Gelbart, William Martin

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Gelbart, William Martin

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Gelbart

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William Martin

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Gelbart, William Martin

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FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
(Oxford University Press, 2015) dos Santos, Gilberto; Schroeder, Andrew J.; Goodman, Joshua L.; Strelets, Victor B.; Crosby, Madeline A.; Thurmond, Jim; Emmert, David B.; Gelbart, William Martin
Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.
The Evolution of the Anopheles 16 Genomes Project
(Genetics Society of America, 2013) Neafsey, Daniel E.; Christophides, George K.; Collins, Frank H.; Emrich, Scott J.; Fontaine, Michael C.; Gelbart, William Martin; Hahn, Matthew W.; Howell, Paul I.; Kafatos, Fotis C.; Lawson, Daniel; Muskavitch, Marc A. T.; Waterhouse, Robert M.; Williams, Louise J.; Besansky, Nora J.
We report the imminent completion of a set of reference genome assemblies for 16 species of Anopheles mosquitoes. In addition to providing a generally useful resource for comparative genomic analyses, these genome sequences will greatly facilitate exploration of the capacity exhibited by some Anopheline mosquito species to serve as vectors for malaria parasites. A community analysis project will commence soon to perform a thorough comparative genomic investigation of these newly sequenced genomes. Completion of this project via the use of short next-generation sequence reads required innovation in both the bioinformatic and laboratory realms, and the resulting knowledge gained could prove useful for genome sequencing projects targeting other unconventional genomes.
A Simple RNA-DNA Scaffold Templates the Assembly of Monofunctional Virus-Like Particles
(American Chemical Society (ACS), 2015) Garmann, Rees; Sportsman, Richard; Beren, Christian; Manoharan, Vinothan; Knobler, Charles M.; Gelbart, William Martin
Using the components of a particularly well-studied plant virus, cowpea chlorotic mottle virus (CCMV), we demonstrate the synthesis of virus-like particles (VLPs) with one end of the packaged RNA extending out of the capsid and into the surrounding solution. This construct breaks the otherwise perfect symmetry of the capsid and provides a straightforward route for monofunctionalizing VLPs using the principles of DNA nanotechnology. It also allows physical manipulation of the packaged RNA, a previously inaccessible part of the viral architecture. Our synthesis does not involve covalent chemistry of any kind; rather, we trigger capsid assembly on a scaffold of viral RNA that is hybridized at one end to a complementary DNA strand. Interaction of CCMV capsid protein with this RNA-DNA template leads to selective packaging of the RNA portion into a well-formed capsid but leaves the hybridized portion poking out of the capsid through a small hole. We show that the nucleic acid protruding from the capsid is capable of binding free DNA strands and DNA-functionalized colloidal particles. Separately, we show that the RNA-DNA scaffold can be used to nucleate virus formation on a DNA-functionalized surface. We believe this self-assembly strategy can be adapted to viruses other than CCMV.
Automatic Categorization of Diverse Experimental Information in the Bioscience Literature
(BioMed Central, 2012) Fang, Ruihua; Schindelman, Gary; Auken, Kimberly Van; Fernandes, Jolene; Chen, Wen; Wang, Xiaodong; Davis, Paul; Tuli, Mary Ann; Marygold, Steven J; Millburn, Gillian; Matthews, Beverley; Zhang, Haiyan; Brown, Nick; Gelbart, William Martin; Sternberg, Paul W
Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.
VectorBase: A Data Resource for Invertebrate Vector Genomics
(Oxford University Press, 2009) Lawson, Daniel; Arensburger, Peter; Besansky, Nora J.; Bruggner, Robert V.; Butler, Ryan; Campbell, Kathryn S.; Christophides, George K.; Christley, Scott; Dialynas, Emmanuel; Hammond, Martin; Hill, Catherine A.; Konopinski, Nathan; Lobo, Neil F.; MacCallum, Robert M.; Madey, Greg; Megy, Karine; Redmond, Seth; Severson, David W.; Stinson, Eric O.; Topalis, Pantelis; Birney, Ewan; Louis, Christos; Collins, Frank H.; Atkinson, Peter; Meyer, Jason; Gelbart, William Martin; Kafatos, Fotis
VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data.
Inferring Genome-Scale Rearrangement Phylogeny and Ancestral Gene Order: A Drosophila Case Study
(BioMed Central, 2007) Bhutkar, Arjun; Gelbart, William Martin; Smith, Temple F
A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes, providing insights into evolutionary chromosomal dynamics.
FlyBase: genomes by the dozen
(Oxford University Press, 2006) Crosby, Madeline; Goodman, Joshua L.; Strelets, Victor B.; Zhang, Peili; Gelbart, William Martin; The FlyBase Consortium
FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.
Analysis of 14 BAC Sequences from the Aedes Aegypti Genome: A Benchmark for Genome Annotation and Assembly
(BioMed Central, 2007) Lobo, Neil F; Campbell, Kathy S; Thaner, Daniel; deBruyn, Becky; Koo, Hean; Gelbart, William Martin; Loftus, Brendan J; Severson, David W; Collins, Frank H
In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology.
Annotation of the Drosophila Melanogaster Euchromatic Genome: A Systematic Review
(BioMed Central, 2002) Misra, Sima; Mungall, Christopher J; Campbell, Kathryn S; Hradecky, Pavel; Huang, Yanmei; Kaminker, Joshua S; Millburn, Gillian H; Prochnik, Simon E; Tupy, Jonathan L; Whitfield, Eleanor J; Bayraktaroglu, Leyla; Bettencourt, Brian R; Celniker, Susan E; de Grey, Aubrey DNJ; Drysdale, Rachel A; Harris, Nomi L; Richter, John; Shu, ShengQiang; Stapleton, Mark; Yamada, Chihiro; Ashburner, Michael; Rubin, Gerald M; Lewis, Suzanna E; Crosby, Madeline; Matthews, Beverley; Smith, Christopher D; Berman, Benjamin P; Russo, Susan; Schroeder, Andrew; Gelbart, William Martin
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.