Systems biology and pharmacology, applications to cancer and brain tumors, combining experiments and modeling with interest in single cells and heterogeneity
Clemson, SC
Joined July 2015
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Birtwistle Lab retweeted
The abstract deadline for #SACB2027 is Friday, Oct 16! Join us Jan 20-23 at CU Anschutz (Aurora, CO). Submissions are open for oral & poster presentations, a special session on Spatial Single-Cell Cancer Systems Biology, and our Postdoc Highlight Session! sacbmeeting.org/
Birtwistle Lab retweeted
Earlier this week I posted an example of a fake western blot provided by ThermoFisher to demonstrate the validity of a p53 antibody. I considered it an amusing curiosity. In fact ThermoFisher has systematically manipulated antibody validation data. Short Thread... 🧵
How can we use detailed mechanistic models of stochastic single-cell behavior to interpret drug dose viability response experiments? Our new paper led by Arnab Mutsuddy describes how using in silico lineage tracing: doi.org/10.1371/journal.pcbi…
The work enables clean comparison of simulations to data by tracking individual division and death events and starting with an asynchronously cycling population, generation of novel analytics such as simulated lineage dendrograms and lineage-resolved biochemical dynamics, studying biological mechanisms related to drug targets, and hypothesis generation for factors associated with drug sensitivity and resistance.
We had a lot of fun with @MarkBlenner over the past several years developing and experimentally demonstrating the concept of fluorescent protein barcodes using spectral readouts, recently published: pubs.acs.org/doi/full/10.102…
That is related to previous work on MuSIC (multiplexing using spectral imaging and combinatorics). pubmed.ncbi.nlm.nih.gov/3033… pubmed.ncbi.nlm.nih.gov/3746….
Our high-throughput, 96-well western blot paper is out! pubs.acs.org/doi/10.1021/acs… If anyone is interested, contact Blotting Innovations–blottinginnovations.com or @BetterBlotting!
From the original pre-print, we added data showing MW ranges resolvable with different acrylamide % gels (overall 10 to 250 kDa), limit-of-detection equivalency with a matched regular western, and a dual color blot (thank you to @AzureBiosystems and their solid instruments!).
Birtwistle Lab retweeted
RNAseq is commonly performed. We compared N=30 wild-type Bl6 mice to an N=30 heterozygotic knockout with a phenotype, and then downsized. We found you need at least an N= 8-12 to avoid a >50% false positive rate. A 2nd line confirmed the finding.
biorxiv.org/content/10.1101/…
Birtwistle Lab retweeted
Professor Edward H.Sargent a Canadian Scientist, who published many papers in top journals i.e., #science and #Nature. He wrote 10 tips on how to write papers. @PhDvibe @PhDVoice @Labiofy #PhDposition #phdlife #PhD #postdoc #chemtwitter #Science #AcademicChatter
Birtwistle Lab retweeted
There's a lot of excitement about foundation models and their ability to learn biology 🧬💻
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
biorxiv.org/content/10.1101/…
ALT Beeswarm plot of the double perturbation predictions. The Additive model outperforms GEARS, scGPT, and scFoundation by a large margin
ALT Line plot of the accuracy of the predictions that are most different from the additive model. The No Change model outperforms GEARS, scGPT, and scFoundation.
ALT Beeswarm plot of the single perturbation predictions. The linear model perform as good as GEARS, scGPT, and scFoundation.
Dr. Xiaoming Lu, who has been a rock in my lab for the past 5 years or so, is relocating to the Raleigh-Durham NC area (Duke, UNC, NC State) with her family, and is looking for a new lab home. If anyone needs someone to build their lab around, she would be an amazing choice.
She is extremely hard working and has solid skills in so many things cell and molecular biology. She is incredible with molecular cloning and with mentoring students. On top of that, for a few recent projects, she taught herself python programming and wrote some pretty complex analysis scripts which was the difference in us getting our experiments to work out (e.g. linear unmixing of spectral flow cytometry data with her as first co-author 10.1021/acs.bioconjchem.4c00246, and non-standard alignment analysis of nanopore sequencing data in a soon to be pre-print with her as first author).
I wish she were staying here but I will be really happy for her to find a new lab to call home!
If anyone is interested, you can message / email me, or email her at [email protected] or [email protected] . If you know of anyone looking for a person like Xiaoming, please do share this with them!
I’m happy to share our recent work exploring how to increase fluorescence multiplexing with antibodies (pubs.acs.org/doi/10.1021/acs…)!
We are excited to see how far we can push this idea! Full spectrum flow cytometry panels are getting quite large (~40; 10.1002/cyto.a.24213), but there is substantial room for combination probes.