Adam Marblestone

Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance Alzheimer's disease (AD) is a relentlessly progressive, fatal neurodegenerative disorder associated with widespread aberrant proteomic changes. The full extent of protein dysfunctions in AD and their ...

The hits keep on coming from @parallelsq.bsky.social! Today we released an exciting use-case for plexDIA in single cell analysis of #alzheimer's disease, characterizing dysregulation of the 20S proteasome. #TeamMassSpec #Proteomics

www.biorxiv.org/content/10.1...

E11 Bio is launching Volara: an open-source Python library for block-wise processing of large volumetric microscopy datasets! 🧪🔬

Volara features block-wise task abstractions, making scalable image processing more accessible, robust, and repeatable.

Read more: e11.bio/blog/volara

Kimina Prover Demo – AI-Powered Proof Validation in Action Try the live demo of Kimina Prover – a new AI-powered assistant for interactive proof validation. Test it now!

Kimina: Interactive mathematical proof assistant. demo.projectnumina.ai #AI #ITP #LeanProver #Math

We just released JMod: an open source software supporting multiplexed DIA.

It supports parallelization in both the mass domain (plexDIA) using small mass offsets and in the time domain (timePlex).

It enabled 27-plex DIA & opens the door to further scaling 🚀

www.biorxiv.org/content/10.1...

Believe it a not, a third multisite connectomic project also lost funding. The multi-PI R01 led by @darbly.bsky.social with myself and @bassemh.bsky.social as co-PIs.

This is the platform that was farthest along, with a known safety record (RFK jr's conspiracies notwithstanding). There are other viable platforms that may work out, but mRNA and SA-mRNA may be the best shot at being able to get a vaccine out within 100 days of a pandemic being recognized

Multiplexed proteomics is getting a big boost 🚀

It's not just speed & scale ...
It's also data quality, depth, rich spectra improving de novo sequencing & accurate quantification.

biorxiv.org/content/10.1...

I am very enthusiastic for improving fragmentation spectra & the research this empowers.

This means increasing the sensitive and scope of sequencing the immunopeptidome ==> better cell therapies.

biorxiv.org/content/10.1...
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Happy to share our tools & resources !

Links to our preprints:

timePlex (multiplexing with time-offsets): www.biorxiv.org/content/10.1...

JMod (search software for joint-modeling): www.biorxiv.org/content/10.1...

PSMtag (novel mass tag for 9-plexDIA): www.biorxiv.org/content/10.1...

Amazing amount of progress made advancing high throughput proteomics in such a short time from the team at @parallelsq.bsky.social 🚀

Increasing throughput in mass spec proteomics requires new ways to model the increased complexity of the spectra.
We are delighted to share JMod, our new open source software developed at @parallelsq.bsky.social , which enables new multiplexing approaches.

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www.biorxiv.org/content/10.1...

We are excited to introduce ‘time’ as a new domain for proteomics multiplexing!

It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA

Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀

🧪 Transforming biomedical discovery needs proteomics that is specific and accurate, but also faster and cheaper

@parallelsq.bsky.social is proud to introduce 9-plex PSMtags: a new mass tag that improves sequencing and increases throughput in sensitive proteomics 👇

www.biorxiv.org/content/10.1...

JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics The throughput of mass spectrometry (MS) proteomics can be increased substantially by multiplexing that enables parallelization of data acquisition. Such parallelization in the mass domain (plexDIA) a...

....and the data analysis program to sift through all these data!
www.biorxiv.org/content/10.1...

Increasing mass spectrometry throughput using time-encoded sample multiplexing Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate at which samples can be analyzed remains limiting. Throughp...

We've also been working on multiplexing with time offsets
www.biorxiv.org/content/10.1...

PSMtags improve peptide sequencing and throughput in sensitive proteomics Mass spectrometry-based proteomics enables comprehensive characterization of protein abundance, function, and interactions. Label-free approaches are simple to implement but challenging to scale to th...

So excited to share our novel mass tags for multiplexing DIAa s DDA data acquisition in BioRxiv
www.biorxiv.org/content/10.1...

