Kitty Murphy

Computational biologists, sign up! 👩‍💻🧑‍💻

Don’t miss out on the chance to share your work and exchange ideas. Abstract deadline: 12th August

See you there 🤓

Super excited to see them at Glastonbury this year! 🎪

Londonomics is back with its second workshop of the year: computer science for bioinformaticians 💡

4 pm @ UCL, with a pizza and drinks social after for an opportunity to network with fellow computational ECRs dotted around London ⚡️

This was a true team effort, and huge thanks go to everyone involved: @sj-marzi.bsky.social, Di Hu, @bartdestrooper.bsky.social, @mancusorenzo.bsky.social, Leen Wolfs, @susanrohde.bsky.social, Gonzalo Leguía Fauró, and Ivana Geric ✨

n/n

Lastly, we were excited to find that regions with increased chromatin accessibility in APOE2 microglia were enriched for vitamin D receptor binding, suggesting vitamin D signalling as a potential protective mechanism and therapeutic avenue.

6/n

Comparison with independent studies showed that APOE2 microglia were enriched for plaque-phagocytosing genes, prompting us to test their phagocytic activity. Using E. coli and myelin, we found that they were indeed more phagocytic than APOE4 microglia.

5/n

Genes downregulated in APOE4-expressing microglia were enriched in putatively protective microglial states, suggesting a failure to transition into these states.

Additionally, cytokine expression was elevated, consistent with previous findings in mouse microglia expressing APOE4.

4/n

We observed consistent differences in gene expression and chromatin accessibility. For example, the cellular migration-related gene CHCHD2 showed higher expression and increased chromatin accessibility near its transcription start site in APOE2 microglia.

3/n

As anticipated, the most pronounced differences were observed between APOE4 (risk-increasing in some populations) and APOE2 (protective).

Expression changes were partly driven by loss of function, but only genes downregulated in APOE4 and KO microglia were enriched for AD risk variants.

2/n

Excited to share that a chapter of my PhD has just been published in Nature Communications!

We profiled the transcriptomic and chromatin landscapes of microglia expressing the different APOE variants, which were xenografted into the brains of an Alzheimer's disease (AD) mouse model 🧠🧬

1/n

And just like that, 5 years in the Marzi lab @sj-marzi.bsky.social have come to an end. Couldn’t have asked for a better team ✨

Super excited to say, I’m switching fields and will be working with ancient human genomes in the Skov lab @lauritsskov.bsky.social in Copenhagen 🇩🇰

Excited to see a part of my PhD work out in the 🌍

We developed CHAS using 🧠 acetylation profiles, but it can be extended! Would love to hear from you if you try it with other tissues and cell types 🫁 🩸🫀

Lucky to have worked on this with an excellent team, more details below 👇🏻

This is a devastating and essential read. Here is a gift link for those without subs. The part about outside perceptions of scientists compared with almost a blue-collar reality is spot on (without even mentioning meager salaries). www.nytimes.com/2025/04/03/o...

Londonomics is back! ⚡️

Join us next Thursday 4pm @ The Francis Crick Institute.

Don’t sleep on this - only one ticket left!

We’re excited to bring you a series of talks and workshops 💥

Kicking things off with all things single-cell analysis with Dr @kristinaulicna.bsky.social 👩‍💻 🧬

More info and FREE tickets (only 1 left!) here: www.eventbrite.com/e/londonomic...

Talk followed by a networking social 🍕

Picture of Cathryn Lewis' research group at the SGDP Centre, waving and smiling.

📬New job 📬 Postdoc role on the AMBER project, to undertake genetic analyses of antidepressant response. Join us! Important science, rich data, nice people. Please repost. @kingsioppn.bsky.social
#depression #statistics #genetics #pharmacogenetics #antidepressants
my.corehr.com/pls/coreport...

openRxiv has arrived!

We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...

#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv

What a line-up! Just in time for international women’s day 💫 congrats!

Comparative characterization of human accelerated regions in neurons - Nature The cis-regulatory functions of human accelerated regions of genomic loci and their potential contribution to human brain evolution are revealed.

Comparative characterization of human accelerated regions in neurons [including brain evolution] www.nature.com/articles/s41...

Thanks to the discovery of sodium channels and experiments in giant squid 🦑 and much more in between, we now have a non-addictive pain treatment 💊

Brilliant storytelling of why long term funding of basic science across disciplines is critical.

I was part of the Marzi lab for my masters, PhD, and now postdoc. @sj-marzi.bsky.social is an enthusiastic scientist and supportive mentor. The science is cool and the people are even cooler. Can’t recommend enough!!! 🤓

Apply apply apply 👇🏻

This would also be a great opportunity to increase interaction between ECRs and PIs at conferences!

Just very happy to have our paper out today! A big thanks to all our co-authors, and to Nikolai and @steinaerts.bsky.social for the teamwork over the past years. If you are interested in using our models for cross-species enhancer studies, check out crested.readthedocs.io/en/stable/mo... 🙂

a cartoon of homer simpson and bart simpson sitting on a couch with the words join us above them . ALT: a cartoon of homer simpson and bart simpson sitting on a couch with the words join us above them .

We are looking to recruit a highly motivated postdoc with cell or molecular biology expertise. Excellent #epigenetics, #chromatin training & networking opportunities @qmulepigenetics.bsky.social
DM me for inquiries
pl apply/share tinyurl.com/m6jnksk5

YouTube video by BillieEilishVEVO Billie Eilish - BIRDS OF A FEATHER (Official Music Video)

Happy Birthday! I had this on repeat: www.youtube.com/watch?v=V9PV... ✨

Londonomics has made the move over to Bluesky 🦋

We now have 200+ members and we’re excited to bring you together at workshops, networking events, and the annual symposium! 💡

We’ll be kicking things off with a NextFlow workshop in March 👀

Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events*

*should be specific to gene regulation

Wide range of Earth’s species are showing a decline in diversity The loss of genetic variation means species may be less resilient to climate change and other stressors

Our long term project has finally been published - genetic diversity is lost worldwide, but we can also make a difference and conservation actions matters.
Find out more in the Science news here
www.science.org/content/arti...
#Consgen

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?

I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Friends and colleagues, I’ve written a book on effective functional genomics study design, which will be available on Amazon in a couple of weeks. Sharing the TOC to spark interest. I hope students and those planning genomics experiments will find it useful! I’ll share updates soon