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Mae Woods

@maewoods.bsky.social

Passionate about compbio | high performance computing | mathematics | digitalization | cell & gene therapy. Opinions are my own. GitHub: https://github.com/MaeWoods

597 Posts1184 Follower1055 Folgt
Kermit Murray@kkmurray.bsky.social · 3w ago

(BioRxiv All) Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics: Single-cell proteomics (SCP) currently lacks validated benchmarking standards, and cell annotation often relies on transcriptomic proxies.… #BioRxiv #MassSpecRSS

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

Single-cell proteomics (SCP) currently lacks validated benchmarking standards, and cell annotation often relies on transcriptomic proxies. Unsupervised clustering offers a proxy-free alternative, but its success depends on biological signal outweighing technical variation. In homogeneous samples this is achievable, but in heterogeneous populations, where closely related cell types differ only subtly, technical variation can dominate the clustering and obscure the biology needed for annotation. To address this, we developed an integrated experimental and computational pipeline for protein-level cell annotation and applied it to human PBMCs as an immune-cell test case. We isolated T cells, B cells, monocytes, and NK cells by negative-selection sorting to build a high-fidelity reference. In parallel, unsorted PBMCs from the same donor were processed on a cellenONE and acquired using label-free DIA on an Orbitrap Astral Zoom. Using the labeled reference, we systematically benchmarked normalization, imputation, and clustering methods to assess their effect on cell-type separation. Unsupervised analysis resolved functional subpopulations within each lineage, and a probabilistic SCP classifier trained on these annotations identified the corresponding cell types and states in the unsorted PBMC fraction, validating the pipeline on unenriched, heterogeneous samples. Together, this work delivers an analytically benchmarked SCP workflow that resolves immune lineage and cell-state heterogeneity in human PBMCs and provides a classifier-ready, protein-level reference for immune-cell assignment.

dlvr.it

Helen Branswell 🇨🇦@helenbranswell.bsky.social · 2mo ago

Have you ever seen this iconic image of the Ebola virus, from the first known outbreak in DRC in 1976? An electron microscopic image, it was captured by #CDC 's Fred Murphy, a virological giant and a very kind interviewee. He died yesterday. He will be missed, but his scientific legacy lives on.

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Wandering Scientist @wandsci.bsky.social · 3mo ago

My go to example of this sort of thing is the study of weird thermophilic bacteria gave us PCR, upon which so much of modern biological research and its many applications (including drug discovery!) depend

Jonathan Pritchard@jkpritch.bsky.social · 3mo ago

People often think about risk as referring to (i): Can the project achieve its specific aims? But really what NIH should want is (ii): studies with low probability of huge long-term impact. Here, think of work on gila monster venoms (leading to GLP-1 meds) or bacterial immune systems (crispr)

Dementia Researcher@dementiaresearcher.bsky.social · 4mo ago

Fully funded PhD at Newcastle University studying NHS hospital care pathways for people with multiple long term conditions using mixed methods and data science. Closing date: 24th May www.dementiaresearcher.nihr.ac.uk/job/phd-mltc...

PhD: MLTC and Hospital Care Pathways - DEMENTIA RESEARCHER

Newcastle University PhD to study hospital care pathways for people with multiple long term conditions, using mixed methods and NHS data.

dementiaresearcher.nihr.ac.uk

The Jackson Laboratory@jax.org · 4mo ago

🧬🧪 New from JAX: Scientists have corrected an extremely rare and life-threatening genetic disease of the liver in mouse models and human patient cells, using the gene-editing approach that served as the basis for the historic, life-saving treatment of Baby KJ Muldoon in 2025.

jax.org

Kaggle@kaggle.com · 4mo ago

Calling NeurIPS 2026 researchers! 🚀 The CFPs for the evaluations & datasets track are officially out, and we want to support you if you're working on a submission. When you build your benchmark on Kaggle Benchmarks, you get complimentary compute, top model access, and exposure to 30M+ users.

Anne Carpenter@drannecarpenter.bsky.social · 5mo ago

I'm moving to Purdue University as a tenured professor this summer! Excited to hire postdocs there and get a lab up and running with @runxishen.bsky.social as co-lead. More details: www.linkedin.com/posts/anneca...

I'm thrilled to announce I'm joining Purdue University as a tenured professor this August! Purdue holds a special place in my heart: its undergraduate program prepared this Indiana farm girl…...

I'm thrilled to announce I'm joining Purdue University as a tenured professor this August! Purdue holds a special place in my heart: its undergraduate program prepared this Indiana farm girl remarkab...

linkedin.com

VivienM@vivienm.bsky.social · 5mo ago

The Association for Computing Machinery (ACM) Prize in Computing has gone to Matei Zaharia for his "visionary development of distributed data systems and computing infrastructure" that has supported large-scale machine learning, analytics and AI. 1/2

Lior Pachter@lpachter.bsky.social · 5mo ago

Happy to see multiple optimizations to the edgePython codebase, with more on the way: github.com/pachterlab/e... I have already experimented with porting to Rust, and have it mostly done (with some extra speedup); useful to complete an end-to-end single-cell Rust ecosystem.

GitHub - pachterlab/edgePython: Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.

Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data. - pachterlab/edgePython

github.com