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9 Publications visible to you, out of a total of 9
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Abstract (Expand)

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of … data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Authors: Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson

Date Published: 29th Jun 2017

Publication Type: Not specified

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Abstract (Expand)

With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of … computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Dedicated to ‘whole-genome assembly-free’ treatments, the Colib’read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. With the Colib’read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.

Authors: Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo

Date Published: 1st Dec 2016

Publication Type: Not specified

Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed.

Abstract (Expand)

Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use … efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency.

Authors: Anne-Sophie Bouchet, Anne Laperche, Christine Bissuel-Belaygue, Cécile Baron, Jérôme Morice, Mathieu Rousseau-Gueutin, Jean-Eric Dheu, Pierre George, Xavier Pinochet, Thomas Foubert, Olivier Maes, Damien Dugué, Florent Guinot, Nathalie Nesi

Date Published: 16th Sep 2016

Publication Type: Not specified

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ

Abstract

Not specified

Authors: Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin

Date Published: 1st Dec 2015

Publication Type: Not specified

Ultraviolet-B wavelengths regulate changes in UV absorption of cleaner fish Labroides dimidiatus mucus.

Abstract (Expand)

High-energy wavelengths in the ultraviolet-B (UVB, 280-315 nm) and the UVA (315-400-nm) portion of the spectrum are harmful to terrestrial and aquatic organisms. Interestingly, UVA is also involved in … the repair of UV induced damage. Organisms living in shallow coral reef environments possess UV absorbing compounds, such as mycosporine-like amino acids, to protect them from UV radiation. While it has been demonstrated that exposure to UV (280-400 nm) affects the UV absorbance of fish mucus, whether the effects of UV exposure vary between UVB and UVA wavelengths is not known. Therefore, we investigated whether the UVB, UVA, or photosynthetically active radiation (PAR, 400-700 nm) portions of the spectrum affected the UV absorbance of epithelial mucus and Fulton's body condition index of the cleaner fish Labroides dimidiatus. We also compared field-measured UV absorbance with laboratory based high-performance liquid chromatography measurements of mycosporine-like amino acid concentrations. After 1 week, we found that the UV absorbance of epithelial mucus was higher in the UVB+UVA+PAR treatment compared with the UVA+PAR and PAR only treatments; after 2 and 3 weeks, however, differences between treatments were not detected. After 3 weeks, Fulton's body condition index was lower for fish in the UVB+UVA+PAR compared with PAR and UVA+PAR treatments; furthermore, all experimentally treated fish had a lower Fulton's body condition index than did freshly caught fish. Finally, we found a decrease with depth in the UV absorbance of mucus of wild-caught fish. This study suggests that the increase in UV absorbance of fish mucus in response to increased overall UV levels is a function of the UVB portion of the spectrum. This has important implications for the ability of cleaner fish and other fishes to adjust their mucus UV protection in response to variations in environmental UV exposure.

Authors: J. P. Zamzow, U. E. Siebeck, M. J. Eckes, A. S. Grutter

Date Published: 22nd Oct 2013

Publication Type: Not specified

Cardiac R2* values are independent of the image analysis approach employed.

Abstract (Expand)

PURPOSE: To determine whether systematic differences were present between myocardial R2* values obtained with two different decay models: truncation and exponential + constant (Exp-C). METHODS: … Single-center cohorts were used to compare black and bright blood sequences separately, and a multicenter cohort of mixed bright and black blood studies was used to assess the generalizability. Truncated exponential estimates were calculated with CMRtools, which uses a single region of interest (ROI) method. Exp-C estimates were calculated using a pixelwise approach. RESULTS: No differences could be distinguished based upon whether a white or black blood sequence was examined. The two fitting algorithms yielded similar R2* values, with R-squared values exceeding 0.997 and a coefficient of variation of 3% to 4%. Results using the pixelwise method yielded a small systematic bias ( approximately 3%) that became apparent in patients with severe iron deposition. This disparity disappeared when Exp-C fitting was used on a single ROI, suggesting that the use of pixelwise mapping was responsible for the bias. In the multicenter cohort, the strong agreement between the two fitting approaches was reconfirmed. CONCLUSION: Cardiac R2* values are independent of the signal model used for its calculation over clinically relevant ranges. Clinicians can compare results among centers using these disparate approaches with confidence.

Authors: A. Meloni, H. Y. Jr Rienhoff, A. Jones, A. Pepe, M. Lombardi, J. C. Wood

Date Published: 15th Oct 2013

Publication Type: Not specified

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.

Abstract (Expand)

BACKGROUND: In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on … the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then introduce an exact algorithm, called KISSPLICE, to extract alternative splicing events. RESULTS: We show that KISSPLICE enables to identify more correct events than general purpose transcriptome assemblers. Additionally, on a 71 M reads dataset from human brain and liver tissues, KISSPLICE identified 3497 alternative splicing events, out of which 56% are not present in the annotations, which confirms recent estimates showing that the complexity of alternative splicing has been largely underestimated so far. CONCLUSIONS: We propose new models and algorithms for the detection of polymorphism in RNA-seq data. This opens the way to a new kind of studies on large HTS RNA-seq datasets, where the focus is not the global reconstruction of full-length transcripts, but local assembly of polymorphic regions. KISSPLICE is available for download at http://alcovna.genouest.org/kissplice/.

Authors: G. A. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M. F. Sagot, P. Peterlongo, V. Lacroix

Date Published: 2nd May 2012

Publication Type: Not specified

Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss).

Abstract (Expand)

There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known … about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout.

Authors: Yvan Le Bras, Nicolas Dechamp, Francine Krieg, Olivier Filangi, René Guyomard, Mekki Boussaha, Henk Bovenhuis, Thomas G Pottinger, Patrick Prunet, Pascale Le Roy, Edwige Quillet

Date Published: 22nd Jun 2011

Publication Type: Not specified

Associations Between the Built Environment and Objective Measures of Sleep: The Multi-Ethnic Study of Atherosclerosis.

Abstract (Expand)

Although dense neighborhood built environments support increased physical activity and lower obesity, these features may also disturb sleep. Therefore, we sought to understand the association between … the built environment and objectively measured sleep. From 2010 to 2013, we analyzed data from examination 5 of the Multi-Ethnic Study of Atherosclerosis, a diverse population from 6 US cities. We fit multilevel models that assessed the association between the built environment (Street Smart Walk Score, social engagement destinations, street intersections, and population density) and sleep duration or efficiency from 1-week wrist actigraphy in 1,889 individuals. After adjustment for covariates, a 1-standard-deviation increase in Street Smart Walk Score was associated with 23% higher odds of short sleep duration (</=6 hours; odds ratio = 1.2, 95% confidence interval: 1.0, 1.4), as well as shorter average sleep duration (mean difference = -8.1 minutes, 95% confidence interval: -12.1, -4.2). Results were consistent across other built environment measures. Associations were attenuated after adjustment for survey-based measure of neighborhood noise. Dense neighborhood development may have multiple health consequence. In promoting denser neighborhoods to increase walkability, it is important to also implement strategies that reduce the adverse impacts of this development on sleep, such as noise reductions efforts.

Authors: D. A. Johnson, J. A. Hirsch, K. A. Moore, S. Redline, A. V. Diez Roux

Date Published: No date defined

Publication Type: Not specified

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