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Protocols specifications


Unique identifier OMICS_02754
Restrictions to use None
Database management system MySQL
Community driven Yes
User data submission Not allowed
Version 4.0
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans


  • NemaBlast
  • NemaBrowse
  • NemaGene
  • NemaPath



  • person_outline Makedonka Mitreva
  • person_outline John Martin

Publications for citations


The Distribution of Lectins across the Phylum Nematoda: A Genome Wide Search

Int J Mol Sci
PMCID: 5297725
PMID: 28054982
DOI: 10.3390/ijms18010091

[…] n addition, transcriptome databases of some plant parasitic nematodes were searched for lectin-like domains as well: Hirschmanniella oryzae [], Meloidogyne graminicola [], Heterodera glycines (, Heterodera avenae [], Pratylenchus coffeae [], and Pratylenchus thornei []. All new hits were checked separately to reduce the number of false positives. The nematode-specific profile w […]


The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates

PMCID: 5039805
PMID: 27677574
DOI: 10.1186/s13071-016-1795-8

[…] sources (golden hamster genome database, GCF_000349665.1, and GenBank Bacterial Sequences database, GBBCT). The processed reads were mapped to the unpublished A. ceylanicum genome (available at http: []), using Tophat 2.0.8 [] with the parameter mate-inner-distance set to 300. Breadth of coverage and read count of individual A. ceylanicum gene transcripts were calculated using Refcov, […]


Paramyosin of canine Onchocerca lupi: usefulness for the diagnosis of a neglected zoonotic disease

PMCID: 5013582
PMID: 27604904
DOI: 10.1186/s13071-016-1783-z

[…] s from other organisms were identified by BLASTp of non-redundant (NCBI,, and parasite-specific databases (,,, Augustus gene prediction, using B. malayi as the training set, was used to predict the full-length genes and proteins from genomic data (http://bioinf.uni-greifswald. […]


Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

BMC Evol Biol
PMCID: 4828791
PMID: 27068610
DOI: 10.1186/s12862-016-0651-y

[…] []. We performed searches against all available nematode clades as well as to Hoplolaimina PPN separately. As outgroups in these searches, we included the genesets from flatworms and Homo sapiens at, but as our main outgroup, we included the genomic sequences for the Tardigrade Hypsibius dujardini []; Tardigrada (water bears) is another basal Ecdysozoa phylum like Nematoda. Also, we […]


Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention

Sci Rep
PMCID: 4746573
PMID: 26856411
DOI: 10.1038/srep20316

[…] re predicted using DESeq2 (version 1.4.5) with an adjusted p-value cutoff of 0.1 according to established protocols. Statistical enrichments are described in . RNA-Seq profiles have been deposited in and a browse-able genome is also available at and WormBase. […]


Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root Knot Nematode Meloidogyne incognita

PLoS One
PMCID: 4339843
PMID: 25710378
DOI: 10.1371/journal.pone.0118269
call_split See protocol

[…] notated and assigned to known functional groups as previously described []. For detection of differentially expressed transcripts in nematodes a publicly available M. incognita database was used ( […]


Looking to check out a full list of citations? institution(s)
The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Microbiology, Immunology & Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA; Department of Internal Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA funding source(s)
Supported by National Institutes of Health (NIH) [AI081803 and GM097435]; NIFA [2013-01109]; OPP [GH 1083853], NIH-NHGRI [U54HG003079], and NIH [AI098639, CA164719 and CA155297]. reviews

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