Story of my life…

Not synteny, but expression profiles with the expectation of some genome/transcriptome disagreement due to population-level variation. Braker and Stringtie were used to make the first pass models, which were then inspected manually and edited with webapollo. The nightmares were the tandem repeats...

Because SCN genomes are population-based, they’re packed with variation and pseudogene artifacts. Tandem duplicates wrecked RNA alignments and distorted gene models. I needed a clean, confidently real set for comparison and now I’ve got it.

Now, just have to wait for the speaker invites and job offers to roll in...

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

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

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

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

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

Release v1.1.7 · Gaius-Augustus/Tiberius ⚠️ New Models available: Diatoms Eudicotyledons Lepidoptera Monocotyledonae Mucoromycota Saccharomycota Sordariomycota Several bugfixes.

With help of international colleagues at @jgi.doe.gov, @oregonstate.edu, and @stockholm-uni.bsky.social, we are relasing new parameters for Tiberius. Thx to Lars Gabriel, @tomasbruna.bsky.social, Samuel Talbot, @chriswheat.bsky.social, @masta.bsky.social - and many others. github.com/Gaius-August...

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

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

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 🧪

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

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...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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?