BEATSON CANCER SEMINAR SERIES,
GLASGOW UK
30 March 2023
Sarah was invited to give a talk in the Glasgow Cancer Seminar Series at the Beatson Institute for Cancer Research.
Really interesting discussions with computational, experimental, and clinician scientists on all things cancer research. Wonderful combination of people, science, and technologies.
CAMBRIDGE FESTIVAL
26 March 2023
This weekend we volunteered at the Cambridge Festival to engage members of the public (or all ages!) with our research. Malina, Cat, Mark and Sarah were all there.
We looked at cells with a virtual microscope, made lungs with paper bags and straws, and pipetted different types of glitter...
And #HeppieTheHepatocyte was on offer at the "Tattoo my Science" event - thanks to Claudia's artwork!
NEW TEAM PHOTO
06 March 2023
We finally have an official lab photo!
Left to right: Hashim Ahmed Nur, Claudia Arnedo Pac, Sarah Aitken, John Connelly, Malina Anghel.
Not pictured: Jose Coehlo-Lima, Áine McColgan
PATHSOC WINTER MEETING
LONDON, UK
02 February 2023
This week John and Sarah attended the PathSoc winter meeting at the Royal Society of Medicine: "Unleashing the edge power of pathology".
John presented his PhD work "Inference of germline and somatic variation using weakly-supervised deep transfer learning".
In the Jean Shanks and Pathological Society Symposium, Sarah presented "Disentangling strand interactions in DNA damage and repair". She was also invited to the National Academic Trainee Network meeting to talk about "Clinician scientists – An insight into the job".
GENOME STABILITY NETWORK MEETING
CAMBRIDGE, UK
13 January 2023
Claudia, Hashim, and Sarah attended the Genome Stability Network today. Lots of very interesting posters, talks, and discussions.
SEASONS GREETING FROM AITKEN LAB
23 December 2022
Celebrating a year of building the Aitken Lab team! And we were joined by our friends from the Histopathology and Light Microscopy Core Facilities.
INTRODUCING DR ARNEDO PAC!
15 December 2022
Congratulations to Claudia, now Dr Arnedo Pac, who successfully defended her PhD thesis today at IRB Barcelona.
CONGRATULATIONS, MALINA!
12 December 2022
Congratulations to Malina Anghel, who graduated today from her Masters degree at Manchester University.
DIGITAL PATHOLOGY AND AI CONGRESS
HEATHROW, UK
07 December 2022
This week is the Digital Pathology and AI Congress!
John Connelly will talk about using Computational Pathology and Machine Learning to predict genomic features from histology images.
The MRC Toxicology Unit Histopathology Facility will present their validation of a multiplex-immunofluourescence assay for neural proteins.
SYMBLS22
CAMBRIDGE, UK
25 November 2022
Hashim Ahmed Nur presented his work today at the Symposium for Biological and Life Sciences 2022.
He presented his work on the cellular responses to platinum-based DNA damaging agents in liver cancer models.
WE ARE HIRING - PHD STUDENTSHIP
01 November 2022
We are hiring: AstraZeneca-Funded Non-Clinical PhD Studentship to join us in October 2023.
Project: Error-corrected sequencing of carcinogenic nitrosamines in a human liver spheroid model
Deadline: 05 December 2022
WELCOME MALINA!
05 October 2022
Today we welcome another new lab member! - Malina Anghel its starting her PhD with us.
Malina joins us from the University of Manchester, where she did her Masters in Tissue Engineering for Regenerative Medicine.
WELCOME CLAUDIA!
03 October 2022
We are delighted to welcome Claudia Arnedo Pac to the lab - she starts her postdoc with us today!
Claudia joins us from the Institute for Research in Biomedicine (IRB) Barcelona, where just did her PhD in Bioinformatics and Biomedicine with Prof. Núria López-Bigas in the Barcelona Biomedical Genomics (BBG) Lab.
WE ARE HIRING - POSTDOC (GENOMICS)
26 September 2022
We are hiring: Postdoctoral researcher (Research Associate) in Genome Biology or Genomics to join our team!
Deadline: 24 October 2022
RIDE ACROSS BRITAIN FOR CRUK
18 September 2022
Sarah completed her end-to-end bike ride of the UK, from Lands End to John O'Groats in September.
