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juliusbogo.bsky.social

@juliusbogo.bsky.social
51 followers 124 following 28 posts
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juliusbogo.bsky.social @juliusbogo.bsky.social · 05/08/2026
One of my favorite takeaways from our new paper: Embryonic cardiomyocytes aren't just small adult cardiomyocytes. During a brief developmental window they actively shape the ventricles. We show PKN2 is essential during this period, but largely dispensable afterward. rdcu.be/fx4jG
rdcu.be
A narrow developmental window defines PKN2’s essential role in ventricular chamber morphogenesis
Communications Biology - Multi-omic and quantitative morphometric analyses define a narrow early developmental window during which cardiomyocytes require PKN2 for ventricular chamber morphogenesis...
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juliusbogo.bsky.social @juliusbogo.bsky.social · 22/07/2026
Quoting Minny from The Help: 'Frying chicken just tend to make you feel better about life.' Well, for me that would be protein purification.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 25/05/2026
I made Conway–Maxwell–Binomial regression on #TMB + #glmmTMB. A bounded-count family that handles both over- and under-dispersion through one parameter.. Demo on coral fertilization data from @benoitpujol.bsky.social #rstats #STEM #biology jbogomolovas2.github.io/Julius-s-Blo...
jbogomolovas2.github.io
Conway–Maxwell–Binomial regression: two-directional dispersion for bounded counts – Julius’s Blog
Data Science, Swimming Analytics, and R Programming
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juliusbogo.bsky.social @juliusbogo.bsky.social · 22/05/2026
Thank you for looking into this! Happy you like it. I will contact Kasper Kristensen and try to sell CMB for TMB. The more I think (and do simulations) this is pretty good addition.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 21/05/2026
Thanks Ben! I jumped the gun already. I dissected how glmmTMB does it so had to work on TMB side too to make it fast, robust, and mean-parametrized (Huang-style, like compois). Would you be willing to look at it? TMB-side: github.com/jbogomolovas... glmmTMB-side: github.com/jbogomolovas...
github.com
GitHub - jbogomolovas2/adcomp at cmb-family
AD computation with Template Model Builder (TMB). Contribute to jbogomolovas2/adcomp development by creating an account on GitHub.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 21/05/2026
Thank you! I am slowly looking into this. If I will get stuck will definitely reach out. I like complicate things so going mean parameterized CMB path.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 20/05/2026
Good point. This would be another great comparator. I will sure give it a try/test in a future. Building data simulator I realized it would be great to have frequentist CMB regression.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 20/05/2026
If you need to compare numbers of proliferating cells, ditch the t-test and go for count regression. You're more likely to get p < 0.05 when a real difference is there. I crunched the numbers: #rstats #statistics #biostats #ScienceSky #AcademicSky #biology jbogomolovas2.github.io/Julius-s-Blo...
jbogomolovas2.github.io
Conway–Maxwell–Poisson vs Welch’s t-test for proliferation count data – Julius’s Blog
Data Science, Swimming Analytics, and R Programming
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juliusbogo.bsky.social @juliusbogo.bsky.social · 03/05/2026
Hierarchical Bayesian models are easier than they sound. I used one to ask whether some Lithuanian news outlets are more negative than others. The naive answer was wrong; partial pooling fixed it. brms + ordinal regression on 4,832 headlines. jbogomolovas2.github.io/Julius-s-Blo...
