Rick Masonbrink

Why does my stdout not have the same number of genes as my written .csv file? Six hours later I figured out that the authors hard-coded to print a max of 7,693 genes to stdout, but all genes to the .csv file. These little unexplained details can kill a bioinformatician....

always always always run the sample data first when testing a new program #bioinformatics

It almost never fails. Something I struggle for hours with last week gets solved in the first hour on monday...

Extracting and Assembling a Mitochondrial and Chloroplast Genome from Nuclear-targeted Nanopore Reads A workbook to help scientists working on bioinformatics projects

The tutorial for how to assemble organellar genomes from nuclear-targeted long reads is ready to be used. Please check it out
bioinformaticsworkbook.org/dataAnalysis...
#Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria

I love creating genome assemblies and gene annotations. I work in the Iowa State Genome Informatics Facility and would love to get another genome project. We do fantastic work for very reasonable fee. If you need bioinformatics support, please request here gif.biotech.iastate.edu/tracking/use...

Trying to get people to find this post, as I spent a lot of time trying to make this tutorial very thorough. Anyone depositing a #genome and #annotation to NCBI? Give this tutorial a try.
#sequencing #assembly #data #deposition #biology

Submitting a BioProject, BioSample, SRA, Genome, and Annotation to NCBI A workbook to help scientists working on bioinformatics projects

The tutorial for depositing a bioproject, biosample, sra entry, genome, or genome and annotation to NCBI is ready. Please give it a try. I would love some feedback from others.
bioinformaticsworkbook.org/dataWranglin...

#genomics #bioinformatics #data

Submitting a BioProject, BioSample, SRA, Genome, and Annotation to NCBI A workbook to help scientists working on bioinformatics projects

The tutorial for depositing a bioproject, biosample, sra entry, genome, or genome and annotation to NCBI is ready. Please give it a try. I would love some feedback from others.
bioinformaticsworkbook.org/dataWranglin...

#genomics #bioinformatics #data

We all make mistakes. Even after 13 years of experience I still need 5 tries to get the files exactly right. #bioinformatics #genomics #ncbi The tutorial for depositing a genome and annotation to NCBI is nearly ready.

Bioinformatics Workbook A tutorial to help scientists design their projects and analyze their data.

I am going through the pains to create a tutorial in the bioinformaticsworkbook.org about how to submit a genome and annotation to NCBI. This is so tricky to do.

Research Plant Pathologist Inga Zasada to Present Dec. 2nd Seminar Research plant pathologist Inga Zasada of the USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Ore., will speak on "How an Applied Nematologist Uses Genomic Tools to Address Plant-Parasiti...

💻 Nematologist Inga Zasada will talk about "How an applied #nematologist uses #genomic_tools to address plant-parasitic #nematode research"
📅 December 2nd, 2024
🕓 4:10 PM
ℹ️ More info and Zoom link through the link below 👇
entnem.ucdavis.edu/news/researc...

Identification and Characterization of a Novel Nematode Pan Allergen (NPA) from Wuchereria bancrofti and their Potential Role in Human Filarial Tropical Pulmonary Eosinophilia (TPE) https://www.biorxiv.org/content/10.1101/2023.12.04.569914v1 Tropical pulmonary eosinophilia (TPE) is a chronic respiratory syndrome associated with Lymphatic Fi

Identification and Characterization of a Novel Nematode Pan Allergen (NPA) from Wuchereria bancrofti and their Potential Role in Human Filarial Tropical Pulmonary Eosinophilia (TPE) https://www.biorxiv.org/content/10.1101/2023.12.04.569914v1

A Major Role of Class III HD-ZIPs in Promoting Sugar Beet Cyst Nematode Syncytium Formation in Arabidopsis https://www.biorxiv.org/content/10.1101/2024.02.15.580549v1 Cyst nematodes use a stylet to secrete plant CLE-like peptide effector mimics into selected root cel

A Major Role of Class III HD-ZIPs in Promoting Sugar Beet Cyst Nematode Syncytium Formation in Arabidopsis https://www.biorxiv.org/content/10.1101/2024.02.15.580549v1

And don't forget: many nematode species have lost them altogether! A huge puzzle.
doi.org/10.1002/wrna...

A Sea Snail Toxin Could Inspire New Diabetes Drugs Sea snails stun their prey with toxins that mimic glucose-regulating hormones.

Sea snails stun their prey with #toxins that mimic glucose-regulating hormones.🧪💊 #Marine #MarineDrugs #DrugDiscovery #PharmSky www.the-scientist.com/a-sea-snail-...

SCNBase

The soybean cyst nematode genomics database has been updated as of last night. SCNBase.org now has all 9 early release H. glycines genomes and annotations. All files are downloadable and accessible through BLAST, feature search, and Jbrowse. The pan-genome paper is coming soon! #science #genomics