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Axe: rapid, competitive sequence read demultiplexing using a trie [article]

Kevin D. Murray, Justin O. Borevitz
2017 bioRxiv   pre-print
Here we implement a rapid algorithm for demultiplexing DNA sequence reads with in-read indixces. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length, and several mismatches per index sequence.
doi:10.1101/160606 fatcat:dk4vkbg4anhd3hjp6ryurgrr4q

Axe: rapid, competitive sequence read demultiplexing using a trie

Kevin D Murray, Justin O Borevitz, Bonnie Berger
2018 Bioinformatics  
Murray This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License  ...  pre-compiled executables available from https://github.com/kdmurray91/axe/releases • Other operating systems: portable source available from https://github.com/kdmurray91/axe/releases Copyright 2014-2017 Kevin  ... 
doi:10.1093/bioinformatics/bty432 pmid:29868827 fatcat:xsfzvp2isrdijjunulqfb4oaoa

Valuing a multistate river: the case of the River Murray*

Darla Hatton MacDonald, Mark D. Morrison, John M. Rose, Kevin J. Boyle
2011 Australian Journal of Agricultural and Resource Economics  
Experimental design Underlying the choice questions shown to respondents is a D b -efficient design (Bliemer and Rose 2006; Bliemer et al. 2009 ).  ...  The priors used in generating the final design were drawn from Bayesian multivariate normal distributions. 3 The resulting design had 32 choice sets with a D b -error of 0.10004.  ...  improvements along the River Murray.  ... 
doi:10.1111/j.1467-8489.2011.00551.x fatcat:ka262ojla5ebjgydevyl3vunae

libqcpp: A C++14 sequence quality control library

Kevin D Murray, Justin O Borevitz
2017 Journal of Open Source Software  
Murray et al., (2017). libqcpp: A C++14 sequence quality control library. Journal of Open Source Software, 2(13), 232, doi:10.21105/joss.00232 1  ... 
doi:10.21105/joss.00232 fatcat:cro4na2enrh6zox6z6bl4pme4a

Genomic constraints to drought adaptation [article]

Collin W Ahrens, Kevin Murray, Richard A Mazanec, Scott Ferguson, Jason G Bragg, Ashley Jones, David T Tissue, Margaret Byrne, Justin O Borevitz, Paul D Rymer
2021 bioRxiv   pre-print
We discovered genetic variation among samples following the approach of Murray et al. (41) .  ...  (a) Population locations with precipitation of the driest month (mm; BIO14); (b-d) trait values (grey) with their best linear unbiased predictions (BLUPs; yellow) for (b) δ 13 C, (c) SLA, and (d) NDVI.  ... 
doi:10.1101/2021.08.07.455511 fatcat:xcpua6kqanhxxo6t5bvzeegowe

Cdc28 Activates Exit from Mitosis in Budding Yeast

Adam D. Rudner, Kevin G. Hardwick, Andrew W. Murray
2000 Journal of Cell Biology  
., 1992; Sorger and Murray, 1992; Booher et al., 1993) .  ...  The plates were incubated at 30ЊC for 2 d. D, 2-CDC28 suppresses CDC28-VF. All strains contain pGAL-MPS1.  ... 
doi:10.1083/jcb.149.7.1361 pmid:10871278 pmcid:PMC2175138 fatcat:n6poxopmzra7nfbr2jzicba5rm

Infographics and digital resources: an international consensus on golf and health

Andrew D Murray, Christian J Barton, Daryll Archibald, Danny Glover, Iain Robert Murray, Kevin Barker, Roger A Hawkes
2018 British Journal of Sports Medicine  
Infographics and digital resources: an international consensus on golf and health Andrew D Murray, 1,2 Christian J Barton, 3, 4 Daryll Archibald, 5, 6 Danny Glover, 7 Iain Robert Murray, 8, 9 Kevin  ... 
doi:10.1136/bjsports-2018-099771 pmid:30245479 pmcid:PMC6241625 fatcat:x7vojnkezjbzbbff66k26hbumi

TraitCapture: genomic and environment modelling of plant phenomic data

Tim B Brown, Riyan Cheng, Xavier RR Sirault, Tepsuda Rungrat, Kevin D Murray, Martin Trtilek, Robert T Furbank, Murray Badger, Barry J Pogson, Justin O Borevitz
2014 Current opinion in plant biology  
(d) TrayScan high throughput phenotyping provided by our partner PSI.  ... 
doi:10.1016/j.pbi.2014.02.002 pmid:24646691 fatcat:2thu6z64vnd63mbppzwtyhygzm

