Szen
@szen.bsky.social
Wellcome Trust Clinical PhD Fellow in the Garnett Lab @sangerinstitute.bsky.social. Interested in cancer plasticity, multiplexed assays, ML, & comp bio.
https://ttszen.com/
https://ttszen.com/
Reposted by Szen
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Group Leader - Generative Biology and AI
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
tinyurl.com
November 7, 2025 at 9:37 AM
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Reposted by Szen
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
biorxiv.org
November 5, 2025 at 2:17 PM
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Reposted by Szen
🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.
Shout out to Tamara Prieto, Dennis Yuan, John Zinno and @ivanraimondi.bsky.social . Thank you to our funders at @themarkfdn.bsky.social
October 14, 2025 at 2:42 PM
🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.
Reposted by Szen
Big, beautiful trees!!
SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.
www.biorxiv.org/content/10.1...
SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.
www.biorxiv.org/content/10.1...
October 14, 2025 at 2:37 PM
Big, beautiful trees!!
SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.
www.biorxiv.org/content/10.1...
SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.
www.biorxiv.org/content/10.1...
Reposted by Szen
We've been screening across many DNA construct structures with variable number/size of interesting regions - e.g. spacer, extension and barcode for prime editing. There wasn't a widely used tool to process these complex structured reads so I ended up developing github.com/allydunham/d....
GitHub - allydunham/dnacomb: CLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected libraries
CLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected libraries - allydunham/dnacomb
github.com
October 13, 2025 at 2:36 PM
We've been screening across many DNA construct structures with variable number/size of interesting regions - e.g. spacer, extension and barcode for prime editing. There wasn't a widely used tool to process these complex structured reads so I ended up developing github.com/allydunham/d....
Reposted by Szen
The @crick.ac.uk is recruiting Early Career Group Leaders
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
Early career group leaders
We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.
www.crick.ac.uk
October 10, 2025 at 8:20 AM
The @crick.ac.uk is recruiting Early Career Group Leaders
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
Reposted by Szen
In our latest paper, I wrote 2 supplementary notes (5 and 6) to briefly recap classical models, starting with Armitage&Doll and moving onto models with different types of clonal expansions. Some readers may find them of interest. [4/4] static-content.springer.com/esm/art%3A10...
static-content.springer.com
October 9, 2025 at 3:29 PM
In our latest paper, I wrote 2 supplementary notes (5 and 6) to briefly recap classical models, starting with Armitage&Doll and moving onto models with different types of clonal expansions. Some readers may find them of interest. [4/4] static-content.springer.com/esm/art%3A10...
Reposted by Szen
A short thread. For years, I have been surprised by how much confusion our discovery of clones carrying cancer-driver mutations in normal tissues has caused in the cancer community. Typical questions like: (1) if you see these mutations in normal cells, are they really cancer drivers?... [1/4]
Our latest work is out in Nature today. In this paper, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people www.nature.com/articles/s41...
Somatic mutation and selection at population scale - Nature
A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.
www.nature.com
October 9, 2025 at 3:29 PM
A short thread. For years, I have been surprised by how much confusion our discovery of clones carrying cancer-driver mutations in normal tissues has caused in the cancer community. Typical questions like: (1) if you see these mutations in normal cells, are they really cancer drivers?... [1/4]
Reposted by Szen
Now published! Our paper on:
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
Sperm sequencing reveals extensive positive selection in the male germline - Nature
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
www.nature.com
October 8, 2025 at 3:51 PM
Now published! Our paper on:
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
Reposted by Szen
Our latest work is out in Nature today. In this paper, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people www.nature.com/articles/s41...
Somatic mutation and selection at population scale - Nature
A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.
www.nature.com
October 8, 2025 at 4:31 PM
Our latest work is out in Nature today. In this paper, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people www.nature.com/articles/s41...
Reposted by Szen
The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
September 20, 2025 at 7:43 AM
The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Reposted by Szen
Scientists are taking the first steps towards the first synthetic human genome.
We’re proud to announce £10 million funding for the SynHG project.
Learn more ⤵️
wellcome.org/news/researc...
We’re proud to announce £10 million funding for the SynHG project.
Learn more ⤵️
wellcome.org/news/researc...
Researchers take first steps to creating synthetic human genomes | Wellcome
Scientists are developing technology to create the first synthetic human chromosome. The ability to write large genomes could transform our understanding of health.
wellcome.org
June 26, 2025 at 4:22 PM
Scientists are taking the first steps towards the first synthetic human genome.
We’re proud to announce £10 million funding for the SynHG project.
Learn more ⤵️
wellcome.org/news/researc...
We’re proud to announce £10 million funding for the SynHG project.
