Colm Ryan
@colmr.bsky.social
Systems biology | Bioinformatics | Cancer | Genetic interactions
https://cancerdata.ucd.ie/
(he / him)
https://cancerdata.ucd.ie/
(he / him)
Reposted by Colm Ryan
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
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)
January 9, 2026 at 4:09 PM
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)
Reposted by Colm Ryan
Great to see this out, collaboration with the Bond lab @sysbioire.bsky.social to understand consequences of EZH2 mutation in T-acute lymphoblastic leukaemia (T-ALL). Congrats to @lefeivret.bsky.social @cosmintudose.bsky.social and other authors not on bluesky!
ashpublications.org/bloodadvance...
ashpublications.org/bloodadvance...
Reduced PRC2 function causes asparaginase resistance in T-ALL by decreasing WNT pathway activity
Key Points. Reduced PRC2 function in T-ALL is associated with asparaginase resistance that is linked to reduced WNT/STOP pathway activity.Asparaginase resi
ashpublications.org
December 5, 2025 at 11:15 AM
Great to see this out, collaboration with the Bond lab @sysbioire.bsky.social to understand consequences of EZH2 mutation in T-acute lymphoblastic leukaemia (T-ALL). Congrats to @lefeivret.bsky.social @cosmintudose.bsky.social and other authors not on bluesky!
ashpublications.org/bloodadvance...
ashpublications.org/bloodadvance...
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.
November 28, 2025 at 3:05 PM
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.
Reposted by Colm Ryan
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
Postdoctoral fellow - Petsalaki Group - NetworkCommons
Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...
tinyurl.com
November 26, 2025 at 5:05 PM
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
Reposted by Colm Ryan
Last chance to register. Hurry Up!
🧬 Excited to announce the 2nd Euro Cancer DepMap Symposium bringing together leading minds in functional genomics, cancer vulnerabilities, AI, CRISPR and anti-cancer target discovery.📍Join us in Milan for cutting-edge science, open discussion & collaboration. #EuroDepMap #CancerResearch #CRISPR
November 3, 2025 at 1:50 PM
Last chance to register. Hurry Up!
Reposted by Colm Ryan
Anyone with a lower h-index than me is ineffectual, while anyone with a higher h-index is just better at playing the game and cutting corners. I'm sorry, that's just how numbers work!
I am completely against the use of citation metrics to evaluate scientists. But if your h-index is less than mine, you kinda have do what I say. I don't make the rules.
October 24, 2025 at 8:23 AM
Anyone with a lower h-index than me is ineffectual, while anyone with a higher h-index is just better at playing the game and cutting corners. I'm sorry, that's just how numbers work!
Reposted by Colm Ryan
🧵1/Exciting news in cancer epigenetics! Our latest research, "AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma", is now available on www.biorxiv.org/content/10.1.... Here's a thread summarizing our findings!👇
#CancerResearch #Epigenetics #Chromatin #Lymphoma
#CancerResearch #Epigenetics #Chromatin #Lymphoma
AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma
The catalytic subunit of Polycomb Repressive Complex 2 (PRC2), EZH2, is recurrently mutated in 25% of diffuse large B-cell lymphomas (DLBCL), causing increased H3K27me3 and decreased H3K27me2 levels. ...
www.biorxiv.org
October 17, 2025 at 7:11 AM
🧵1/Exciting news in cancer epigenetics! Our latest research, "AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma", is now available on www.biorxiv.org/content/10.1.... Here's a thread summarizing our findings!👇
#CancerResearch #Epigenetics #Chromatin #Lymphoma
#CancerResearch #Epigenetics #Chromatin #Lymphoma
Reposted by Colm Ryan
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...
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
October 7, 2025 at 4:11 PM
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...
blog.genesmindsmachines.com/p/we-still-c...
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...
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
September 29, 2025 at 4:11 PM
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...
academic.oup.com/nargab/artic...
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...
rdcu.be
September 24, 2025 at 2:54 PM
Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw
Reposted by Colm Ryan
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...
jobs.icr.ac.uk
September 19, 2025 at 7:38 AM
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...
Reposted by Colm Ryan
📢 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...
🗓️ 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
September 17, 2025 at 10:05 AM
📢 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...
🗓️ 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...
Reposted by Colm Ryan
Join Us! @ioriolab.bsky.social
🚨 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...
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
September 11, 2025 at 4:31 PM
Join Us! @ioriolab.bsky.social
Reposted by Colm Ryan
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...
biorxiv.org
September 9, 2025 at 1:30 PM
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
Reposted by Colm Ryan
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
September 7, 2025 at 5:02 PM
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...
just a month to go until the International Conference on Systems Biology #ICSB2025 kicks off in Dublin, still time to submit a poster abstract!
📢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
Submit your poster abstract here: icsb2025.com
#personalisedmedicine #computationalmodelling
@precisiononcire.bsky.social
September 5, 2025 at 1:23 PM
just a month to go until the International Conference on Systems Biology #ICSB2025 kicks off in Dublin, still time to submit a poster abstract!
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
September 5, 2025 at 8:50 AM
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...
Reposted by Colm Ryan
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
September 3, 2025 at 11:53 AM
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
Reposted by Colm Ryan
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...
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
www.ucd.ie
August 27, 2025 at 11:15 AM
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...
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...
Reposted by Colm Ryan
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.
It easily takes A YEAR from first contact, even if everything goes to plan on both sides.
August 27, 2025 at 9:35 AM
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.
It easily takes A YEAR from first contact, even if everything goes to plan on both sides.
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
August 20, 2025 at 11:00 AM
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...
Reposted by Colm Ryan
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...
rdcu.be
July 30, 2025 at 8:29 AM
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
Reposted by Colm Ryan
This is one of those awesome "I always wanted to do that experiment" papers. And a great 🧵.
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 🧪
July 27, 2025 at 1:04 AM
This is one of those awesome "I always wanted to do that experiment" papers. And a great 🧵.