Colin Semple
@csemple.bsky.social
Genomics, bioinformatics; attempting to say useful things about cancer and evolution.
Institute of Genetics and Cancer, University of Edinburgh
https://institute-genetics-cancer.ed.ac.uk
https://semplelab.com
Institute of Genetics and Cancer, University of Edinburgh
https://institute-genetics-cancer.ed.ac.uk
https://semplelab.com
Pinned
Colin Semple
@csemple.bsky.social
· Jul 1
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer - Nature Communications
Tumour evolution and heterogeneity in high grade serous ovarian cancer (HGSOC) remains poorly characterised. Here, the authors investigate the genomic landscape of HGSOC and reveal two distinct evolut...
www.nature.com
New publication from the lab!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Colin Semple
Looking for a new opportunity in computational genomics? Join our group @uoe-igc.bsky.social @edinburgh-uni.bsky.social
Deadline September 1!
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Deadline September 1!
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Lecturer in Computational Genomics
Establishing an innovative research line as Lecturer in Computational Genomics related to reproductive disorders and genomic medicine. This Lecturer post is full-time (35 hours per week); however, we ...
elxw.fa.em3.oraclecloud.com
August 8, 2025 at 1:07 PM
Looking for a new opportunity in computational genomics? Join our group @uoe-igc.bsky.social @edinburgh-uni.bsky.social
Deadline September 1!
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
Deadline September 1!
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
New publication from the lab!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer - Nature Communications
Tumour evolution and heterogeneity in high grade serous ovarian cancer (HGSOC) remains poorly characterised. Here, the authors investigate the genomic landscape of HGSOC and reveal two distinct evolut...
www.nature.com
July 1, 2025 at 1:34 PM
New publication from the lab!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Colin Semple
tl;dr — this EO co-opts the language of open science to implement a system of political control wherein presidential appointees are given broad latitude to designate any number of reasonable scientific activities and inferences as scientific misconduct, and to penalize those involved accordingly.
Restoring Gold Standard Science
By the authority vested in me as President by the Constitution and the laws of the United States of America, including section 7301 of title 5, United
www.whitehouse.gov
May 24, 2025 at 9:28 PM
tl;dr — this EO co-opts the language of open science to implement a system of political control wherein presidential appointees are given broad latitude to designate any number of reasonable scientific activities and inferences as scientific misconduct, and to penalize those involved accordingly.
Reposted by Colin Semple
Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
May 6, 2025 at 2:59 PM
Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
Building AI models or the data to train them?
Core funding of >$130M a year for a faculty of ~30.
www.nature.com/naturecareer...
acrobat.adobe.com/id/urn:aaid:...
pls RT!
New publication from the lab! We used a machine learning approach to predict chromatin loop dynamics during human spermatogenesis - and find these structures do not direct gene expression but may drive the positioning of recombination events
bmcbiol.biomedcentral.com/articles/10....
bmcbiol.biomedcentral.com/articles/10....
CTCF-anchored chromatin loop dynamics during human meiosis - BMC Biology
Background During meiosis, the mammalian genome is organised within chromatin loops, which facilitate synapsis, crossing over and chromosome segregation, setting the stage for recombination events and...
bmcbiol.biomedcentral.com
March 24, 2025 at 1:09 PM
New publication from the lab! We used a machine learning approach to predict chromatin loop dynamics during human spermatogenesis - and find these structures do not direct gene expression but may drive the positioning of recombination events
bmcbiol.biomedcentral.com/articles/10....
bmcbiol.biomedcentral.com/articles/10....
Reposted by Colin Semple
Watching the US take a wrecking ball to science 💔 🤯
Reminder of the importance of doing science in the open. Put data, software, resources in public domain, where no single govt can erase them. This is our collective knowledge. Distributed data systems are essential.
www.nature.com/articles/s41...
Reminder of the importance of doing science in the open. Put data, software, resources in public domain, where no single govt can erase them. This is our collective knowledge. Distributed data systems are essential.
www.nature.com/articles/s41...
Genomic data sharing: you don’t know what you’ve got (till it’s gone) - Nature Reviews Genetics
Reflecting on the core values of early data sharing agreements, the Bermuda Principles and the Fort Lauderdale Agreement, Kathryn E. Holt and Michael Inouye emphasize the need to reaffirm our commitme...
www.nature.com
March 17, 2025 at 9:08 PM
Watching the US take a wrecking ball to science 💔 🤯
Reminder of the importance of doing science in the open. Put data, software, resources in public domain, where no single govt can erase them. This is our collective knowledge. Distributed data systems are essential.
www.nature.com/articles/s41...
Reminder of the importance of doing science in the open. Put data, software, resources in public domain, where no single govt can erase them. This is our collective knowledge. Distributed data systems are essential.
www.nature.com/articles/s41...
