News archive

June 2019 - James and Patricia have successfully graduated. Congratulations to both of you and best of luck with your future endeavours.

May 2019 - Richard and Mela have received a Grant from the Principal's Teaching Award Scheme for a project on Building Biological Models in Minecraft.

April 2019 - We have a poster at BNA 2019 in Dublin! Richard Fitzpatrick, Tara M O'Driscoll, Ayisha Mahmood, David C. Sterratt, Melanie I Stefan. Rule-based modelling of AMPA receptor regulation at the synapse. Ayisha and Mela will be in Dublin to present it.

March 2019 - Preprint: Matthew C. Pharris, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy, Melanie I. Stefan, Tamara L. Kinzer-Ursem. A Multi-State Model of the CaMKII Dodecamer Suggests a Role for Calmodulin in Maintenance of Autophosphorylation. bioRxiv 575712 [DOI]

February 2019 - Our visiting students Crystal and Kevin have completed their internship and have returned to Zhejiang University International Campus in Haining, China, to complete their studies.

January 2019 - We have obtained a grant to study Biomedical Microfluidics from the Zhejiang University International Campus. The project is a collaboration between several research groups at Zhejiang Unviersity and the University of Edinburgh, and led by Sebastian Leptihn.

January 2019 - Mela is talking about Modelling signalling events in dendritic spines at the European Bioinformatics Institute on Thursday, 24 January.

January 2019 - Mela is talking about Studying learning and memory using computer models at the Cambridge University Biological Society on Wednesday, 23 January.

January 2019 - We welcome visiting student Wenkai Ye (Kevin) to the Stefan Lab. Kevin is a third-year student in Biomedical Sciences at ZJU/UoE in Haining, China. During his visit here in Edinburgh, he will work on modelling interactions between mGluR and NMDA recetpors.

January 2019 - We welcome new Honours students James Schofield and Patricia Cambalova and new MSc student Georgios Rodamnakis to the Stefan Lab.

January 2019 - We welcome visiting student Jiang Lifei (Crystal) to the Stefan Lab. Crystal is currently studying in the joint Edinburgh-Zhejiang degree programme in Haining, China, and is visiting our lab in Edinburgh for a few weeks to work on modelling CaMKII regulation.

2018

December 2018 - Mela has passed her tenure review! Happy holidays everyone!

November 2018 - Kyle Robertson, who did a Nuffield Research Placement in our lab this summer, has just won a CREST Gold Award for his work on modelling Sonic Hedgehog signalling. Congratulations Kyle!

October 2018 - Mela is speaking at ICSB 2018 on Multi-scale modelling of hyperpolarisation-gated synaptic plasticity. This project involved Stefan Lab alumni Yubin Xie and Marcel Kazmierczyk.

October 2018 - We welcome Christine Lee as a new PhD student in the Stefan Lab. Christine will be based at the ZJU-UoE Institute in Haining, China and will be working on developing learning analytics software.

September 2018 - Preprint: Yubin Xie, Marcel Kazmierczyk, Bruce P Graham , Mayank B. Dutia, and Melanie I Stefan. A multi-scale model reveals cellular and physiological mechanisms underlying hyperpolarisation-gated synaptic plasticity. bioRxiv 418228 [DOI]

August 2018 - We will be at the Scottish Neuroscience Group meeting in Dundee on Friday, 31 August. Richard will be presenting his poster on AMPA receptor modelling.

August 2018 - Kyle presented his poster on Computational modelling of the Sonic Hedgehog signalling pathway at the Nuffield Foundation Celebration Event.

August 2018 - Marios and Sagar have successfully completed their final presentations for their MSc in Integrative Neuroscience and are now on to new adventures. Congratulations and best of luck to both of you!

July 2018 - Check out our Poster at FENS 2018: S. Arora, S. Roman-Garcia, M. Stefan. Calcium signalling in Alzheimer's Disease: a computational model. Poster G007 on Tuesday afternoon! Sagar will be there to present.

July 2018 - Kyle Robertson will join the Stefan Lab over the summer as a Nuffield student. Kyle will be supervised by Richard and will work on models of Sonic Hedgehog signalling.

July 2018 - Ayisha Mahmood has been awarded a Biomedical Sciences Summer Vacation Scholarship and will be joining the Stefan Lab to work on computational models of neuronal protein degradation

June 2018 - Paper published: N.A. Viswan, G.V. HarshaRani, M.I. Stefan, U.S. Bhalla (2018). FindSim: a Framework for Integrating Neuronal Data and Signaling Models. Front Neuroinform, 12:38.

June 2018 - WikiJournal of Science launched. Read more about the aims and scope of WikiJournal of Science or browse through volume 1, issue 1

June 2018 - Paper accepted: N.A. Viswan, G.V. HarshaRani, M.I. Stefan, U.S. Bhalla (2018). FindSim: a Framework for Integrating Neuronal Data and Signaling Models. Front Neuroinform, in press.

May 2018 Medical Research Scotland has granted a vacation scholarship for Marcel to continue his work on computational modelling of hyperpolarisation-mediated plasticity in MVN neurons.

May 2018 Mela will be speaking at the EMBL in the UK meeting at the Royal Society of Edinburgh on Monday, 21 May.

May 2018 Congratulations to Abaz, Grant, Marcel and Pierce, who have successfully submitted their Honours dissertations.

April 2018 Sagar presented a poster at the FENS Computational Neuroscience of Prediction Conference in Copenhagen, Denmark.

March 2018 Mela wrote a guest commentary about failure in science (in German) for APA Science.

February 2018 Mela is speaking at the Neural Dynamics Forum, University of Bristol on 2.2.2018.

January 2018 - We are happy to welcome four new Honours students to the Stefan Lab. Abaz Shehu, Grant Herpich, Marcel Kazmierczyk (co-supervised with Mayank Dutia), and Pierce Ryu span a range of disciplines and research interests.

January 2018 - New MSc students joining the lab: We are very happy to welcome two new students from the MSc Inetegrative Neuroscience to the lab: Marios Diamantopoulos (co-supervised with Emanuel Busch) will be working on Calcium signalling in C. elegans. Sagar Arora will be working on spatial stochastic modelling of signalling in the spine.

January 2018 - Congratulations to Zale on passing his MSc! Zale did very interesting work on analysing the neural network of C. Elegans.

2017

December 2017 - Congratulations to long-term collaborator and friend Dr. Ranjita Dutta Roy for successfully defending her PhD at Karolinska Institutet!

November 2017 - Mela is talking about academic failure and how to deal with it at CNIC PhDay in Madrid.

November 2017 - Richard is presenting a poster at Neuroscience 2017: R. Fitzpatrick, U.S. Bhalla, M.I. Stefan. Towards a maximalist AMPAR-centric biochemical model of the synapse and its application in neurodevelopmental disease research.

November 2017 - Poster at Neuroscience 2017: M.C. Pharris, T. L. Kinzer-Ursem, M.I. Stefan. A rule-based, multi-state model of the CaMKII holoenzyme

October 2017 - PhD position available: Work on Calcium signalling in C elegans with us and with Emanuel Busch's Lab.

October 2017 - Paper published: K. Bonham, M.I. Stefan (2017). Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology. PLoS Comput Biol 13(10): e1005134. [DOI]

October 2017 - Mela will be talking about chemical signalling in space at the University of St. Andrews on 24 October.

September 2017 - Mela will be talking about her and Kadri's work on methods for modelling actin dynamics at the V International Conference on Particle-Based Methods on 27 September.

August 2016 - Lewis and Isla presented posters about their summer research placements at the Nuffield Foundation Celebration Event in Edinburgh.

August 2017 - Mela will be talking about Computational models of neuronal biochemistry at the Scottish Neuroscience Group Meeting in Aberdeen.

August 2017 - Paper published: R. Dutta Roy, Christian Rosenmund, M.I. Stefan (2017). Cooperative Binding Mitigates the High-Dose Hook Effect. BMC Sys Bio 11:74. [DOI]

August 2017 - Congratulations to Salvador and Tara for submitting their dissertations for their Informatics MSc!

July 2017 - We were proud to host two visitors for an afternoon during the Science Insights programme at the University of Edinburgh. Our two students were able to learn about spatial modelling in MCell by going through our introductory tutorial.

July 2017 - Paper accepted for BMC Systems Biology: Dutta Roy et al. Cooperative Binding Mitigates the High-Dose Hook Effect.

July 2017 - Having both successfully graduated, Susana and Jana are both coming back as research assistants to work in the lab this summer. Susana is wrapping up her work on modelling CaMKII interactions with NMDA receptors. In the meantime, Jana is modelling mGluR-NMDAR signalling as part of a project supported by the Edinburgh Neuroscience RS Macdonald seedcorn fund.

