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Colm Ryan

@colmr.bsky.social

360 followers 408 following 78 posts

Systems biology | Bioinformatics | Cancer | Genetic interactions cancerdata.ucd.ie (he / him)

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Colm Ryan @colmr.bsky.social · 04/09/2026

Bernard came back from his placement @ebi.embl.org bearing gifts...

Sticker from the Perturbation Catalogue stating "Would I rather catalogue a thousand perturbations once or one perturbation a thousand times? Easy. Both."

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Colm Ryan @colmr.bsky.social · 09/01/2026

Enjoying 'Why Machines Learn' by Anil Ananthaswamy, including this anecdote highlighting that there's always more that *could* be in a PhD but that you have to draw a line somewhere. Guyon here is Isabelle Guyon, who was later key to the development of SVMs (especially the kernel trick)

Photo containing the following text: "Their paper was published a year before Guyon defended her Ph.D. thesis, for which she had tested numerous algorithms for linear classification—but none of these was an optimal margin classifier, meaning the algorithms found some linear boundary, not necessarily the best one. Guyon could have used Krauth and Mézard's algorithm to implement an optimal margin classifier; she didn't. "One of the examiners of my Ph.D. asked me why I did not implement the algorithm of Mézard and Krauth and benchmark it against the other things I was trying. I said, 'Well, I didn't think it would make that much of a difference,'" Guyon told me. "But the reality is that I just wanted to graduate, and I didn't have time."

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Colm Ryan @colmr.bsky.social · 28/11/2025

Replacing my still functioning 2017 Mac because it's no longer compatible with our two factor authentication software (preventing me logging on to any work related system). This really doesn't seem optimal.

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Colm Ryan @colmr.bsky.social · 30/05/2025

Pairs with these sorts of regulatory relationships are enriched in synthetic lethality – when one gene gets deleted, cells become dependent on the other for survival – suggesting these relationships can identify new therapeutic targets. The cartoon below illustrates the proposed model.

Cartoon illustrating proteomic compensation between paralogs

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Colm Ryan @colmr.bsky.social · 14/02/2025

Congrats to Anjan Venkatesh, who passed his viva @ucddublin.bsky.social this morning. Thanks to extern @pedrobeltrao.bsky.social, intern Denis Shields and chair Dimitris Chatzopoulos. cc @ucddublin.bsky.social @ucdcs.bsky.social

Picture of Anjan Venkatesh after his Viva alongside his supervisor and examiners

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Colm Ryan @colmr.bsky.social · 29/01/2025

We will be hosting the International Conference on Systems Biology (ICSB) in Dublin this year – 5-9th October icsb2025.com/registration/ #ICSB2025

Flier for the ICSB2025 conference in Dublin 5-9 October 2025

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Colm Ryan @colmr.bsky.social · 23/01/2025

this table evaluates the methods on an actual combinatorial screen where we have data on both the identified SL pairs and the set of screened pairs (real negatives instead of random sampling!). in this case, all methods perform significantly worse than the analyses presented elsewhere in the paper.

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