The final tally was: • 978 miles / 1574 kilometres • 56,931 feet climbed • 9 days • 2 wheels • 1 tent • 39 bananas • 0 punctures
Thanks to generous sponsorship from friends, family, and colleagues I reached my fundraising target for Cancer Research UK.
Any final donations are of course welcome!
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
EUROPEAN CONGRESS OF PATHOLOGY
BASEL, SWITZERLAND
07 September 2022
John Connelly and Jose Coelho-Lima both gave talks this week at the European Congress of Pathology in Basel, Switzerland.
Here is a glimpse of John's brilliant talk on "Predicting genetic variation from quantitative tissue phenotypes using explainable machine learning".
Jose presented his clinical project "Cardiac arrest with successful cardiopulmonary resuscitation induces histologic changes that correlate with survival time and lead to misdiagnosis in sudden arrhythmic death syndrome"
CAMBRIDGE BIOSCIENCES DTP SYMPOSIUM
25 July 2022
Hashim Ahmed Nur attended the Cambridge Biosciences DTP Symposium.
HELLO AND GOODBYE!
30 June 2022
Today we said goodbye to Jose Coelho-Lima, who has finished his NIHR Academic Clinical Fellowship with us, and heading back to clinical work (for now).
We also welcomed John Connelly to the lab, who is joining us from Prof. Martin Taylor's lab at our sister Unit, the MRC Human Genetics Unit in Edinburgh.
PULMONARY PATHOLOGY SOCIETY MEETING, CORK, IRELAND
27 June 2022
Jose Coelho-Lima attended the Pulmonary Pathology Society meeting in Cork.
EUROPEAN CONGRESS ON DIGITAL PATHOLOGY (ECDP). BERLIN, GERMANY
16 June 2022
John Connelly attended the European Congress on Digital Pathology in Berlin.
His work was selected for an oral presentation: "Using machine learning to infer whole genome duplication from tumour nuclear morphology".
NEW PREPRINT: STRAND-RESOLVED MUTAGENICITY OF DNA DAMAGE AND REPAIR
10 June 2022
Strand-resolved mutagenicity of DNA damage and repair
We recently discovered that some DNA lesions (damaged bases) segregate unrepaired into daughter cells for multiple generations, thereby generating combinatorial genetic diversity (Aitken et al., 2020). We have now leveraged this discovery to learn more about how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair (Anderson et al., 2022).
Read the preprint here.
Read Sarah's tweetorial here.
#StrandInteractions
EMBO CANCER EVOLUTION
RIMINI, ITALY
20 May 2022
Sarah was invited to the EMBO Workshop: The many faces of cancer evolution to present unpublished work from the LCE Consortium "Disentangling strand interactions in DNA damage and repair".
#StrandInteractions
IRB BARCELONA, INVITED SEMINAR
27 April 2022
Sarah was invited to deliver the IRB Barcelona Research Seminar for the Computational Biology and Preclinical Models of Cancer research nodes.
"Disentangling strand interactions in DNA damage and repair"
WE ARE HIRING: COMPUTATIONAL POSTDOC
14 April 2022
We are hiring: Postdoctoral researcher (Research Associate) in Computational Biology or Bioinformatics to join us summer/autumn 2022.
Deadline: 28 April 2022
CONTRA CONFERENCE, ANDERMATT
12 April 2022
Sarah was invited to present at the Computational Oncology Conference organised by CONTRA (Computational ONcology TRaining Alliance Innovative Training Network).
"Re-running cancer evolution in vivo to disentangle DNA damage and repair"
First in-person conference since the pre-COVID era. Enthusiastic and engaged participants. And great snow...
MEDICAL MASTERCLASSES
07 April 2022
During the Cambridge Festival 2022, two of our lab members were invited by the Department of Pathology to give Medical Masterclasses aimed at Year 12 pupils from all backgrounds interested in medicine (not just at Cambridge), followed by a Q&A with current medical students.
Jose Coelho-Lima, our Academic Clinical Fellow, discussed the role of artificial intelligence in medicine and clinical research.
And Sarah talked about "Putting pathology under the microscope".
FIRST YEAR PHD TALKS
23 March 2022
Hashim, and all of the other first year PhD students at the MRC Toxicology Unit presented an overview of their project to the other students and group leaders. Well done!
