Simone Zaccaria
@zaccasimo.bsky.social
CRUK Career Development Fellow
Group Leader of @ccg-ucl.bsky.social at the UCL Cancer Institute, @CRUKLungCentre, and Visiting Scientist at the Francis Crick
W: http://www.ucl.ac.uk/cancer/zaccaria-lab
W: https://sites.google.com/view/ccgresearchgroup
Group Leader of @ccg-ucl.bsky.social at the UCL Cancer Institute, @CRUKLungCentre, and Visiting Scientist at the Francis Crick
W: http://www.ucl.ac.uk/cancer/zaccaria-lab
W: https://sites.google.com/view/ccgresearchgroup
Pinned
Simone Zaccaria
@zaccasimo.bsky.social
· Nov 29
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Reposted by Simone Zaccaria
New @natgenet.nature.com paper from the brilliant @eszterlakatos.bsky.social presents evidence that chromatin alterations disrupt antigen presentation & neoantigens in colorectal cancer. Also that immune escape is part of the "Big Bang", at the outset of CRC growth. www.nature.com/articles/s41...
Epigenetically driven and early immune evasion in colorectal cancer evolution - Nature Genetics
This study nominates immune escape as an early event in colorectal cancer and shows how this can be driven through both genetic and epigenetic changes.
www.nature.com
November 5, 2025 at 4:36 PM
New @natgenet.nature.com paper from the brilliant @eszterlakatos.bsky.social presents evidence that chromatin alterations disrupt antigen presentation & neoantigens in colorectal cancer. Also that immune escape is part of the "Big Bang", at the outset of CRC growth. www.nature.com/articles/s41...
Reposted by Simone Zaccaria
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 Simone Zaccaria
Huge congratulations to the lead applicants to our Development Fund 2025 on their innovative ideas! 👏 Özgen Deniz; Jonathan Fisher; Paul Grevitt; Jit Sarkar; Adam C Sedgwick; Emmanouil Stylianakis; and @zaccasimo.bsky.social 🎉 Find out more about their projects here: www.colcc.ac.uk/development-...
Development Fund
CRUK City of London Centre Development Fund
The CRUK City of London Centre brings together the discovery science of the Crick and the cross-disciplinary, translational and clinical expertise at UCL,...
www.colcc.ac.uk
September 25, 2025 at 11:55 AM
Huge congratulations to the lead applicants to our Development Fund 2025 on their innovative ideas! 👏 Özgen Deniz; Jonathan Fisher; Paul Grevitt; Jit Sarkar; Adam C Sedgwick; Emmanouil Stylianakis; and @zaccasimo.bsky.social 🎉 Find out more about their projects here: www.colcc.ac.uk/development-...
Reposted by Simone Zaccaria
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature
Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.
www.nature.com
September 10, 2025 at 3:21 PM
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
Reposted by Simone Zaccaria
🧨Exciting new pre-print 🧨 Introducing ppmSeq - cost effective, scalable dual-strand 🧬🧬 sequencing. Scalability & ultra-low error in one! A game changer for somatic genome discovery science and cfDNA clinical apps. Check out thread for deets!
Highly accurate sequencing OR high throughput? We refuse to choose.
Introducing ppmSeq, a method built to deliver both. Our latest from the @landau.bsky.social lab with Ultima Genomics
👀👀👀
See ⬇️ for a primer on the next frontier of genomics
www.biorxiv.org/content/10.1...
Introducing ppmSeq, a method built to deliver both. Our latest from the @landau.bsky.social lab with Ultima Genomics
👀👀👀
See ⬇️ for a primer on the next frontier of genomics
www.biorxiv.org/content/10.1...
Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules
Distinguishing real biological variation in the form of single-nucleotide variants (SNVs) from errors is a major challenge for genome sequencing technologies. This is particularly true in settings whe...
www.biorxiv.org
August 14, 2025 at 6:11 PM
🧨Exciting new pre-print 🧨 Introducing ppmSeq - cost effective, scalable dual-strand 🧬🧬 sequencing. Scalability & ultra-low error in one! A game changer for somatic genome discovery science and cfDNA clinical apps. Check out thread for deets!
🚨 We're hiring a sequencing technician in #TRACERx!
