In November I attended the Festival of Biologics (FoB) 2022 conference in Basel, Switzerland. Originally a set of different conferences (now called agendas) that has merged into a single conference, FoB focuses on anything related to biologics. One of the agendas is an antibody specific agenda, derived from the former European Antibody Congress. This year the antibodies agenda had more than 100 talks across multiple tracks, covering many different aspects of using antibodies as therapeutics, making it an exciting conference for an antibody enthusiast. However, while FoB does include talks on machine learning and bioinformatics, most are focused solely on experimental work. Another drawback is that the majority of the talks are by industry, with the few academic speakers almost all also representing a company. This meant that of the few talks about computational methods and tools for protein design, most felt more like a commercial rather than a research presentation. Nonetheless, FoB is still an interesting conference to attend when you are working on applied research for antibody therapeutics. It is an amazing opportunity to hear about which antibody specific problems companies are trying to overcome, which are deemed solved and which are the future problems to solve.
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Thinking of going to a conference
As so many members of the group have never attended an in-person conference, I thought it might be worth answering the question “why do people attend conferences?”
First- up, we should remember that flying around the world is not a zero cost to the planet, so all of us lucky enough to be able to travel should think hard every time before we choose to do so.
This means it’s really important to make sure that we know why we are going to any conference and maximise the benefits from attendance. Below are a few things to think about in terms of why you attend a conference and what to do when you are there, but this is definitely not a complete list, more a starter for four.
Continue reading5th AI in Chemistry meeting
A few weeks ago we attended the RSC’s 5th AI in Chemistry conference at Churchill College, Cambridge. It featured research and discussions on a broad range of topics and was attended by a diverse set of more than 200 researchers from academia and industry, including six Opiglets.
Continue readingVaccines and vino
Recently, I was fortunate enough to attend and present at GSK’s PhD and Postdoc workshop in Siena, Italy. The workshop spanned two days and I had a brilliant time there – Siena itself is beautiful, I ate fantastic food, and I learnt a huge amount about all stages of vaccine production.
Unfortunately, due to confidentiality, I can’t go into great detail about others’ current research, however I have provided a short overview of the five main areas the workshop focused on below.
Continue readingISMB 2022 – July 10-14 Madison, Wisconsin
Madison, Wisconsin, a place known for its superb selection of craft beverages, for having Wisconsin’s Best Cheese Curds, and, most importantly, for hosting the 2022 annual international conference on Intelligent Systems for Molecular Biology (ISMB). Fortunately, we (Lewis and Tobias) got to attend this year’s ISMB and get a taste of Madison. The 2022 conference is the 30th ISMB conference and has grown to become the world’s largest bioinformatics/computational biology conference with nearly 600 presented talks. We therefore got to hear a wide range of different and interesting talks.
Continue reading5th Artificial Intelligence in Chemistry Symposium
The lineup for the Royal Society of Chemistry’s 5th “Artificial Intelligence in Chemistry” Symposium (Thursday-Friday, 1st-2nd September 2022) is now complete for both oral and poster presentations. It really is a fantastic selection of topics and speakers and it is clear this event is now a highlight of the scientific calendar. Our very own Prof. Charlotte M. Deane, MBE will be giving a keynote.
It marks a return to in-person meetings: it will be held at Churchill College, Cambridge, with a conference dinner at Trinity Hall.
More details are here: https://www.rscbmcs.org/events/aichem22/.
Registration for in person attendance is open until Monday 29th August 17:00 (BST).
It is also possible to register for virtual attendance; the meeting will be broadcast on Zoom.
AIRR Community Meeting VI May 17-19
Eve, Brennan and I were delighted to attend the sixth AIRR (adaptive immune receptor repertoire) Community Meeting: Exploring New Frontiers in San Diego. Eve and I had been awaiting this meeting for a mere 3 years, since it was announced during the last in-person AIRR Community Meeting back in 2019. Fortunately, San Diego did not disappoint.
After a rocky start (featuring many hours stuck in traffic on the M40, one missed flight and one delayed flight), we made it to California! The three day conference had ~230 participants (remote and in-person) and featured great talks from academia and industry. We particularly enjoyed keynote talks from Dennis Burton on rational vaccine design using broadly neutralising antibodies, Gunilla Karlsson Hedestam on functional consequences of allelic variation, Shane Crotty on covid and HIV vaccine design, and Atul Butte on uses of electronic health record data and how we should all found start-ups.