📣 TWO EXCITING NEW LEAN LECTURES!

Just released: Two Strachey Lectures from @compscioxford.bsky.social featuring Leo de Moura (Chief Architect, Lean FRO) and Kevin Buzzard (Professor, Imperial College). A thread on these must-see talks 🧵👇

#LeanLang #LeanProver

Imprint Labs Launches to Pioneer "Forensic Immunology" For Chronic Disease Imprint has raised $15 million to decode the body's immune memory for understanding chronic diseases, such as long-COVID and psychiatric disorders.

📣Major thanks to @faylinphd.bsky.social at GEN News for this lovely piece on IMPRINT! It was a pleasure for our founders — @beckbrachman.bsky.social, @victorgreiff.bsky.social, and Raymond Alvarez — to speak about our mission and research, and being NYC's first FRO.

@convergentresearch.bsky.social

✨E11 Bio is hiring a Chief of Staff / Project Manager!

This unique role blends scientific project management with day-to-day operations—and gives you a front-row seat and bird’s-eye view as we advance the field of connectomics toward mammalian brains.

Job posting: jobs.lever.co/convergentre...

This week, PTI will be sharing 4 preprints, including:

⬛️ New tools & mass tags for plexDIA

⬛️ 27-plex DIA enabling 500 samples / day

⬛️ Improved de novo sequencing of peptides

⬛️ Protein degradation dysregulation in Alzheimer's

Check out @parallelsq.bsky.social for updates

🚀

Come work with us at EvE Bio in Durham, NC!

EvE's Assay Dev team is looking for a pharmacology scientist to develop new cell-based screening assays. While this is a temporary position (filling in for a scientist on family leave) it has potential to become permanent.
jobs.lever.co/convergentre...

Wake up, babe. EvE Bio's data release #4 just dropped.

1.4k Rx drugs, 85 targets & counting:
237,490 combinations screened (mode/target/compound)
8 median agonists per target (potency < 1 uM)
31 median antagonists per target (potency < 1uM)

🧪Browse or DL (for non-commercial use) at evebio.org/data

🧪 EvE Bio's biggest public data release (#4) yet!

1.4k Rx drugs screened for 24 new potential off-targets including adrenergic, apelin, muscarinic, dopamine, gastrin-releasing, orexin, 5-HT, neuromedin, opioid, prostaglandin, sphingosine, somatostatin & neuromedin receptors. evebio.org/data

Excited to co-found and help lead @imprintlabs.bsky.social —a focused effort to decode the immune system’s memory through cutting-edge computation and experimentation. Grateful to be on this journey with an exceptional team.

Press Release May 2025 — Imprint FRO Imprint FRO launches with $15M in funding

🧵 Today, IMPRINT, a pioneering new nonprofit initiative, is announcing $15 million in philanthropic funding to advance our work to decode the body's immune memory and uncover the causes of chronic diseases.

#Immunology #Biotech #BiotechResearch

Jobs — Imprint FRO Join our team—current openings at Imprint

Looking for a job in immunology or biotech research?
✨IMPRINT is #hiring! ✨

Join us to help revolutionize how we decode the body’s immune memory, uncover the causes of chronic diseases, and drive breakthroughs in autoimmunity and neuropsychiatric research.

#BiotechJobs #Immunology #sciencejobs

It seems likely that the brain directs more or less energy to different sets of neurons based on their importance to carrying out current task, but do we know the mechanism by which it does that? Does it make neurons spike more/less often and if so how? Or is it an open question? #neuroscience

Nonprofit Cultivarium nets $10M to build tools for researchers studying fungi and archaea Bioengineering nonprofit Cultivarium is embarking on a three-year journey to develop tools and resources for scientists studying fungi and archaea, backed by $10 million in funding from the London- | ...

And via @FierceBiotech www.fiercebiotech.com/research/non...

We're gearing up to tackle new kingdoms of life, thanks to generous support from @wellcometrust.bsky.social. Get in touch!

Read more on our blog: cultivarium.substack.com/p/fungi-and-...