Kevin Stachelek

Scott Edmunds cuts the cake at the 2025 GigaScience birthday party at ISMB/ECCB 2025

An open letter about the recent cuts at GigaScience: www.open-bio.org/2025/09/30/2...
(open for signatures until the end of October)

#OpenScience #OpenData #GigaScience

TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing Nature Communications - The authors report TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA sequencing. TEQUILA-seq uncovers transcript isoforms and RNA...

rdcu.be/eITLE

GitHub - MorrissyLab/mosaicMPI: mosaicMPI: mosaic multi-resolution program integration mosaicMPI: mosaic multi-resolution program integration - MorrissyLab/mosaicMPI

I ran NMF via github.com/MorrissyLab/... with scRNA-seq data. I don’t recall any installation struggles

Ok, my buddies and I were ALL ABUZZ as we read about #nanonext last night 👀 Have you seen it?! Data exchange between R and Python made way more accessible? I have questions!! www.tidyverse.org/blog/2025/09...

#databs #rstats #python

Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing. #SingleCell #scRNAseq #FullLengthRNA #GigaByte
gigabytejournal.com/articles/158

Video: How Los Angeles Police Officers Broke Protocols and Injured Protesters A Times analysis of videos and interviews with police, protesters and legal experts found that officers misused 40-mm sponge rounds at immigration-raid protests.

I contributed footage to this excellent visual investigation from @devonlum.bsky.social at the @nytimes.com www.nytimes.com/video/world/...

Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored an AI researcher going back to school for immunology

HIGHLY recommend reading this if you work in the intersection of AI and biology: rachel.fast.ai/posts/2025-0...

then again, perhaps don't read it if you want that flashy Nature paper

Ohtani bored watching Dodgers take BP vs the Yankees

‘The Rehearsal’ Finale Reveals What Season 2 Was Really About — and It’s Not Just Planes: TV Review In the Season 2 finale of his HBO series 'The Rehearsal', Nathan Fielder reveals what the aviation-centric season was really about.

I wrote about the finale of THE REHEARSAL s2: variety.com/2025/tv/revi...

Just a reminder that Öztürk is in jail for writing this op-ed. That’s it. This is despicable.
www.tuftsdaily.com/article/2024...

Everyone loves describing their dissertation research to non-academics, right? Now try that on the witness stand in a second language on a Zoom connection from ICE custody!

YouTube video by Pediatric Oncology Knowledge Center Accelerating Childhood Cancer Research through Data Science Training Workshops

Hear from Drs. Eric Wafula and Elena Vasileva who sat down with us to share their experiences at Data Lab training workshops! Learn why they believe our #SingleCell #RNASeq courses are essential for #PediatricCancer researchers who want to perform their own analysis.

The working knowledge and accessory command line skills that I learned from this book were essential in moving beyond scattered tutorials. Thanks for writing it!

my god

Untangling the hairball using statistical inference – Tiago P. Peixoto Inverse Complexity Lab

"The seductive futility of network visualization"

skewed.de/lab/posts/ha...

The federal tech workers facing down DOGE What it's like to be a federal worker during the dark days of Elon Musk's DOGE campaign

As DOGE began infiltrating government agencies and targeting federal staff for termination, I started interviewing tech workers on the front lines. With the mass layoffs unfolding today, and with their permission, I'm sharing their stories.

This is what it's been like to endure Musk's campaign.

A yellow and brown bog shaped like a heart in a darker forested area.

Happy Valentine’s Day to all the bog lovers out there. This heart shaped bog is in the beautiful Northwest Territories, Canada. Often unappreciated, bogs will win your love with their beauty, mystery, and strength. They clean our water, produce food and biodiversity, and store carbon. Let’s ♥️ them

Revised and Extended: What's Happening Inside the NIH and NSF

I’ve unfortunately needed to add more material to my post from yesterday. The re-election of Donald Trump is looking like the biggest act of American self-destruction since the Civil War.

Same link, new title and some updates.

