The Experts below are selected from a list of 3726 Experts worldwide ranked by ideXlab platform
Paul W. Sternberg - One of the best experts on this subject based on the ideXlab platform.
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Vennter - An interactive analysis tool for WormBase interaction data using Venn diagrams.
microPublication biology, 2020Co-Authors: Jaehyoung Cho, Sibyl Gao, Lincoln Stein, Paul W. SternbergAbstract:WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the Interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. In WormBase, genetic interaction data is defined as a phenotypic deviation of double mutants (or any other genetic perturbations) from single mutant phenotypes and the control phenotype. Regulatory interactions are defined by how perturbation of one gene or gene product affects the expression of another gene or the localization of its gene product. Physical interactions represent molecular associations between genes and gene products from C. elegans (Grove et al. 2018). Each type of interaction data is essential to understanding certain aspects of the biological process mediated by the two interacting genes. However, integrating information from these three types of interaction data is critical to reading the biological context. Understanding the logical relations between different types of interaction data provides a vital clue on how to tackle a gene-to-gene interaction within this context. To achieve this goal, we introduce a new tool for analyzing these logical relations among the interaction data using a Venn diagram, named Vennter (Venn diagram for interaction). Venn diagrams are very useful for displaying similarities and distinctions between different data sets of interest, especially when they are area-proportional to the amount of information presented. Vennter consists of three circles, each representing one of the three different interaction data types. The size of any area within the interactive Venn diagram corresponds to the number of unique interactor genes pertaining to that region. Figure 1A shows an example of a Vennter diagram for selected genes (daf-2, daf-15, daf-16, and let-363) which play key roles in the Insulin/IGF-1 and TOR-dependent signaling pathway. These results exhibit distinct patterns of overlap among their interaction data. In some cases, the differences might reflect differences in prior scientific approaches to studying these genes as well as the availability of annotated interaction data in WormBase. Vennter is fully interactive for analyzing interactor genes from different sets of interaction data. By clicking on any single or multiple area in combination, one can easily obtain all gene names corresponding to the selected area (represented by hashed lines) in Vennter. The number of selected genes is shown next to the ‘View selected genes’ button (see arrows). From there, one can open a popup window called ‘Browse gene set’ which contains a comprehensive list of interactor genes shown in alphabetic order. This list can be copied or downloaded in diverse formats, and for the user’s convenience, each gene name is linked to its unique WormBase gene page. Under the same ‘Browse gene set’ window, Vennter also offers other functions for further analysis of selected genes, such as direct links to the batch analysis tools ‘SimpleMine’ and ‘Gene-set Enrichment Analysis’ (Figure 1B) which can help to query the gene list more conveniently and efficiently. To demonstrate yet another aspect of Vennter, we can look at the high-throughput physical protein-protein interaction data, which comprise long lists of genes. To date, WormBase has curated 86.9% of physical protein-protein interaction data from these high-throughput studies (Cho et al. 2018). However, identifying the functional relevance of such large amounts of interacting gene candidates can often be quite challenging to researchers. To improve this, Vennter provides more organized and relevant information to researchers by evaluating overlapping information between physical, genetic, and/or regulatory interactions, which enables researchers to more easily measure the confidence and biological relevance of their gene candidates of interest. For the C. elegans research community, Vennter can help compare and integrate the different types of interaction data available. It also provides hyperlinks to other useful WormBase tools in order to analyze the gene interactor list in a more efficient and automated manner.
