Rick Masonbrink
@naturesenigma.bsky.social
I am a bioinformatic scientist working in the Iowa State Genome Informatics Core. Maintainer of SCNBase.org for soybean cyst nematode genomics. Science and nature are my work and my fun.
Reposted by Rick Masonbrink
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
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
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
m.yale.edu
January 14, 2026 at 1:10 PM
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
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
January 12, 2026 at 1:17 AM
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
Reposted by Rick Masonbrink
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...
Release v1.1.7 · Gaius-Augustus/Tiberius
⚠️ New Models available:
Diatoms
Eudicotyledons
Lepidoptera
Monocotyledonae
Mucoromycota
Saccharomycota
Sordariomycota
Several bugfixes.
github.com
October 24, 2025 at 6:37 PM
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
January 12, 2026 at 12:43 AM
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
January 12, 2026 at 12:41 AM
Reposted by Rick Masonbrink
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 🧪
How do gonads and sex chromosomes contribute to regional sex differences in the brain? 🤔
Our new preprint summarizes >5 years of work on this question, combining structural neuroimaging and snRNAseq within a sample of >850 mice.
www.biorxiv.org/content/10.6...
Thread below …
Our new preprint summarizes >5 years of work on this question, combining structural neuroimaging and snRNAseq within a sample of >850 mice.
www.biorxiv.org/content/10.6...
Thread below …
Gonadal and sex chromosomal contributions to sex differences in mammalian brain organization
Sex differences in brain development may contribute to well-known sex differences in behavior and neuropsychiatric risk - making it important to comprehensively map and mechanistically annotate normat...
www.biorxiv.org
January 11, 2026 at 8:44 PM
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 🧪
Reposted by Rick Masonbrink
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...
#Invertebrate 🧪
www.sciencedirect.com/science/arti...
January 10, 2026 at 1:32 AM
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...
#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
January 11, 2026 at 7:48 PM
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
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
January 11, 2026 at 7:10 PM
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
January 11, 2026 at 6:54 PM
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
January 11, 2026 at 5:00 PM
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
January 11, 2026 at 4:27 PM
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
January 10, 2026 at 11:00 PM
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
January 10, 2026 at 10:37 PM
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
January 10, 2026 at 10:24 PM
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
January 10, 2026 at 10:09 PM
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
January 10, 2026 at 10:06 PM
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
January 10, 2026 at 10:03 PM
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
January 10, 2026 at 9:51 PM
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
January 9, 2026 at 10:51 PM
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
January 9, 2026 at 10:32 PM
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
January 9, 2026 at 10:09 PM
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
Reposted by Rick Masonbrink
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?
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?
December 15, 2025 at 3:09 PM
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?
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
January 9, 2026 at 9:34 PM
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