prevalence of gestational diabetes mellitus (GDM) amongst black South African women, describe GDM-associated risk factors and clinical management, and evaluate the efficacy of the fasting...
The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769.
Kerstin Howe, Melinda Dwinell, Mary Shimoyama, Craig Corton, Emma Betteridge, Alexander Dove, Michael A Quail, Michelle Smith, Laura Saba, Robert W Williams, Hao Chen, Anne E Kwitek, Shane A McCarthy, Marcela Uliano-Silva, William Chow, Alan Tracey, James Torrance, Ying Sims, Richard Challis, Jonathan Threlfall, Mark Blaxter
Oct 22, 2021
We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20...
Two Winthrop Graduates Picked for Winthrop University Board of Trustees
Winthrop University
Jan 01, 0001
Janet Smalley `72 of Walhalla, South Carolina, was re-elected to the Third Congressional District seat. Shane Duncan `98 of Greenville, South Carolina, was elected to the Fourth Congressional District seat replacing Scott...
Published by: Winthrop University
The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758.
Dan Mead, Rob Ogden, Anna Meredith, Gabriela Peniche, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Nadine Holmes, Victoria Wright, Matt Loose, Michael A Quail, Shane A McCarthy, Kerstin Howe, William Chow, James Torrance, Joanna Collins, Richard Challis, Richard Durbin, Mark Blaxter
Dec 15, 2021
We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is...
Insights into human genetic variation and population history from 929 diverse genomes.
Anders Bergström, Shane A McCarthy, Ruoyun Hui, Mohamed A Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm, Hélène Blanché, Jean-François Deleuze, Howard Cann, Swapan Mallick, David Reich, Manjinder S Sandhu, Pontus Skoglund, Aylwyn Scally, Yali Xue, Richard Durbin, Chris Tyler-Smith
Feb 19, 2020
The genome sequence of the brown trout, Salmo trutta Linnaeus 1758.
Tom Hansen, Per Gunnar Fjelldal, Sigbjørn Lien, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A McCarthy, William Chow, Kerstin Howe, James Torrance, Jonathan Wood, Ying Sims, Leanne Haggerty, Richard Challis, Jonathan Threlfall, Daniel Mead, Richard Durbin, Mark Blaxter
Nov 17, 2021
We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded...
Digging Deeper: The Impact of Depth on Soil Organic Matter Stabilization Dynamics in a Forage System
Finnleigh Shane Doherty
Jan 01, 0001
Utilizing agriculture as a resource to mitigate the increased atmospheric CO2 fueling the climate crisis requires transformation of soils from a carbon (C) source into a C sink by investing in root-microbial communities to...
Forage Crops depth soil organic matter POX-C Mineralizable C ATR- FTIR Spectroscopy analytical chemistry biogeochemistry Organic chemistry Soil Science
Published by: Ursinus College
Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.
Wentao Shi, Andrea Massaia, Sandra Louzada, Juliet Handsaker, William Chow, Shane McCarthy, Joanna Collins, Pille Hallast, Kerstin Howe, Deanna M Church, Fengtang Yang, Yali Xue, Chris Tyler-Smith
Nov 26, 2019
BACKGROUND: Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they...
Winthrop Board of Trustees Welcomes New Member
Winthrop University
Jan 01, 0001
Quick Facts
The South Carolina General Assembly appointed Ed Driggers '92 to the Congressional District 4 seat that was vacated by Shane Duncan '98. He holds a Master of Business Administration degree from Winthrop and a...
Published by: Winthrop University
Birth, expansion, and death of VCY -containing palindromes on the human Y chromosome
Wentao Shi, Andrea Massaia, Sandra Louzada, Juliet Handsaker, William Chow, Shane McCarthy, Joanna Collins, Pille Hallast, Kerstin Howe, Deanna M. Church, Fengtang Yang, Yali Xue, Chris Tyler-Smith
Oct 13, 2020
Abstract: Background: Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a...
The Grizzly, October 10, 2019
Kevin Leon, Gillian McComeskey, Colleen Murphy, Lillian Vila Licht, Jen Joseph, Daniel Walker, Rosalia Murphy
Jan 01, 0001
"Si, se Puede!" Speaker Series Debuts Charles Rafferty Reads his Brief and Humorous Poems Highlights from the Annual Security and Fire Safety Report Meet this Year's "Lantern" Editor A Fresh New Look for the Ursinus Website ...
Ursinus College Collegeville Pennsylvania newspaper Ana Pena Charles Rafferty campus safety Nicole Kosar Lantern Erin Hovey Mike Moronese Eric Hoffman cultural history Higher Education Liberal Studies Social History United States History
Published by: Ursinus College
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Jie Huang, Bryan Howie, Shane McCarthy, Yasin Memari, Klaudia Walter, Josine L Min, Petr Danecek, Giovanni Malerba, Elisabetta Trabetti, Hou-Feng Zheng, UK10K consortium, Giovanni Gambaro, J Brent Richards, Richard Durbin, Nicholas J Timpson, Jonathan Marchini, Nicole Soranzo
Jun 25, 2018
Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts...
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