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Phenotype and gene ontology enrichment as guides for disease modeling in C. elegans
2017Co-Authors: David Angeles-albores, Raymond Y N Lee, Juancarlos Chan, Paul W. SternbergAbstract:Genome-wide experiments have the capacity to generate massive amounts of unbiased data about an organism. In order to interpret this data, dimensionality reduction techniques are required. One approach is to annotate genes using controlled languages and to test experimental datasets for term enrichment using probabilistic methods. Although gene, phenotype and anatomy ontologies exist for C. elegans, no unified software offers enrichment analyses of all the ontologies using the same methodology. Here, we present the WormBase Enrichment Suite, which offers users the ability to test all nematode ontologies simultaneously. We show that the WormBase Enrichment Suite provides valuable insight into different biological problems. Briefly, we show that phenotype enrichment analysis (PEA) can help researchers identify disease phenologs, phenotypes that are homologous across species, which can inform disease modeling in C. elegans. The WormBase Enrichment Suite analysis can also shed light on RNA-seq datasets by showing what molecular functions are enriched, which phenotypes these functions are implicated in and what tissues are overrepresented in the dataset. Finally, we explore the phenotype-anatomy relationship, showing that a small subset of highly specific tissues are disproportionately likely to cause an Egl phenotype, but inferring tissue expression from an Egl phenotype is limited to the largest tissues.
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© 2012 Landes Bioscience. Do not distribute.
2016Co-Authors: Paul Kersey, Paul W. SternbergAbstract:WormBase (www.WormBase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase’s role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE
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WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 2007. 35(Database issue
2015Co-Authors: Lisa R Girard, Todd W Harris, Lincoln D. Stein, Igor Antoshechkin, Paul W. Sternberg, Tristan J Fiedler, Felicia Carvalho, Michael Han, Martin ChalfieAbstract:WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters con-tain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infras-tructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field
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This PDF file includes: Materials and Methods Figs. S1 to S6
2015Co-Authors: Weiwei Zhong, Paul W. Sternberg, Tables To S SAbstract:All data used in this study are publicly available open access data. Reference data sets We obtained our training set data from WormBase (1). For positives, we collected all available yeast-two-hybrid and genetic interaction data in WormBase excluding un-cloned loci and self-interactions. The final positive training set contained 4,687 gene pairs (seven pairs interact both genetically and physically). For negatives, we downloaded the complete 3,296 combinations of cis markers from WormBase excluding pairs overlapping with the positive set. We also constructed a testing set independent of the training set to detect over-fitting problems. For testing set positives, we extracted 5,515 gene pairs from the KEGG pathway database (2). We took the KEGG data as our testing set rather than the training set because some KEGG database knowledge was derived from orthologous gene data rather than direct evidence in C. elegans. Only three gene pairs in this set overlap with the training set positives, indicating the independency of the two data sets. For negatives, we generated 5,000 random gene pairs with the percentage of annotated gene
Juancarlos Chan - One of the best experts on this subject based on the ideXlab platform.
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WormBase a modern model organism information resource
Nucleic Acids Research, 2019Co-Authors: Todd W Harris, Paul Davis, Ranjana Kishore, Scott Cain, Juancarlos Chan, Wen J Chen, Christian A Grove, Valerio Arnaboldi, Hansmichael Muller, Cecilia NakamuraAbstract:WormBase (https://WormBase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.
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WormBase 2017: molting into a new stage.
Nucleic acids research, 2017Co-Authors: Raymond Y N Lee, Kevin L Howe, Paul Davis, Todd W Harris, Scott Cain, Juancarlos Chan, Wen J Chen, Sibyl Gao, Valerio Arnaboldi, Christian A GroveAbstract:WormBase (http://www.WormBase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
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Phenotype and gene ontology enrichment as guides for disease modeling in C. elegans
2017Co-Authors: David Angeles-albores, Raymond Y N Lee, Juancarlos Chan, Paul W. SternbergAbstract:Genome-wide experiments have the capacity to generate massive amounts of unbiased data about an organism. In order to interpret this data, dimensionality reduction techniques are required. One approach is to annotate genes using controlled languages and to test experimental datasets for term enrichment using probabilistic methods. Although gene, phenotype and anatomy ontologies exist for C. elegans, no unified software offers enrichment analyses of all the ontologies using the same methodology. Here, we present the WormBase Enrichment Suite, which offers users the ability to test all nematode ontologies simultaneously. We show that the WormBase Enrichment Suite provides valuable insight into different biological problems. Briefly, we show that phenotype enrichment analysis (PEA) can help researchers identify disease phenologs, phenotypes that are homologous across species, which can inform disease modeling in C. elegans. The WormBase Enrichment Suite analysis can also shed light on RNA-seq datasets by showing what molecular functions are enriched, which phenotypes these functions are implicated in and what tissues are overrepresented in the dataset. Finally, we explore the phenotype-anatomy relationship, showing that a small subset of highly specific tissues are disproportionately likely to cause an Egl phenotype, but inferring tissue expression from an Egl phenotype is limited to the largest tissues.