Join world-leading teams at @TheCrick & @uclcancer, working at the forefront of cancer research.
Want to apply cutting-edge genomic tech to understand cancer evolution? Apply now!
👉 www.ucl.ac.uk/work-at-ucl/...
#Genomics #CancerResearch
Join world-leading teams at @TheCrick & @uclcancer, working at the forefront of cancer research.
Want to apply cutting-edge genomic tech to understand cancer evolution? Apply now!
👉 www.ucl.ac.uk/work-at-ucl/...
#Genomics #CancerResearch
UCL – University College London
UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).
www.ucl.ac.uk
July 14, 2025 at 12:44 PM
🚨 We're hiring a sequencing technician in #TRACERx!
Join world-leading teams at @TheCrick & @uclcancer, working at the forefront of cancer research.
Want to apply cutting-edge genomic tech to understand cancer evolution? Apply now!
👉 www.ucl.ac.uk/work-at-ucl/...
#Genomics #CancerResearch
Join world-leading teams at @TheCrick & @uclcancer, working at the forefront of cancer research.
Want to apply cutting-edge genomic tech to understand cancer evolution? Apply now!
👉 www.ucl.ac.uk/work-at-ucl/...
#Genomics #CancerResearch
Reposted by Simone Zaccaria
1 in 2 people will get cancer in their lifetime. Our team'll still run @cancerresearchuk.org Muddy Race also this May to highlight the importance of funding cancer research and improving patient outcomes
Please support us if you can! #RaceforLife
👉 fundraise.cancerresearchuk.org/team/computa...
Please support us if you can! #RaceforLife
👉 fundraise.cancerresearchuk.org/team/computa...
Computational Cancer Genomics (CCG) Research Group
We are the Computational Cancer Genomics (CCG) Lab at the UCL Cancer Institute, a group of passionate scientists and clinicians who work on developing computational methods to unravel cancer's mysteri...
fundraise.cancerresearchuk.org
May 14, 2025 at 12:59 PM
1 in 2 people will get cancer in their lifetime. Our team'll still run @cancerresearchuk.org Muddy Race also this May to highlight the importance of funding cancer research and improving patient outcomes
Please support us if you can! #RaceforLife
👉 fundraise.cancerresearchuk.org/team/computa...
Please support us if you can! #RaceforLife
👉 fundraise.cancerresearchuk.org/team/computa...
Reposted by Simone Zaccaria
Not only are you a brilliant PI and an incredible mother, but you’re also a role model for women in science. Your strength and dedication inspire us all!
Not long after I started my lab, a prominent scientist told me it was “impossible” to be a successful PI and a mother
Don’t ever let the naysayers tell you it can’t be done - of course it can!
#HappyMothersDay this weekend to all the amazing scientist mamas raising their wonderful kids 🥰
Don’t ever let the naysayers tell you it can’t be done - of course it can!
#HappyMothersDay this weekend to all the amazing scientist mamas raising their wonderful kids 🥰
May 10, 2025 at 5:15 AM
Not only are you a brilliant PI and an incredible mother, but you’re also a role model for women in science. Your strength and dedication inspire us all!
I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Who else is going? Register here and don't miss it! invt.io/1bxbyktm0wq
I'm participating the ISMB/ECCB 2025 conference, join me!
Register now
invt.io
April 7, 2025 at 8:36 PM
I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Who else is going? Register here and don't miss it! invt.io/1bxbyktm0wq
Huge congratulations to now PhD @alexsteinresearch.bsky.social and supervisor @benjaminwerner.bsky.social , well deserved! It has been a pleasure to listening to and discussing such a great amount of work and how it all came together
Congratulations to a successful viva Dr. @alexsteinresearch.bsky.social
Many thanks to @cancerevo.org and @zaccasimo.bsky.social to be examiners!
Many thanks to @cancerevo.org and @zaccasimo.bsky.social to be examiners!
March 21, 2025 at 5:49 PM
Huge congratulations to now PhD @alexsteinresearch.bsky.social and supervisor @benjaminwerner.bsky.social , well deserved! It has been a pleasure to listening to and discussing such a great amount of work and how it all came together
Reposted by Simone Zaccaria
To what extent is cancer development deterministic and predictable..?