July 2017 - Zale is spending time on-site in Edinburgh this July to work on his MSc project on modelling the C. elegans brain.

July 2017 - Congratulations to our two Honours graduates, who both graduated on Friday, 7 July: Susana in Neuroscience, and Jana in Medical Biology.

July 2017 - We are happy to welcome two new summer students, Isla Smith and Lewis Strachan. They are both on a Nuffield Research Placement.

July 2017 - Poster accepted for Neuroscience 2017: R. Fitzpatrick, U.S. Bhalla, M.I. Stefan. Towards a maximalist α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-centric biochemical model of the synapse and its application in neurodevelopmental disease research

June 2017 - Melanie has been selected for the GSO Leadership academy and will be travelling to Boston and Darmstadt for leadership training over the coming year.

June 2017 - Melanie will be speaking at the BMS Learning and Teaching Forum on Wednesday, 21 June about her experience with the Edinburgh/Zhejiang Biomedical Sciences degree programme.

June 2017 - Our two Honours students Jana and Susana have done extremely well and will both graduate in early July. Congratulations!

June 2017 - Updated preprint on BioRxiv: Dutta Roy et al. Cooperative Binding Mitigates the High-Dose Hook Effect.

June 2017 - We are welcoming three Informatics MSc students: Nazanin Zamani Behabadi and Tara O'Driscoll will work on rule-based modelling of CaMKII in a project co-supervised with David C. Sterratt. Salvador García González (co-supervised with Dragan Gasevic) will work on developing a learning analytics package.

June 2017 - I was nominated for a Best Research or Dissertation Supervisor Award from the Edinburgh University Students' Association.

May 2017 - We are looking for a PhD student to work with the Busch lab and with us on Calcium signalling in C. elegans neurons. The project will involve both experiments and computational modelling. [More info]

May 2017 - Richard has been awarded a fellowship from the Neuroresearchers Fund. This will allow him to travel to Bangalore over the summer to work on autism modelling with our collaborators in the Bhalla Lab.

May 2017 - Jana and Susana have both submitted their Honours dissertations and are one step closer to graduation. Congratulations!

May 2017 - We have received a grant from the Edinburgh Neuroscience RS MacDonald Seedcorn Fund, in collaboration with Sergiy Sylantyev and Noboru Komiyama. This will allow us to investigate interactions between mGluR and NMDA receptors.

April 2017 - Kadri's work on Methods for modelling actin dynamics in MCell has been accepted for presentation at the V International Conference on Particle-Based Methods.

April 2017 - Mela is back on the International Campus at Zhejiang University in late April/early May to teach Integrative Biomedical Sciences 1 and Introduction to Cellular and Molecular Biology 1.

Arpil 2017 - Prof. Tamara Kinzer-Ursem from Purdue University is visiting the Stefan lab for a few days. She will talk about Multidisciplinary approaches for precise descriptions of protein function at the CIP Seminar on 11 April.

Arpil 2017 - Mela is presenting a talk on Computational models of postsynaptic signalling at the School of Informatics

March 2017 - Lab alumnus Yubin Xie has been offered a PhD position in the Cornell/Weill Cornell/MSKCC Tri-Institutional PhD Program in Computational Biology & Medicine and will start there in July. Congratulations and all the best with this next scientific adventure, Yubin!

March 2017 - Mela is lecturing on Long-term potentiation in Neuroscience 3 at the University of Edinburgh on Friday.

February 2017 - Melanie is back on the International Campus at Zhejiang University from 25 February to 18 March to teach Integrative Biomedical Sciences 1 and Introduction to Cellular and Molecular Biology 1.

January 2017 - Richard is presenting his MSc work on Enactivising Memory at the Neural Control Systems Meeting at 9:30 on Monday, 13.2. in HRB 174.

January 2017 - Melanie is at the Wellcome Trust in London to speak about her CV of Failures

January 2017 - We welcome our two new Honours students Jana Finžgar and Susana Román García to the lab. They will work on computatoinal models of different aspects of synaptic plasticity.

2016

December 2016 - Poster on using digital games in undergraduate education: L. Ferrington, M.I. Stefan, S.-H. Wang, J. McCluskey, K. Meyer (2016). Using educational digital games to improve the engagement and performance of Applied Pharmacology students in an undergraduate cell biology course. Pharmacology 2016, London, UK

December 2016 - Melanie is back on the International Campus at Zhejiang University until Christmas to teach Biomedical Sciences 1.

