Programme events

Upcoming events 

XDF Programme Annual Symposium 2024 - 8th November 2024

Short talks from our current fellows and 3 invited keynote speakers from academia and industry. 

More details on the Institute of Genetics and Cancer website.

Past events

XDF Programme Annual Symposium 2022 - 5 October 2022

The Cross-Disciplinary Fellowships (XDF) Programme Annual Symposium 2022 will include presentations from some of our cross-disciplinary Fellows as well as short talks from session chairs Dr Catalina Vallejos and Dr Linus Schumacher. The XDF Fellows’ talks will cover a broad spectrum of topics in quantitative biomedicine. The Symposium will take place in the Institute of Genetics and Cancer (South seminar room: S1.14) but is planned as a “hybrid style meeting” with the possibility of joining online. The talks will be open to the University of Edinburgh community - if you are not based in the Institute of Genetics and Cancer but would like to attend in IGC or obtain online meeting details please contact Dr Arek Welman [A.Welman@ed.ac.uk] in advance.

Schedule:

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Opening of the Symposium

10:00-10:10       Prof Chris Ponting: Introduction from XDF Programme Lead

Session 1:

10.10 - 10.25    Dr Catalina Vallejos: Foreword from the session Chair

10.25 - 10.40    Dr Andreas Kapourani

10.40 - 10.55    Dr Andrew Papanastasiou

10.55 - 11.10    Dr Lyndsay Kerr

11.10 - 11.25    Dr Eric Latorre Crespo

11.25 – 11:45    Short break

Session 2:

11.45 - 12.00    Dr Linus Schumacher: Foreword from the session Chair

12.00 - 12.15    Dr Vanessa Smer Barreto

12.15 - 12.30    Dr Didier Devaurs

12.30 - 12.45    Dr Lucy Martin

12.45 - 13.00    Dr Michael Nicholson

Titles of presentations:

Andreas Kapourani: "Multimodal decoding of human liver regeneration"

Andrew Papanastasiou: "Probing the regulation of eye-field specification using organoid multi-omics"

Lyndsay Kerr: “Assessing the heterogeneity of methylation patterns within single molecules using Nanopore sequencing data”

Eric Latorre Crespo: "Measuring genetic and epigenetic processes of ageing in blood "

Vanessa Smer Barreto: "Senolytics and machine learning: from discovery to design"

Didier Devaurs: “Making deep mutational scanning actionable for the interpretation of protein variant effects”

Lucy Martin: "The role of senescence in glioblastoma radiation therapy"

Michael Nicholson: "Modelling the effects of mutational processes and selection in determining cancer evolutionary trajectories"

XDF Programme Tutorials

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XDF Programme Tutorials represent a relaxed and informal way of introducing complex biomedical concepts to scientists coming to life sciences from other disciplines. They are delivered by researchers from the Institute of Genetics and Cancer and by invited colleagues from other parts of the University of Edinburgh. The tutorials are primarily aimed at the Fellows accepted for our XDF Programme but are open to wider research community, particularly postdocs and PhD-students  with non-biomedical backgrounds, who would like to fill gaps in their knowledge and get better understanding of concepts and language used in biomedicine. Questions and discussions during these meetings are highly encouraged.

You can watch some of past tutorials using links available on the XDF Programme Tutorials website.

One-To-One Meetings

These meetings are designed to provide an opportunity for the XDF’s to discuss the progress and any other issues of relevance directly with the XDF Programme Lead Professor Ponting. 

"Catch up" meetings with XDF Programme Directors

"Catch up" meetings of the XDF Programme Fellows with the Programme Directors and Scientific Administrator are organised to discuss Fellows' progress, outcomes of their projects and other important matters.

Past events

5 October 2022

In October 2022 the Institute of Genetics and Cancer (IGC) celebrated its cross-disciplinary science with the XDF Programme Annual Symposium 2022. The event, organised by Dr Arkadiusz Welman and opened by Professor Chris Ponting, took place in the Edinburgh Cancer Research seminar room. It included scientific presentations from the Programme Fellows and short talks from invited session chairs: Dr Catalina Vallejos Meneses (MRC Human Genetics Unit) and Dr Linus Schumacher (Centre for Regenerative Medicine), who reflected on their own paths to cross-disciplinarity. The Symposium was broadcasted online to enable better accessibility for people who were unable to travel to IGC.

