matthew bendall - mlbendall.bsky.social

Computational biologist @WeillCornell focusing on methods development, genomics, and the retrotranscriptome. Previously: @CBI_at_GWU @GWSMHS @jgi

[matthew bendall - mlbendall.bsky.social @mlbendall]

At the DC #StandUpForScience rally on Friday.

The question was “why are you here?” She came up with this on her own! (I helped her with the spelling)

So proud of her!

@michelebendall

[matthew bendall - mlbendall.bsky.social @mlbendall]

7/ 🔗“A single-cell transposable element atlas of human cell identity” Cell Reports Methods, 2025. https://t.co/cXoNMebzp4

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

[matthew bendall - mlbendall.bsky.social @mlbendall]

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

https://t.co/bOLX1XWBAA

[matthew bendall - mlbendall.bsky.social @mlbendall]

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.

https://t.co/paLB0MgOgD

[matthew bendall - mlbendall.bsky.social @mlbendall]

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

[matthew bendall - mlbendall.bsky.social @mlbendall]

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

[matthew bendall - mlbendall.bsky.social @mlbendall]

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.

[matthew bendall - mlbendall.bsky.social @mlbendall]

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: @CellRepMethods

@TheNixonLab @HOPEforHIVCure @WCM_ID

https://t.co/QM6Kcbbf4E

[matthew bendall - mlbendall.bsky.social @mlbendall]

@DCPoliceTraffic Does the 15th street closure (U to Mass) apply to the cycle track/ protected bike lane for bicycle travel?

[matthew bendall - mlbendall.bsky.social @mlbendall]

🚨 Excited to share our latest work: 🚨

We show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!

Locus-specific human endogenous retroviruses reveal lymphoma subtypes: iScience https://t.co/UGjqNxaxyC

@TheNixonLab @WCM_ID

[Daniella Fodera @DaniellaFodera]

This piece on the impacts of science funding cuts to young researchers and the future of science is so well said by a Nobel Prize winner 🙏🏻
https://t.co/puMpzfJxnC

[matthew bendall - mlbendall.bsky.social @mlbendall]

Find this post on 🦋: https://t.co/a5oFiM6iRx

[matthew bendall - mlbendall.bsky.social @mlbendall]

At the DC #StandUpForScience rally on Friday.

The question was “why are you here?” She came up with this on her own! (I helped her with the spelling)

So proud of her!

@michelebendall

[Robert Schwartz @RobSchwartzLab]

Do you or a family member have a medical illness? My NIH study section that reviews cutting edge medical research was cancelled before review. This means delayed research and discoveries. Please call your representatives and senators to support the @NIH and biomedical research.

[matthew bendall - mlbendall.bsky.social @mlbendall]

I’ve seen my feed go from almost all TEs (pre 2022) to almost nothing. Just discovered #TEsky 🦋

[matthew bendall - mlbendall.bsky.social @mlbendall]

@3RDuarte @ISPGnet @powell_tim_r Congrats Diego!

[Xiaoyu Zhuo @XiaoyuZhuo]

Our paper about TE's regulatory functions using ENCODE data has been published! https://t.co/9ngI3POHrc @twang5 @CedricFeschotte We confirmed TEs contributed 25% of regulatory elements in the human genome. We also investigated how different TEs contributed differently. /1

[David Sinclair @davidasinclair]

Exciting new research shows retrotransposons, ancient viruses making up ~1/2 our DNA, can create precise biological clocks to measure our rate of aging. This is the tip of the iceberg… 🧵

[TimePie (focus on anti-aging science) @TimePieChina]

The study shows that #retroelement #DNA #methylation can create precise age-predicting #epigenetic clocks and reveals their unique signals and utility in aging research.
By @mlbendall, @VarunDw, Lishomwa C. Ndhlovu, et al.
https://t.co/udkGqn3hLE

[Cedric🧬➰🧬Feschotte @CedricFeschotte]

💥Excited to unleash ENCOTE: Encyclopedia of Transposable Elements with cis-regulatory activity in the human genome!
Collab w @twang5 for #ENCODE led by🔥trio Alan Du, Jason Chobirko & @XiaoyuZhuo
TEs = 25% of all cCREs = 200,000+ elements!!
Deep dive! 1/n https://t.co/t9xacOAOAQ

[matthew bendall - mlbendall.bsky.social @mlbendall]

@GianniNigita @CELLECTA @CellPressNews @KeystoneSymp This link was in the front: https://t.co/llt7bPWD6e

[matthew bendall - mlbendall.bsky.social @mlbendall]

These coloring books from #KSTE23 are a hit! (Getting us a few quiet hours at home) Molecular biologist in training? Thank you @CELLECTA @CellPressNews @KeystoneSymp

[matthew bendall - mlbendall.bsky.social @mlbendall]

@GianniNigita @CELLECTA @CellPressNews @KeystoneSymp They were being distributed at a recent conference (Keystone Symposia) courtesy of Cell Press and CELLECTA