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
January 15, 2025 at 7:32 PM
To what extent is cancer development deterministic and predictable..?
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Reposted by Simone Zaccaria
A big moment for our Centre - the first algorithm to identify cells responsible for aggressive tumour growth.
SPRINTER can measure proliferation of distinct clones within the same tumour, using DNA sequencing data. This could facilitate better prediction of cancer progression, informing treatment.
SPRINTER can measure proliferation of distinct clones within the same tumour, using DNA sequencing data. This could facilitate better prediction of cancer progression, informing treatment.
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
December 18, 2024 at 10:27 AM
A big moment for our Centre - the first algorithm to identify cells responsible for aggressive tumour growth.
SPRINTER can measure proliferation of distinct clones within the same tumour, using DNA sequencing data. This could facilitate better prediction of cancer progression, informing treatment.
SPRINTER can measure proliferation of distinct clones within the same tumour, using DNA sequencing data. This could facilitate better prediction of cancer progression, informing treatment.
Reposted by Simone Zaccaria
How much do algorithmic and experimental choices drive the accuracy of reconstructing tumour evolution?
In this Cancer Research commentary, @zaccasimo.bsky.social and I discuss a recent Nature Biotech benchmarking paper exploring this question:
bit.ly/3VAMRQs
In this Cancer Research commentary, @zaccasimo.bsky.social and I discuss a recent Nature Biotech benchmarking paper exploring this question:
bit.ly/3VAMRQs
Tumor Evolution Reconstruction Is Heavily Influenced by Algorithmic and Experimental Choices
Tumor progression is an evolutionary process during which cells acquire distinct genetic alterations. Several cancer evolutionary studies reconstruct this evolutionary process by applying bulk DNA seq...
bit.ly
December 16, 2024 at 11:56 AM
How much do algorithmic and experimental choices drive the accuracy of reconstructing tumour evolution?
In this Cancer Research commentary, @zaccasimo.bsky.social and I discuss a recent Nature Biotech benchmarking paper exploring this question:
bit.ly/3VAMRQs
In this Cancer Research commentary, @zaccasimo.bsky.social and I discuss a recent Nature Biotech benchmarking paper exploring this question:
bit.ly/3VAMRQs
🚨 Very proud of this commentary led by @rijazaidi.bsky.social reasoning on the impact of methods and experimental design on cancer evolution understanding, motivated by the outstanding work of @TheBoutros, @VanLooLab, @kellrott et al
Original work 👉 doi.org/10.1038/s415...
Our Commentary 👇
Original work 👉 doi.org/10.1038/s415...
Our Commentary 👇
December 16, 2024 at 3:47 PM
🚨 Very proud of this commentary led by @rijazaidi.bsky.social reasoning on the impact of methods and experimental design on cancer evolution understanding, motivated by the outstanding work of @TheBoutros, @VanLooLab, @kellrott et al
Original work 👉 doi.org/10.1038/s415...
Our Commentary 👇
Original work 👉 doi.org/10.1038/s415...
Our Commentary 👇
Reposted by Simone Zaccaria
Reposting this list of #cancer #evolution scientists, in case its useful for the many newcomers.
I've started a list of people working on #cancer #evolution. Many more to be added, so do let me know if that is you. Also if you would like to be removed. go.bsky.app/QuAF4Mo
December 6, 2024 at 9:46 AM
Reposting this list of #cancer #evolution scientists, in case its useful for the many newcomers.
Reposted by Simone Zaccaria
So proud that our paper introducing SPRINTER to characterise clone proliferation through cancer evolution is out in Nature Genetics!
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
December 5, 2024 at 9:36 AM
So proud that our paper introducing SPRINTER to characterise clone proliferation through cancer evolution is out in Nature Genetics!
🎉 Hugely honoured & happy to be selected for the
@embopress.org EMBO Young Investigator Programme 2024!
Exciting opportunity for our group @ccg-ucl.bsky.social & grateful for the support of @uclofficial.bsky.social @uclnews.bsky.social & funders @cancerresearchuk.org
www.embo.org/press-releas...
@embopress.org EMBO Young Investigator Programme 2024!