LANDS END TO JOHN O'GROATS FOR CRUK
20 February 2022
Sarah is cycling from Lands End to John O'Groats in September
• 970miles • 1552km • 9 days • 2 wheels • 1 tent •
Although I am a daily, all-weather cyclist, this will be a massive challenge - so I've signed up via Cancer Research UK to give something back for the generous support that I have received from them over the years, and I would be massively grateful for any sponsorship and for generally helping to spread the word:
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
I also have another page for the Red Cross to show solidarity with the people of Ukraine and other countries who need humanitarian aid and support from the Disasters Emergency Committee.
LIVER CANCER EVOLUTION CONSORTIUM (HYBRID) MEETING
01 February 2022
This week we hosted the Liver Cancer Evolution Consortium meeting at the MRC Toxicology Unit. A truly hybrid meeting, with attendees from Edinburgh, Barcelona, Heidelberg, Hinxton, and Cambridge.
AND THEN THERE WERE FOUR!
12 January 2022
This week Hashim and Jose both joined our team.
L to R: (me), Hashim, Jose, and John.
Hashim Ahmed Nur is a MRC PhD student working on molecular and genomic responses to DNA damaging agents.
Jose Coehlo-Lima is a postdoctoral NIHR Academic Clinical Fellow, working on computational analysis of clinical histology images of lung cancers.
John Connelly is a Wellcome Trust Clinical PhD Student (University of Edinburgh). He is using machine learning to detect mutational processes in digitised pathology images of liver tumours.
CAMBRIDGE HEPATOLOGY RESEARCH SEMINAR
14 December 2021
Sarah was invited to present our work on Lesion Segregation at the monthly Eastern Liver Network Cambridge Hepatology Research Seminar.
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EMBL CANCER GENOMICS
22 November 2021
Sarah presented the next instalment from the Liver Cancer Evolution Consortium at EMBL Cancer Genomics: "Re-running cancer evolution in vivo: a high-resolution multi-omics approach"
WE ARE HIRING: PHD STUDENT
16 November 2021
We are hiring: Phd studentship to join us in October 2022.
Characterisation of 3D liver models for discovery toxicology and pathology
Deadline: 02 December 2021
CRUK CAMBRIDGE INSTITUTE RETREAT
22 October 2021
Sarah was invited to present our work on Lesion Segregation at the CRUK Cambridge Institute annual retreat.
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WE ARE HIRING: PHD STUDENT
16 September 2021
We are hiring: Phd studentship to join us in January 2022.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 27 September 2021
AITKEN LAB: DAY ONE
01 September 2021
First day at the Medical Research Council Toxicology Unit in the School of Biological Sciences at the University of Cambridge.
WE ARE HIRING: PHD STUDENT
04 June 2021
We are hiring: Phd studentship to join us in October 2021.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 18 June 2021
WE ARE MOVING TO THE MRC TOXICOLOGY UNIT, UNIVERSITY OF CAMBRIDGE
02 June 2021
The Aitken Lab will open at the MRC Toxicology Unit, University of Cambridge in autumn 2021.
2022
SEASONS GREETING FROM AITKEN LAB
23 December 2022
Celebrating a year of building the Aitken Lab team! And we were joined by our friends from the Histopathology and Light Microscopy Core Facilities.
INTRODUCING DR ARNEDO PAC!
15 December 2022
Congratulations to Claudia, now Dr Arnedo Pac, who successfully defended her PhD thesis today at IRB Barcelona.
CONGRATULATIONS, MALINA!
12 December 2022
Congratulations to Malina Anghel, who graduated today from her Masters degree at Manchester University.
DIGITAL PATHOLOGY AND AI CONGRESS
HEATHROW, UK
07 December 2022
This week is the Digital Pathology and AI Congress!
John Connelly will talk about using Computational Pathology and Machine Learning to predict genomic features from histology images.
The MRC Toxicology Unit Histopathology Facility will present their validation of a multiplex-immunofluourescence assay for neural proteins.
SYMBLS22
CAMBRIDGE, UK
25 November 2022
Hashim Ahmed Nur presented his work today at the Symposium for Biological and Life Sciences 2022.
He presented his work on the cellular responses to platinum-based DNA damaging agents in liver cancer models.
