9 results on '"Rachel Lyne"'
Search Results
2. The InterMine Android app: Cross-organism genomic data in your pocket
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Julie Sullivan, Yo Yehudi, Gos Micklem, Rachel Lyne, Daria Komkova, Komkova, Daria [0000-0003-2428-7061], Lyne, Rachel [0000-0001-8050-402X], Yehudi, Yo [0000-0003-2705-1724], Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository
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Databases, Factual ,Computer science ,Biological database ,Genomics data ,InterMine ,computer.software_genre ,General Biochemistry, Genetics and Molecular Biology ,Android app ,World Wide Web ,03 medical and health sciences ,Gene search ,Android (operating system) ,General Pharmacology, Toxicology and Pharmaceutics ,Organism ,030304 developmental biology ,Biological data ,0303 health sciences ,General Immunology and Microbiology ,Software Tool Article ,030302 biochemistry & molecular biology ,Articles ,General Medicine ,Genomics ,Data access ,Mobile phone ,computer ,Mobile device ,Cell Phone ,Software ,Data integration - Abstract
InterMine is a data integration and analysis software system that has been used to create both inter-connected and stand-alone biological databases for the analysis of large and complex biological data sets. Together, the InterMine databases provide access to extensive data across multiple organisms. To provide more convenient access to these data from Android mobile devices, we have developed the InterMine app, an application that can be run on any Android mobile phone or tablet. The InterMine app provides a single interface for data access, search and exploration of the InterMine databases. It can be used to retrieve information on genes and gene lists, and their relatives across species. Simple searches can be used to access a range of data about a specific gene, while links to the InterMine databases provide access to more detailed report pages and gene list analysis tools. The InterMine app thus facilitates rapid exploration of genes across multiple organisms and kinds of data.
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- 2019
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3. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
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L. Dick, Mark S. Guyer, D. Mecenas, William C. Spencer, Ming Sin Cheung, Sebastian D. Mackowiak, Tao Liu, A. Vielle, Abby F. Dernburg, Mitzi Morris, Bradley I. Arshinoff, Sheldon J. McKay, Amber Leahey, Thea A. Egelhofer, Lukas Habegger, Michael Snyder, Teruaki Takasaki, Roger P. Alexander, Stuart K. Kim, Ashish Agarwal, Ting Han, A. Leo Iniguez, Eric L. Van Nostrand, Gos Micklem, S. Taing, Ekta Khurana, Joel Rozowsky, Beijing Wu, Steven Henikoff, Adrian Carr, Philip Green, Angie S. Hinrichs, A. Muroyama, Jason D. Lieb, Paul Lloyd, Yaniv Lubling, P. Scheid, Kevin Y. Yip, Stefan R. Henz, Chao Cheng, Jiang Du, Mei Zhong, P. Alves, Elicia Preston, Zhi John Lu, Vishal Khivansara, Robert H. Waterston, J. Janette, C. Slightam, Frank J. Slack, David M. Miller, Eo Stinson, Nikolaus Rajewsky, Eran Segal, Jing Leng, Tony Hyman, R. Robilotto, C. Shou, Gunnar Rätsch, Eric C. Lai, Mihail Sarov, X. Shirley Liu, Isabel J. Latorre, A. Chateigner, Francois Gullier, Raymond K. Auerbach, W. James Kent, Sergio Contrino, Jeremy Brouillet, Lincoln Stein, T. Phippen, Andrea Sboner, Marco Mangone, Georg Zeller, Hoang Pham, Mark Gerstein, Michael J. MacCoss, Siew Loon Ooi, Cathleen M. Brdlik, D. Vafeados, Nicole L. Washington, Andreas Rechtsteiner, Peter J. Good, Susan Strome, Galt P. Barber, Kristin C. Gunsalus, John I. Murray, Valerie Reinke, Luke Dannenberg, Masaomi Kato, M. Jensen, X. Feng, John Kim, Kahn Rhrissorrakrai, H. Holster, Kohta Ikegami, Christina M. Whittle, M. Gutwein, Rachel Lyne, Wei Niu, Richard J.H. Smith, LaDeana W. Hillier, P. Kolasinska-Zwierz, Heidi Rosenbaum, Andréa C. Dosé, Xingliang Zhou, Marc D. Perry, Rajkumar Sasidharan, Rebecca F. Lowdon, Arshad Desai, Z. Zha, J. Brennan, Guilin Wang, P. Ruzanov, Brent Ewing, Gennifer E. Merrihew, Kim Rutherford, Reto Gassmann, Elise A. Feingold, Fabio Piano, Julie Ahringer, E. Kephart, Lucas Lochovsky, Sevinc Ercan, Suzanna E. Lewis, Ksenia Voronina, Koon-Kiu Yan, Jorja G. Henikoff, Hyunjin Shin, Hiram Clawson, and Ghia Euskirchen
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Gene expression profiling ,Genetics ,Multidisciplinary ,biology ,Chromosome ,Genomics ,Genome project ,biology.organism_classification ,Gene ,Genome ,Caenorhabditis elegans ,Chromatin - Abstract
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.
