iiinova — where your digital self keeps evolving

Rick Masonbrink @naturesenigma.bsky.social · 15/09/2026

As a bioinformatician, you have to be okay with repetition. Making tweak after tweak to the same figure may seem boring, but can also be fantastically exciting if it addresses a biological question.

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Rick Masonbrink @naturesenigma.bsky.social · 04/08/2026

Scientific journals: why require a full reformat into “proper” section order before I even know if the paper will be sent for review? If another equally strong journal will evaluate the manuscript as submitted, why add extra hoops at the front end?

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Reposted by Rick Masonbrink

Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Rick Masonbrink @naturesenigma.bsky.social · 16/06/2026

After years of writing scientific papers, I've written a new book Extreme Complaining: A Comprehensive Guide to the Art of Dissatisfaction This groundbreaking work explores the foundations of grumpiness, the mechanics of annoyance, and evidence-based ways to find fault in absolutely everything

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Reposted by Rick Masonbrink

Katharina Hoff @katharinahoff.bsky.social · 08/04/2026

Story of my life…

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Rick Masonbrink @naturesenigma.bsky.social · 02/04/2026

The dedication, the confidence, the walmart bags! #bicycling #commute

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Rick Masonbrink @naturesenigma.bsky.social · 02/04/2026

I manually annotated the every gene in the Heterodera glycines genome. Has anyone else survived this? Learned a ton—but wow, what a test of patience. #genomics #bioinformatics #nematology

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Jeffrey Townsend @jeffreytownsend.bsky.social · 14/01/2026

Movement matters in the fight against cancer. Muscles actually outcompete tumors for glucose, starving them of the fuel they need to grow. Even modest activity — like regular walks — reshapes metabolism in ways that may slow tumor progression. 🧪 m.yale.edu/dd8j

m.yale.edu

How Exercise Slows Tumor Growth

In her latest study, Rachel Perry, PhD, of Yale School of Medicine, reveals one of the clearest mechanisms to date behind a question patients often ask: Why

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Rick Masonbrink @naturesenigma.bsky.social · 12/01/2026

Andrew Scaboo presents research suggesting that nonfunctional alpha-snap genes in soybean provide resistance to the soybean cyst nematode. Soybean is absolutely screaming “study my small RNAs!” #PAG33 #Soybean #nematodes

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Rick Masonbrink @naturesenigma.bsky.social · 12/01/2026

Ben Mansfield’s research shows that cultivated tomatoes become more responsive to immune signals like flg22 as they get older. Wild tomato (S. pennellii) does the opposite, being highly sensitive at 4 weeks with a dramatic reduction at 10 weeks. 🤯 #PlantScience #Evolution #Tomato #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 12/01/2026

Sai Thejas Babanna shows a rare biological phenomenon: Pre-anthesis Embryonic Inflorescence Greening (PEIG) In certain grasses (Pooideae), the immature flower spike turns green while still buried deep inside the leaf sheaths, which seems to correlate with spikelet survival #PlantSci #Barley #PAG33

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Reposted by Rick Masonbrink

Ed Hagen @edhagen.net · 11/01/2026

More evidence that sex chromosomes, and not just sex hormones, contribute to phenotypic sex differences, sometimes working together, and sometimes in opposition, at least in mouse brains 🧪

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Veeloxxy Bites @the-episiarch.bsky.social · 10/01/2026

Hexametra angusticaecoides is a nematode worm that usually infects lizards, (see: dailyparasite.blogspot.com/2020/08/hexa...) but this study found bats infected with this worm, possibly from eating insect prey which are usually eaten by lizards. #Invertebrate 🧪 www.sciencedirect.com/science/arti...