Presentations by the Fellows covered the following topics:

Dr Andreas Kapourani: "Multimodal decoding of human liver regeneration"

Dr Andrew Papanastasiou: "Probing the regulation of eye-field specification using organoid multi-omics"

Dr Lyndsay Kerr: “Assessing the heterogeneity of methylation patterns within single molecules using Nanopore sequencing data”

Dr Eric Latorre Crespo: "Measuring genetic and epigenetic processes of ageing in blood "

Dr Vanessa Smer Barreto: "Senolytics and machine learning: from discovery to design"

Dr Didier Devaurs: “Making deep mutational scanning actionable for the interpretation of protein variant effects”

Dr Lucy Martin "The role of senescence in glioblastoma radiation therapy"

Dr Michael Nicholson "Modelling the effects of mutational processes and selection in determining cancer evolutionary trajectories"

The event attracted significant interest from across the University with visitors from the School of Informatics, many attendees in the room and online, and multiple exciting research discussions.

26 October 2021

A "catch up" meeting of the XDF Programme 2020 Fellows with the Programme Directors and Scientific Administrator to discuss their "final project" proposals. 

20 September 2021 - XDF Programme Annual Symposium 2021

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The Cross-Disciplinary Fellowships (XDF) Programme Annual Symposium 2021 included presentations from some of our cross-disciplinary Fellows. The talks covered a broad spectrum of topics in quantitative biomedicine. They were delivered online using Zoom virtual room and were open to the University community. Details below:

Seminar Titles:

Ava Khamseh "Current gold standards in population genetics: Can we do better?"

Mattia Marenda "Investigating how SAF-A nuclear protein regulates genome organisation by coupling super-resolution microscopy and polymer modelling."

Andrew Papanastasiou "scEnhance: computational discovery of cell and gene specific regulatory elements using single-cell datasets."

Chantriolnt - Andreas Kapourani "scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution."

Eric Latorre Crespo "A mathematical perspective on age-related clonal haematopoiesis."

Lyndsay Kerr "Understanding DNA methylation using mathematical models."

Vanessa Smer Barreto "Senolytics discovery with machine learning and open data."

1 April 2021

Important update for the XDF Programme: the Institute of Genetics and Molecular Medicine has been renamed the Institute of Genetics and Cancer (IGC) to better reflect its scientific strengths.

23 March 2021

A "catch up" meeting of the XDF Programme Fellows 2020 with the XDF Programme Directors and the Scientific Administrator to discuss experiences and review progress. The meeting took place online due to Covid situation.

11 January 2021

A "catch up" meeting of the XDF Programme 2019 Fellows with the Programme Directors and Scientific Administrator to discuss their "final project" proposals. The meeting took place online due to Covid situation.

January 2021

Due to ongoing Covid situation Prof Tim Aitman stepped down from the XDF Programme "Directors' Board" to concentrate on his leadership of the TestEd project that provides Covid testing for the University staff and students. He also got involved in formation of a cancer liquid biopsy spin off company BioCaptiva. 

4 November 2020

A "catch up" meeting of the XDF Programme Fellows 2020 with the XDF Programme Directors and the Scientific Administrator to discuss experiences and review progress. The meeting took place online due to Covid situation. It discussed first rotation project proposals from Drs Didier Devaurs and Michael Nicholson and the second rotation project from Dr Lucy Martin. 

29 September 2020 - The XDF Programme Annual Scientific Meeting 2020

In 2020 due to Covid situation the annual XDF Programme scientific meeting happened online as a "Mini-symposium" opened to local research community. The meeting was attended by all XDF Programme Fellows, Programme Directors, Scientific Administrator and others. It included presentations from XDFs 2018 about their ongoing work:

Chantriolnt - Andreas Kapourani "scMET: Bayesian modelling of DNA methylation heterogeneity at single cell resolution"

Andrew Papanastasiou "Enhancing chromatin accessibility signal at single-cell level using DNA sequence features"

Ava Khamseh "Pressing challenges for quantitative biomedicine: Causality, Bias and ‘Big Data’ "

Mattia Marenda "Unveil the properties of SAF-A/RNA mesh by using Super-Resolution Microscopy and Molecular Dynamics Simulations" 

The meeting was followed by a "catch up" of XDF Programme 2018 Fellows with the Programme Directors and Scientific Administrator to discuss their progress, needs and career ambitions, and to reflect on the Programme activities so far.  