Flavonoid intake and its association with atrial fibrillation

Nicola P. Bondonno, Kevin Murray, Catherine P. Bondonno, Joshua R. Lewis, Kevin D. Croft, Cecilie Kyrø, Gunnar Gislason, Anne Tjønneland, Augustin Scalbert, Aedin Cassidy, Jonathan P. Piccini, Kim Overvad (+2 others)
2020 Clinical Nutrition  
0.84 (0.75, 0.95)] but not in low-to-moderate alcohol consumers [<20 g/d: 0.97 (0.89, 1.07)].  ...  flavonoid intake of 1000 mg/day was associated with a lower risk of AF in smokers [0.86 (0.77, 0.96)] but not in non-smokers [0.96 (0.88, 1.06)], and a lower risk of AF in high alcohol consumers [>20 g/d:  ...  )], compared to those consuming 173 mg/d.  ... 
doi:10.1016/j.clnu.2020.04.025 pmid:32386860 fatcat:b5hydf5xojcsljey5gw7s3n7pa

Proposed U.S. regulation of gene-edited food animals is not fit for purpose

Alison L. Van Eenennaam, Kevin D. Wells, James D. Murray
2019 npj Science of Food  
Dietary DNA is generally regarded as safe to consume, and is a routine ingredient of food obtained from any living organism. Millions of naturally-occurring DNA variations are observed when comparing the genomic sequence of any two healthy individuals of a given species. Breeders routinely select desired traits resulting from this DNA variation to develop new cultivars and varieties of food plants and animals. Regulatory agencies do not evaluate these new varieties prior to commercial release.
more » ... ene editing tools now allow plant and animal breeders to precisely introduce useful genetic variation into agricultural breeding programs. The U.S. Department of Agriculture (USDA) announced that it has no plans to place additional regulations on gene-edited plants that could otherwise have been developed through traditional breeding prior to commercialization. However, the U.S. Food and Drug Administration (FDA) has proposed mandatory premarket new animal drug regulatory evaluation for all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies. This runs counter to U.S. biotechnology policy that regulatory oversight should be triggered by unreasonable risk, and not by the fact that an organism has been modified by a particular process or technique. Breeder intention is not associated with product risk. Harmonizing the regulations associated with gene editing in food species is imperative to allow both plant and animal breeders access to gene editing tools to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.
doi:10.1038/s41538-019-0035-y pmid:31304275 pmcid:PMC6550240 fatcat:7mo4vtcx6jc63iohivgkj6sqze

A Plasminogen Activator Inhibitor-1 Promoter Polymorphism and Idiopathic Interstitial Pneumonia

Kevin K. Kim, Kevin R. Flaherty, Qi Long, Noboru Hattori, Thomas H. Sisson, Thomas V. Colby, William D. Travis, Fernando J. Martinez, Susan Murray, Richard H. Simon
2003 Molecular Medicine  
The normal fibrinolytic activity within the alveolar space is suppressed in fibrotic lung diseases in part because of increased levels of plasminogen activator inhibitor-1 (PAI-1). Studies with animals have shown that inhibition of the plasminogen system by PAI-1 increases the generation of pulmonary fibrosis. To determine if a similar relationship occurs in human fibrotic lung diseases, we took advantage of a polymorphism (4G/5G) that occurs in the promoter region of the human PAI-1 gene and
more » ... fluences the expression of PAI-1. We hypothesized that the 4G/4G genotype, because of its association with higher levels of PAI-1, would occur in patients with idiopathic interstitial pneumonia more frequently than in a control population. PAI-1 promoter genotype was determined in 88 well-characterized patients with idiopathic interstitial pneumonia consisting of 62 patients with usual interstitial pneumonia and 26 with nonspecific interstitial pneumonia. DNA was extracted from paraffinembedded biopsy tissue and the genotype identified by polymerase chain reaction and restriction endonuclease digestion. We found that the distribution of PAI-1 genotypes in the idiopathic interstitial pneumonia population was similar to that of a large control population. However, subgroup analysis showed that patients with nonspecific interstitial pneumonia were more likely than the control population to have the promoter genotype (4G/4G) that is associated with higher levels of PAI-1. A similar pattern in PAI-1 polymorphism was not seen in the usual interstitial pneumonia subgroup. The results of this study support the conclusion that PAI-1 expression influences the development of nonspecific interstitial pneumonia in a similar manner to what occurs in animal models of pulmonary fibrosis. Patients with usual interstitial pneumonia did not show the same relationship with PAI-1 genotype.
doi:10.1007/bf03402107 fatcat:lpg5ebwi6fevjeql7fenogjroe

kWIP: The k-mer Weighted Inner Product, a de novo Estimator of Genetic Similarity [article]