jbogomolovas2.github.io
“And I’m looking for the funnies”: sentiment in Lithuanian news headlines – Julius’s Blog
Data Science, Swimming Analytics, and R Programming
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Reposted by @juliusbogo.bsky.social
Måns Thulin @mansthulin.bsky.social · 19/11/2024
Looking for a book that covers both statistics and R programming? Check out my book Modern Statistics with R! Coding, visualisation, regression, ML & more. 📖 Read it for free: www.modernstatisticswithr.com 📚 Get printed copies: tinyurl.com/mswrbook #Rstats #statistics #datascience #machinelearning
Modern Statistics with R - the author holding the book
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juliusbogo.bsky.social @juliusbogo.bsky.social · 13/04/2026
Your weight has a weekly cycle and a yearly cycle. 3 years of daily weigh-ins confirm it: Monday heaviest → Thursday lightest January heaviest → September lightest New blog post breaking it all down with GAMs in R: jbogomolovas2.github.io/Julius-s-Blog/posts/weight_fluctations/ #rstats #datascience
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Reposted by @juliusbogo.bsky.social
Nur Shahir, PhD (Hire me!) @gigiomics.bsky.social · 23/03/2026
Goals for my blog - a mini-series on the microbiome - recap of my experience with NLP - posting my posit:conf experience as a virtual participant (I have.....one post drafted and I think I may have been over ambitious 🥲)
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juliusbogo.bsky.social @juliusbogo.bsky.social · 05/04/2026
Best way to learn something is to use it on a problem you care about. I've been getting into GAMs, so I built a swim base pace tracker — something #Garmin doesn't offer. #rstats #dataviz #swimming jbogomolovas2.github.io/Julius-s-Blog/posts/swim-css-pipeline/
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juliusbogo.bsky.social @juliusbogo.bsky.social · 18/11/2025
Our latest paper is out. We show that smaller is sometimes better- by trimming out a large portion of the #ALPK3 kinase we create a functional miniALPK3 that fits into an AAV vector and treats ALPK3 cardiomyopathy. doi.org/10.1161/CIRC...
doi.org
American Heart Association Journals
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juliusbogo.bsky.social @juliusbogo.bsky.social · 08/07/2025
It was fun distraction to participate International Cherry Blossom Prediction Competition organized by @georgemasonu.bsky.social. Not the winner, but not shabby for a first try. jbogomolovas2.github.io/Julius-s-Blo...
jbogomolovas2.github.io
Cherry Bloom Prediction – Julius’s Blog
Data Science, Swimming Analytics, and R Programming
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Reposted by @juliusbogo.bsky.social
juliusbogo.bsky.social @juliusbogo.bsky.social · 10/04/2025
Our new paper in @commsbio.bsky.social. We show that Tnnt2 intronic RNAscope probe reliably identifies cardiomyocytes —even through mitosis and nuclear envelope breakdown—overcoming the limitations of traditional CM identification methods. www.nature.com/articles/s42...
nature.com
Intronic RNAscope probes enable precise identification of cardiomyocyte nuclei and cell cycle activity - Communications Biology
Intronic RNA probes precisely identify cardiomyocyte nuclei or chromatin throughout the cell cycle during embryonic cardiomyocyte proliferation and precisely identify cardiomyocyte nuclei in adult hea...
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juliusbogo.bsky.social @juliusbogo.bsky.social · 10/04/2025
Our new paper in @commsbio.bsky.social. We show that Tnnt2 intronic RNAscope probe reliably identifies cardiomyocytes —even through mitosis and nuclear envelope breakdown—overcoming the limitations of traditional CM identification methods. www.nature.com/articles/s42...
nature.com
Intronic RNAscope probes enable precise identification of cardiomyocyte nuclei and cell cycle activity - Communications Biology
Intronic RNA probes precisely identify cardiomyocyte nuclei or chromatin throughout the cell cycle during embryonic cardiomyocyte proliferation and precisely identify cardiomyocyte nuclei in adult hea...
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juliusbogo.bsky.social @juliusbogo.bsky.social · 07/04/2025
Our paper on #ALPK3 is out in JAHA. We demonstrate that loss of ALPK3 and established factor for genetic cardiomyopathy leads to accumulation of thick filament components, possibly via MuRFs - muscle specific E3 ubiquitin ligases. doi.org/10.1161/JAHA...
doi.org
α Protein Kinase 3 Is Essential for Neonatal and Adult Cardiac Function | Journal of the American Heart Association
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juliusbogo.bsky.social @juliusbogo.bsky.social · 25/03/2025
If it ain't green and glow in the dark it ain’t #science. Leftovers from #mClover3 fluorescent protein purification
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juliusbogo.bsky.social @juliusbogo.bsky.social · 18/03/2025
Great work! As github does not have discussion option I thought would ask here: what would be best practical workflow to invent synthesis-worthy binders for particular protein? Use “naive” model with filters or preference aligned one that is currently available or train one?