Summer/Autumn 2020

XDF Programme Fellows increasingly contribute to educational activities at the Institute and the University level, this includes talks within the Institute's Statistical Seminar Series, appointment of XDF 2018 Fellow Dr Ava Khamseh as lecturer in  Biomedical Artificial Intelligence and other activities.

9 June 2020

A "catch up" meeting of the XDF Programme 2019 Fellows with the Programme Directors and Scientific Administrator to discuss their progress, outcomes of the second rotation projects and third rotation project proposals.  The meeting also included discussion of the first rotation project proposal by the first-to-join 2020 Fellow - Dr Lucy Martin. Due to ongoing COVID-19 situation the meeting took place in a virtual space using modern videoconferencing technology.

April 2020

The recruitment of XDF Programme 2020 Fellows has been completed following highly competetive process. The 2020 recruitment round was samewhat more complicated due to the COVID-19 pandemic but nonetheless very succesful with three new Fellows appointed. 

February 2020 - Doctor Diego Oyarzún and Doctor Matthias Hennig join the XDF Programme "Directors' Board" as Professor Guido Sanguinetti steps down due to other commitments 

Dr Oyarzún and Dr Hennig have backgrounds in systems and control theory and computational neuroscience, respectively. Their appointment strengthens the informatics site of the XDF Programme and provides new impetus for collaborative projects between IGMM and the School of Informatics.

6 February 2020 

A "catch up" meeting of the XDF Programme 2019 Fellows with the Programme Directors and Scientific Administrator to discuss their progress, outcomes of the first rotation projects and second rotation project proposals. The meeting took place in the Institute of Genetics and Molecular Medicine.

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October 2019 - Professor Ian Tomlinson - the incoming Director of the Edinburgh Cancer Research Centre, joins the XDF Programme as a member of  the"Directors' Board"

Prof Tomlinson joins the original set of XDF Programme Directors (Professors Chris Ponting, Jane Hillston, Guido Sanguinetti, Margaret Frame and Tim Aitman) to provide additional input (particularly in the area of cancer research) and to strenghten the Programme's mentorship and supervision capabilities.

Ian's work focuses on colorectal cancer, but extends to several other cancer types. He is especially keen to integrate work across a variety of biomedical areas, including human patient cohorts and clinics, animal models of disease and biomathematics. 

21 October 2019

A "catch up" meeting of the XDF Programme 2018 Fellows with the Programme Directors and Scientific Administrator to discuss their "final project" proposals. The meeting took place in the School of Informatics.

14 October 2019

 A "catch up" meeting of the XDF Programme 2019 Fellows with the Programme Directors and Scientific Administrator to discuss their first rotation project proposals. The meeting took place in the School of Informatics.

19 August - 6 September 2019 XDF Programme Induction Period

The XDF Programme 2019 Fellows were introduced to the Institute of Genetics & Molecular Medicine, School of Informatics and the University of Edinburgh. As in 2018, the induction period was very intensive and consisted of a broad spectrum of activities including Prof jane Hillston's and Prof Margaret Frame's overviews of the School of Informatics and IGMM respectively, Prof Tim Aitman's "Reflections on the XDF Programme so far", talks from the 2018 Fellows on their XDF Programme progress and experiences so far, new Fellows (2019 Fellows) introductory presentations to the local scientific community, "Cross-disciplinary workshop" from the Institute for Academic Development (Dr Sara Shinton),  Prof Chris Ponting's introduction into "How should we do science" and many others. For technical reasons the induction activities were delivered over 3 weeks rather than condenced into one week as in 2018, but it all worked out equally well. The "breaks" between the formal induction activities were used by 2019 Fellows to meet investigators who submitted XDF Project proposals and discuss opportunities before making decisions on their first rotation projects. 

