You may be able to make them “feature barcodes” like an ADT library by putting them into a csv and referencing that with -feature_ref and running the CITE-seq workflow. That would bypass star but would require the custom library has the same structure as the ADT with barcode and UMI in R1.

would love to be added!

Amazing starter pack, would love to join the list!

Hoping to engage with everyone on here to discuss science. Reach out for collaboration. If you made it this far, PDFs of everything and links to open source software are on this website mattpm.net !

Prior to all this I focused on clinical diagnostics with @drchrishourigan.bsky.social pubmed.ncbi.nlm.nih.gov/27544285/. I'm returning to the clinical lab for residency training where I aim to develop clinical tools to prognosticate, treat and reprogram immune system subtypes across diseases.

This pairs well conceptually w/ our earlier work showing how the same temporally stable immune setpoint correlates with later plasmablast activity with differing context-dependent outcomes:
- productive vaccine response in healthy people
-disease flares in SLE patients
www.nature.com/articles/s41...

With Chen Zhao, Arun Rajan, & colleagues at NCI, we identified a stable immune setpoint featuring TEMRA cells, metabolic rewiring, and elevated resting inflammatory tone in DCs—all linked to myositis following anti PD-L1. (updates soon)
www.biorxiv.org/content/10.1...
jitc.bmj.com/content/9/Su...

If we can identify a baseline immune state linked to later outcomes, we can risk-stratify patients and intervene earlier. For example, oncologists would benefit from knowing the likelihood of a patient developing immune-related adverse events (e.g. severe autoimmunity) after checkpoint inhibition.

Using the dsb method and mixed modeling/network analysis, we found that high responders to seasonal flu vaccines have a "Naturally Adjuvanted" baseline immune setpoint—mimicking the cell states specifically induced by an adjuvanted vaccine. doi.org/10.1016/j.im...

With @tsanglab.bsky.social, I focused on advancing the concept of measuring homeostatic baseline immune system setpoints in humans. This framework was a cornerstone for how I thought about advancing precision medicine in immunology (far beyond vaccination alone). pubmed.ncbi.nlm.nih.gov/26187853/

I used dsb in Ken Smith's lab, where Aimee Hanson and I observed stress erythropoiesis and the multicell circuitry of inflammatory anemia in humans, which was related to long-term symptoms post-viral infection. www.nature.com/articles/s41...

These experiments inspired our simple method for ADT denoising, dsb, which has been widely adopted and is available for R and Python github.com/niaid/dsb