Mark

RNAseq counting tools are not perfect. I simulated 240 GTEx samples to test multiple tools. Below I show the difference between actual and estimated counts for each simulated sample. But, what is causing this? And will it affect differential expression? (1/7) #Bioinformatics

@JohnHolbein1 Not really sure this means what you think. E.g. if someone shows a plot with only differentially expressed genes, the z scores will be shifted to the left and right. Nobody wants to see a heatmap with 20k rows

Look at the distribution of z-values from medical research!

@MedscapeErik @Mozziebites Which genotype?

Japanese encephalitis virus is spreading in Australia. Experts are calling for increased awareness of this potentially dangerous disease. Protection against mosquitoes, which bear the virus, is encouraged. @Mozziebites #infectiousdiseases2025 #Australia medscape.com/viewarticle/ja…

anndata 0.12 is out now! We have lots of great features that we hope address some persistent needs. Here are some of the highlights!

Short Tweetorial about a recent publication from our lab by @Sanbomics on detecting cellular #senescence in scRNA-seq data nature.com/articles/s4146… in @NatureComms with a great @sanbomics video tutorial youtube.com/watch?v=mc7rnl… #computationalbiology #aging

Thrilled to share this new publication from our lab on muscle wasting in #Cancer and #vascularbiology, spearheaded by Young-Mee Kim in @NatureCancer nature.com/articles/s4301…. Here is a tweetorial on #cachexia, #cancersurvivorship and #cardiovascular #health @thisisUIC

We show that muscle vasculature loss precedes cancer cachexia and identify PGC1α and INHBA as causal factors. This was a huge effort with several models, clinical biopsies, massive amounts of imaging, sequencing, bioinformatics, and much more. nature.com/articles/s4301…

@JDVance How many hearings has Trump had? Maybe we should deport him.

Call me crazy but if you got two hearings and a valid deportation order then you shouldn’t be in the United States.

@iaincheeseman Didn’t it arise from an endosymbiosis between archaea and bacteria? Is the host cell a bit anachronistic in this graphic? Not my expertise area, but I did just read some Nick Lane 😅

New preprint countdown! Mitochondria are cells within our cells. They need the same core activities - replication, transcription, translation. How do cells enable these diverse activities in both compartments? We uncover an unexpected strategy with ancient origins. Stay tuned!

@wc_ratcliff Unfortunately still get 100x more engagement here on some posts. Waiting for a day this isn’t the case and I can be gone forever.

Scientists, is it even worth the effort to post here anymore? For comparison, my twitter post about two recent big papers got a whopping 5 likes. My post at the other place got a lot of community engagement. Either the community here is dead, or algo attention is pay to play.

1/: Excited to share our new study led by Luke Zappia on feature selection methods for single-cell RNA-seq data, now published @naturemethods ! We explore how choosing features impacts reference atlases & downstream analyses. 📊📚 nature.com/articles/s4159…

@Ella_Maru I think this depends on the disease quite a bit. Maybe in chronic disease but not acute

@Sanbomics Congratulations Mark! Is senescence-driven inflammation a stronger disease trigger than cell loss?

Senescent cells contribute to disease and are found in many tissues but are hard to analyze because markers have been derived in culture and do not account for cell-type differences. Here, we define new signatures based on millions of single cells (1/5) nature.com/articles/s4146…

There are three primary ways to use SenePy: 1) as an input list in any tool that takes a gene list, such as gene set enrichment. 2) senescence scoring directly on single-cell data. 3) Database to search for senescence markers in a specific cell type. (5/5)

In addition to aging, SenePy is widely applicable in many disease contexts. We show how it can be applied to cancer, heart disease, and infection. Here is an example of senescent-like foci in infarction spatial data (4/5)

@dna_rosenberg Parse is great and cheap but still many reasons to do bulk. To sequence 5M cells at 20k reads/cell requires at least 10 S4 flow cells. That’s at least ~150k USD. Of course you don’t need to do all 5M but still need >10k reads per cell if you care about quality

Time to go big on your single cell experiments! 5M cells and 384 samples in a single experiment. No reason to ever do bulk RNA-seq again.

@nomad421 Still waiting for the promised day one reduction in grocery prices

The Trump Bump!

@TedNugent You own a store. Your store gets robbed. Elon, out of his mind on ketamine, sh*ts on the floor and incoherently blames the delivery man with proof he scribbled on a napkin. You believe him. Your store goes bankrupt. You’re an idiot.

@DaleStarkA10 Bro doesn’t know what the House of Representatives is