A5013939926- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Research Data Management Practices
- Fungal and yeast genetics research
- Advanced Proteomics Techniques and Applications
- Insect symbiosis and bacterial influences
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- Leadership, Human Resources, Global Affairs
- International Business and FDI
- Long-Term Effects of COVID-19
- Housing, Finance, and Neoliberalism
- Plant and animal studies
- Entrepreneurship Studies and Influences
- Water Quality and Resources Studies
- Service-Learning and Community Engagement
- Environmental Conservation and Management
- Agricultural economics and policies
- Academic Writing and Publishing
Brigham and Women's Hospital
2023
University of Cambridge
2007-2022
Czech Academy of Sciences, Biology Centre
2017
Ontario Institute for Cancer Research
2011
Abstract FlyMine is a data warehouse that addresses one of the important challenges modern biology: how to integrate and make use diversity volume current biological data. Its main focus genomic proteomics for Drosophila other insects. It provides web access integrated at number different levels, from simple browsing construction complex queries, which can be executed on either single items or lists.
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) provides high-quality curated genomic, genetic, and molecular information on the genes their products of budding yeast cerevisiae. To accommodate increasingly complex, diverse needs researchers for searching comparing data, SGD has implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine (http://yeastmine.yeastgenome.org). is...
Abstract Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex integration requirements and a need for fast customizable query facility. Using InterMine, large biological can be created from range heterogeneous sources, extensible model allows easy new types. The analysis tools include flexible builder, genomic region search library ‘widgets’ performing various statistical analyses. results exported in many commonly used formats....
The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the thaliana genome sequence and associated annotation. was conceived as framework that allows research community to develop release 'modules' integrate, analyze visualize data may reside at remote sites. current implementation provides an indexed database of core genomic information. These are made available through feature-rich web applications provide search, mining,...
In an effort to comprehensively characterize the functional elements within genomes of important model organisms Drosophila melanogaster and Caenorhabditis elegans, NHGRI organism Encyclopaedia DNA Elements (modENCODE) consortium has generated enormous library genomic data along with detailed, structured information on all aspects experiments. The modMine database (http://intermine.modencode.org) described here been built by modENCODE Data Coordination Center allow broader research community...
InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the interface can be re-used in many other applications: to find filter data; export it flexible structured way; upload, use, manipulate analyze lists; provide for retrieval of sequence segments, statistical analysis tools. Here we describe these features discuss how they used separately or combinations support integrative...
Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order effectively achieve this goal, it is critical that researchers have high quality datasets available them, in standard format, also suite tools with which analyse such form experimentally testable hypotheses from them. The PSI-MI XML interchange format was initially published 2004, expanded 2007 enable download data. PSI-XML2.5 designed describe...
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 widespread conservation gene sequence function amongst eukaryotes, allowing insights from model help decipher in a wider range species. The InterMOD consortium is developing an infrastructure based around InterMine data warehouse system integrate functional number key organisms, leading way...
Abstract Summary InterMineR is a package designed to provide flexible interface between the R programming environment and biological databases built using InterMine platform. The offers access query builder library of term enrichment tools framework, as well interoperability with other Bioconductor packages. This facilitates automation data retrieval tasks downstream analysis existing statistical in environment. Availability implementation free open source, released under LGPL licence...
Toxoplasma gondii ( T. ) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it still not fully known which genetic or epigenetic factors are involved regulating virulence traits of . There on-going efforts to elucidate mechanisms stage transition process via application high-throughput epigenomics, genomics proteomics techniques. Given range experimental conditions typical yield from such techniques, a new challenge...
A number of different molecular interactions data download formats now exist, designed to allow access these valuable by diverse user groups. These include the PSI-XML and MITAB standard interchange developed Molecular Interaction workgroup HUPO-PSI in addition other, use-specific downloads produced other resources. The onus is currently on ensure that a piece software capable read/writing all necessary versions each format. This problem may increase, as providers strive meet ever more...
The DAGViewer BioJS component is a reusable JavaScript made available as part of the project and intended to be used display graphs structured data, with particular emphasis on Directed Acyclic Graphs (DAGs). It enables users embed representations such ontologies or phylogenetic trees, in hyper-text documents (HTML). This generic, since it capable (given appropriate configuration) displaying any kind data that organised graph. features this which are useful for examining filtering large...
Abstract Patients with chronic anemia, or low blood hemoglobin levels, are frequently subjected to the cost, inconvenience, and discomfort of traditional hematology analyzer-based measurements levels via complete counts. Elimination need for count testing screening is an unmet clinical that we previously addressed by developing a non-invasive smartphone app estimates image analysis fingernail bed images. In this work, present additional data yielding significant improvement upon our...
Abstract HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration analysis compiled from experimental, computational curated sources. Built using the InterMine integration platform, includes genes, proteins, pathways, expression levels, Single nucleotide polymorphism (SNP), diseases more, into single searchable database. promotes integrative analysis, approach in modern biology allows...
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 widespread conservation gene sequence function amongst eukaryotes, allowing insights from model help decipher in a wider range species. The InterMOD consortium is developing an infrastructure based around InterMine data warehouse system integrate functional number key organisms, leading way...
The EBI Complex Portal is a manually curated, unifying resource of macromolecular complexes from model organisms. Each entry has unique and stable identifier links participating molecule to their reference database (UniProt, ChEBI RNAcentral). complex annotated with information about stoichiometry, topology structural assembly, function, complex-centric Gene Ontology terms evidence codes. Complexes are extensively cross-referenced ChEMBL, EMDB, Experimental Factor Ontology, Intenz, MatrixDB,...
Abstract HumanMine ( www.humanmine.org ) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration analysis compiled from experimental, computational curated sources. Built using the InterMine integration platform, includes genes, proteins, pathways, expression levels, SNPs, diseases more, into single searchable database. promotes integrative analysis, approach in modern biology allows many sources evidence be...
<ns4:p><ns4:bold>Summary: </ns4:bold>The InterMineTable component is a reusable JavaScript as part of the BioJS project. It enables users to embed powerful table-based query facilities in their websites with access genomic data-warehouses such <ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.flymine.org">http://www.flymine.org</ns4:ext-link>, which allow perform flexible queries over wide range integrated data...
<ns4:p><ns4:bold>Summary: </ns4:bold>The InterMineTable component is a reusable JavaScript as part of the BioJS project. It enables users to embed powerful table-based query facilities in their websites with access genomic data-warehouses such <ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.flymine.org">http://www.flymine.org</ns4:ext-link>, which allow perform flexible queries over wide range integrated data...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe new Science Building at Millsaps CollegeJ. Magruder Sullivan Cite this: J. Chem. Educ. 1930, 7, 5, 1058Publication Date (Print):May 1, 1930Publication History Received3 August 2009Published online1 May 1930Published inissue 1 1930https://doi.org/10.1021/ed007p1058RIGHTS & PERMISSIONSArticle Views52Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF...