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Simone Zaccaria

@zaccasimo.bsky.social
277 followers 152 following 37 posts

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: www.ucl.ac.uk/cancer/zaccaria-lab W: sites.google.com/view/ccgresearchgr…

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Simone Zaccaria @zaccasimo.bsky.social · 21h
Huge congrats, Mariam @jamal-hanjani-lab.bsky.social!🎉 So well deserved. Having had the privilege of working closely with you, I know firsthand the vision, energy and collaborative spirit you bring. I have no doubt you will have an enormously positive impact on @cancerresearchuk.org & on all of us 🎉
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Cancer Research UK @cancerresearchuk.org · 23h
We’re pleased to announce Professor Mariam Jamal-Hanjani as our new Chief Clinician! 🎉 Mariam is Professor of Cancer Genomics and Metastasis at UCL Cancer Institute and has led on a number of our key research initiatives. Join us in welcoming her to the role! cruk.ink/4jGWABC
cruk.ink
Cancer Research UK appoints Professor Mariam Jamal-Hanjani as its new chief clinician - Cancer Research UK - Cancer News
Cancer Research UK has appointed Professor Mariam Jamal-Hanjani as its new chief clinician.
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Simone Zaccaria @zaccasimo.bsky.social · 05/10/2026
Who? 🧑‍💻 Bioinformatics, CS, maths, physics, or any quantitative background. You should be excited by algorithms & cancer evolution. Sequencing experience is a bonus, not a must. Programme & eligibility 👉 colcc.ac.uk/black-leader... Please share 🙏
colcc.ac.uk
Black Leaders PhD Recruitment Process
The CRUK CoL Centre Black Leaders in Cancer PhD Programme Applications for the CRUK CoL Centre Black Leader in Cancer PhD programme starting in September 2027 are open Application through Cancer Research UK/ Windsor Fellowship required in addition - OPEN NOW CRUK CoL Centre Black Leaders
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Simone Zaccaria @zaccasimo.bsky.social · 05/10/2026
The twist 🧠 The same single-cell data also reads out replication timing, a window into each cell's epigenetic state. You'll link ecDNA to the cell states and plasticity that drive resistance, beyond the amplified oncogenes themselves 👇 www.nature.com/articles/s41...
nature.com
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...
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Simone Zaccaria @zaccasimo.bsky.social · 05/10/2026
Why single cells?🔬 Bulk sequencing averages millions of cells into a blurry signal. Single-cell genomics lets us read the genome of each cancer cell individually, so we can watch tumours evolve and diversify cell by cell. For something as chaotic as ecDNA, that's a game changer
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Simone Zaccaria @zaccasimo.bsky.social · 05/10/2026
Why ecDNA? 🔄 Unlike chromosomes, these oncogene-carrying circles split randomly when cells divide. Cancers can crank oncogene copies up or down within a few generations and outpace treatment. How this evolves through metastasis & therapy is still a mystery.
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Simone Zaccaria @zaccasimo.bsky.social · 05/10/2026
🚨 PhD opportunity at @ccg-ucl.bsky.social! Build AI & computational tools to catch ecDNA in single cells: rogue DNA circles that let cancer beat therapy With @jamal-hanjani-lab.bsky.social & @benjaminwerner.bsky.social Black Leaders in Cancer PhD at UCL CI 👇 www.colcc.ac.uk/2027-blic-ph...
colcc.ac.uk
2027 BLiC PhD project Zaccaria
Computational single-cell investigation of extrachromosomal DNA and replication-timing alterations shaping metastatic cancer Primary supervisor: Simone Zaccaria, UCL Secondary supervisors: Benjamin Werner, Queen Mary University of London; Mariam Jamal-Hanjani, UCL Project High-level copy-number amplification of oncogenes is a common mechanism of cancer activation and a major source of intratumoural heterogeneity, poor outcomes, and treatment resistance .