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WormBase 2016 expanding to enable helminth genomic research
Nucleic Acids Research, 2016Co-Authors: Kevin L Howe, Paul Davis, Bruce J Bolt, Scott Cain, Juancarlos Chan, Wen J Chen, J Done, Thomas A Down, Sibyl Gao, Christian A GroveAbstract:WormBase (www.WormBase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.WormBase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
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WormBase 2014: new views of curated biology
Nucleic Acids Research, 2013Co-Authors: Todd W Harris, Juancarlos Chan, Wen J Chen, J Done, Christian A Grove, Tamberlyn Bieri, Paul H Davis, Joachim Baran, Abigail Cabunoc, Kevin L HoweAbstract:WormBase (http://www.WormBase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.
Todd W Harris - One of the best experts on this subject based on the ideXlab platform.
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WormBase a modern model organism information resource
Nucleic Acids Research, 2019Co-Authors: Todd W Harris, Paul Davis, Ranjana Kishore, Scott Cain, Juancarlos Chan, Wen J Chen, Christian A Grove, Valerio Arnaboldi, Hansmichael Muller, Cecilia NakamuraAbstract:WormBase (https://WormBase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.
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Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Christian A Grove, Kevin L Howe, Michael Paulini, Paul Davis, Todd W Harris, Raymond Y N Lee, Ranjana Kishore, Scott Cain, Wen J Chen, Daniela RacitiAbstract:WormBase ( www.WormBase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.
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WormBase 2017: molting into a new stage.
Nucleic acids research, 2017Co-Authors: Raymond Y N Lee, Kevin L Howe, Paul Davis, Todd W Harris, Scott Cain, Juancarlos Chan, Wen J Chen, Sibyl Gao, Valerio Arnaboldi, Christian A GroveAbstract:WormBase (http://www.WormBase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
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WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 2007. 35(Database issue
2015Co-Authors: Lisa R Girard, Todd W Harris, Lincoln D. Stein, Igor Antoshechkin, Paul W. Sternberg, Tristan J Fiedler, Felicia Carvalho, Michael Han, Martin ChalfieAbstract:WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters con-tain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infras-tructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field
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Methods for Data Mining and Comparative Genomics
2015Co-Authors: Todd W Harris, Lincoln D. SteinAbstract:WormBase is a comprehensive repository for information on Caenorhabditis elegans and related nematodes. Although the primary web-based interface of WormBas
Kevin L Howe - One of the best experts on this subject based on the ideXlab platform.
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Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Bruce J Bolt, Faye H. Rodgers, Myriam Shafie, Paul Kersey, Matthew Berriman, Kevin L HoweAbstract:WormBase ParaSite ( parasite.WormBase.org ) is a comprehensive resource for the genomes of parasitic nematodes and flatworms (helminths). It currently includes genomic data for over 100 helminth species, adding value by way of consistent functional annotation, gene comparative analysis and gene expression analysis. We provide several ways of exploring the data including a choice of genome browsers, genome and gene summary pages, text and sequence searching, a query wizard, bulk downloads, and programmatic interfaces. WormBase ParaSite is released three to six times per year, and is developed in collaboration with WormBase ( www.WormBase.org ) and Ensembl Genomes ( www.ensemblgenomes.org ).
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Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Christian A Grove, Kevin L Howe, Michael Paulini, Paul Davis, Todd W Harris, Raymond Y N Lee, Ranjana Kishore, Scott Cain, Wen J Chen, Daniela RacitiAbstract:WormBase ( www.WormBase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.
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WormBase 2017: molting into a new stage.
