matthew.bendall
@mlbendall.bsky.social
Computational biologist @WeillCornell focusing on methods development, genomics, and the retrotranscriptome.
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.
July 22, 2025 at 5:20 PM
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.
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!
TY: @bhavyasighs.bsky.social @hamarillo.bsky.social @3rduarte.bsky.social @weillcornell.bsky.social
🔄 RT to share with colleagues in #singlecell and #genomics!
July 22, 2025 at 2:47 PM
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!
TY: @bhavyasighs.bsky.social @hamarillo.bsky.social @3rduarte.bsky.social @weillcornell.bsky.social
🔄 RT to share with colleagues in #singlecell and #genomics!
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...
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
July 22, 2025 at 2:47 PM
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...
www.eurekalert.org/news-release...
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.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
July 22, 2025 at 2:47 PM
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.com/nixonlab/ste...
4/ This TE atlas uncovers novel signatures within immune compartments, offering new avenues for cellular taxonomy and understanding TE biology in health and disease.
July 22, 2025 at 2:47 PM
4/ This TE atlas uncovers novel signatures within immune compartments, offering new avenues for cellular taxonomy and understanding TE biology in health and disease.
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
The surprising finding? TE activity signatures distinctly mark cell types and subsets—sometimes even more sharply than conventional mRNA markers
July 22, 2025 at 2:47 PM
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
The surprising finding? TE activity signatures distinctly mark cell types and subsets—sometimes even more sharply than conventional mRNA markers
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.
July 22, 2025 at 2:47 PM
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.
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
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
May 20, 2025 at 8:44 PM
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
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
Bottom line: HERV expression can uncover hidden lymphoma biology 🧫
🧬 Inform classification
🧬 Refine prognosis
🧬 Suggest new therapeutic targets
A new frontier for cancer retrotranscriptomics!
7/
🧬 Inform classification
🧬 Refine prognosis
🧬 Suggest new therapeutic targets
A new frontier for cancer retrotranscriptomics!
7/
May 20, 2025 at 8:44 PM
Bottom line: HERV expression can uncover hidden lymphoma biology 🧫
🧬 Inform classification
🧬 Refine prognosis
🧬 Suggest new therapeutic targets
A new frontier for cancer retrotranscriptomics!
7/
🧬 Inform classification
🧬 Refine prognosis
🧬 Suggest new therapeutic targets
A new frontier for cancer retrotranscriptomics!
7/
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/
Clusters enriched for plasma cell-like signatures had the poorest survival — a finding invisible in gene-only classifications.
6/
May 20, 2025 at 8:44 PM
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/
Clusters enriched for plasma cell-like signatures had the poorest survival — a finding invisible in gene-only classifications.
6/
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/
Some "unclassified" DLBCLs actually fit into new HERV-defined groups — with distinct survival outcomes! 📉📈
5/
May 20, 2025 at 8:44 PM
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/
Some "unclassified" DLBCLs actually fit into new HERV-defined groups — with distinct survival outcomes! 📉📈
5/
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/
- 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/
May 20, 2025 at 8:44 PM
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/
- 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/
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/
- 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/
May 20, 2025 at 8:44 PM
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/
- 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/
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/
2/
May 20, 2025 at 8:44 PM
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/
2/
What does this mean for DCPS teachers/admins? Are they required to comply?
March 26, 2025 at 6:39 PM
What does this mean for DCPS teachers/admins? Are they required to comply?
Thanks Bhavya glad she has scientists like you to look up to!
March 9, 2025 at 3:25 AM
Thanks Bhavya glad she has scientists like you to look up to!
Reposted by matthew.bendall
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.
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
March 8, 2025 at 4:12 PM
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.
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.
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!
March 8, 2025 at 5:35 PM
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!
My writing (non-spell checked) would support this conclusion. But somehow I can spell correctly when I’m coding?
March 8, 2025 at 4:51 AM
My writing (non-spell checked) would support this conclusion. But somehow I can spell correctly when I’m coding?
There was one poster, forget exactly what it was but something about ELONgated MUSKrats. She was so pleased when she got it.
March 8, 2025 at 4:42 AM
There was one poster, forget exactly what it was but something about ELONgated MUSKrats. She was so pleased when she got it.
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.
Glad I didn’t have to get into it with this one.
March 8, 2025 at 4:35 AM
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.
Glad I didn’t have to get into it with this one.