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- 2010
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4. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
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Rachel Lyne, Daniela Butano, Jelena Aleksic, Richard N. Smith, Fengyuan Hu, Mike Lyne, Kim Rutherford, Sergio Contrino, Xavier Watkins, Radek Stepan, Gos Micklem, Adrian Carr, Matthew Wakeling, Julie Sullivan, and Alex Kalderimis
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Statistics and Probability ,Databases, Factual ,Computer science ,Databases and Ontologies ,Biological database ,computer.software_genre ,Biochemistry ,Data type ,Set (abstract data type) ,03 medical and health sciences ,0302 clinical medicine ,Data Mining ,Molecular Biology ,030304 developmental biology ,Internet ,0303 health sciences ,Biological data ,Database ,Computational Biology ,Genomics ,Data warehouse ,Computer Science Applications ,Applications Note ,Computational Mathematics ,Computational Theory and Mathematics ,Data model ,Database Management Systems ,Programming Languages ,Web service ,computer ,Algorithms ,030217 neurology & neurosurgery - Abstract
Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. Availability: Freely available from http://www.intermine.org under the LGPL license. Contact: ku.ca.mac.neg@melkcim.g Supplementary information: Supplementary data are available at Bioinformatics online.
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- 2012
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5. InterMOD: integrated data and tools for the unification of model organism research
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Richard N. Smith, Pushkala Jayaraman, Rama Balakrishnan, Elizabeth A. Worthey, Steven B. Neuhauser, Gail Binkley, Julie Sullivan, Lincoln Stein, J. D. Wong, Jelena Aleksic, Sierra A. T. Moxon, J. Michael Cherry, Monte Westerfield, Todd W. Harris, Quang M. Trinh, Rachel Lyne, Benjamin C. Hitz, Gos Micklem, Simon N. Twigger, Andrew Vallejos, Howie Motenko, Joel Richardson, Christian Pich, and Kalpana Karra
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Unification ,Databases, Factual ,media_common.quotation_subject ,ved/biology.organism_classification_rank.species ,Biology ,computer.software_genre ,Article ,Data modeling ,03 medical and health sciences ,Consistency (database systems) ,0302 clinical medicine ,Comparative research ,Databases, Genetic ,Animals ,Function (engineering) ,Model organism ,030304 developmental biology ,media_common ,0303 health sciences ,Multidisciplinary ,Genome ,Models, Genetic ,ved/biology ,Genomics ,Data science ,Data warehouse ,DECIPHER ,Data mining ,computer ,030217 neurology & neurosurgery - Abstract
Model organisms are widely used for understanding basic biology and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene function in a wider range of species. The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to improved cross-species research. So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models and created analysis tools and links between data from different species. The project unites a number of major model organism databases, improving both the consistency and accessibility of comparative research, to the benefit of the wider scientific community.
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- 2013
6. modMine: flexible access to modENCODE data
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Richard N. Smith, Paul Lloyd, Rachel Lyne, Lincoln Stein, Sergio Contrino, Alexis Kalderimis, Daniela Butano, E. O. Stinson, Nicole L. Washington, Suzanna E. Lewis, Julie Sullivan, Adrian Carr, Z. Zha, E. Kephart, P. Ruzanov, Gos Micklem, Marc D. Perry, Kim M. Rutherford, Fengyuan Hu, Seth Carbon, Lyne, Rachel [0000-0001-8050-402X], Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository
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Genomic data ,Genome, Insect ,Gene Expression ,Genomics ,Biology ,Bioinformatics ,Genome ,03 medical and health sciences ,User-Computer Interface ,0302 clinical medicine ,Research community ,Databases, Genetic ,Genetics ,Animals ,Caenorhabditis elegans ,030304 developmental biology ,0303 health sciences ,Genome, Helminth ,Internet ,business.industry ,Articles ,Data science ,Metadata ,Drosophila melanogaster ,Encyclopedia ,The Internet ,business ,030217 neurology & neurosurgery - Abstract
In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.
