@pedalheadphx
🇨🇦 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
🔄 Inversions predispose to recurrent deletions and duplications in chromsome 15q13.3. 🔁
Using de-novo assemblies of 10 patient-parent trios, we investigated how recurrent copy-number variants (CNVs) in the 15q13.3 locus arise.
www.biorxiv.org/content/10.6...
A brief tour (1/17)
My future rig, first R2 I’ve seen in the wild #Rivian @rivianofficial.bsky.social can’t wait for a real production version. I must want one paid to charge just to take a peak
Figure in general from probably 30 years ago, give or take a few
Remember having this one
Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.
Feel free to drop me some feedback as an issue on the repo
github.com/Psy-Fer/kuva
crates.io/crates/kuva/...
Sounds promising,
Appreciate your effort, enjoyed following and glad the hashtag was picked up in my sequencing tech feed
The real costs today are people, library prep cost, and storage. We advertise 30x analytical genomes (90Gb!=30x) at $475, so true $100 sequencing costs would bring it down a lot, assuming no platform duplicates, to around $200 covering people, service contracts, library prep and data distribution.
Wasn’t the $100 genome already reached by Ultima Genomics? This is just press release for an instrument you can get this fall if you are the select few. Real question is where will Roche price their instrument and will Illumina get to that same price point with the 35B announcement.
Argh, overtime, come on 🇨🇦 just need one past the goalie, US goalie is keeping them in the game
@rahulbanerjeemd.bsky.social seeing in the airport, so have not read it, first question is if this is the rare hyper mutated myeloma cases. But nice to see people try checkpoint inhibitors again, lots of anecdotal reports of good responses
www.nature.com/articles/s41...
Not sure how this can be possible with a therapeutic with such a long half life. Dosing a checkpoint inhibitor before or after 3PM changes outcome. If true maybe the early bird gets the immune system
dplyr 1.2.0 is out now and we are SO excited!
- `filter_out()` for dropping rows
- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools
These are huge quality of life wins for #rstats!
tidyverse.org/blog/2026/02...
Good till June for reagent purchase based on communication we got yesterday but we already decommissioned ours last summer seeing the writing on the wall. Bit embarrassed to acknowledge the paper weight but open spot in the lab now for a new challenger
Fair comment, just worry uninformed care teams use it to stop therapy thinking is established to be comparable to adaptive.
Good concept, but very dangerous to use before details are published. I’m very skeptical of myeloma MRD by flow on the blood samples and clinically dangerous to assume results are comparable to BM Euroflow NGF or adaptive BM NGS
Welcome
Fantastic work from a world class group @ucalgary.bsky.social led by Nizar Bahlis and up and coming rock star Holly Lee who are leading the world in understanding how #myeloma patients become resistant to immunotherapies
Albertans signing a petition to leave Canada should be taken out back and beaten to a pulp, stupid Alberians
Awesome news,
Figure illustrating some content of the Python course for biology students at UniBonn
“Analysis of Biological Data with Python” started today for biology bachelor students 🧬🐍
Want to learn Python for data analysis?
Slides are freely available:
github.com/bpucker/teac...
#Python #DataAnalysis #Biology #OpenScience #BigData #Bioinformatics #DataScience @puckerlab.bsky.social
Also very cool: a study from 2024 found that in Scottish women fully vaccinated with the HPV vaccine in 2008, *no* cases of cervical cancer have been found. Not a single one. 100% success rate.
Co-author: "It is [now] possible to make cervical cancer a rare disease.”
www.bbc.co.uk/news/article...
Lamar to Flowers
B - t(11;14), is the answer you are looking for BUT by the new IMS/IMWG high risk consensus genomic staging only C - deletion 17p is NOT standard risk so the correct answer in 2026 is A, B, AND D!
Registration is OPEN! 🧬 Join the CGC on January 27th for an essential webinar: "Guidelines for the testing and reporting of cytogenetic results for risk stratification of multiple myeloma."
🗓 Date: Tuesday, Jan 27, 2026 🕐 Time: 1:00 PM – 2:00 PM ET 🔗 Register Here: buff.ly/vlo99BZ
I just recalled some older Nanopore data and started fixing the assembly when I came across a 'weird' contig. Blasting it generated a lot of almost perfect hits to 'plasmids' all across the tree of life. Turns out it was the spike in control DNA that comes with the ONT library prep kit...
{ggview} can print plots to Viewer (Rstudio or Positron) with true scaling. Adjust plot settings and see the final proportions immediately.
Save the plot once 👌
e.g.:
ggplot(...) +
ggview::canvas(width = 220, height = 220*2/3, units = "mm", dpi = 300)
per @nrennie.bsky.social #datavis #rstats
"Japanese curry, Officer's mess, Battleship Mikasa, c. 1906. | Old Tokyo" A group of men in white uniforms of Japanese traditional design sit on the floor around a tablecloth spread with rice dishes and curries.
Thiamine (vitamin B1) is essential to metabolism & deficiencies produce a condition called beriberi.
I want to tell the story of why the Japanese Army suffered from it until 1926, while the Japanese Navy did NOT after 1884.
A cautionary tale about science denialism & the resulting policy choices.
San Antonio Breast Cancer Symposium Original Article | Dec. 9, 2025 | NEJM.org Teclistamab plus Daratumumab in Relapsed or Refractory Multiple Myeloma (MajesTEC-3) Figure 2. Overall Survival. The NEJM identity sits at the bottom.
In relapsed or refractory multiple myeloma, teclistamab plus daratumumab significantly prolonged progression-free survival as compared with DPd or DVd (83.4% vs. 29.7%) and had higher response rates. Full MajesTEC-3 phase 3 trial results: nej.md/4431DUD
#SABCS25 | @sabcs.bsky.social
#ash25 Another potentially practice changing study presented by myeloma superstar Marivi Mateos - Ph3 of Tec-Dara in RR MM #mmsm 1/n
