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Martin, Ryan

Publications and source records attributed to Martin, Ryan.

4 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Non-stationary Geostatistical Modeling: A Case Study Comparing LVA Estimation Frameworks

Incorporating locally varying anisotropy (LVA) in geostatistical modeling improves estimates for structurally complex domains where a single set of anisotropic parameters modeled globally do not account for all geological features. In this work, the properties of two LVA-geostatistical modeling frameworks are explored through application to a complexly folded gold deposit in Ghana. The inference of necessary parameters is a significant requirement of geostatistical modeling with LVA; this work focuses on the case where LVA orientations, derived from expert geological interpretation, are used to improve the grade estimates. The different methodologies for inferring the required parameters in this context are explored. The results of considering different estimation frameworks and alternate methods of parameterization are evaluated with a cross-validation study, as well as visual inspection of grade continuity along select cross sections. Results show that stationary methodologies are outperformed by all LVA techniques, even when the LVA framework has minimal guidance on parameterization. Findings also show that additional improvements are gained by considering parameter inference where the LVA orientations and point data are used to infer the local range of anisotropy. Considering LVA for geostatistical modeling of the deposit considered in this work results in better reproduction of curvilinear geological features.

58 GEOSCIENCES↗