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

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

Story of my life…

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

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

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 🧪

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?

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

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

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

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

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

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

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...

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...

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

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.

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.

💻 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

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...

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

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