To "celebrate" the inauguration I've donated money to Planned Parenthood, Translifeline and The Trevor Project. The next few years are going to be chaotic so I'll be striving to ignore the things outside my control while doing my best to support the communities that I can help.

Hello! We’re the Alex’s Lemonade Stand Foundation Childhood Cancer Data Lab. 👋 We build data and analysis tools and offer workshops designed to accelerate pediatric cancer research. Check us out at ccdatalab.org! We’re excited to connect with the community and share our resources with you.

Since I'm seeing it everywhere:

I worked in LA City Hall when the budget passed. Our office voted No. But the idea that LAFD was "defunded" to increase the LAPD budget is not accurate. Both got increases due to salary hikes. LAFD's deal just happened after the budget process -- LAPD's was before.

Wildfire danger: Southern California braces for 'life-threatening' Santa Ana winds Power shutoffs are planned as wind gusts up to 100 mph could rattle the region for several days this week.

UPDATED: Mountain wave windstorm could bring gusts up to 100 mph in Pasadena, other parts of LA County from Tuesday-Wednesday.

“Everyone needs to be prepared for a very dangerous, destructive and potentially life-threatening windstorm."
#CAwx
www.sfchronicle.com/weather/arti...

Hey there! We've got some fantastic news to share! We have a fresh batch of Western Straight 3x3 Alfalfa Pasture blocks for just $200 each when picked up. The attached scale ticket photos confirm that these bales average 886.667 lbs per bale – I have been selling hay for over a decade and if I did not see the scale ticket I would not believe it! At just $500 a ton (remember, we sell by the bale, not weight), these are a steal. And here's the best part – these giant bales aren't compressed, so they'll flake apart when you open them, revealing their amazing leaf retention and stunning appearance. They're from the same supplier who provides our awesome 3-string western alfalfa bales. We're open Monday to Friday from 9am to 6:30pm and weekends from 10am to 6pm. If you have any questions, feel free to call or text us at [hidden information]. And when texting or facebook messeging , feel free to ask more than just "Is this available?" Let's chat about these incredible bales! We Do offer Delivery services.

Let’s chat about these incredible bales!

It is that time of the year again when @odedrechavi.bsky.social and I do our annual “your favorite paper of the year” thread. Now only on Bluesky! Please link to your favorite paper in the comments and say a few words why you loved it so much. Happy holidays and happy reading!

A perfect thesis is never finished and a finished thesis is never perfect

Check out this bombshell publication by Michael Fischbach @mfgrp.bsky.social and coworkers @stanford-chemh.bsky.social @stanfordmedicine.bsky.social, imagine a cancer immune therapy/vaccine where treatment begins and ends with a painless topical skin treatment! 🤯

www.nature.com/articles/s41...

Keck School of Medicine of University of Southern California A Dissertation Defense by Kevin Stachelek Candidate for Doctor of Philosophy Cancer Biology and Genomics “Retinoblastoma progression-related somatic copy number alterations correlate with altered transcriptomic states and cell cycle distributions” Mentor: David Cobrinik, M.D., Ph.D. Wednesday, Dec 4th, 2024, 9:30AM PST Norman Topping Tower (NTT) 7409 USC/Norris Comprehensive Cancer Center and Hospital, 1441 Eastlake Ave, Los Angeles, CA 90033

I'll be presenting my dissertation defense as part of the USC PIBBS PhD program in Cancer Biology and Genomics a week from today. This will be a summary of my years of work to better understand retinoblastoma genetics. Nervous and excited!

Thanks! tflow was really important in getting me started with targets. The biggest hurdles have been difficulty managing ggplots and consequently using filename targets. I like to have per figure targets with plot and possibly corresponding table outputs. Working to reorient around smaller functions

How does this work if you are operating on a single df in a series of operations? Do you have slight variations on the df name? Am I understanding your point?

Clonally related cells are transcriptomically similar -- enough to get surprisingly great recall and precision when grouping cells into clones.
t.co/WCKKSF0dFR

Yes, I'm still a pseudotime hater -- this is a distinct approach. Data don't even need to be in a tree shape.