Learn more ⤵️
wellcome.org/news/researc...
Reposted by Szen
I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...
Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology
The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...
www.nature.com
June 23, 2025 at 6:19 AM
I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...
Reposted by Szen
Cancer Plasticity Atlas To Improve Cancer Therapies
#HelmholtzMunich joins @sangerinstitute.bsky.social & @parse.bsky.social to build the Cancer Plasticity Atlas, using #AI & single-cell data to model therapy response.
👉 t1p.de/13ifi
@fabiantheis.bsky.social
@mgarnett.bsky.social
#CancerResearch
#HelmholtzMunich joins @sangerinstitute.bsky.social & @parse.bsky.social to build the Cancer Plasticity Atlas, using #AI & single-cell data to model therapy response.
👉 t1p.de/13ifi
@fabiantheis.bsky.social
@mgarnett.bsky.social
#CancerResearch
June 13, 2025 at 6:27 AM
Cancer Plasticity Atlas To Improve Cancer Therapies
#HelmholtzMunich joins @sangerinstitute.bsky.social & @parse.bsky.social to build the Cancer Plasticity Atlas, using #AI & single-cell data to model therapy response.
👉 t1p.de/13ifi
@fabiantheis.bsky.social
@mgarnett.bsky.social
#CancerResearch
#HelmholtzMunich joins @sangerinstitute.bsky.social & @parse.bsky.social to build the Cancer Plasticity Atlas, using #AI & single-cell data to model therapy response.
👉 t1p.de/13ifi
@fabiantheis.bsky.social
@mgarnett.bsky.social
#CancerResearch
Reposted by Szen
Announcing a new collaboration with @parse.bsky.social @www.helmholtz-munich.de to develop a #Cancer Plasticity Atlas.
The reference map will help predict the effect of cancer drugs - where resistance might develop and where to target future treatment efforts.
www.sanger.ac.uk/news_item/pi...
The reference map will help predict the effect of cancer drugs - where resistance might develop and where to target future treatment efforts.
www.sanger.ac.uk/news_item/pi...
Pioneering cancer plasticity atlas will help predict response to cancer therapies
Utilising novel organoid perturbation and Artificial Intelligence (AI) platforms, the aim is to create a comprehensive dataset to fuel foundational drug discovery models and cancer research.
www.sanger.ac.uk
June 12, 2025 at 4:17 PM
Announcing a new collaboration with @parse.bsky.social @www.helmholtz-munich.de to develop a #Cancer Plasticity Atlas.
The reference map will help predict the effect of cancer drugs - where resistance might develop and where to target future treatment efforts.
www.sanger.ac.uk/news_item/pi...
The reference map will help predict the effect of cancer drugs - where resistance might develop and where to target future treatment efforts.
www.sanger.ac.uk/news_item/pi...
Reposted by Szen
That’s all for #VariantEffect25! This was my first time live sketching a conference, it was a really fun and interesting experience. The science was fantastic, i learnt so much!!
Big thanks to everyone who shared any of my sketches or spoke to me about them, i really appreciate it.
Big thanks to everyone who shared any of my sketches or spoke to me about them, i really appreciate it.
May 23, 2025 at 2:08 PM
That’s all for #VariantEffect25! This was my first time live sketching a conference, it was a really fun and interesting experience. The science was fantastic, i learnt so much!!
Big thanks to everyone who shared any of my sketches or spoke to me about them, i really appreciate it.
Big thanks to everyone who shared any of my sketches or spoke to me about them, i really appreciate it.
Reposted by Szen
Check this out if you're interested in #crispr #baseeditor. Congratulations Cansu for creating this wonderful tool.
🚨 Excited to share our latest preprint!
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments https://www.biorxiv.org/content/10.1101/2025.05.19.654892v1
May 22, 2025 at 4:48 PM
Check this out if you're interested in #crispr #baseeditor. Congratulations Cansu for creating this wonderful tool.
Reposted by Szen
Check out the first session for the upcoming GRC conference on synthetic lethality in oncology www.grc.org/synthetic-le.... Top flight speakers - Simon Powell (MSK), Chris Lord (ICR), and plenary talk from William Sellers (Broad Inst.). What a start! It's not too late to register.
May 22, 2025 at 4:51 PM
Check out the first session for the upcoming GRC conference on synthetic lethality in oncology www.grc.org/synthetic-le.... Top flight speakers - Simon Powell (MSK), Chris Lord (ICR), and plenary talk from William Sellers (Broad Inst.). What a start! It's not too late to register.
Reposted by Szen
🚨 Excited to share our latest preprint!