A dead Pipistrellus kuhlii, partially dissected revealing a Hexametra angusticaecoides in the subcutaneous tissue

Suggested life cycle of Hexametra angusticaecoides with chameleons and other squamates being the parasite's usual definitive host and bats as accidental, dead-end host

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Rick Masonbrink @naturesenigma.bsky.social · 11/01/2026

Jana Seiler used CRISPR to show that DSX+ neurons are essential for processing sensory stimuli. Chemogenetic inhibition shows that silencing these specific neurons causes workers to ignore the Queen Mandibular Pheromone (QMP) #PAG33 #Neuroscience #Honeybees #Genetics

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Reposted by Rick Masonbrink

Kathleen Rhoades @kathleenrhoades.bsky.social · 10/01/2026

Today I learned the fababean chromosome 1 is larger than the entire human genome #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 11/01/2026

What’s happening with Ireland's honeybees? Julia Jones found that while pest-herb-fungicides in pollen are relatively low, they are still affecting bee gut bacteria. Exposure to these chemicals decreased 30+ beneficial bacteria like Lactobacillus and Snodgrassella. #BeeHealth #Microbiome #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 11/01/2026

Martin Hasselmann’s research shows East African honeybees use a 600kb chromosomal inversion to thrive at high altitudes. Highland bees are mostly homozygous for the inversion, which is linked to lower expression of Octopamine receptor beta-1 (linked to memory & foraging). #BeeScience #PAG2026 #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 11/01/2026

Modest Markus Sommer suggests that 8-23% of rice genes in the Ensembl annotation might not actually be real proteins. PSAURON is a new, fast tool that uses deep learning to assign a "protein likelihood" score to your gene models, helping to clean up false positives in your annotation. #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 11/01/2026

Aleksey Zimin presents EVIANN (Evidence-based Annotation) While it does not drastically increase the accuracy over existing tools, its speed is ultrafast, can use ONT transcripts, creates UTRs and lncRNAs. #Bioinformatics #Genomics #Coding #PAG33 #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Research by Venkatasubbu Thirulogachandar combines high-resolution sequencing, spatial validation (sm-FISH), and mutations to dissect barley primordia. He tracked where genes express revealing that HvMND6 acts as an axillary meristem coordinator #Barley #PlantSci #Genomics #PAG33 #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Song Li’s benchmarking shows that for single cell genomics gene co-expression, Pearson correlation and bicor on raw counts actually outperform filtered or scaled data. Surprisingly, using raw counts provided more reliable metrics than traditional normalization or scaling. #singlecell #pag33 #pag2026

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Single cell genomics rigor: where mathematicians confuse biologists resulting in reduced dimensions that confuse mathematicians. #PAG2026 #PAG33 #SingleCell #Genomics

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Vidya S. Vuruputoor's work on Funaria hygrometrica shows how whole-genome duplication triggers an immediate genomic shock in moss, largely mediated by transposable elements and methylation patterns in up to 14% of the gene space. #PlantSci #Genetics #Evolution #PAG33 #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Allison Roberts' work in Physcomitrium patens (moss) shows fundamental differences between the standard cellulose machinery (CESA) and its more agile cousin (CSLD). CESA-deficient moss looks normal at first, its buds lose integrity and literally burst. #PlantSci #CellBiology #Moss #PAG33 #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Han Yang uses B chromosomes in maize to show they cause DSB with knobs, but more importantly also can cause nondisjunction of the entire A genome, creating diploid sperm. Because maize can heterofertlilize, these triploid embryos can survive. Very cool work #maize #PAG2026 #PAG33 #Cytogenetics

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Rick Masonbrink @naturesenigma.bsky.social · 10/01/2026

Research by Xingtan (Vera) Yu provides a high-resolution look at how heat stress (HS) effectively reprograms the bovine mammary gland, forcing cells to prioritize survival over milk production. #DairyScience #Heatstress #AgTech #PAG33 #PAG2026

