Ashley Wong
ashleywong.bsky.social
Ashley Wong
@ashleywong.bsky.social
PhD candidate studying cancer evolution @icr.ac.uk | MBiochem grad @ox.ac.uk | she/her
Reposted by Ashley Wong
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
Reposted by Ashley Wong
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&nbsp;sequencing, with an&nbsp;error rate&nbsp;lower than five errors&nbsp;per billion base pairs&nbsp;and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection&nbsp;and&nbsp;the generation of high-resolution&nbsp;selection&nbsp;maps across coding and non-coding sites for many genes.
www.nature.com
October 8, 2025 at 4:31 PM
Reposted by Ashley Wong
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
Reposted by Ashley Wong
Grrrr. We don't call protein phosphorylation or acteylation epiproteomics. So let's not call RNA modification epitranscriptomics. In fact, realisitically, epigenetics has so many definitions, some of them non-overlapping, that this whole epi-XXXX (genetics/genomics whatever) is just not helping us.
August 21, 2025 at 7:36 AM
Reposted by Ashley Wong
My wonderful colleage Colin Kleanthous is raising money for the MND association. Please support Colin in this worthy endeavor! www.justgiving.com/page/colin-k...
(Please repost!)
Colin Kleanthous' fundraiser for Motor Neurone Disease Association
Help Colin Kleanthous raise money to support Motor Neurone Disease Association
www.justgiving.com
July 15, 2025 at 7:21 AM
Reposted by Ashley Wong
Using barcodes 📊 to track cancer 💊 resistance evolution: is it clonal selection or plasticity? @fwhiting.bsky.social‬ knows! His new "Evolutionary Informed Resistance Assays" (EIRAs) framework infers resistance evolution dynamics from barcode diversity data. www.nature.com/articles/s41... @icr.ac.uk
Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding - Nature Communications
Understanding the dynamics of how drug resistance originates in cancer remains crucial, but it is not possible to observe them directly. Here, the authors construct a mathematical framework to infer d...
www.nature.com
June 20, 2025 at 12:49 PM
Reposted by Ashley Wong
Social media grump Kamila has finally made it onto Bluesky!

Please check out my new perspective on metastasis evolution in @natrevcancer.nature.com if you need a reprieve from the news.

I tried my best to develop some new conceptual thoughts here, you be the judge whether I succeeded.
May 21, 2025 at 12:06 AM
Reposted by Ashley Wong
dATAC: our new method for simultaneous very high quality whole genome sequencing and chromatin accessibility profiling of single cells. We used dATAC to trace epigenome clonal evolution in colon cancer. Devised by the extraordinarily talented @maxmossner.bsky.social

www.biorxiv.org/content/10.1...
Single cell multi-omic whole genome sequencing and chromatin accessibility profiling reveals genome-epigenome coevolution in colorectal cancer
Epigenetic alterations co-evolve with genetic mutations to drive carcinogenesis and treatment response. Resolving genome-epigenome coevolution requires accurate multi-omic single cell measurement. Her...
www.biorxiv.org
April 23, 2025 at 3:42 PM
Reposted by Ashley Wong
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Reposted by Ashley Wong
Quite an essay on the basis of cancer entitled "The End of the Genetic Paradigm of Cancer" @plosbiology.org arguing against the primacy of somatic mutations (traditional model) and cells, invoking gene regulatory networks and tissue
journals.plos.org/plosbiology/...
March 18, 2025 at 6:25 PM