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Colm Ryan

@colmr.bsky.social

330 followers 390 following 49 posts

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

cancerdata.ucd.ie

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Reposted by Colm Ryan

Claus Wilke @clauswilke.com · 2d

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

Colm Ryan @colmr.bsky.social · 10d

We think this work will be useful for 1) those choosing an existing method to score a genetic interaction screen and 2) those developing new genetic interaction scoring systems as it provides a framework for benchmarking. Thanks to @researchireland.ie for funding!

Colm Ryan @colmr.bsky.social · 10d

We find that no single method performs best across all screens, but one (Gemini) performs well across most and has an available R package (Gemini).

Colm Ryan @colmr.bsky.social · 10d

1) we develop a benchmark that allow us to compare the performance of different scoring methods when applied to a single screen and 2) we systematically apply this benchmark to 5 scoring methods applied across 5 published screens.

Colm Ryan @colmr.bsky.social · 10d

Multiple methods for scoring genetic interactions from combinatorial screens have been published, but comparison across methods has been limited. Most published screens use distinct scoring methods, making comparison across published work difficult. Here we make two contributions....

Colm Ryan @colmr.bsky.social · 10d

Hamda's paper is out: benchmarking different genetic interaction scoring methods for identifying synthetic lethal interactions from combinatorial CRISPR screens.

academic.oup.com/nargab/artic...

Benchmarking genetic interaction scoring methods for identifying synthetic lethality from combinatorial CRISPR screens

Abstract. Synthetic lethality (SL) is an extreme form of negative genetic interaction, where simultaneous disruption of two non-essential genes causes cell

academic.oup.com

Colm Ryan @colmr.bsky.social · 15d

Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw

Synthetic lethality in cancer drug discovery: challenges and opportunities

Nature Reviews Drug Discovery - This Review outlines recent advances in synthetic lethality, from CRISPR-based discovery and machine learning-guided prioritization of gene pairs to new phenotypic...

Reposted by Colm Ryan

Chris Lord and Andrew Tutt’s Lab Institute of Cancer Research @icrlordlab.bsky.social · 20d

We're hiring ! Specifically....we are seeking to appoint a creative and motivated Postdoctoral Training Fellow to study how drug resistance emerges in homologous recombination defective (HRD) breast cancers and how this could be targeted. jobs.icr.ac.uk/vacancies/13...

PDTF - Homologous Recombination Defective Cancers ( Profs Chris Lord and Andrew Tutt) in Chelsea | The Institute of Cancer Research

View details and apply for this PDTF - Homologous Recombination Defective Cancers ( Profs Chris Lord and Andrew Tutt) vacancy in Chelsea . Salary: Dependent on relevant Postdoctoral exp...

Reposted by Colm Ryan

Francesco Iorio @francescoiorio.bsky.social · 22d

📢 The 2nd European Cancer Dependency Map Symposium is coming!
🗓️ 20 Nov 2025
📍 Human Technopole, Milan
Join us for a one-day dive into:
🔹 Cancer genomics
🔹 CRISPR screening
🔹 AI-driven target discovery
With the patronage of AIRC
🔗 humantechnopole.it/en/trainings...

2nd European Cancer Dependency Map Symposium - Human Technopole

The 2nd European Cancer Dependency Map Symposium is a scientific event open to the national and international scientific community working in computational genomics, pharmacogenomics, and therapeutic ...

humantechnopole.it

Reposted by Colm Ryan

Francesco Iorio @francescoiorio.bsky.social · 28d

Join Us! @ioriolab.bsky.social

IorioLab @ioriolab.bsky.social · 28d

🚨 We’re hiring! 🚨 looking for a computational postdoc to lead an exciting project at the intersection of AI, CRISPR, multi-omics, and cancer genomics.
Join us to design the next generation of genetic interaction screens and uncover new synthetic lethalities
www.linkedin.com/jobs/view/42...

Human Technopole hiring Postdoc in Cancer Synthetic Lethality Prediction and AI-Driven Target Discovery in Milan, Lombardy, Italy | LinkedIn

Posted 2:37:53 PM. APPLICATION CLOSING DATE: October 12, 2025Human Technopole (HT) is an interdisciplinary life…See this and similar jobs on LinkedIn.

www.linkedin.com

Reposted by Colm Ryan

Cosmin Tudose @cosmintudose.bsky.social · Sep 9

Pleased that the 2nd part of my PhD is now available as a preprint! Here, we investigated the epigenomic and transcriptomic changes occurring upon PRC2 depletion in AML cells. biorxiv.org/content/10.1.... A thread🧵1/17

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

Background Polycomb Repressive Complex 2 (PRC2) modulates chromatin accessibility and architecture to direct tissue-specific gene expression. PRC2 function is frequently altered in cancer by loss-of-f...

Reposted by Colm Ryan

John Doench @johndoench.bsky.social · Sep 7

Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...

Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design

The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...

www.biorxiv.org

Colm Ryan @colmr.bsky.social · Sep 5

just a month to go until the International Conference on Systems Biology #ICSB2025 kicks off in Dublin, still time to submit a poster abstract!

Systems Biology Ireland @sysbioire.bsky.social · Sep 5

📢We've extended our poster abstract deadline to Sept 22 to accommodate anyone returning to campus who would still like to submit & attend #ICSB2025! Please spread the word!

Submit your poster abstract here: icsb2025.com

#personalisedmedicine #computationalmodelling
@precisiononcire.bsky.social

Colm Ryan @colmr.bsky.social · Sep 5

new from @cosmintudose.bsky.social What happens when tumor suppresor EZH2 is mutated in acute myeloid leukaemia? How does it change transcription, chromatin accessibility & drug response? The Bond lab created CRISPR mutants to find out & Cosmin put it all together www.biorxiv.org/content/10.1...

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

Background Polycomb Repressive Complex 2 (PRC2) modulates chromatin accessibility and architecture to direct tissue-specific gene expression. PRC2 function is frequently altered in cancer by loss-of-f...

www.biorxiv.org

Reposted by Colm Ryan

UCD School of Computer Science @ucdcs.bsky.social · Sep 3

Article by Pádraig Cunningham and Barry Smyth in Communications of the ‪@acm.org‬ analyses the differences in quality and practices of new Open Access and traditional Computer Science journals. bit.ly/41KKQ7s

montage of figures from the article and headshots of the authors

Reposted by Colm Ryan

Eric Conway @conwayer1.bsky.social · Aug 27

Delighted that our work on EZH2 dominant negativity in Weaver syndrome is now out in Genes & Development!

This exciting work on chromatinopathies 🧬 was in collab with @adrianbracken.bsky.social and spearheaded by Orla Deevy.

@ucddublin.bsky.social @ucd-sbbs.bsky.social

www.ucd.ie/newsandopini...

UCD co-lead breakthrough discovering genetic mechanism driving Weaver syndrome

Reposted by Colm Ryan

Gautam Dey @gautamdey.bsky.social · Aug 27

Final year PhD students, I know you’re desperately trying to finish experiments/revisions/submissions/write a thesis & just survive - but please spare a few minutes to apply to your dream postdoc labs.

It easily takes A YEAR from first contact, even if everything goes to plan on both sides.

Colm Ryan @colmr.bsky.social · Aug 20

looks like a super resource, congrats on getting it out! I think having a large number of GIs measured in a single genetic background will be a really useful complement to DepMap. we're only starting to dig into the data now, will let you know how we get on!

Colm Ryan @colmr.bsky.social · Aug 20

Monumental effort from @maxbillmann.bsky.social and colleagues, quantifying genetic interactions among 4 million human gene pairs. Lots of features associated with genetic interaction & GI degree conserved from yeast. www.biorxiv.org/content/10.1...

A global genetic interaction map of a human cell reveals conserved principles of genetic networks

We generated a genome-scale, genetic interaction network from the analysis of more than 4 million double mutants in the haploid human cell line, HAP1. The network maps ∼90,000 genetic interactions, in...

www.biorxiv.org

Colm Ryan @colmr.bsky.social · Jul 31

I too am 'programming' with Claude! it's fun isn't it?

Reposted by Colm Ryan

Chris Lord and Andrew Tutt’s Lab Institute of Cancer Research @icrlordlab.bsky.social · Jul 30

With super Roman Chabanon and Sophie Postal Vinay, we show that inhibition of RNA editor ADAR1 causes a new form of BRCA synthetic lethality>autocrine inferferon poisoning. Relevant for ADAR1 drug discovery. Could provide a mechanistically different approach than PARPi. rdcu.be/eyo6t

Autocrine interferon poisoning mediates ADAR1-dependent synthetic lethality in BRCA1/2-mutant cancers

Nature Communications - The RNA editing enzyme ADAR1 blocks interferon responses triggered by cytosolic RNA sensors, and has been proposed as a potential target in immuno-oncology. Here, the...

Reposted by Colm Ryan

Traver Hart @traver.bsky.social · Jul 27

This is one of those awesome "I always wanted to do that experiment" papers. And a great 🧵.

Mark Peifer (He, him) @peiferlabunc.bsky.social · Jul 26

To better treat cancer, we need to understand its underlying biology. Despite decades of research, some fundamental questions remain unanswered. One is why certain key tumor suppressor or oncogenes lead to cancer predominantly in single tissue: e.g. Rb in the retina, or APC in the colon 1/n 🧪

Diagram illustrating the two-hit model of retinoblastoma

Colm Ryan @colmr.bsky.social · Jul 29

congrats Tríona!

Colm Ryan @colmr.bsky.social · Jul 29

when an Irish funding agency launches a new grant call in July with a deadline in August it's hard to feel that researcher well-being is one of their priorities...

Colm Ryan @colmr.bsky.social · Jul 29

I'm not the person to ask!