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WormBase 2016: expanding to enable helminth genomic research

Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas Down, Sibyl Gao, Christian Grove, Todd W. Harris, Ranjana Kishore (+22 others)
2015 Nucleic Acids Research  
WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.  ...  WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes.  ...  We would like to thank him for his guidance and leadership.  ... 
doi:10.1093/nar/gkv1217 pmid:26578572 pmcid:PMC4702863 fatcat:h3yxwojkojgszivof7ahs6fprq

WormBase 2017: molting into a new stage

Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller (+18 others)
2017 Nucleic Acids Research  
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  ...  WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide.  ...  It has now expanded to include almost all nematode and platyhelminth genomes, thus providing an integrated resource for exploring the genome biology of helminths in the evolutionary context of their free-living  ... 
doi:10.1093/nar/gkx998 pmid:29069413 pmcid:PMC5753391 fatcat:5rholx7nqvaurox74fnyrulgs4

Caenorhabditis elegans: nature and nurture gift to nematode parasitologists

Gustavo Salinas, Gastón Risi
2017 Parasitology  
We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance.  ...  We review key fields, such as genomics, drug discovery and genetics, where C. elegans and nematode parasite research have convened.  ...  Microfluidics is another technology in which C. elegans advances can fuel helminth research. This technology enables experiments that are otherwise impossible with conventional methods.  ... 
doi:10.1017/s0031182017002165 pmid:29208057 fatcat:atjsdg6ksndefpxjqx5djg4zfm

The genetic basis of adaptive evolution in parasitic environment from the Angiostrongylus cantonensis genome

Lian Xu, Meng Xu, Xi Sun, Junyang Xu, Xin Zeng, Dai Shan, Dongjuan Yuan, Ping He, Weiming He, Yulan Yang, Shiqi Luo, Jie Wei (+14 others)
2019 PLoS Neglected Tropical Diseases  
We undertake comparative analyses with representative helminth genomes and explore transcriptomic data throughout key developmental life-cycles of the parasite.  ...  Overall, we find several potential adaptive evolutionary signatures in A. cantonensis, and also in some other helminths with similar traits.  ...  WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 2016; 44(D1):D774-80.  ... 
doi:10.1371/journal.pntd.0007846 pmid:31751335 pmcid:PMC6871775 fatcat:vg6qgv3kdnaihcesawprp3doia

Post-genomic progress in helminth parasitology

Paul McVeigh
2020 Parasitology  
genomics tools with which to test biological hypotheses.  ...  To reflect this progress, the 2019 Autumn Symposium of the British Society for Parasitology was held in Queen's University Belfast on the topic of 'post-genomic progress in helminth parasitology'.  ...  The helminth post-genomic revolution has seen a confluence of expanded genomic data with improved proteomic technologies, where in a two-way relationship, genome sequencing data has helped to improve protein  ... 
doi:10.1017/s0031182020000591 pmid:32252832 pmcid:PMC7284816 fatcat:2th5suz54bgdhfkcumqne65ewi

The NIH-NIAID Schistosomiasis Resource Center at the Biomedical Research Institute: Molecular Redux

James J. Cody, Wannaporn Ittiprasert, André N. Miller, Lucie Henein, Margaret M. Mentink-Kane, Michael H. Hsieh, Jennifer Keiser
2016 PLoS Neglected Tropical Diseases  
The SRC has and will continue to monitor and contribute to advances in the field in order to support these research efforts with an expanding array of molecular reagents.  ...  the critical raw materials needed to carry out this important research.  ...  Acknowledgments The authors would like to thank Dr. Matty Knight for her helpful discussions on the history of the SRC and Kelson Bruce (BEI Resources) for help compiling data on reagent requests.  ... 
doi:10.1371/journal.pntd.0005022 pmid:27764112 pmcid:PMC5072641 fatcat:7fag3vpkcffatcy4ledhjnz2hq

KinFin: Software for taxon-aware analysis of clustered protein sequences [article]

Dominik R Laetsch, Mark L Blaxter
2017 bioRxiv   pre-print
The field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms.  ...  A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyse protein cluster presence and absence in different species groups as a guide to biology  ...  -M., Nakamura, C., Nuin, P., Paulini, 21 M., Raciti, D. and Sternberg, P.W. 2016. WormBase 2016: expanding to enable helminth genomic 22 research. Nucleic Acids Research 44(D1), pp. D774-80.  ... 
doi:10.1101/159145 fatcat:7dtjocxdgjhv5klsp72wdqb7y4

Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing [article]

Stephen R Doyle, Geetha Sankaranarayanan, Duncan Berger, Pablo D Jimenez Castro, James Bryant Collins, Thomas Crellen, Maria A Durque-Correa, Peter Ellis, Tegegn G Jaleta, Roz Laing, Kirsty Maitland, Catherine McCarthy (+13 others)
2019 bioRxiv   pre-print
Whole genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications.  ...  immature helminth samples.  ...  We thank Alison Elliot for access to S. mansoni samples collected  ... 
doi:10.1101/616672 fatcat:w6kmxnhrenebrninlen4bfcteq

Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation [article]

