BDB-Lab Spring 2023 Updates

Looking forward. Luis and Svetlana will meet the EMBARK collaborators for the annual project progress discussion in Paris (April 2-4). Please feel free to get in touch if you will be in Paris!

Yiqian is presenting a poster and its associated flash talk titled “With small ORFs come great datasets: the global microbial small ORFs catalog (GMSC)” at the Microproteins 2023 conference, in Denmark (May 31 - June 2).

Marija is giving a rapid fire talk and a poster presentation titled “A global survey of eco-evolutionary pressures acting on horizontal gene transfer” at ASM Microbe 2023, in Houston (TX, USA) (June 15-19; her talk is on the 16th of June). Feel free to get in touch with her to meet at the conference.

Anna is giving a flash presentation titled “Exploring the dog gut microbiome within a large-scale investigation of animal gut metagenomes” at FEMS 2023, in Hamburg (9-13 July).

Focus of the Quarter

We have had a YouTube channel for a while, but it lay dormant until early this year. However, we decided to start publishing there as an alternative way to communicate our science.

Our channel so far contains primarily two types of videos: (1) those showcasing our scientific work and (2) those providing tutorials for the computational tools that we develop. For tutorials, we also provide a GitHub repository with all the materials.

We highly encourage viewers/readers to reach out with requests and questions. In fact, some of our videos have already been inspired by user feedback. Please feel free to reach out and subscribe to the channel.

Other BDB-Lab Updates

People.  We welcome Fernando Gil (@_Fernando_Gil on Twitter), a biosciences student at Fudan who recently joined to support the dog gut microbiome project. We welcome Daniel Adediran (@danieladedira13 on Twitter), Seun Olufemi (@SeunOlufemi9 on Twitter), and Anne Staff, who will join us as remote interns at the end of Spring 2023. 

Manuscripts. The SemiBin2 manuscript is conditionally accepted at ISMB (which will be published as a special issue of Bioinformatics).

Online resources & tools. We released SemiBin v1.5, which is the first beta version of SemiBin2.

Conferences/talks. Luis gave a talk titled “SemiBin: using self-supervised deep learning for better metagenomics binning“ organized by the Faculty of Mathematics (University of Belgrade) & Serbian Society for Bioinformatics & Computational Biology (see YouTube version).

We had a guest in our group meeting: Anna Abramova, who benchmarked different metagenomic assembly tools to recover antimicrobial resistance genes.

Others. We started to share questionnaires with dog owners in Shanghai for the dog gut microbiome project (read more about the project here).

Get in touch. Feel free to get in touch, by email, by Twitter DM, schedule a Zoom coffee, or join our discord.