December 2016 - Poster on using quizzes to improve undergraduate student performance: M.I. Stefan, C. McMullen, S.-H. Wang, C.D Etchells, and L. Ferrington (2016). Can optional online quizzes increase student engagement, retention and performance in an undergraduate cell biology and physiology course? Creativity in Science Teaching, Society for Experimental Biology, London, UK

December 2016 - Poster at Creativity in Science Teaching: L. Ferrington, M.I. Stefan, S.-H. Wang, J. McCluskey, K. Meyer (2016). Using educational digital games to improve the engagement and performance of Applied Pharmacology students in an undergraduate cell biology course. Creativity in Science Teaching, Society for Experimental Biology, London, UK

December 2016 - Kadri's time in Edinburgh has come to an end and she is going back to Sweden to finish her MSc studies at the Karolinska Institutet. Best of luck for the future, Kadri!

December 2016 - PhD position open: In a joint project with the Busch lab, you would be working on Calcium signalling in C. elegans neurons. [More info]

November 2016 - Updated preprint of our paper about Cooperativity and the high-dose hook effect (with Ranjita Dutta Roy and Christian Rosenmund) is now available on biorxiv.

November 2016 - The NCS grant writing group is meeting in HRB 174 at 10:30 on Monday, 21 November. Nathalie Rochefort is going to talk.

November 2016 - We welcome Zale Cao as a new PhD student in the lab. Zale will be placed on the International Campus at Zhejiang and will work on spaced-repetition learning

October 2016 - Melanie published a short piece about cooperativity in the Journal of Mathematical Biology. Read it here.

October 2016 - The NCS grant writing group is meeting in HRB 174 at 9:30 on Monday, 10 October (note the slightly earlier time). Gareth Leng is going to talk.

October 2016 - Undergraduate student interested in doing a research placement next summer? Now is a good time to get in touch!

September 2016 - Melanie is off to China for five weeks to teach the first incoming class of students in the joint Zhejiang University/University of Edinburgh undergraduate degree in Biomedical Sciences

September 2016 - We welcome Richard Fitzpatrick, who is starting his PhD on modelling intellectual disabilities and autism spectrum disorders

September 2016 - Yubin has graduated with distinction and left the lab for new adventures in Chicago. Good luck Yubin!

September 2016 - Excellence presented his poster about Computer simulation of a biochemical memory system at the Nuffield Foundation Celebration Event in Edinburgh.

August 2016 - Melanie submitted a new paper with Kevin S. Bonham from Harvard Medical School: Gender disparity in computational biology research publications. Get the preprint on bioRxiv or read more on Kevin's blog

August 2016 - Poster about using educational games for undergraduates: K. Meyer, L. Ferrington, M.I. Stefan, S.-H. Wang (2016). ENGAGE: Using educational digital games to improve student engagement and performance in an undergraduate cell biology course. Scottish Crucible Forum, Glasgow, UK

August 2016 - We welcome Kadri Pajo who is a visiting MSc student from Karolinska Institute. Kadri will work on modelling CaMKII interactions with the actin cytoskeleton.

August 2016 - It's Yubin's dissertation defense today!

August 2016 - It's the last day in the lab for Excellence, who was working with us on a Nuffield Research Placement over the summer. Excellence is going back to St Columba's High School for now. But we do hope he will join us again at the University of Edinburgh in the future!

July 2016 - Yubin has submitted his MSc dissertation on multi-scale modelling of hyperpolarisation-mediated synaptic plasticity

July 2016 - Melanie is teaching at the Okinawa Collaborative International Undergraduate Workshop. Look here for materials relating to her session on modelling central pattern generators.

July 2016 - We welcome Excellence Ogunbayo, who is joining our lab for the summer through a Nuffield Research Placement. Excellence will be working on modelling biochemical interactions necessary for memory formation.

July 2016 - New Poster: Y. Xie, B. Graham, M. Dutia, M.I. Stefan. Multi-scale Modelling of Hyperpolarisation Mediated Synaptic Plasticity.

July 2016 - Yubin is headed to Cambridge to participate in the WGC Advanced Course on In Silico Systems Biology

June 2016 - Yubin has presented his work on Multi-scale Modelling of Hyperpolarisation controlled Synaptic Plasticity to his peers in the Edinburgh-Zhejiang Biomedical Sciences MSc Programme

June 2016 - The NCS grant writing group is meeting in HRB 174 at 10:30 on Monday, 23 May. John Menzies is going to talk about working within big collaborative grant projects.