Kevin D Murray, Christfried Webers, Cheng Soon Ong, Justin O Borevitz, Norman Warthmann
2016 bioRxiv   pre-print
D S 2 and D * 2 [36, 43, 2] ).  ...  An inner product between k-mer counts has long been used in the field of alignment free phylogenetics, where it is referred to as the D 2 statistic.  ... 
doi:10.1101/075481 fatcat:axtzbxdlh5hwpf4jrncp7tkaoy

NovelPseudomonas fluorescensSeptic Sacroiliitis in a Healthy Soldier

David A. Lindholm, Clinton K. Murray, Kevin S. Akers, Seth D. O'Brien, Joseph F. Alderete, Todd J. Vento
2013 Military medicine  
Lindholm D. A., Murray C. K., Akers K. S., O'Brien S. D., Alderete J. F., Vento T.  ... 
doi:10.7205/milmed-d-13-00114 pmid:23929064 fatcat:jhx7js3ijrhprljq3j6k4gtwpa

Higher Habitual Flavonoid Intake Is Associated with Lower Atherosclerotic Cardiovascular Disease Hospitalizations

Frederik Dalgaard, Nicola Bondonno, Kevin Murray, Catherine P Bondonno, Joshua R Lewis, Kevin D Croft, Cecilie Kyrø, Gunnar Gislason, Augustin Scalbert, Aedin Cassidy, Anne Tjønneland, Kim Overvad (+1 others)
2019 Social Science Research Network  
Flavonoids, compounds found in plant-based foods and beverages, might ameliorate vascular damage and atherosclerosis. Therefore, our aim was to assess the association between flavonoid intake and hospital admissions due to atherosclerotic cardiovascular disease. Methods In this prospective cohort study, participants from the Danish Diet, Cancer, and Health Study were crosslinked with Danish nationwide registries. Eligible participants were aged 50-65 years, had no previous history of
more » ... otic cardiovascular disease, and had completed a food-frequency questionnaire at baseline. We examined associations between flavonoid intake (calculated from food-frequency questionnaires with use of the Phenol-Explorer database) and hospital admissions for atherosclerotic cardiovascular disease, ischaemic heart disease, ischaemic stroke, or peripheral arterial disease. We obtained hazard ratios (HRs) using restricted cubic splines based on Cox proportional hazards models. Findings Of the participants recruited to the Danish Diet, Cancer, and Health study between 1993 and 1997, our study population was comprised of 53 552 participants, with a median follow-up of 21 years (IQR 15-22). During follow-up, 8773 participants were admitted to hospital for atherosclerotic cardiovascular disease. We observed non-linear associations between flavonoid intake and hospital admissions, plateauing at total flavonoid intakes of approximately 1000 mg per day. Compared with an intake of 175 mg per day, an intake of 1000 mg per day was associated with a 14% lower risk of atherosclerotic cardiovascular disease (HR 0·86, 95% CI 0·81-0·91). For disease subtypes, we observed a 9% lower risk of ischaemic heart disease (0·91, 0·85-0·98), a non-significant 9% lower risk of ischaemic stroke (0·91, 0·82-1·01), and a 32% lower risk of peripheral artery disease (0·68, 0·60-0·78). The overall associations were stronger in smokers than in non-smokers, as well as stronger in consumers of high (>20 g per day) quantities of alcohol than in those consuming low-to-moderate (≤20 g per day) quantities. Interpretation Our results suggest that ensuring an adequate consumption of flavonoid-rich foods, particularly in subpopulations at risk of atherosclerosis such as smokers and consumers of high quantities of alcohol might mitigate some of the risk of atherosclerotic cardiovascular disease. More studies are needed to support and validate these data.
doi:10.2139/ssrn.3416721 fatcat:7hqsmqwthnbapo53nrbfvochxi

Saccade and pursuit on an active head/eye platform

Kevin J Bradshaw, Philip F McLauchlan, Ian D Reid, David W Murray
1994 Image and Vision Computing  
Graph (d) plots the instantaneous difference between the current head position and that required by the saccade demand.  ...  (a) angular position; (b) angular velocity; (c) angular accelerations; and (d) errors between demand and current position.  ... 
doi:10.1016/0262-8856(94)90067-1 fatcat:svwqygomq5arzfvol3tc62jlj4
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