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Rachel Shahan’s team used a scRNAseq atlas to track root cells in 12-hour increments ove 10 days. They found that MADS-box TFs, the same ones that control flowering time, also regulate the root's transition from juvenile to adult in arabidopsis! #PlantScience #Roots #Aging #Genetics #PAG2026 #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Kevin Cox presented Expansion Microscopy: using a swellable hydrogel to enlarge cells physically moving cellular structures apart, allowing nanoscale imaging on a standard light microscope. I wonder if this can translate to better chromosome squashes? #Microscopy #Jim_Birchler #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Agata Daszkowska-Golec highlights a "genetic flip" where removing two components of the cap-binding complex (CBC) actually creates hormone insensitivity though single mutants are highly sensitive. CBC loss disturbs the spliceosome and interacts with SERRATE (SE) to alter mRNA metabolism. #PAG33

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Reposted by Rick Masonbrink

Andrew Severin @andrewseverin.bsky.social · 15/12/2025

For example, you shouldn't use a splice-aware RNA-Seq aligner like STAR on reads from a prokaryotic organism. 🧬 🖥️ #PAG33 I think this is why it can be challenging to teach bioinformatics. There is so much knowledge that needs to be taught! What other examples can you think of?

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Legumes usually fix nitrogen in their roots, but Sesbania rostrata does it in the stem. Haofei Luo used EMS to find that ARP1 is a key transcription factor, and when overexpressed, can induce stem nodule-like structures in a relates species. #PlantSci #Legumes #Symbiosis #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Mengran Yang presents that damaged plant cells leak ATP. This extracellular ATP (eATP) acts as a DAMP, triggering defense responses. The receptor P2K1 phosphorylates PERK15, which links eATP signaling directly to the Salicylic Acid (SA) pathway and the master immune regulator NPR1. #PAG33 #Immunity

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

New pangenome research by Giacomo Bongiorno on Eragrostis curvula is uncovering the secrets of diplosporous apomixis. By building a pangenome across 10 species, researchers identified the PVA31 gene—found exclusively in apomictic genotypes. #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

What’s the secret to apple apomixis? Researchers used 15x depth sequencing on 1,200+ embryos across 22 species to find the culprit in chr 5. Apomicts share unique chr5 k-mers surrounded by LTR retros and "shotgun blasted" non-syntenic regions that contain cyclin B genes #PlantGenetics #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 09/01/2026

Apomixis in Boechera isn't a quirk—it’s driven by fragile genomic sites, B chromosomes, and chromosome fissions. Key takeaway: Evolution is reusing these fragile regions repeatedly to trigger apomixis. Not just dosage, but structural evolution! #PlantSci #Evolution #Genetics #PAG33

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Rick Masonbrink @naturesenigma.bsky.social · 11/12/2025

Respect is non-negotiable. Every person, every interaction. If you can’t do that, move along.

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Rick Masonbrink @naturesenigma.bsky.social · 04/06/2025

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....

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Rick Masonbrink @naturesenigma.bsky.social · 02/06/2025

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

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Rick Masonbrink @naturesenigma.bsky.social · 12/05/2025

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

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Rick Masonbrink @naturesenigma.bsky.social · 30/04/2025

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...

gif.biotech.iastate.edu

Iowa State University Genome Informatics Facility - Login and Create submission form

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Rick Masonbrink @naturesenigma.bsky.social · 11/04/2025

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

bioinformaticsworkbook.org

Submitting a BioProject, BioSample, SRA, Genome, and Annotation to NCBI

A workbook to help scientists working on bioinformatics projects

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Rick Masonbrink @naturesenigma.bsky.social · 11/04/2025

bioinformaticsworkbook.org

Submitting a BioProject, BioSample, SRA, Genome, and Annotation to NCBI

A workbook to help scientists working on bioinformatics projects

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Rick Masonbrink @naturesenigma.bsky.social · 26/03/2025

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.

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Rick Masonbrink @naturesenigma.bsky.social · 24/02/2025

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.

bioinformaticsworkbook.org

Bioinformatics Workbook

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

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David Pires @david1822.bsky.social · 27/11/2024

💻 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...

entnem.ucdavis.edu

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...

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