Reposted by Colin Semple
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
February 12, 2025 at 5:04 PM
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Reposted by Colin Semple
#postdoctoral traineeships in the Hide Lab in Alzheimer's disease omics and in cancer immunoediting. #Spatial #snSeq? Integration?#compBiol We grow people and celebrate diversity @harvardmed.bsky.social @bidmcreseach.bsky.social @bidmc-cancercenter.bsky.social
learn more: shorturl.at/97TpL
learn more: shorturl.at/97TpL
February 19, 2025 at 7:08 PM
#postdoctoral traineeships in the Hide Lab in Alzheimer's disease omics and in cancer immunoediting. #Spatial #snSeq? Integration?#compBiol We grow people and celebrate diversity @harvardmed.bsky.social @bidmcreseach.bsky.social @bidmc-cancercenter.bsky.social
learn more: shorturl.at/97TpL
learn more: shorturl.at/97TpL
Delighted to see this work emerge - exploiting a large in vivo mouse mutagenesis experiment to study evolutionary interactions between the nuclear and mitochondrial genomes during early tumourigenesis:
bsky.app/profile/bior...
bsky.app/profile/bior...
Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis https://www.biorxiv.org/content/10.1101/2025.02.11.637769v1
February 17, 2025 at 11:03 AM
Delighted to see this work emerge - exploiting a large in vivo mouse mutagenesis experiment to study evolutionary interactions between the nuclear and mitochondrial genomes during early tumourigenesis:
bsky.app/profile/bior...
bsky.app/profile/bior...
Reposted by Colin Semple
Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis https://www.biorxiv.org/content/10.1101/2025.02.11.637769v1
February 16, 2025 at 5:51 AM
Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis https://www.biorxiv.org/content/10.1101/2025.02.11.637769v1
Reposted by Colin Semple
American science is under attack
Opinion piece by Dr Harold Varmus, Nobel Prize winner, former director of the #NIH and the #NCI 🧪
“Perhaps what’s most disheartening is what feels like the absence of widespread opposition to this unraveling”
www.nytimes.com/2025/02/14/o...
Opinion piece by Dr Harold Varmus, Nobel Prize winner, former director of the #NIH and the #NCI 🧪
“Perhaps what’s most disheartening is what feels like the absence of widespread opposition to this unraveling”
www.nytimes.com/2025/02/14/o...
Opinion | American Science is Under Attack (Gift Article)
The Trump administration hobbles research and endangers the public health.
www.nytimes.com
February 14, 2025 at 1:58 PM
American science is under attack
Opinion piece by Dr Harold Varmus, Nobel Prize winner, former director of the #NIH and the #NCI 🧪
“Perhaps what’s most disheartening is what feels like the absence of widespread opposition to this unraveling”
www.nytimes.com/2025/02/14/o...
Opinion piece by Dr Harold Varmus, Nobel Prize winner, former director of the #NIH and the #NCI 🧪
“Perhaps what’s most disheartening is what feels like the absence of widespread opposition to this unraveling”
www.nytimes.com/2025/02/14/o...
Reposted by Colin Semple
Building on our discovery of #LesionSegregation, @mikespencerchapman.bsky.social and colleagues from @sangerinstitute.bsky.social find that some DNA lesions can persist in humans for months or years!
"Prolonged persistence of mutagenic DNA lesions in somatic cells"
www.nature.com/articles/s41...
"Prolonged persistence of mutagenic DNA lesions in somatic cells"
www.nature.com/articles/s41...
Prolonged persistence of mutagenic DNA lesions in somatic cells - Nature
Persistent DNA lesions can occur throughout the human lifespan and can remain in the genome of affected cells for several years and generate a substantial proportion of the mutational burden.
www.nature.com
January 15, 2025 at 5:21 PM
Building on our discovery of #LesionSegregation, @mikespencerchapman.bsky.social and colleagues from @sangerinstitute.bsky.social find that some DNA lesions can persist in humans for months or years!
"Prolonged persistence of mutagenic DNA lesions in somatic cells"
www.nature.com/articles/s41...
"Prolonged persistence of mutagenic DNA lesions in somatic cells"
www.nature.com/articles/s41...
Reposted by Colin Semple
To what extent is cancer development deterministic and predictable..?
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
January 15, 2025 at 7:32 PM
To what extent is cancer development deterministic and predictable..?
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Does the germline genome affect that predictability...?
Preprint: www.biorxiv.org/content/10.1...
Reposted by Colin Semple
🌟NEW PREPRINT ALERT!🌟
We are very pleased to introduce #StrainDifferences: “Genetic background sets the trajectory of cancer evolution”
www.biorxiv.org/content/10.1...
🧵[1/12]
We are very pleased to introduce #StrainDifferences: “Genetic background sets the trajectory of cancer evolution”
www.biorxiv.org/content/10.1...
