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matthew.bendall @mlbendall.bsky.social · Jul 22

Hi Rebecca, for the data in the paper paper and in the current version of the software, we are removing genic (exonic) reads downstream of the Stellarscope output matrix. Future plans are to implement this as an option in the main workflow.

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matthew.bendall @mlbendall.bsky.social · Jul 22

7/ 🔗 “A single-cell transposable element atlas of human cell identity” Cell Reports Methods, 2025. doi.org/10.1016/j.cr...

TY: @bhavyasighs.bsky.social @hamarillo.bsky.social @3rduarte.bsky.social @weillcornell.bsky.social

🔄 RT to share with colleagues in #singlecell and #genomics!

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matthew.bendall @mlbendall.bsky.social · Jul 22

6/ 💡 Key takeaway: TEs aren’t "genomic junk"—they’re informative regulators of cell identity and offer additional layers of biological insight.

www.eurekalert.org/news-release...

Turning 'junk' DNA into gold

Mining the rich uncharted territory of the genome or genetic material of a cancer cell has yielded gold for Princess Margaret scientists: new protein targets for drug development against prostate canc...

www.eurekalert.org

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matthew.bendall @mlbendall.bsky.social · Jul 22

5/ Stellarscope is open‑source, scalable, and built to integrate with existing scRNA‑seq workflows—empowering labs to explore TE dynamics at single‑cell resolution.

github.com/nixonlab/ste...

GitHub - nixonlab/stellarscope: Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing

Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing - nixonlab/stellarscope

github.com

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matthew.bendall @mlbendall.bsky.social · Jul 22

4/ This TE atlas uncovers novel signatures within immune compartments, offering new avenues for cellular taxonomy and understanding TE biology in health and disease.

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matthew.bendall @mlbendall.bsky.social · Jul 22

3/ Applied to human PBMCs, it quantifies locus‑specific TE expression, which was previously hidden in standard scRNA‑seq pipelines

The surprising finding? TE activity signatures distinctly mark cell types and subsets—sometimes even more sharply than conventional mRNA markers

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matthew.bendall @mlbendall.bsky.social · Jul 22

2/ A major challenge with scRNA-seq is the low per-cell read depth - instead of having 30M reads to inform the model, we are lucky if we get 30K! To overcome this, we developed "pooling modes", where we can borrow strength from other cells to help reassign ambiguous reads.

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matthew.bendall @mlbendall.bsky.social · Jul 22

🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.

A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...

@hamarillo.bsky.social #TEHub #singlecell #genomics

A single-cell transposable element atlas of human cell identity

Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying locus-specific transposable element expression in single-cell RNA sequencing data. The authors profile human PBMCs a...

www.cell.com

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matthew.bendall @mlbendall.bsky.social · May 20

Read the full story here:
doi.org/10.1016/j.is...

A special congratulations to FIRST AUTHOR @bhavyasighs.bsky.social

Thanks to an amazing team and collaborators! @ecesarman.bsky.social @heymannjonas.bsky.social @hamarillo.bsky.social @weillcornell.bsky.social

#lymphoma #HERV #bioinformatics

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matthew.bendall @mlbendall.bsky.social · May 20

Bottom line: HERV expression can uncover hidden lymphoma biology 🧫

🧬 Inform classification
🧬 Refine prognosis
🧬 Suggest new therapeutic targets

A new frontier for cancer retrotranscriptomics!
7/

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matthew.bendall @mlbendall.bsky.social · May 20

Importantly, HERV-based subtypes predict prognosis.

Clusters enriched for plasma cell-like signatures had the poorest survival — a finding invisible in gene-only classifications.

6/

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matthew.bendall @mlbendall.bsky.social · May 20

In DLBCL, we identified 7 distinct HERV-driven subtypes, refining the traditional 3-subtype COO model.

Some "unclassified" DLBCLs actually fit into new HERV-defined groups — with distinct survival outcomes! 📉📈

5/

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matthew.bendall @mlbendall.bsky.social · May 20

Findings:

- Healthy B-cells show dynamic HERV activity during differentiation.
- Lymphomas retain HERV signatures from their cell of origin (COO).
- BL subtypes cluster by EBV status better with HERVs than with genes!

4/

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matthew.bendall @mlbendall.bsky.social · May 20

We created the first locus-specific map of HERV activity in:
- Healthy B cells (Naïve, Memory, Germinal Center subtypes)
- Diffuse large B-cell lymphoma (DLBCL)
- Follicular lymphoma (FL)
- Burkitt lymphoma (BL)
🎯 Using RNAseq + #Telescope quantification.

3/

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matthew.bendall @mlbendall.bsky.social · May 20

Endogenous retroelements (EREs), like HERVs, make up ~8% of the human genome. Their expression is often overlooked — but we found they hold key information about B-cell identity, both in healthy germinal centers and in malignancy!

2/

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matthew.bendall @mlbendall.bsky.social · May 20

🚨 Excited to share our latest work: 🚨

@bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!

Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful...

#TEsky #TEworldwide
1/

Locus-specific human endogenous retroviruses reveal lymphoma subtypes

Genomics; Virology

www.cell.com

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matthew.bendall @mlbendall.bsky.social · Mar 26

What does this mean for DCPS teachers/admins? Are they required to comply?

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matthew.bendall @mlbendall.bsky.social · Mar 26

This is very upsetting

Brad Johnson @climatebrad.hillheat.com · Mar 26

ICE agents are attempting to enter DC public schools today, have been turned away at least one school so far.

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matthew.bendall @mlbendall.bsky.social · Mar 9

Thanks Bhavya glad she has scientists like you to look up to!

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Reposted by matthew.bendall

Sara Rouhi @rouhiroo.bsky.social · Mar 8

She’s our future!! DC was ⚡️!

Hope we can continue ✊✊✊ by SIGNING/SHARING the declaration to #defendresearch from #censorship and erasure

Join us and share widely #standupforscience: tinyurl.com/3bwuc38f bc #scienceforall is the only kind of science worth doing.

Declaration To Defend Research Against U.S. Government Censorship

This Declaration is a call to action for the scholarly communication community and additional stakeholders to condemn and resist recent acts by the U.S. government to censor scholarly research. We ca...

tinyurl.com

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matthew.bendall @mlbendall.bsky.social · Mar 8

Yes! Unfortunately as DC residents we have no (voting) representation. For all those who do have representation in the US please contact your representatives and let them know that preserving science is important for us now and for the generations to come!

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matthew.bendall @mlbendall.bsky.social · Mar 8

My writing (non-spell checked) would support this conclusion. But somehow I can spell correctly when I’m coding?

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matthew.bendall @mlbendall.bsky.social · Mar 8

There was one poster, forget exactly what it was but something about ELONgated MUSKrats. She was so pleased when she got it.

matthew.bendall @mlbendall.bsky.social · Mar 8

I spent a lot of the rally trying to explain the posters to my 7yo daughter who is just starting to read. Like, “why did they write f-word trump?”

Glad I didn’t have to get into it with this one.

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