Nematode.net (Database resource)

Nematode.net is a website dedicated to the dissemination of roundworm information to the community of Helminth scientists.  This site provides users an interface enabling users to search for multifactorial combinations of species-omics properties associated with 73 nematode species.

Trematode.net (Database resource)

Trematode.net is a website dedicated to the dissemination of flatworm information to the community of Helminth scientists.  This site provides users an interface enabling users to search for multifactorial combinations of species-omics properties associated with 17 trematode species.

modDFS (Software)

modDFS is a tool enabling users to assess Kegg module completeness.  modDFS is available at SourceForge.net by following the ‘modDFS’ link above.

Helminth Genomics Workshop – Genome handbook

The ‘Genomics’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:

Helminth_Bioinformatics_Workshop_2015_GENOMICS

Helminth Genomics Workshop – Transcriptome handbook

The ‘Transcriptome’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:

Helminth_Bioinformatics_Workshop_2015_TRANSCRIPTOMICS

Helminth Genomics Workshop – Variome handbook

The ‘Variome’ section of the handbook from our 2015 Bioinformatics Workshop for Helminth Genomics:

Helminth_Bioinformatics_Workshop_2015_VARIOME

Kinase annotation for helminths (Protocol)

We’ve developed a protocol for annotating kinase domains in nematodes and platyhelminthes and published the method on the Nature Protocol Exchange:

Kinase annotation for helminths

Genomic and transcriptomic data production for helminths (Protocol)

We’ve published our protocols for genomic and transcriptomic data production, assembly and quality control on the Nature Protocol Exchange:

Genomic and transcriptomic data production for helminths

Defining ‘core genes’ for Helminths (Protocol)

We published our method for defining sets of core genes for nematodes, trematodes and cestodes for use in training gene predictors in the Nature Protocol Exchange:

Finding set of “core genes” for Nematoda, Trematoda and Cestoda

Comparative analysis of metabolism in parasitic worms (Protocol)

We’ve published a method for the characterizing and comparing the metabolic potential of worm parasites in the Nature Protocol Exchange:

Comparative analysis of metabolism in parasitic worms

Annotating metabolic enzymes in parasitic worm proteomes (Protocol)

In collaboration with Dr. John Parkinson’s lab we’ve developed a protocol for annotating metabolic enzymes in parasitic worms

Annotating metabolic enzymes in parasitic worm proteomes