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 readingCategory Archives: Conferences
5th 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.
Continue readingHighlights from the European Antibody Congress 2021
Last month, I was fortunate enough to be able to attend (in person!) and present at the Festival of Biologics European Antibody Congress (9-11 November, 2021) in Basel, Switzerland. The Festival of Biologics is an annual conference, which brings together researchers from industry and academia. It was an excellent opportunity to learn about exciting research and meet people working in the antibody development field.
Here are some of my highlights from the European Antibody Congress, with a focus on antibody design and engineering:
Continue readingFive 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 readingISMB 2021: epitope prediction tools
I recently had the opportunity to present my work on antibody virtual screening at the 2021 ISMB/ECCB virtual conference. In this blogpost, I want to summarise two research projects presented in the 3DSIG immunoinformatics session (in which I also presented my work) highlighting two different avenues of approaching epitope prediction (and immunoinformatics questions in general): Structure-based (Epitope3D) and sequence-based (SeRenDIP-CE).
Continue readingAIRR Community Meeting V – December 2020
We attended the virtual Adaptive Immune Receptor Repertoire (AIRR) Community Meeting in early December. The three day conference is usually held every 18 months and covered a range of research talks, software demonstrations and poster presentations on the latest TCR and BCR (antibody) research. While we missed certain elements that were present at the last AIRR community meeting (namely focaccia), it was a really interesting meeting with technology all running very smoothly.
Given our current research on SARS-CoV-2 antibodies, we particularly enjoyed the work presented by Armita Nourmohammad from the University of Washington on “Dynamics of BCR in Covid”, based on the preprint on medRxiv. The research identified 34 significantly expanded rare clonal lineages shared among patients with SARS-CoV-2, which are potential candidates for covid response. In particular, the analysis includes an assessment of whether an antibody sequence identified in different individuals (known as a shared or public sequence) is likely to be found due to inherent biases in antibody recombination. Shared antibody sequences which are calculated as unlikely to be shared are potentially a response to a shared exposure such as SARS-CoV2, rather than randomly found in the antibody repertoire. In this way, Nourmohammed and colleagues identified ‘rare’ antibodies which were identified in more individuals than would statistically be expected, and therefore might be worthy of further experimental analysis.
A theme common across a short talk and poster by Hadas Neuman (Bar-Ilan) and a poster by Kenneth Hoehn (Yale), was class-switching dynamics revealed by phylogenetic inference (from IgM to IgA in the human gut in the former, and IgE and IgG4 in a paediatric patient with peanut allergy in the latter). Kenneth Hoehn’s poster also looked at B-cell differentiation during HIV infection – this can all be read about in this preprint. The methods developed in the paper for discrete trait analysis of differentiation, isotype switching and B-cell migration are implemented in the new R package dowser (https://bitbucket.org/kleinstein/dowser) which is part of the Immcantation suite (http://immcantation.org).
It was also really nice to see evidence of the burgeoning use of single-cell sequencing for immune repertoire profiling, with posters by Igor Snapkov (UiO), Indu Khatri (Leiden University Medical Centre), Nick Borcherding (Washington University in St. Louis) all using single-cell technologies, and a talk by Ivelin Georgiev on LIBRA-seq.
If you missed the conference and have had your interest piqued, some of the conference talks are available at the AIRRC youtube channel.
We look forward to AIRRC6, Dec 7 – 11, 2021!
Sarah and Eve