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates (+2 others)
2016 bioRxiv   pre-print
Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models.  ...  The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations.  ...  ., et al. (2016) WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res., 44, D774-80. 5 47.  ... 
doi:10.1101/087239 fatcat:td5frmusmfal5pa56hjnonv44u

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing

Stephen R. Doyle, Geetha Sankaranarayanan, Fiona Allan, Duncan Berger, Pablo D. Jimenez Castro, James Bryant Collins, Thomas Crellen, María A. Duque-Correa, Peter Ellis, Tegegn G. Jaleta, Roz Laing, Kirsty Maitland (+14 others)
2019 Frontiers in Genetics  
Whole-genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications.  ...  Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole-genome sequencing of individual immature helminth samples  ...  Reference genomes from each of the test species were obtained from the helminth genome repository WormBase Parasite (Howe et al., 2017) Release 12.  ... 
doi:10.3389/fgene.2019.00826 pmid:31616465 pmcid:PMC6764475 fatcat:7cjbi25fuvavti5al2olglc2fi

UDP-glycosyltransferase family in Haemonchus contortus: Phylogenetic analysis, constitutive expression, sex-differences and resistance-related differences

Petra Matoušková, Lenka Lecová, Roz Laing, Diana Dimunová, Heiko Vogel, Lucie Raisová Stuchlíková, Linh Thuy Nguyen, Pavlína Kellerová, Ivan Vokřál, Jiří Lamka, Barbora Szotáková, Marián Várady (+1 others)
2018 International Journal for Parasitology: Drugs and Drug Resistance  
The progress of genome sequencing has enabled an assessment of the UGT multigene family in Haemonchus contortus (family Trichostrongylidae, Nematoda), a hematophagous gastrointestinal parasite of small  ...  Caenorhabditis elegans, a free-living model nematode, revealed several single member homologues, a lack of the dramatic gene expansion seen in C. elegans, but also several families (UGT365, UGT366, UGT368) expanded  ...  to their target molecule (Kotze and Prichard, 2016) .  ... 
doi:10.1016/j.ijpddr.2018.09.005 fatcat:jh3676psyffjrjkjm763wbpcu4

Revisiting the Phylogenetic History of Helminths Through Genomics, the Case of the New Echinococcus oligarthrus Genome

Lucas L. Maldonado, Juan Pablo Arrabal, Mara Cecilia Rosenzvit, Guilherme Corrêa De Oliveira, Laura Kamenetzky
2019 Frontiers in Genetics  
The first parasitic helminth genome sequence was published in 2007; since then, only ∼200 genomes have become available, most of them being draft assemblies.  ...  Nevertheless, despite the medical and economical global impact of helminthic infections, parasite genomes in public databases are underrepresented.  ...  Eval: a software package for analysis of genome annotations. BMC Bioinform. 4, 50. doi: 10.1186/1471-2105-4-50 Kinkar, L., Laurimäe, T., Sharbatkhori, M., Mirhendi, H., Kia, E.  ... 
doi:10.3389/fgene.2019.00708 pmid:31440275 pmcid:PMC6692484 fatcat:ebm6zxt77vg3tdgpodwnxzyhku

Comparative genomics of the major parasitic worms

2018 Nature Genetics  
This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms.  ...  We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism.  ...  Assemblies and annotation are available at WormBase and WormBase-ParaSite (https://parasite.wormbase.org/).  ... 
doi:10.1038/s41588-018-0262-1 pmid:30397333 pmcid:PMC6349046 fatcat:ksx7pyge2vc2pjsaoktseodwym

The genome of Onchocerca volvulus, agent of river blindness

James A. Cotton, Sasisekhar Bennuru, Alexandra Grote, Bhavana Harsha, Alan Tracey, Robin Beech, Stephen R. Doyle, Matthew Dunn, Julie C. Dunning Hotopp, Nancy Holroyd, Taisei Kikuchi, Olivia Lambert (+15 others)
2016 Nature Microbiology  
Methods Parasite material for genome sequencing All O. volvulus parasite material used for genome sequencing was collected in the research facility at the Tropical Medicine Research Station, Kumba, Cameroon  ...  Further species-specific gene models were provided to MAKER using comparative algorithms against the genome: genBlastG (ref. 78 ) output of C. elegans gene models (WormBase 79 ) and RATT (Rapid Annotation  ... 
doi:10.1038/nmicrobiol.2016.216 pmid:27869790 pmcid:PMC5310847 fatcat:64gyzdb37bh2dlr25rjhb4iblq

The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes

Astra S Bryant, Elissa A Hallem
2021 G3: Genes, Genomes, Genetics  
Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis.  ...  Here, we describe this web-based tool and demonstrate how it may be used to analyze genome-wide codon bias in Strongyloides species.  ...  High-quality reference genomes for many parasitic nematode species are now available (Hunt et al. 2016; Howe et al. 2017; International Helminth Genomes Consortium 2019) , and are a critical resource  ... 
doi:10.1093/g3journal/jkab146 pmid:33914084 pmcid:PMC8496300 fatcat:zenehghs3vf2jcif6zplgzae5e
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