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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...
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...
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
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...
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...
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...
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
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
The Ursinus Weekly, October 28, 1976
Ursinus News in Brief: Fourteen chosen for Who's who; P.M. Rabin "dismayed"; Garnet squad spoils Homecoming McCarthy rep visits Ursinus State candidates view higher education An evening of one acts Comment: Exercise your...
Ursinus College Collegeville Pennsylvania newspaper Who's who Yitzhak Rabin Football Eugene McCarthy Frank Brown G. Sieber Pancoast Jay R. Stover ProTheatre election 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...
Identifying the Use of Anonymising Proxies to Conceal Source IP Addresses
The detection of unauthorised users can be problematic for techniques that are available at present if the nefarious actors are using identity hiding tools such as anonymising proxies or Virtual Private Networks (VPNs). This...
Published by: IGI Global Scientific Publishing
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...
Detection of Anonymising Proxies Using Machine Learning
Network Proxies and Virtual Private Networks (VPN) are tools that are used every day to facilitate various business functions. However, they have gained popularity amongst unintended userbases as tools that can be used to hide...
Published by: IGI Global Scientific Publishing
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 genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758.
Dan Mead, Frank Hailer, Elisabeth Chadwick, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan Doulcan, Olga Dudchenko, Arina Omer, David Weisz, Erez Lieberman Aiden, Shane McCarthy, Kerstin Howe, Ying Sims, James Torrance, Alan Tracey, Richard Challis, Richard Durbin, Mark Blaxter
May 01, 2020
We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is...
Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
Aug 15, 2018
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these...
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...
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...
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
The Ursinus Weekly, May 13, 1971
Charles Chambers, Linda Mills, Judith Earle, Lesa Spacek, Carol Barenblitt, David Mowere, Jane Siegel, Dave Dillman, Candy Silver, Glen Greenberg, Peter von Sothen, Mike Powers
Jan 01, 0001
'71 CCC forms plans for frosh H. Salisbury of "New York Times" to speak at 1971 Commencement U.C. Sigma Xi chooses new '71 members Campus Chest caps drive with carnival Application trend up as class of 1975 fills Area...
Ursinus College Collegeville Pennsylvania newspaper Central Coordinating Committee Harrison Evans Salisbury Sigma Xi Campus Chest admissions lacrosse Budget grading system Michele Gil Richard Sorensen Limerick nuclear power plant I never sang for my father track team tennis golf cultural history Higher Education Liberal Studies Social History United States History
Published by: Ursinus College
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