Nucleic acids research, 2017Co-Authors: Raymond Y N Lee, Kevin L Howe, Paul Davis, Todd W Harris, Scott Cain, Juancarlos Chan, Wen J Chen, Sibyl Gao, Valerio Arnaboldi, Christian A GroveAbstract:WormBase (http://www.WormBase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
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WormBase parasite a comprehensive resource for helminth genomics
Molecular and Biochemical Parasitology, 2017Co-Authors: Kevin L Howe, Bruce J Bolt, Myriam Shafie, Paul Kersey, Matthew BerrimanAbstract:The number of publicly available parasitic worm genome sequences has increased dramatically in the past three years, and research interest in helminth functional genomics is now quickly gathering pace in response to the foundation that has been laid by these collective efforts. A systematic approach to the organisation, curation, analysis and presentation of these data is clearly vital for maximising the utility of these data to researchers. We have developed a portal called WormBase ParaSite (http://parasite.WormBase.org) for interrogating helminth genomes on a large scale. Data from over 100 nematode and platyhelminth species are integrated, adding value by way of systematic and consistent functional annotation (e.g. protein domains and Gene Ontology terms), gene expression analysis (e.g. alignment of life-stage specific transcriptome data sets), and comparative analysis (e.g. orthologues and paralogues). We provide several ways of exploring the data, including genome browsers, genome and gene summary pages, text search, sequence search, a query wizard, bulk downloads, and programmatic interfaces. In this review, we provide an overview of the back-end infrastructure and analysis behind WormBase ParaSite, and the displays and tools available to users for interrogating helminth genomic data.
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WormBase 2016 expanding to enable helminth genomic research
Nucleic Acids Research, 2016Co-Authors: Kevin L Howe, Paul Davis, Bruce J Bolt, Scott Cain, Juancarlos Chan, Wen J Chen, J Done, Thomas A Down, Sibyl Gao, Christian A GroveAbstract:WormBase (www.WormBase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.WormBase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
Igor Antoshechkin - One of the best experts on this subject based on the ideXlab platform.
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WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res, 2007. 35(Database issue
2015Co-Authors: Lisa R Girard, Todd W Harris, Lincoln D. Stein, Igor Antoshechkin, Paul W. Sternberg, Tristan J Fiedler, Felicia Carvalho, Michael Han, Martin ChalfieAbstract:WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters con-tain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infras-tructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field
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Additional file 7: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
2015Co-Authors: Adler Dillman, Igor Antoshechkin, Marissa Macchietto, Camille Porter, Alicia Rogers, Brian Williams, Ming-min Lee, Zane Goodwin, Edwin LewisAbstract:Additional Cufflinks gene and isoform annotations for S. carpocapsae . The file was generated by combining Cufflink’s transcript annotations for four developmental stages (embryo, L1, IJ, and adult) with the Augustus-predicted gene annotations (.gtf format). Gene and isoform IDs beginning with “CUFF” were predicted by Cufflinks, whereas ones beginning with “L596_” were predicted by Augustus. The Augustus annotations here match the WormBase gene annotations for S. carpocapsae. (GTF 55690 kb
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WormBase a comprehensive resource for nematode research
Nucleic Acids Research, 2010Co-Authors: Todd W Harris, Juancarlos Chan, Wen J Chen, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Norie De La Cruz, Paul H Davis, Margaret Duesbury, Ruihua FangAbstract:WormBase (http://www.WormBase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.
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WormBase 2007.
Nucleic acids research, 2007Co-Authors: Anthony Rogers, Paul Davis, Juancarlos Chan, Wen J Chen, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Jolene FernandesAbstract:WormBase (www.WormBase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences.
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WormBase: new content and better access
Nucleic Acids Research, 2006Co-Authors: Tamberlyn Bieri, Juancarlos Chan, Wen J Chen, Nansheng Chen, Igor Antoshechkin, Carol Bastiani, Darin Blasiar, Philip Ozersky, Payan Canaran, Paul DavisAbstract:WormBase (http://WormBase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.