June 2016 - We are looking for a PhD student to work on Multi-scale modelling of neuronal signalling pathways in intellectual disability/autism spectrum disorders. Apply here before Friday, 17 June.

May 2016 - Melanie is talking about Modelling Calcium Signalling in the Brain at Kinetics on the Move in Heidelberg, Germany.

May 2016 - The NCS grant writing group is meeting in HRB 174 at 9:30 on Monday, 23 May. Julia Schiemann is going to talk about her experiences with securing a personal fellowship.

April 2016 - Melanie is talking about the Postdoc to PI transition in an event hosted by the George Square Postdoc Society and the Wellcome Trust.

April 2016 - Paper published: N. Rodriguez, J.-B. Pettit, P. Dalle Pezze, L. Li, A. Henry, M.P. van Iersel, G. Jalowicki, M. Kutmon, K.N. Natarajan, D. Tolnay, M.I. Stefan, C.T Evelo, and N. Le Novère (2016). The Systems Biology Format Converter BMC Bioinformatics, 17:154. DOI

April 2016 - Paper on the Systems Biology Format Converter accepted for publication: N. Rodriguez, J.-B. Pettit, P. Dalle Pezze, L. Li, A. Henry, M.P. van Iersel, G. Jalowicki, M. Kutmon, K.N. Natarajan, D. Tolnay, M.I. Stefan, C.T Evelo, and N. Le Novère (2016). The Systems Biology Format Converter. BMC Bioinformatics, in press.

April 2016 - Melanie has been selected for the Scottish Crucible programme for Scotland's Future Research Leaders.

March 2016 - Yubin has been selected to participate in the WGC Advanced Course: In Silico Systems Biology this coming July.

March 2016 - Presenting for the BMTO Teaching Network at the University of Edinburgh: What can we learn from online learning data?

February 2016 - Slides for the Biomedical Sciences 3 Tutorial about Brain Training are now available here.

January 2016 - I am giving a talk about Computational modelling of synaptic proteins at Zhejiang University's annual Biomedical Sciences Meeting.

January 2016 - Visiting Zhejiang University to meet our colleagues and collaborate on the Dual Award Honours degree program in Biomedical Sciences, which is due to launch in September

January 2016 - I am giving a talk about teaching statistical thinking in context at the ASE Conference in Birmingham on 7 January.

2015

November 2015 - Happy to welcome my new MSc student, who joins from Zhejiang University. Yubin Xie will be working on modelling post-synaptic integration of converging spike trains.

November 2015 - We went to the Meeting of the LERU e-learning working group in Utrecht to talk about our ideas about using learning technologies to support students studying in their second language.

October 2015 - Our poster (H.C. Besche, M.I. Stefan, Y. Liu, R.W. King, A. Sullivan. Assessing item quality in open-book online readiness assessment exercises using student feedback and item response time.) won the Abstract Award in Undergraduate Medical Education Research at HMS Medical Education Day.

October 2015 - We are presenting a poster on item quality in open-book online quizzes at the Harvard Medical School Academy Medical Education Day.

September 2015 - I am now a member of the Physiological Society.

September 2015 - Talked about my research on neuronal Calcium signalling at the CMVM Centres' Symposium.

August 2015 - Back from Decoding the Brain, our international collaborative undergraduate workshop at OIST. Updated readings and course materials for my modules can be found here.

July 2015 - Slides and lecture materials for my Maths for Physics for Biology workshop at OIST are now online

July 2015 - Paper submitted: R. Dutta Roy, M.I. Stefan. Cooperative Binding Mitigates the High-Dose Hook Effect. Read the preprint on bioRxiv.

July 2015 - I will be teaching a series of quantitative workshops at OIST this summer. Course materials and further readings

June 2015 - The team of Edinburgh-Zhejiang lecturers has officially taken up work. Read up more about the four of us on the CIP news page.

April 2015 - New paper: M.I. Stefan, J.L. Gutlerner, R.T. Born, M. Springer (2015). The quantitative methods boot camp: teaching quantitative thinking and computing skills to graduate students in the life sciences. PLoS Comput Biol, 11(4): e1004208. DOI

April 2015 - I have a new job as a Lecturer (for US-Americans: assistant professor) in the Edinburgh-Zhejiang dual degree program in Biology. I will be based at the School of Biomedical Sciences at the University of Edinburgh.