Paulini, Michael [class:all]
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99 results (0.015 seconds)
- person: Michael Paulini European Molecular Biology Laboratory - The European Bioinformatics Institute; Hinxton, United Kingdom
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- paper:
- antibody: WBAntibody00001736
- paper:
- antibody: WBAntibody00001163
- antibody: WBAntibody00001350
[
International Worm Meeting,
2011] Next generation sequencing has provided many laboratories with the means to sequence whole nematode genomes. At WormBase we have created standards to streamline the integration and presentation of this data. This enables small nematode communities to use the comprehensive information available for Caenorhabditids in context of their research species. Using comparative genomics with/against highly curated nematodes, sparse and rough genomes can have interesting features annotated. I will outline the integration process using the examples of Trichinella spiralis and Strongyloides ratti and describe some possible use cases, such as creating list of potential anti-helminthic drug targets.
[
International Worm Meeting,
2019] WormBase (http://www.wormbase.org) is a central data repository for genetic and genomic data relating to C. elegans and other well studied nematodes. WormBase is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org), an effort to align data representation and curation workflows between the major model organism databases (MODs). We will present an update on the curation of nematode genomes outside the Caenorhabditis genus, demonstrate how we use data-mining to add information from current and historical publications, and show examples of the use and benefit to the nematode community. The genome of Trichuris muris has been added by WormBase to act as a representative reference genome for Blaxter clade I group. WormBase have performed first-pass annotation of the genome and manual curation of selected gene structures, with the aim of helping with annotation efforts of closely related Trichuris species. We have also added an updated version of the Pristionchus pacificus genome. This represents the start of a formal collaboration between WormBase and pristionchus.org on the joint maintenance and curation of the reference annotation. Finally, the curation of the Brugia malayi genome is ongoing, and reference annotation provided by WormBase is being used by research groups to analyse the evolution of filarial nematodes and the diseases they cause.
[
International Worm Meeting,
2013] Since 2011, the number of nematode species represented in WormBase increased by half from 12 to 19. These species can be divided into close relatives of Caenorhabditis elegans and parasitic nematodes. In addition the in-depth curation of a limited set of core species has been extended, with the support of the wider research community, to include Brugia malayi, a nematode of clade III and one of the causative agents of lymphatic filariasis in human. Support for multiple alternative reference genomes for a single species (like Ascaris suum somatic/germline assemblies) has been added. To support the extension of WormBase to non-Caenorhabditis species and provide a standardised nomenclature across nematodes, we have also extended our gene-naming service to include B.malayi and helped to provide a first pass gene nomenclature based on a combination of publications and predictions through orthologs. Another development focus was the mapping procedure for RNAi and expression probes, which now allows for more accurate mappings in a species-agnostic way. Also the use of RNASeq by WormBase increased and mappings of RNASeq libraries deposited in the Short Read Archive are not only provided as BAM files, but are also post processed and used in the curation process providing information on TSL sites, splicing, expression asymmetry, polycistronic transcripts and tissue and life-stage specific expression levels (available through SPELL). This is supplemented by the integration sequence features from modENCODE data, like transcription factor, RNA polymerase II and histone binding sites as well as genelets and transcripts.
Antibody against SYN-4, from Michael Glotzer. syx-4
Tunez I, Rubio-Lopez LC, Aguilera-Portillo G, Silva-Palacios A, Evaristo-Priego Y, Santamaria A, Galvan-Arzate S, Cortez-Nunez S, Aschner M, Rangel-Lopez E, Chen P, Colonnello A, Robles-Banuelos B, Garcia-Contreras R
[
Neurotox Res,
2020] One of the authors has incorrect family name spelling in the original article<sub>.</sub> Michael Ashner should read as Michael Aschner.
Rabbit polyclonal peptide antibody against SPD-2 (a gift from Michael Glotzer). spd-2
Antibody against RAB-3, provided by Michael Nonet, Washington University, St. Louis, MO. rab-3
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