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Simone Zaccaria @zaccasimo.bsky.social · 15/06/2026
Join us In London for #MAP2026 to think how we can shape the next generation of molecular precision oncology! #esmomeetings 👇
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Simone Zaccaria @zaccasimo.bsky.social · 20/05/2026
On a personal note, it was incredibly special to finally wear the gown from my own graduating university, @unimib. Thanks @ucl.ac.uk for this! 🇮🇹🎓 A wonderful reminder of where my pathway started at @unimib Informatica, and of @paolabonizzoni who, in turn, supported me at the time 🙏
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Simone Zaccaria @zaccasimo.bsky.social · 20/05/2026
Huge thanks to @ucl.ac.uk for organising such a wonderful celebration & infinitely grateful to everyone who supported along the way 🙏 🙏 @uclmedsci.bsky.social @cancerresearchuk.org @MRC @wellcometrust.bsky.social @cruk-cityoflondon.bsky.social @Rosetrees 🙏
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Simone Zaccaria @zaccasimo.bsky.social · 20/05/2026
🎓ABSOLUTELY BURSTING WITH PRIDE! Huge congrats to our @ccg-ucl.bsky.social first doctoral graduates: Dr @rijazaidi.bsky.social, Dr @abibunkum.bsky.social & Dr @ojlucas.bsky.social!🎉 Whatever pathways they choose next, I have no doubt these brilliant minds will lead critical advances in our society!
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Trevor Graham @trevorgraham.bsky.social · 08/05/2026
In colon, stem cells divide & so do the crypts they reside in: a multi-level evolutionary process. D Mallo, P Bousquets @heathergrant.bsky.social @calumgabbutt.bsky.social have made "PhyPhum" to lineage trace somatic evolution in human glandular tissues www.biorxiv.org/content/10.6... @icr.ac.uk
biorxiv.org
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Simone Zaccaria @zaccasimo.bsky.social · 01/05/2026
🚨 Huge honour to have helped supervise this landmark PEACE study! New insights into metastasis + a unique dataset of unprecedented resolution on metastatic evolution and dissemination that we hope will drive future advances. 🙏 @cancerresearchuk.org @uclhresearch.bsky.social Please take a look 👇
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Jamal-Hanjani Lab @jamal-hanjani-lab.bsky.social · 29/04/2026
Using MACHINA from @braphael.bsky.social's lab to infer metastatic migration patterns, we found that NSCLC primaries had multiple seeding subclones more often than a single seeding subclone. 4/9
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Jamal-Hanjani Lab @jamal-hanjani-lab.bsky.social · 29/04/2026
Through the integration of the #PEACE autopsy programme, which allows high breadth metastasis sampling, with the #TRACERx lung study, we collected and studied 501 primary and metastatic tumour samples from 24 patients with non-small cell lung cancer (NSCLC) enrolled in the both studies. 2/9
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Jamal-Hanjani Lab @jamal-hanjani-lab.bsky.social · 29/04/2026
Excited to share our ‘Evolutionary characterization of lung cancer metastasis’ in #TRACERx & #PEACE, published today in @nature.com in collaboration with @charlesswanton.bsky.social @nickymcgranahan.bsky.social @zaccasimo.bsky.social at @ucl.ac.uk & @crick.ac.uk. www.nature.com/articles/s41...
nature.com
Evolutionary characterization of lung cancer metastasis - Nature
DNA-sequencing data from primary tumours and paired metastases from participants in the TRACERx lung study and PEACE autopsy programme are used to analyse the metastatic diversity of advanced non-smal...
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Trevor Graham @trevorgraham.bsky.social · 01/12/2025
We held the first #CANPOP symposium today (cancer population genetics club) @icr.ac.uk. 6 excellent & didactic talks, all applying mathematical #popgen theory to dissect somatic evolutionary dynamics: spanning the full range of pre-cancer, metastasis through to 6000 year old transmissible cancer...
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Trevor Graham @trevorgraham.bsky.social · 05/11/2025
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...
nature.com
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.
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Dan Landau @landau.bsky.social · 14/10/2025
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...
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Cancer Research UK City of London Centre @cruk-cityoflondon.bsky.social · 25/09/2025
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-...
colcc.ac.uk
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,...
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Simone Zaccaria @zaccasimo.bsky.social · 12/09/2025
Congratulations everyone, outstanding work!
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Trevor Graham @trevorgraham.bsky.social · 10/09/2025
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...
nature.com
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.
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Dan Landau @landau.bsky.social · 14/08/2025
🧨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!
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Simone Zaccaria @zaccasimo.bsky.social · 14/07/2025
🚨 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
ucl.ac.uk
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).
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Computational Cancer Genomics (CCG) Research Group @ccg-ucl.bsky.social · 14/05/2025
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...
fundraise.cancerresearchuk.org
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...
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rociosotillo.bsky.social @rociosotillo.bsky.social · 10/05/2025
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!
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Simone Zaccaria @zaccasimo.bsky.social · 07/04/2025
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
invt.io
I'm participating the ISMB/ECCB 2025 conference, join me!