🧵[1/12]
Genetic background sets the trajectory of cancer evolution
Human cancers are heterogeneous. Their genomes evolve from genetically diverse germlines in complex and dynamic environments, including exposure to potential carcinogens. This heterogeneity of humans,...
www.biorxiv.org
January 15, 2025 at 7:19 PM
🌟NEW PREPRINT ALERT!🌟
We are very pleased to introduce #StrainDifferences: “Genetic background sets the trajectory of cancer evolution”
www.biorxiv.org/content/10.1...
🧵[1/12]
We are very pleased to introduce #StrainDifferences: “Genetic background sets the trajectory of cancer evolution”
www.biorxiv.org/content/10.1...
🧵[1/12]
We are hiring a new postdoctoral bioinformatician!
Come and work with us on multidisciplinary cancer genomics projects at the Institute of Genetics and Cancer in Edinburgh:
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
institute-genetics-cancer.ed.ac.uk
semplelab.com
Come and work with us on multidisciplinary cancer genomics projects at the Institute of Genetics and Cancer in Edinburgh:
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
institute-genetics-cancer.ed.ac.uk
semplelab.com
January 9, 2025 at 8:41 PM
We are hiring a new postdoctoral bioinformatician!
Come and work with us on multidisciplinary cancer genomics projects at the Institute of Genetics and Cancer in Edinburgh:
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
institute-genetics-cancer.ed.ac.uk
semplelab.com
Come and work with us on multidisciplinary cancer genomics projects at the Institute of Genetics and Cancer in Edinburgh:
elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
institute-genetics-cancer.ed.ac.uk
semplelab.com
Reposted by Colin Semple
The SIDB PhD programme with projects on neurodevelopmental disorders (including one from our lab) is now open for applications. Good stipend, excellent environment and a beautiful city sidb.org.uk/phds/
November 20, 2024 at 9:30 AM
The SIDB PhD programme with projects on neurodevelopmental disorders (including one from our lab) is now open for applications. Good stipend, excellent environment and a beautiful city sidb.org.uk/phds/
Reposted by Colin Semple
Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits https://www.biorxiv.org/content/10.1101/2023.11.09.566307v1
Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits https://www.biorxiv.org/content/10.1101/2023.11.09.566307v1
Abstract CTNNB1, the gene encoding beta-catenin, is a frequent target for oncogenic mutations activa
www.biorxiv.org
November 14, 2023 at 3:09 AM
Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits https://www.biorxiv.org/content/10.1101/2023.11.09.566307v1
Reposted by Colin Semple
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer https://www.biorxiv.org/content/10.1101/2024.01.12.575376v1
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer https://www.biorxiv.org/content/10.1101/2024.01.12.575376v1
Deciphering the structural variation across tumour genomes is crucial to determine the events drivin
www.biorxiv.org
January 15, 2024 at 8:54 PM
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer https://www.biorxiv.org/content/10.1101/2024.01.12.575376v1
Reposted by Colin Semple
Protein structural context of cancer mutations reveals molecular mechanisms and identifies novel candidate driver genes https://www.biorxiv.org/content/10.1101/2024.03.21.586131v1
Protein structural context of cancer mutations reveals molecular mechanisms and identifies novel candidate driver genes https://www.biorxiv.org/content/10.1101/2024.03.21.586131v1
Advances in structure determination and computational modelling are enabling us to study the protein
www.biorxiv.org
March 27, 2024 at 9:47 AM
Protein structural context of cancer mutations reveals molecular mechanisms and identifies novel candidate driver genes https://www.biorxiv.org/content/10.1101/2024.03.21.586131v1
Reposted by Colin Semple
How Musk broke Twitter and helped elect Trump
(Location: Tesla European HQ, Amsterdam)
www.youtube.com/watch?v=iX3v...
(Location: Tesla European HQ, Amsterdam)
www.youtube.com/watch?v=iX3v...
TESLA = TRUMP
YouTube video by Led By Donkeys
www.youtube.com
November 9, 2024 at 10:39 AM
How Musk broke Twitter and helped elect Trump
(Location: Tesla European HQ, Amsterdam)
www.youtube.com/watch?v=iX3v...
(Location: Tesla European HQ, Amsterdam)
www.youtube.com/watch?v=iX3v...
Reposted by Colin Semple
We are happy to announce the release of a new #nf-core workflow -- #oncoanalyser performs an exhaustive analysis of single-patient cancer sequencing data using methods developed by the Hartwig Medical Foundation Australia. (1/5)
August 26, 2024 at 9:33 AM
We are happy to announce the release of a new #nf-core workflow -- #oncoanalyser performs an exhaustive analysis of single-patient cancer sequencing data using methods developed by the Hartwig Medical Foundation Australia. (1/5)