WE ARE HIRING - PHD STUDENTSHIP
01 November 2022
We are hiring: AstraZeneca-Funded Non-Clinical PhD Studentship to join us in October 2023.
Project: Error-corrected sequencing of carcinogenic nitrosamines in a human liver spheroid model
Deadline: 05 December 2022
WELCOME MALINA!
05 October 2022
Today we welcome another new lab member! - Malina Anghel its starting her PhD with us.
Malina joins us from the University of Manchester, where she did her Masters in Tissue Engineering for Regenerative Medicine.
WELCOME CLAUDIA!
03 October 2022
We are delighted to welcome Claudia Arnedo Pac to the lab - she starts her postdoc with us today!
Claudia joins us from the Institute for Research in Biomedicine (IRB) Barcelona, where just did her PhD in Bioinformatics and Biomedicine with Prof. Núria López-Bigas in the Barcelona Biomedical Genomics (BBG) Lab.
WE ARE HIRING - POSTDOC (GENOMICS)
26 September 2022
We are hiring: Postdoctoral researcher (Research Associate) in Genome Biology or Genomics to join our team!
Deadline: 24 October 2022
RIDE ACROSS BRITAIN FOR CRUK
18 September 2022
Sarah completed her end-to-end bike ride of the UK, from Lands End to John O'Groats in September.
The final tally was: • 978 miles / 1574 kilometres • 56,931 feet climbed • 9 days • 2 wheels • 1 tent • 39 bananas • 0 punctures
Thanks to generous sponsorship from friends, family, and colleagues I reached my fundraising target for Cancer Research UK.
Any final donations are of course welcome!
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
EUROPEAN CONGRESS OF PATHOLOGY
BASEL, SWITZERLAND
07 September 2022
John Connelly and Jose Coelho-Lima both gave talks this week at the European Congress of Pathology in Basel, Switzerland.
Here is a glimpse of John's brilliant talk on "Predicting genetic variation from quantitative tissue phenotypes using explainable machine learning".
Jose presented his clinical project "Cardiac arrest with successful cardiopulmonary resuscitation induces histologic changes that correlate with survival time and lead to misdiagnosis in sudden arrhythmic death syndrome"
CAMBRIDGE BIOSCIENCES DTP SYMPOSIUM
25 July 2022
Hashim Ahmed Nur attended the Cambridge Biosciences DTP Symposium.
HELLO AND GOODBYE!
30 June 2022
Today we said goodbye to Jose Coelho-Lima, who has finished his NIHR Academic Clinical Fellowship with us, and heading back to clinical work (for now).
We also welcomed John Connelly to the lab, who is joining us from Prof. Martin Taylor's lab at our sister Unit, the MRC Human Genetics Unit in Edinburgh.
PULMONARY PATHOLOGY SOCIETY MEETING, CORK, IRELAND
27 June 2022
Jose Coelho-Lima attended the Pulmonary Pathology Society meeting in Cork.
EUROPEAN CONGRESS ON DIGITAL PATHOLOGY (ECDP). BERLIN, GERMANY
16 June 2022
John Connelly attended the European Congress on Digital Pathology in Berlin.
His work was selected for an oral presentation: "Using machine learning to infer whole genome duplication from tumour nuclear morphology".
NEW PREPRINT: STRAND-RESOLVED MUTAGENICITY OF DNA DAMAGE AND REPAIR
10 June 2022
Strand-resolved mutagenicity of DNA damage and repair
We recently discovered that some DNA lesions (damaged bases) segregate unrepaired into daughter cells for multiple generations, thereby generating combinatorial genetic diversity (Aitken et al., 2020). We have now leveraged this discovery to learn more about how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair (Anderson et al., 2022).
Read the preprint here.
Read Sarah's tweetorial here.
#StrandInteractions
EMBO CANCER EVOLUTION
RIMINI, ITALY
20 May 2022
Sarah was invited to the EMBO Workshop: The many faces of cancer evolution to present unpublished work from the LCE Consortium "Disentangling strand interactions in DNA damage and repair".
#StrandInteractions
IRB BARCELONA, INVITED SEMINAR
27 April 2022
Sarah was invited to deliver the IRB Barcelona Research Seminar for the Computational Biology and Preclinical Models of Cancer research nodes.
