Search Results - "CONTRINO, Sergio"

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data by SMITH, Richard N, ALEKSIC, Jelena, STEPAN, Radek, SULLIVAN, Julie, WAKELING, Matthew, WATKINS, Xavier, MICKLEM, Gos, BUTANO, Daniela, CARR, Adrian, CONTRINO, Sergio, FENGYUAN HU, LYNE, Mike, LYNE, Rachel, KALDERIMIS, Alex, RUTHERFORD, Kim

“…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…”
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Araport: the Arabidopsis information portal by Krishnakumar, Vivek, Hanlon, Matthew R, Contrino, Sergio, Ferlanti, Erik S, Karamycheva, Svetlana, Kim, Maria, Rosen, Benjamin D, Cheng, Chia-Yi, Moreira, Walter, Mock, Stephen A, Stubbs, Joseph, Sullivan, Julie M, Krampis, Konstantinos, Miller, Jason R, Micklem, Gos, Vaughn, Matthew, Town, Christopher D

“…The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome…”
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ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery by Krishnakumar, Vivek, Contrino, Sergio, Cheng, Chia-Yi, Belyaeva, Irina, Ferlanti, Erik S, Miller, Jason R, Vaughn, Matthew W, Micklem, Gos, Town, Christopher D, Chan, Agnes P

“…ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant…”
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Cross-organism analysis using InterMine by Lyne, Rachel, Sullivan, Julie, Butano, Daniela, Contrino, Sergio, Heimbach, Joshua, Hu, Fengyuan, Kalderimis, Alex, Lyne, Mike, N. Smith, Richard, Štěpán, Radek, Balakrishnan, Rama, Binkley, Gail, Harris, Todd, Karra, Kalpana, A. T. Moxon, Sierra, Motenko, Howie, Neuhauser, Steven, Ruzicka, Leyla, Cherry, Mike, Richardson, Joel, Stein, Lincoln, Westerfield, Monte, Worthey, Elizabeth, Micklem, Gos

“…Summary InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative…”
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Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress by Mukherjee, Gaurab, Abeygunawardena, Niran, Parkinson, Helen, Contrino, Sergio, Durinck, Steffen, Farne, Anna, Holloway, Ele, Lilja, Per, Moreau, Yves, Oezcimen, Ahmet, Rayner, Tim, Sharma, Anjan, Brazma, Alvis, Sarkans, Ugis, Shojatalab, Mohammadreza

“…ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant…”
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InterMine: extensive web services for modern biology by Kalderimis, Alex, Lyne, Rachel, Butano, Daniela, Contrino, Sergio, Lyne, Mike, Heimbach, Joshua, Hu, Fengyuan, Smith, Richard, Stěpán, Radek, Sullivan, Julie, Micklem, Gos

“…InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that…”
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Sharing sensitive data in life sciences: an overview of centralized and federated approaches by Rujano, Maria A, Boiten, Jan-Willem, Ohmann, Christian, Canham, Steve, Contrino, Sergio, David, Romain, Ewbank, Jonathan, Filippone, Claudia, Connellan, Claire, Custers, Ilse, van Nuland, Rick, Mayrhofer, Michaela Th, Holub, Petr, Álvarez, Eva García, Bacry, Emmanuel, Hughes, Nigel, Freeberg, Mallory A, Schaffhauser, Birgit, Wagener, Harald, Sánchez-Pla, Alex, Bertolini, Guido, Panagiotopoulou, Maria

“…Abstract Biomedical data are generated and collected from various sources, including medical imaging, laboratory tests and genome sequencing. Sharing these…”
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modMine: flexible access to modENCODE data by Contrino, Sergio, Smith, Richard N., Butano, Daniela, Carr, Adrian, Hu, Fengyuan, Lyne, Rachel, Rutherford, Kim, Kalderimis, Alex, Sullivan, Julie, Carbon, Seth, Kephart, Ellen T., Lloyd, Paul, Stinson, E. O., Washington, Nicole L., Perry, Marc D., Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E., Stein, Lincoln D., Micklem, Gos

“…In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and…”
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HumanMine: advanced data searching, analysis and cross-species comparison by Lyne, Rachel, Bazaga, Adrián, Butano, Daniela, Contrino, Sergio, Heimbach, Joshua, Hu, Fengyuan, Kalderimis, Alexis, Lyne, Mike, Reierskog, Kevin, Stepan, Radek, Sullivan, Julie, Wise, Archie, Yehudi, Yo, Micklem, Gos

“…HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated…”
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Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE by Trinh, Quang M, Jen, Fei-Yang Arthur, Zhou, Ziru, Chu, Kar Ming, Perry, Marc D, Kephart, Ellen T, Contrino, Sergio, Ruzanov, Peter, Stein, Lincoln D

“…Funded by the National Institutes of Health (NIH), the aim of the Model Organism ENCyclopedia of DNA Elements (modENCODE) project is to provide the biological…”
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modMine: flexible access to modENCODE data by Contrino, Sergio, Smith, Richard N., Butano, Daniela, Carr, Adrian, Hu, Fengyuan, Lyne, Rachel, Rutherford, Kim, Kalderimis, Alex, Sullivan, Julie, Carbon, Seth, Kephart, Ellen T., Lloyd, Paul, Stinson, E. O., Washington, Nicole L., Perry, Marc D., Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E., Stein, Lincoln D., Micklem, Gos

“…In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and…”
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COM e: the ontology of bioinorganic proteins by Degtyarenko, Kirill, Contrino, Sergio

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COMe: the ontology of bioinorganic proteins by Degtyarenko, Kirill, Contrino, Sergio

“…Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects…”
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The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details by Washington, Nicole L, Stinson, E O, Perry, Marc D, Ruzanov, Peter, Contrino, Sergio, Smith, Richard, Zha, Zheng, Lyne, Rachel, Carr, Adrian, Lloyd, Paul, Kephart, Ellen, McKay, Sheldon J, Micklem, Gos, Stein, Lincoln D, Lewis, Suzanna E

“…The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize…”
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ArrayExpress: a public database of gene expression data at EBI by Rocca-Serra, Philippe, Brazma, Alvis, Parkinson, Helen, Sarkans, Ugis, Shojatalab, Mohammadreza, Contrino, Sergio, Vilo, Jaak, Abeygunawardena, Niran, Mukherjee, Gaurab, Holloway, Ele, Kapushesky, Misha, Kemmeren, Patrick, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sansone, Susanna-Assunta

“…ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate…”
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The ArrayExpress gene expression database: a software engineering and implementation perspective by Sarkans, Ugis, Parkinson, Helen, Lara, Gonzalo Garcia, Oezcimen, Ahmet, Sharma, Anjan, Abeygunawardena, Niran, Contrino, Sergio, Holloway, Ele, Rocca-Serra, Philippe, Mukherjee, Gaurab, Shojatalab, Mohammadreza, Kapushesky, Misha, Sansone, Susanna-Assunta, Farne, Anna, Rayner, Tim, Brazma, Alvis

“…Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While…”
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The role SWISS-PROT and TrEMBL play in the genome research environment by Junker, Vivien, Contrino, Sergio, Fleischmann, Wolfgang, Hermjakob, Henning, Lang, Fiona, Magrane, Michele, Jesus Martin, Maria, Mitaritonna, Nicoletta, O’Donovan, Claire, Apweiler, Rolf

“…SWISS-PROT, a curated protein sequence data bank, contains not only sequence data but also annotation relevant to a particular sequence. The annotation added…”
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