14 August 2019 - The XDF Programme Annual Scientific Meeting 2019

The XDF Programme Annual Scientific Meeting 2019 took place on Wednesday 14 August 2019 in Raeburn Hotel, the XDF Programme 2018 Fellows reflected upon their progress and experiences from the Programme to date. They also discussed future strategic developments with the XDF Programme Directors and Scientific Administrator. 

12 June 2019

A "catch up" meeting of the XDF Programme Fellows with the XDF Programme Directors and the Scientific Administrator to discuss experiences and review progress. The meeting took place in the MRC Institute of Genetics & Molecular Medicine.

7 May 2019 and 14 May 2019 - Edinburgh Interviews

The 2019 international competition for the Cross-disciplinary postdoctoral fellowships  attracted 81 applications. Preselected candidates were invited for a formal interview in Edinburgh. Edinburgh Interviews took place on the 7th and 14th of May 2019. The candidates discussed their skills, interests and motivations to join the XDF Programme with the Programme Directors. They also had discussions with group leaders from the MRC Institute of Genetics & Molecular Medicine and the School of Informatics. Accompanied by the cross-disciplinary fellows recruited a yer before (XDFs 2018) they toured both places and got first hand insights into the life and work at IGMM, School of Informatics and University of Edinburgh.

1 May 2019 - CGEM Annual Away Day

On the 1 May 2019 the researchers and support staff from the Centre for Genomic & Experimental Medicine (CGEM) engaged in scientific discussions and networking activities during annual Away Day. The 2019 Away Day was organised at the Royal Society of Edinburgh and included a dedicated "complex data" session during which XDF Programme Fellows discussed their scientific interests and outcomes of their research projects performed in the IGMM and the School of Informatics. 

11th March 2019 – 15th March 2019 - Biomedical Data Science School

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Biomedicine is increasingly a data rich science. Turning this data into knowledge requires statistical and computational expertise to handle and interrogate large and complex data sets. This week-long school was focused on delivering training on cutting-edge methodologies to analyse high-throughput biological data sets, covering both the theoretical foundations and the practical applications. The school was aimed at early career researchers (PhD students, postdocs) with a foundational knowledge of statistics/ machine learning and an interest in applying/ developing analysis tools for high-throughput data.

The format of the school consisted of lectures in the mornings, and practical tutorials in the afternoon. There were many opportunities for school participants to present their work in a special, half-day workshop session.

Lecturers included:

• Prof John Marioni, CRUK Cancer Institute Cambridge and European Bioinformatics Institute;
• Prof Magnus Rattray, University of Manchester
• Dr Gabriele Schweikert, University of Dundee and University of Tubingen
• Dr Andrea Sottoriva, Institute of Cancer Research, London
• Dr Catalina Vallejos, Institute of Genetics and Molecular Medicine and Alan Turing Institute
• Dr Diego Oyarzun, School of Informatics and School of Biological Sciences, University of Edinburgh
• Dr Duncan Sproul, Institute of Genetics and Molecular Medicine
• Prof Davide Marenduzzo, School of Physics and Astronomy, University of Edinburgh

19 February 2019

A "catch up" meeting of the XDF Programme Fellows with the XDF Programme Directors and the Scientific Administrator in the School of Informatics. The discussions focused on the outcomes and experiences from first rotation projects as well as on second rotation projects proposals.

11 January 2019 – Visit to Edinburgh Genomics

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On Friday 11 January 2019 the XDF Programme Fellows accompanied by the Programme Scientific Administrator visited the Edinburgh Genomics (https://genomics.ed.ac.uk/) facility at the Roslin Institute (https://www.ed.ac.uk/roslin).

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Over the past years genomic technologies have revolutionised biomedical sciences and made real impact in the clinic, for example in genetic disease diagnosis and oncology. They often provide big sets of complex data that are sometimes very difficult to analyse.

Edinburgh Genomics has established a global reputation for the provision of advanced genomics services. They produce high quality, high volume data for a number of customers and collaborators from across academia, government and industry. Their activities include delivering high-quality next-generation sequencing data from RNA and DNA samples, whole genome sequencing, genotyping and microarray gene expression analyses as well as bioinformatics analysis. This is achieved by employing cutting-edge technology platforms (including Illumina NovaSeq, HiSeq X and MiSeq platforms and the Pacific Biosciences Sequel) and sophisticated industry-standard procedures implemented by a team of highly trained experts.