Register now
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Simone Zaccaria @zaccasimo.bsky.social · 21/03/2025
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
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Martin Taylor @mstaylor.bsky.social · 15/01/2025
To what extent is cancer development deterministic and predictable..? Does the germline genome affect that predictability...? Preprint: www.biorxiv.org/content/10.1...
Manuscript logo, phylogenetic tree of mouse strains with different but highly reproducible patterns of cancer evolution. Demonstrated by rerunning cancer evolution in a controlled system.
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Cancer Research UK City of London Centre @cruk-cityoflondon.bsky.social · 18/12/2024
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.
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Rija Zaidi @rijazaidi.bsky.social · 16/12/2024
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
bit.ly
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...
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Simone Zaccaria @zaccasimo.bsky.social · 16/12/2024
🚨 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 👇
doi.org
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction - Nature Biotechnology
Benchmarking of tumor subclonal reconstruction algorithms finds that interalgorithm variability overwhelms intertumor variability and identifies key quality metrics.
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Trevor Graham @trevorgraham.bsky.social · 06/12/2024
Reposting this list of #cancer #evolution scientists, in case its useful for the many newcomers.
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Olivia Lucas @ojlucas.bsky.social · 05/12/2024
So proud that our paper introducing SPRINTER to characterise clone proliferation through cancer evolution is out in Nature Genetics!
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Simone Zaccaria @zaccasimo.bsky.social · 05/12/2024
🎉 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...
embo.org
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
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Simone Zaccaria @zaccasimo.bsky.social · 03/12/2024
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...
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Marc Williams @marcjwilliams.bsky.social · 03/12/2024
Our paper on chromosomal abnormalities in normal breast tissue from BRCA carriers came out last week. www.nature.com/articles/s41...
nature.com
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.
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Sophie Ward @sophie-ward.bsky.social · 29/11/2024
What an absolute pleasure to be collaborating with such an incredibly talented team!! SPRINTER out today in Nature Genetics 🧬
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Alex Frankell @afrankell.bsky.social · 29/11/2024
A great pleasure to work with @zaccasimo.bsky.social and his team on this elegant data and tool.
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
Thank you, Trevor!
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
Thank you, Wei! 😊
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Qian Du @qianxidu.bsky.social · 29/11/2024
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!
tinyurl.com
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...
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
All of this was really only possible thanks to the support of our funders @cancerresearchuk.org also inc @RosetreesT @bcrfcure.bsky.social @wellcometrust.bsky.social , our teams @uclofficial.bsky.social @thecrick.bsky.social @CRUKLungCentre, and the patients & participants #TRACERx #PEACEautopsy
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
This is also the first step and output of my @cancerresearchuk.org Career Development Fellowship, and you can read its overall vision and goal in a recent @cancerresearchuk.org 's blog post 👇 news.cancerresearchuk.org/2024/02/27/u...
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
This was led by stellar @ojlucas.bsky.social and wouldn't have been possible without @charlesswanton.bsky.social @NnennayaKanu cosupervision, @sophie-ward.bsky.social key collaboration, @rijazaidi.bsky.social @abibunkum.bsky.social key contributions and help of many others inc. Mariam and Nicky
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
📰Read full story 👉 rdcu.be/d1S6m 🖥️SPRINTER is fully available in GitHub 👉 github.com/zaccaria-lab... 🚆Distributed through Bioconda (with also related container) 👉 bioconda.github.io/recipes/spri... 💾also with a reproducible capsule in CodeOcean👉 doi.org/10.24433/CO.... pic.x.com/zpL2rhbRhl
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
Finally, we proved SPRINTER’s broad applicability on prev datasets of 61,914 TNBC and HGSC cells and found other key insights for high prolif clones: ❗️Increased single-cell rates of genomic variants ‼️Enrichment of prolif-related gene amplifications ❔-> Evolutionary advantage?
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
When integrating serial ctDNA samples across 4 timepoints, we found differential ctDNA shedding between clones, with high prolif clones shedding more ctDNA 🚨It shows that previous similar observations obtained across different tumors also hold for distinct clones within a tumor
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
What's their role? We reconstructed met dissemination patterns and found that: 1. high prolif clones seeded most mets disseminating from other mets 2. met-seeding clones had high proliferation ❔-> association between high prolif and met seeding potential of individual clones
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Simone Zaccaria @zaccasimo.bsky.social · 29/11/2024
Maybe non-genetic? Leveraging SPRINTER, we developed an approach to identify clone-specific altered replication timing (ART) ‼️ We found ART unique to the high prolif and metastatic clones affecting key genes like KRAS, and with associated expression changes from matched RNA-seq
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