Upcoming 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 Drs 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:
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
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
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 date for the XDF Programme: the Institute of Genetics and Molecular Medicine has been renamed the Institute of Genetics and Cancer (ICG) to beter 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.
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.