We had fun delivering a tutorial on OPIG antibody tools and, most importantly, we all won AIRR t-shirts in the raffle (potentially we were the only people who noticed how to enter on the conference app). Highlights outside of the conference included paddle boarding and seeing hummingbirds, pelicans, sealions, seals, ‘Garibaldi’ the state fish, and meeting Bob the golden retriever at a surfing shop. We’re now off to find jobs on the West Coast so we can live at the beach….
The AIRR community has many webinars and talks available on their youtube channel https://www.youtube.com/c/AIRRCommunity
Sarah, Eve & Brennan
Antibodies as Drugs: Keystone Symposia
Between the 27th April and 1st of May, I was very fortunate to be able attend the Antibodies as Drugs Keystone Symposium and give my first conference talk internationally, in which I spoke about the methods our group has developed for using structure to make predictions about where an antibody binds relative to other antibodies. This included paratyping [1], Ab-Ligity [2] and most recently SPACE [3].
I will preface this by saying that lots of the work people spoke about was unpublished, which was so exciting, but makes for a difficult blog post to write. To avoid any possibility of putting my foot in my mouth I will keep the science very surface level. The conference was held at the Keystone resort in Colorado, and the science combined with a kind of landscape I have never experienced before made for an extremely cool experience. This meeting was originally combined with a protein design meeting, and the two were split by COVID – this meant that in-silico methods were the minority in the program, but I didn’t mind that as the computational work that was presented was quite diverse so it was definitely a good representation of the field still. I also really enjoyed the large number of infectious disease talks in which we got a good range of the major human pathogens – ebolaviruses, SARS-CoV-2 of course, dengue, hantaviruses, metapneumovirus, HIV, TB and malaria all featured. The bispecific session was another highlight for me. The conference was very well organised and I liked how we were all asked to share a fun fact about ourselves – one speaker shared that he is a Christmas tree farmer in his spare time (I won’t share his name in case he is keeping that under wraps). That made me reconsider how fun I can truly consider myself…
Without turning this into a travel blog, I also want to add that Keystone was insanely beautiful and make you look at some pics I got.
NeurIPS 2021 Conference Feedback
Held annually in December, the Neural Information Processing Systems meetings aim to encourage researchers using machine learning techniques in their work – whether it be in economics, physics, or any number of fields – to get together to discuss their findings, hear from world-leading experts, and in many years past, ski. The virtual nature of this year’s conference had an enormously negative impact on attendees’ skiing experiences, but it nevertheless was a pleasure to attend – the machine learning in structural biology workshop, in particular, provided a useful overview of the hottest topics in the field, and of the methods that people are using to tackle them.
This year’s NeurIPS highlighted the growing interest in applying the newest Natural Language Processing (NLP) algorithms on proteins. This includes antibodies, as seen by two presentations in the MLSB workshop, which focused on using these algorithms for the discovery and design of antibodies. Ruffolo et al. presented their version of a BERT-inspired language model for antibodies. The purpose of such a model is to create representations that encapsulate all information of an antibody sequence, which can then be used to predict antibody properties. In their work, they showed how the representations could be used to predict high-redundancy sequences (a proxy for strong binders) and how continuous trajectories consistent with the number of mutations could be observed when using umap on the representations. While such representations can be used to predict properties of antibodies, another work by Shuai et al. instead focused on training a generative language model for antibodies, able to generate a region in an antibody based on the rest of the antibody. This can then potentially be used to generate new viable CDR regions of variable length, better than randomly mutating them.
Continue readingAntibody Engineering and Therapeutics Conference
I was invited to speak at the Antibody Engineering and Therapeutics Conference (presenting mine and Matt’s recently published epitope profiling paper), in San Diego (December 12th – 16th). Unfortunately, the pandemic had other ideas so I decided not to travel but luckily the conference was hybrid.
The conference included 1 day of pre-conference workshops and 4 days of presentations from academic and industry, with livestreaming of the initial keynotes (including one from Charlotte). Remaining talks were recorded and made available after the conference. I’ve highlighted a few of my favourite talks and conference themes, with links to papers where available.
Naturally, a lot of the presented research related to covid-19. I was speaking in the ‘Antibody Repertoires and Covid-19’ session, where there were interesting presentations from Professor Eline Luning Prak from the University of Pennsylvania and Elaine Chen from Vanderbilt University analysing antibody responses in covid-recovered individuals, and comparing vaccine responses in covid-recovered vs covid-naiive individuals. Other talks around SARS-CoV-2 vaccines included Dr Laura Walker from Adimab/Adagio Therapeutics comparing BCR repertoire responses to different types of vaccinations, and the effect of using different booster types.
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