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments https://www.biorxiv.org/content/10.1101/2025.05.19.654892v1
May 22, 2025 at 1:21 PM
🚨 Excited to share our latest preprint!
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
@mgarnett.bsky.social @mattcoelho.bsky.social
We introduce BEstimate, a flexible, comprehensive tool for designing and interpreting CRISPR-based editing experiments.
#CRISPR #BEstimate #BaseEditor
Reposted by Szen
I'm incredibly grateful to have been selected as one of the best talks at the Downing College Postgraduate Conference 2025, an honour I shared with brilliant Ms Herrick-Doyle, from Oxford, Lincoln College, whose presentation was truly inspiring.
@downingcollege.bsky.social
@downingcollege.bsky.social
May 13, 2025 at 2:59 PM
I'm incredibly grateful to have been selected as one of the best talks at the Downing College Postgraduate Conference 2025, an honour I shared with brilliant Ms Herrick-Doyle, from Oxford, Lincoln College, whose presentation was truly inspiring.
@downingcollege.bsky.social
@downingcollege.bsky.social
Reposted by Szen
Learn about the future of synthetic lethality in oncology at the upcoming Gordon Research Conference. This is the inaugural meeting and WOW what a lineup! We have a truly phenomenal program, with top speakers from academia and industry. Check it out at the link below.
www.grc.org/synthetic-le....
www.grc.org/synthetic-le....
2025 Synthetic Lethality Approaches in Oncology Conference GRC
The 2025 Gordon Research Conference on Synthetic Lethality Approaches in Oncology will be held in Portland, Maine. Apply today to reserve your spot.
www.grc.org
May 12, 2025 at 8:11 PM
Learn about the future of synthetic lethality in oncology at the upcoming Gordon Research Conference. This is the inaugural meeting and WOW what a lineup! We have a truly phenomenal program, with top speakers from academia and industry. Check it out at the link below.
www.grc.org/synthetic-le....
www.grc.org/synthetic-le....
Reposted by Szen
Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
May 6, 2025 at 2:59 PM
Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
Reposted by Szen
We’re looking for Computational Scientists to join our team in advancing cutting-edge research at the intersection of spatial genomics and AI.
Check it out:
lnkd.in/ezruccHF
lnkd.in/e2siGM_9
Check it out:
lnkd.in/ezruccHF
lnkd.in/e2siGM_9
Ensocell hiring AI Scientist in Hinxton, England, United Kingdom | LinkedIn
Posted 12:12:35 PM. The OpportunityAt Ensocell we are building AI models to elucidate the pathogenesis of chronic…See this and similar jobs on LinkedIn.
lnkd.in
March 18, 2025 at 6:32 PM
We’re looking for Computational Scientists to join our team in advancing cutting-edge research at the intersection of spatial genomics and AI.
Check it out:
lnkd.in/ezruccHF
lnkd.in/e2siGM_9
Check it out:
lnkd.in/ezruccHF
lnkd.in/e2siGM_9
Reposted by Szen
Excited to announce that we're recruiting a Staff scientist at the Sanger Institute to investigate drug resistance mechanisms in cancer using gene editing.
Interested?
Apply here:
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Interested?
Apply here:
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
March 12, 2025 at 1:50 PM
Excited to announce that we're recruiting a Staff scientist at the Sanger Institute to investigate drug resistance mechanisms in cancer using gene editing.
Interested?
Apply here:
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Interested?
Apply here:
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Reposted by Szen
How does a young person who loves both science and art decide on a career? Seattle Hub's Dr. Jonas Koeppel has a theory.
@alleninstitute.bsky.social
@jonaskoeppel.bsky.social
@chanzuckerberg.bsky.social
@sudpinglay.bsky.social
brotmanbaty.org/news/promisi...
@alleninstitute.bsky.social
@jonaskoeppel.bsky.social
@chanzuckerberg.bsky.social
@sudpinglay.bsky.social
brotmanbaty.org/news/promisi...
Promising Young Scientist: Jonas Koeppel Overcomes a Professional Dilemma and Later Joins ‘Super Cool’ SeaHub | Brotman Baty Institute
BBI
brotmanbaty.org
March 11, 2025 at 6:07 PM
How does a young person who loves both science and art decide on a career? Seattle Hub's Dr. Jonas Koeppel has a theory.
@alleninstitute.bsky.social
@jonaskoeppel.bsky.social
@chanzuckerberg.bsky.social
@sudpinglay.bsky.social
brotmanbaty.org/news/promisi...
@alleninstitute.bsky.social
@jonaskoeppel.bsky.social
@chanzuckerberg.bsky.social
@sudpinglay.bsky.social
brotmanbaty.org/news/promisi...