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juliusbogo.bsky.social @juliusbogo.bsky.social · 11/02/2025
Great distraction I would enjoy. Will blossom datasets be provided on website, or I have to register to obtain them?
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juliusbogo.bsky.social @juliusbogo.bsky.social · 07/02/2025
New work on how and when Indo-europeans emerged. Nice to see how Marijas Gimbutas Kurgan hypothesis has been verified using ancient DNA approach and new insights and details obtained.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 07/02/2025
Wow. Impressive work!
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juliusbogo.bsky.social @juliusbogo.bsky.social · 02/02/2025
Very likely successful cloning of HDR template for knock-in (ccdB present in source plasmid, sequencing pending). Still got the cloning touch! 🧬 #KeepCalmAndCarryOn
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Reposted by @juliusbogo.bsky.social
Addgene @addgene.bsky.social · 27/01/2025
Hey Bluesky! If you're an Addgene fan, you might want to sign up for our quarterly newsletter. Each edition contains the latest Addgene news, hot plasmids, new viral vectors, and a coupon. Click the link below to browse old editions and join our mailing list! www.addgene.org/news...
addgene.org
Addgene: Newsletters from Addgene
Read Addgene's quarterly newsletters which include information on the latest molecular biology techniques, articles, and plasmids in our collection.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 27/01/2025
Coral, comes in R and as web server: Metz, K. S. et al. Coral: Clear and Customizable Visualization of Human Kinome Data. Cell Syst. 7, 347–350.e341 (2018).
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juliusbogo.bsky.social @juliusbogo.bsky.social · 25/01/2025
Small but mighty .🐦‍🔥
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juliusbogo.bsky.social @juliusbogo.bsky.social · 24/01/2025
We took a “no cell shall be left behind” approach which wouldn’t be possible without #Cellpose, #TrackMate by @jytinevez.bsky.social , #Fiji and #rstats analysis and visualization with GlmmTMB, emmeans and #SuperPlots and microscopy cores at UCSD. Plasmids available from @addgene.bsky.social
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juliusbogo.bsky.social @juliusbogo.bsky.social · 24/01/2025
Our biosensor revealed that PKN2 is constitutively active at the plasma membrane—a previously unappreciated hotspot for basal PKN2 activity! Paralleling ROCK signalling. Not every kinase needs triger for activation. Inhibitor first paradigm is worth looking into.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 24/01/2025
We compared our newly identified peptide to existing ones (from literature and the kinase substrate atlas) and found that ours shows superior sensitivity—perfect for building a PKN biosensor. rdcu.be/d7o0G
rdcu.be
An atlas of substrate specificities for the human serine/threonine kinome
Nature - Analysis of the kinase activity of 300 protein Ser/Thr kinases reveals that the substrate specificity of the kinome is substantially more diverse than expected and is driven extensively by...
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juliusbogo.bsky.social @juliusbogo.bsky.social · 24/01/2025
To find the substrate we dephosphorylated cell lysate, heated up, and then rephosphorylated them to reveal the most suitable PKN substrate peptide (KESTREL). This method helped us discover a new, highly sensitive substrate for PKN.
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juliusbogo.bsky.social @juliusbogo.bsky.social · 24/01/2025
Excited to share our new paper on a PKN biosensor—and how to build more! We only have a handful of kinase biosensors out there; now that ExRai backbone @jinzhanglab “anything you can do I can do better” for excising sensors real bottleneck is finding new substrates. go.nature.com/42rUgpO
go.nature.com
Illuminating understudied kinases: a generalizable biosensor development method applied to protein kinase N - Communications Biology
Development of genetically encoded fluorescent biosensor allows real-time visualization of PKN kinase activity, revealing sustained activity at the plasma membrane and demonstrating a new approach for...
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