The visit was overviewed by Dr Javier Santoyo-Lopez (Clinical Genomics Facility Manager). He provided a comprehensive introduction to genomic technologies used in the facility in the form of a very interesting presentation. This was followed by detailed description of wet-lab working procedures and experimental set up during a highly informative laboratory tour. The visit concluded with a discussion of data analysis pipelines, complex data problems/opportunities that could be of interest to the XDF Programme Fellows and a “Questions & Answers” session.

6 December 2018

A "catch up" meeting of the XDF Programme Fellows with the XDF Programme Directors and the Scientific Administrator to discuss experiences and review progress. The meeting took place in the MRC Institute of Genetics & Molecular Medicine.

24 October 2018 - Selection of 1st rotation projects

After an intensive exploratory period in the IGMM and the School of Informatics including conversations with many local investigators the XDF Programme Fellows met with XDF Programme Directors and Scientific Administrator to reflect upon their first weeks on the Programme and discuss their first rotation projects selections.

20 - 24 August 2018 - XDF Programme Induction Week

The aim of the XDF Programme Induction Week was to introduce the Cross-disciplinary Fellows recruited in 2018 to the research community in Edinburgh, to discuss expectations towards them and to present the structure of the Programme and the challenges lying ahead. The Fellows were also familiarised with working practices in the MRC IGMM and the School of Informatics.

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On Monday they were welcomed to the University of Edinburgh by the XDF Programme Directors and Scientific Administrator, and presented with personal copies of the book “Molecular Biology of the Cell” by Bruce Alberts et al. This was followed by Fellows’ presentations on “who they are” to the local research community. After a lunch break Professor Jane Hillston (in her role as a Head of the School of Informatics) and Professor Margaret Frame (in her role as the MRC IGMM director) provided overview of administrative structures and scientific activities within the School of Informatics and the MRC Institute of Genetics & Molecular Medicine respectively. The day was concluded with an outdoor integration event during which the Fellows, guided by Prof. Ponting and Dr Welman, climbed Arthur's Seat – a famous Edinburgh’s landmark.

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Tuesday started with a “Meet and Mingle Event” during which the XDF Programme Fellows met some other IGMM scientist who transitioned into biomedicine from other disciplines before them. It was great opportunity to get some useful advice and first-hand tips. This was followed by meeting with the IGMM Communications Team over a cuppa in the Nucleus Café and “How should we do science?” discussion with Professor Ponting in the afternoon.

Wednesday represented an “IGMM Cross-disciplinary day” during which the Fellows listened to career summaries and research talks from a few IGMM and the School of Informatics PI’s including Dr Catalina Vallejos, Dr Riccardo Marioni, Prof Helen Colhoun, Dr Duncan Sproul,  Prof Guido Sanguinetti and Prof J Douglas Armstrong.

On Thursday the Fellows were introduced to the IGMM infrastructure and met people from different IGMM support teams including HR, finances, IGMM operations, design studio and computing. This was followed by a seminar from the IGMM IT team. The Fellows spent the afternoon in the School of Informatics, where they were introduced to operating procedures and their working space there.

On Friday the XDF Programme Fellows received an introduction to the IGMM health, safety and wellbeing by Rosie Russell and attended a workshop on cross-disciplinarity that was prepared and delivered by Dr Emily Woollen from the Institute for Academic Development.

15 May 2018 and 24 May 2018 - Edinburgh Interviews

The 2018 international competition for the Cross-disciplinary postdoctoral fellowships attracted 83 applications. Preselected candidates were invited for a formal interview in Edinburgh. Edinburgh Interviews took place on the 15th and 24th of May 2018. The candidates discussed their analytical skills, interests in biomedicine and motivations to join the XDF Programme with the Programme Directors. They also had conversations with group leaders from the MRC Institute of Genetics & Molecular Medicine and the School of Informatics. Accompanied by local postdocs and PhD students they toured both places and got first hand insights into the life and work at IGMM, School of Informatics and University of Edinburgh.