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Reposted by Simone Zaccaria

Cancer Research UK City of London Centre @cruk-cityoflondon.bsky.social · 13d

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

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Simone Zaccaria @zaccasimo.bsky.social · 26d

Congratulations everyone, outstanding work!

Reposted by Simone Zaccaria

Trevor Graham @trevorgraham.bsky.social · 28d

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

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Reposted by Simone Zaccaria

Dan Landau @landau.bsky.social · Aug 14

🧨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!

Alex @alexpellancheng.bsky.social · Aug 14

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...

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

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Simone Zaccaria @zaccasimo.bsky.social · Jul 14

🚨 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 – 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

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Reposted by Simone Zaccaria

Computational Cancer Genomics (CCG) Research Group @ccg-ucl.bsky.social · May 14

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...

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

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Reposted by Simone Zaccaria

rociosotillo.bsky.social @rociosotillo.bsky.social · May 10

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!

Johanna Joyce @johannajoyce.bsky.social · May 9

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 🥰

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Simone Zaccaria @zaccasimo.bsky.social · Apr 7

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

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Simone Zaccaria @zaccasimo.bsky.social · Mar 21

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

Benjamin Werner @benjaminwerner.bsky.social · Mar 20

Congratulations to a successful viva Dr. @alexsteinresearch.bsky.social

Many thanks to @cancerevo.org and @zaccasimo.bsky.social to be examiners!

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Reposted by Simone Zaccaria

Martin Taylor @mstaylor.bsky.social · Jan 15

To what extent is cancer development deterministic and predictable..?

Does the germline genome affect that predictability...?

Preprint: www.biorxiv.org/content/10.1...

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Reposted by Simone Zaccaria

Cancer Research UK City of London Centre @cruk-cityoflondon.bsky.social · Dec 18

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.

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

🚨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👇
🧵👇

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

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Reposted by Simone Zaccaria

Rija Zaidi @rijazaidi.bsky.social · Dec 16

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

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

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Simone Zaccaria @zaccasimo.bsky.social · Dec 16

🚨 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 👇

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Reposted by Simone Zaccaria

Trevor Graham @trevorgraham.bsky.social · Dec 6

Reposting this list of #cancer #evolution scientists, in case its useful for the many newcomers.

Trevor Graham @trevorgraham.bsky.social · Nov 12

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

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Reposted by Simone Zaccaria

Olivia Lucas @ojlucas.bsky.social · Dec 5

So proud that our paper introducing SPRINTER to characterise clone proliferation through cancer evolution is out in Nature Genetics!

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

🚨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👇
🧵👇

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

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Simone Zaccaria @zaccasimo.bsky.social · Dec 5

🎉 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...

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

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Simone Zaccaria @zaccasimo.bsky.social · Dec 3

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...

Qian Du @qianxidu.bsky.social · Nov 29

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!

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

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Reposted by Simone Zaccaria

Marc Williams @marcjwilliams.bsky.social · Dec 3

Our paper on chromosomal abnormalities in normal breast tissue from BRCA carriers came out last week.
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

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Reposted by Simone Zaccaria

Sophie Ward @sophie-ward.bsky.social · Nov 29

What an absolute pleasure to be collaborating with such an incredibly talented team!!

SPRINTER out today in Nature Genetics 🧬

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

🚨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👇
🧵👇

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

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Reposted by Simone Zaccaria

Alex Frankell @afrankell.bsky.social · Nov 29

A great pleasure to work with @zaccasimo.bsky.social and his team on this elegant data and tool.

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

🚨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👇
🧵👇

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

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Simone Zaccaria @zaccasimo.bsky.social · Nov 29

Thank you, Trevor!

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

Thank you, Wei! 😊

Reposted by Simone Zaccaria

Qian Du @qianxidu.bsky.social · Nov 29

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!

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

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Simone Zaccaria @zaccasimo.bsky.social · Nov 29

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

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

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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