Category Archives: Talks

A short account of the talks given by the OPIG group members and their highly esteemed guests.

Conference Summary: MGMS Adaptive Immune Receptors Meeting 2024

On 5th April 2024, over 60 researchers braved the train strikes and gusty weather to gather at Lady Margaret Hall in Oxford and engage in a day full of scientific talks, posters and discussions on the topic of adaptive immune receptor (AIR) analysis!

Continue reading

Conference feedback: AI in Chemistry 2023

Last month, a drift of OPIGlets attended the royal society of chemistry’s annual AI in chemistry conference. Co-organised by the group’s very own Garrett Morris and hosted in Churchill College, Cambridge, during a heatwave (!), the two days of conference featured aspects of artificial intelligence and deep machine learning methods to applications in chemistry. The programme included a mixture of keynote talks, panel discussion, oral presentations, flash presentations, posters and opportunities for open debate, networking and discussion amongst participants from academia and industry alike. 

Continue reading

Out of Band Management

We’ve all had things go wrong with computers, however when they go catastrophically wrong, there’s often little you can do other than to be physically on site to reinstall. This doesn’t have to be the case though. Most PCs have a tiny secondary processor which can allow full remote control of a computer that’s crashed, unresponsive or even switched off.

Continue reading

Experience at a Keystone Symposium

From 19th-22nd February I was fortunate enough to participate in the joint Keystone Symposium on Next-Generation Antibody Therapeutics and Multispecific Immune Cell Engagers, held in Banff, Canada. Now in their 51st year, the Keystone Symposia are a comprehensive programme of scientific conferences spanning the full range of topics relating to human health, from studies on fundamental bodily processes through to drug discovery.

Continue reading

LaTeX Beamer Template with Logos

Alternative Title: The tragic story of how I got trapped making slides with latex.

Typically after giving a presentation at least one person will approach me and ask if they could have access to my custom latex template to make slides with beamer that don’t look rubbish.

TL;DR Yes you can: https://github.com/npqst/latex-beamer-template

Continue reading

Tales of an OPIG Jamboree

Jamboree
(1) a large gathering, as of a political party or the teams of a sporting league, often including a program of speeches and entertainment.;
(2) a large gathering of members of the Boy Scouts or Girl Scouts, usually nationwide or international in scope

Oxford Dictionary

This October marks twenty years since our supreme leader, Charlotte Deane, came to Oxford to start the first protein informatics group in this university.

Twenty years is a really long time, and at OPIG we like to celebrate things in style. From the beginning, it was clear that we would be doing what we know best: get together, consume lots of food and drinks, and perhaps talk about science. But, frankly, that’s what we do all the time. This simply wasn’t enough to celebrate two decades of scientific production. So Charlotte entrusted several of us with an ambitious goal: to reach out to our former members, and to ask them to join us, in Oxford, to celebrate two decades of protein informatics. And that’s what we did.

For two months, we painstakingly tracked down every person that has ever been part of our group, and attempted to gather their contact details to invite them to Oxford. Attempted to, for the most part. While LinkedIn gave us some early victories, some alumni had managed to cover their tracks very well, including one person we could only found after tracking down their three previous jobs. Nevertheless, after much digging, we managed to find updated contact details for every person that has ever passed by our lab, and nearly thirty of these former alumni (almost 50% of them!) made their way to Oxford on October 8th* to hold the first OPIG Jamboree.

From the first student (Sanne Abeln, rightmost in the second row) to the most recent (Kate, whose hair can barely be seen on the leftmost third row), we are all here!
Continue reading

The SARS-CoV-2 protein spike glycosylation not only shields but primes binding by providing structural stability too

Yep, it is very well known that the sugar coating (aka glycosylation) of viruses makes them invisible to the immune system, a strategy so effective that like in the case of HIV, whose spike is almost entirely covered by glycans, makes it so difficult to target by the human immune system.

Unsurprisingly, coronaviruses such as SARS, MERS, and SARS-CoV-1(2) not only benefit from this evolutionary strategy but there is evidence now that sugars provide stability to their spikes to be effective binders by glueing the spike chains, hence making them infectious.

This is the major finding of this paper that introduces very interesting results from all-atom MD simulations of a fully glycosylated model of the  SARS-CoV-2 spike protein embedded in a realistic viral membrane. Researchers aimed to look into the stability of the protein spike (A, B, and C) chains in the “open” and “closed” conformation and how these changed upon key residue mutations to test how glycans sitting in the inter-chain space affect stability. It also aimed at quantifying glycans’ shielding effect from molecules ranging from 2 to 15 Angstroms, i.e., from small-sized to peptide- and antibody-sized molecules.  

Continue reading

Five Nuggets of Wisdom for Chairing at a Conference

I recently spoke at the Festival of Biologics 2021 conference in Basel (in-person, just in time!), and was lucky enough to be offered the chance to chair a session of talks. As this was the first time I’d ever been asked to do this, I asked Charlotte for some hints to make things go more smoothly. I found her advice very useful, so I thought I’d share it here for other first-time “chairers”!

Continue reading

Prediction of Parkinson subtypes at COXIC 2020

Last week I attended the COXIC seminar (joint seminar Oxford – Imperial focused on networks and complex systems) organised by Florian Klimm from Imperial College London (and former OPIG member!). We had several interesting at the seminar. However, one of them caught my eye more than the rest. It was the talk of Dr Sanjukta Krishnagopal (UCL) titled Predicting Parkinson’s Sub-types through Trajectory Clustering in Bipartite Networks​, of which I will give a quick insight. Hope you like it (at least) as much as I did!

This blogpost is based on these two articles:

  1. Sanjukta Krishnagopal, Rainer Von Coelln, Lisa Shulman, Michelle Girvan. “Identifying and predicting Parkinson’s disease subtypes through trajectory clustering via bipartite networks” PloS one (2020)​
  2. Sanjukta Krishnagopal. “Multi-later Trajectory Clustering Network Algorithm for Disease Subtyping” Biomedical Physics & Engineering Express (2020)​
Continue reading