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- 2011
7. The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
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Rachel Lyne, Lincoln Stein, Nicole L. Washington, P. Ruzanov, Suzanna E. Lewis, Richard N. Smith, Z. Zha, E. Kephart, Marc D. Perry, E. O. Stinson, Adrian Carr, Paul Lloyd, Gos Micklem, Sergio Contrino, Sheldon J. McKay, Lyne, Rachel [0000-0001-8050-402X], Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository
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Design elements and principles ,Biology ,General Biochemistry, Genetics and Molecular Biology ,World Wide Web ,03 medical and health sciences ,Software ,Databases, Genetic ,Animals ,Humans ,Center (algebra and category theory) ,Caenorhabditis elegans ,030304 developmental biology ,Protocol (science) ,Internet ,0303 health sciences ,Genome ,business.industry ,fungi ,030302 biochemistry & molecular biology ,DNA ,Genomics ,Metadata ,Drosophila melanogaster ,Encyclopedia ,Original Article ,The Internet ,Data set (IBM mainframe) ,General Agricultural and Biological Sciences ,business ,Information Systems - Abstract
The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at http://www.modencode.org. Database URL: http://www.modencode.org.
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- 2011
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8. FlyMine: an integrated database for Drosophila and Anopheles genomics
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Richard J.H. Smith, Peter McLaren, Xavier Watkins, Matthew Wakeling, Steve Russell, Julie Sullivan, Kenji Mizuguchi, Philip North, Kim Rutherford, Tom Riley, Gos Micklem, Mark Woodbridge, Debashis Rana, Hilde Janssens, Francois Guillier, Rachel Lyne, Andrew Varley, Kathryn S. Lilley, Michael Ashburner, Wenyan Ji, Lyne, Rachel [0000-0001-8050-402X], Lilley, Kathryn [0000-0003-0594-6543], Russell, Steve [0000-0003-0546-3031], Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository
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Genomics ,Computational biology ,03 medical and health sciences ,0302 clinical medicine ,Software ,Web page ,Anopheles ,Databases, Genetic ,Animals ,Drosophila ,030304 developmental biology ,0303 health sciences ,Focus (computing) ,Biological data ,biology ,business.industry ,Volume (computing) ,InformationSystems_DATABASEMANAGEMENT ,biology.organism_classification ,Data science ,Data warehouse ,3. Good health ,ComputingMethodologies_PATTERNRECOGNITION ,business ,030217 neurology & neurosurgery - Abstract
This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for Drosophila and Anopheles., FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists.
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- 2006
9. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data
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Christopher J. Penkett, Jürg Bähler, Gabriella Rustici, Cordelia Langford, Dongrong Chen, Rachel Lyne, David Vetrie, Gavin Burns, Juan Mata, Lyne, Rachel [0000-0001-8050-402X], Mata, Juan [0000-0002-5514-3653], Apollo - University of Cambridge Repository, and Mata, Juan Ignacio [0000-0002-5514-3653]
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Normalization (statistics) ,Microarray ,lcsh:QH426-470 ,PROTEINS ,lcsh:Biotechnology ,Genes, Fungal ,Computational biology ,Biology ,Genome ,03 medical and health sciences ,vectors ,SCHIZOSACCHAROMYCES-POMBE ,lcsh:TP248.13-248.65 ,Schizosaccharomyces ,Genetics ,hybridization ,030304 developmental biology ,GENE-EXPRESSION ,DNA Primers ,Fluorescent Dyes ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,Gene Expression Profiling ,030302 biochemistry & molecular biology ,DNA microarray ,Reproducibility of Results ,Genomics ,biology.organism_classification ,MEIOSIS ,Gene expression profiling ,lcsh:Genetics ,normalization ,Coding strand ,Schizosaccharomyces pombe ,MODULES ,Biotechnology ,Research Article - Abstract
Background: The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays.|Results: We designed PCR primers to amplify specific probes (180-500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (similar to13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts.|Conclusions: This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website., RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.
- Published
- 2003
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