Thinking about how plants and animals, who independently evolved multicellularity, both landed on the spatial expression of transcription factors as the way to figure out where all the parts go.
Jonathan Keats, PhD 🇨🇦
@pedalheadphx.bsky.social
🇨🇦 boiling in the Arizona desert and not riding my bikes enough. Cancer researcher focused on multiple myeloma and clinical genomics at TGen, part of City of Hope. Creator of MyelomaSky and Sequencing Tech feeds. Director, Collaborative Sequencing Center
Sitting at the airport in Salt Lake City, some lady is leading a call for the Nevada elections and keeps saying, “I’m in California” wondering does she not know where she is or doesn’t want to say she is in Utah?
Glacier water in Argentina 🇦🇷 6,720 m above sea level.
When your hotel during the 🇫🇷 Tour de France is so questionable that sleeping on the balcony feels like the better option 😅 🇳🇴 Anders Halland Johannessen and 🇳🇴 Tobias Halland Johannessen (Uno-X Mobility)
🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/
Home - bwa-mem3
Accelerated short-read alignment, derived from bwa-mem2
bwa-mem3.readthedocs.io
Cause I didn’t know about it till today. Appreciate all the work you and the FG team do!
Nils Homer@nilshomer.com · 2mo agoFaster samtools sort, why aren't you using it? github.com/fg-labs/mako
I’ve seen the northern light many times growing up but this is an amazing perspective
In case you missed it: last night, CBS News awarded the Mike Wallace Memorial Scholarship to Santiago Campos, a high school journalist. In accepting, he took the time to condemn the direction of CBS News to much surprise and applause from the audience.
Sounds like something worth a read
Christine Mayr@christinemayr.bsky.social · 3mo agoIf you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.
After largely running our clinical whole genome sequencing test for #myeloma, JAYseq, in stealth mode for the last 6 months I am extremely proud to see the culmination of years of research effort by my team at TGen and collaborators around the world come to fruition in a clinical test.
TGen@tgenresearch.bsky.social · 3mo agoTGen launches JAYseq, a 72 hour whole genome test for multiple myeloma. TGen’s JAYseq™ test provides oncologists with a comprehensive molecular profile of a patient’s myeloma tumor using a single test. #MultipleMyeloma #Genomics #PrecisionMedicine #TGen #CityOfHope #MMRF #ALTSeq
NASA releases insane new image of the mighty hexagonal storm on Saturn's North Pole.
For those who still work with SPSS files, but want to import them into #rstats If you want to retain user defined missing values in your data (-98 = refused), don't forget to add the "user_na = TRUE" argument if you are using haven::read_sav(). Otherwise, user-defined missing values import as NA.
Well that’s a first, patient with a translocation breaking two tumor suppressors in one event, TENT5C and BIRC3
Hey look science makes your life better
Elizabeth Jacobs, PhD@elizabethjacobs.bsky.social · 4mo agoHPV vaccines have been shown to substantially reduce cervical cancer in women, and a paper published just days ago has also shown that cancers in males are also significantly reduced with vaccination. jamanetwork.com/journals/jam...
Gotta pull this one down, finally understand basket versus umbrella designs
Nature Portfolio@natureportfolio.nature.com · 4mo agoA Perspective in Nature Medicine outlines five fundamental tenets to promote clinically meaningful, reproducible, scalable and equitable health outcomes through precision medicine. go.nature.com/3PVIcZD 🔒
I have been a PI for ~23 years now. Some of the things we do routinely in the lab now in molecular biology, genetics/genomics, I would never have believed possible when I started in science more than 30 years ago. But somehow fixing a broken microwave door latch mechanism is beyond me.
Crystal clear sunrise today. Photo taken this morning on Glastonbury Tor.
We are thrilled to announce that Positron Server is now available for academic use via JupyterHub! This gives students a robust #RStats & #Python data science IDE without needing a local install or new infrastructure. Learn more: positron.posit.co/blog/posts/2...
I recently shared a blog post written by Britt DeVries on how she used ChatGPT to create REDCap data dictionaries. I was so inspired by her post that I wrote my own on my experience using Claude to create a data dictionary draft. cghlewis.com/blog/claude_...
Creating data dictionary drafts using Claude | Crystal Lewis
This post walks through an example of the documentation and prompts you can provide to Claude Sonnet 4.6 to get a working draft of a data dictionary for a data collection form.
cghlewis.com
“Brothers and sisters, this is our God: Jesus, King of Peace, who rejects war, whom no one can use to justify war,” Leo said. “He does not listen to the prayers of those who wage war, but rejects them, saying: ‘Even though you make many prayers, I will not listen: your hands are full of blood.’”
LongcalID, This sounds promising, bringing variant calling of most types in a single process, now if we could just add copy number, but at least this brings together phased SNV/INDEL calling with SV calling and maybe some somatic mosaic detection. @lh3lh3.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org