"Disentangling strand interactions in DNA damage and repair"
WE ARE HIRING: COMPUTATIONAL POSTDOC
14 April 2022
We are hiring: Postdoctoral researcher (Research Associate) in Computational Biology or Bioinformatics to join us summer/autumn 2022.
Deadline: 28 April 2022
CONTRA CONFERENCE, ANDERMATT
12 April 2022
Sarah was invited to present at the Computational Oncology Conference organised by CONTRA (Computational ONcology TRaining Alliance Innovative Training Network).
"Re-running cancer evolution in vivo to disentangle DNA damage and repair"
First in-person conference since the pre-COVID era. Enthusiastic and engaged participants. And great snow...
MEDICAL MASTERCLASSES
07 April 2022
During the Cambridge Festival 2022, two of our lab members were invited by the Department of Pathology to give Medical Masterclasses aimed at Year 12 pupils from all backgrounds interested in medicine (not just at Cambridge), followed by a Q&A with current medical students.
Jose Coelho-Lima, our Academic Clinical Fellow, discussed the role of artificial intelligence in medicine and clinical research.
And Sarah talked about "Putting pathology under the microscope".
FIRST YEAR PHD TALKS
23 March 2022
Hashim, and all of the other first year PhD students at the MRC Toxicology Unit presented an overview of their project to the other students and group leaders. Well done!
LANDS END TO JOHN O'GROATS FOR CRUK
20 February 2022
Sarah is cycling from Lands End to John O'Groats in September
• 970miles • 1552km • 9 days • 2 wheels • 1 tent •
Although I am a daily, all-weather cyclist, this will be a massive challenge - so I've signed up via Cancer Research UK to give something back for the generous support that I have received from them over the years, and I would be massively grateful for any sponsorship and for generally helping to spread the word:
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
I also have another page for the Red Cross to show solidarity with the people of Ukraine and other countries who need humanitarian aid and support from the Disasters Emergency Committee.
LIVER CANCER EVOLUTION CONSORTIUM (HYBRID) MEETING
01 February 2022
This week we hosted the Liver Cancer Evolution Consortium meeting at the MRC Toxicology Unit. A truly hybrid meeting, with attendees from Edinburgh, Barcelona, Heidelberg, Hinxton, and Cambridge.
AND THEN THERE WERE FOUR!
12 January 2022
This week Hashim and Jose both joined our team.
L to R: (me), Hashim, Jose, and John.
Hashim Ahmed Nur is a MRC PhD student working on molecular and genomic responses to DNA damaging agents.
Jose Coehlo-Lima is a postdoctoral NIHR Academic Clinical Fellow, working on computational analysis of clinical histology images of lung cancers.
John Connelly is a Wellcome Trust Clinical PhD Student (University of Edinburgh). He is using machine learning to detect mutational processes in digitised pathology images of liver tumours.
2021
CAMBRIDGE HEPATOLOGY RESEARCH SEMINAR
14 December 2021
Sarah was invited to present our work on Lesion Segregation at the monthly Eastern Liver Network Cambridge Hepatology Research Seminar.
EMBL CANCER GENOMICS
22 November 2021
Sarah presented the next instalment from the Liver Cancer Evolution Consortium at EMBL Cancer Genomics: "Re-running cancer evolution in vivo: a high-resolution multi-omics approach"
WE ARE HIRING: PHD STUDENT
16 November 2021
We are hiring: Phd studentship to join us in October 2022.
Characterisation of 3D liver models for discovery toxicology and pathology
Deadline: 02 December 2021
CRUK CAMBRIDGE INSTITUTE RETREAT
22 October 2021
Sarah was invited to present our work on Lesion Segregation at the CRUK Cambridge Institute annual retreat.
WE ARE HIRING: PHD STUDENT
16 September 2021
We are hiring: Phd studentship to join us in January 2022.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 27 September 2021
AITKEN LAB: DAY ONE
01 September 2021
First day at the Medical Research Council Toxicology Unit in the School of Biological Sciences at the University of Cambridge.
WE ARE HIRING: PHD STUDENT
04 June 2021
We are hiring: Phd studentship to join us in October 2021.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 18 June 2021
WE ARE MOVING TO THE MRC TOXICOLOGY UNIT, UNIVERSITY OF CAMBRIDGE
02 June 2021
The Aitken Lab will open at the MRC Toxicology Unit, University of Cambridge in autumn 2021.