Exciting opportunity for our group @ccg-ucl.bsky.social & grateful for the support of @uclofficial.bsky.social @uclnews.bsky.social & funders @cancerresearchuk.org
www.embo.org/press-releas...
Twenty-seven scientists become EMBO Young Investigators – Press releases – EMBO
The group leaders join an international network of nearly 800 life scientists and receive financial support
www.embo.org
December 5, 2024 at 12:02 PM
🎉 Hugely honoured & happy to be selected for the
@embopress.org EMBO Young Investigator Programme 2024!
Exciting opportunity for our group @ccg-ucl.bsky.social & grateful for the support of @uclofficial.bsky.social @uclnews.bsky.social & funders @cancerresearchuk.org
www.embo.org/press-releas...
@embopress.org EMBO Young Investigator Programme 2024!
Exciting opportunity for our group @ccg-ucl.bsky.social & grateful for the support of @uclofficial.bsky.social @uclnews.bsky.social & funders @cancerresearchuk.org
www.embo.org/press-releas...
We are so grateful to @qianxidu.bsky.social for this outstanding News&Views piece highlighting our recent SPRINTER work and framing it so beautifully within the literature. A truly valuable resource! 🙏
Read it here: 👉 doi.org/10.1038/s415...
🧵 Dive into SPRINTER's work: 👉 bsky.app/profile/zacc...
Read it here: 👉 doi.org/10.1038/s415...
🧵 Dive into SPRINTER's work: 👉 bsky.app/profile/zacc...
Single cell genomics was a breakthrough in understanding cancer heterogeneity. Incredible work by Lucas et al. in breaking the next barrier, cancer proliferation heterogeneity tinyurl.com/mjuuk7kt
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
tinyurl.com
December 3, 2024 at 7:16 PM
We are so grateful to @qianxidu.bsky.social for this outstanding News&Views piece highlighting our recent SPRINTER work and framing it so beautifully within the literature. A truly valuable resource! 🙏
Read it here: 👉 doi.org/10.1038/s415...
🧵 Dive into SPRINTER's work: 👉 bsky.app/profile/zacc...
Read it here: 👉 doi.org/10.1038/s415...
🧵 Dive into SPRINTER's work: 👉 bsky.app/profile/zacc...
Reposted by Simone Zaccaria
Our paper on chromosomal abnormalities in normal breast tissue from BRCA carriers came out last week.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations - Nature Genetics
Single-cell DNA sequencing identifies recurrent copy number changes in healthy breast tissue from women with wild-type or germline BRCA1 or BRCA2 mutations.
www.nature.com
December 3, 2024 at 4:08 PM
Our paper on chromosomal abnormalities in normal breast tissue from BRCA carriers came out last week.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Simone Zaccaria
What an absolute pleasure to be collaborating with such an incredibly talented team!!
SPRINTER out today in Nature Genetics 🧬
SPRINTER out today in Nature Genetics 🧬
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
November 29, 2024 at 7:38 PM
What an absolute pleasure to be collaborating with such an incredibly talented team!!
SPRINTER out today in Nature Genetics 🧬
SPRINTER out today in Nature Genetics 🧬
Reposted by Simone Zaccaria
A great pleasure to work with @zaccasimo.bsky.social and his team on this elegant data and tool.
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
November 29, 2024 at 7:02 PM
A great pleasure to work with @zaccasimo.bsky.social and his team on this elegant data and tool.
Reposted by Simone Zaccaria
Single cell genomics was a breakthrough in understanding cancer heterogeneity. Incredible work by Lucas et al. in breaking the next barrier, cancer proliferation heterogeneity tinyurl.com/mjuuk7kt
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
tinyurl.com
November 29, 2024 at 12:44 PM
Single cell genomics was a breakthrough in understanding cancer heterogeneity. Incredible work by Lucas et al. in breaking the next barrier, cancer proliferation heterogeneity tinyurl.com/mjuuk7kt
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
Honoured I was invited to write the News&Views. tinyurl.com/yc27a4ac
Both out now in Nature Genetics!
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics
Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...
doi.org
November 29, 2024 at 1:25 PM
🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others
Out now👇
🧵👇
Out now👇
🧵👇