Super grateful that our scETM work (from my summer internship with Dr. Yue Li, in collab. with Huiyu Cai and @tangjian.bsky.social) was recognized with an honourable mention at SIB PhD Paper Award competition. Many thanks to the jury and congrats to @meyerdh.bsky.social and Can Chen! #bc2basel

✨ I’m honored and grateful to have received the SIB Bioinformatics PhD Paper Award 2025 for part of my PhD work.

Thank you for your guidance and inspiration @bjornschumacher.bsky.social

#SIBAwards #bc2basel #Bioinformatics

That's a wrap on [BC]² 2025 in Basel! 3 absolutely fantastic days full of cutting-edge science and brilliant discussions. Left feeling energized by the inspiring talks, workshops, and the amazing computational biology community. Huge thanks to the organizers @sib.swiss #bc2basel

That will be all for this year’s [BC]² 2025. Thank you to all the speakers, sponsors and attendees for making this edition such a success. We wish you a safe journey home 👋 and see you at @eccb-europe.bsky.social in 2026 and at the next edition of [BC]² in 2027! #bc2basel

We’ve reached the last session of [BC]² 2025 with the closing keynote address from Julia Merkenschlager who is presenting (remotely) on immunology. Title of her talk: “Affinity maturation: Against the odds” #bc2basel

Congratulations to all #posterprize winners!
#bc2basel

Qingyao Huang​ for
“Fostering Sustainability and Environmental Awareness at Work​” #bc2basel #posterprize

Siyuan Luo​ for
“On metrics for subpopulation detection in single-cell and spatial omics data​” #bc2basel #posterprize

Océane Follonier​ @oceanef.bsky.social for
“From bytes to binders: design, score and optimize​” #bc2basel #posterprize

Laura Voitl​
“Identifying Genetic Variants for a Mendelian Trait using Long Read Sequencing in Three Domestic Animal Species​” #bc2basel #posterprize

Benjamin Heiniger​ for
“Proteogenomics identifies conserved and lineage-specific novel small proteins in clinical Mycobacterium tuberculosis reference strains​” #bc2basel #posterprize

Alen Stambolliu​ for
“Deciphering Retrotransposable Elements dynamics in tumor-infiltrating lymphocytes through combination of short- and long-read single-cell RNA sequencing​” #bc2basel #posterprize

Poster prize winners for #bc2basel 2025 are: Cassandra Litchfield​ for “Integrating FFPE derived Whole Genome Sequencing into Routine Molecular Pathology: Validation and Establishment of a Bioinformatics Workflow​” and…

Our [BC]²INGO GAME was won by Nosihle Msomi. Congratulations! #bc2basel

Come chat about text mining and #biodiversity trait #data at my poster R4 at #bc2basel

Thanks to all the speakers of the great 'Integrative Bioinformatics for Evolutionary and Environmental Processes' session at #bc2basel, chaired by Anne-Florence Bitbol and Anna-Sapfo Malaspinas:
Eline Lorenzen, Ludovico Calabrese, Tristan Gollmart, Nadia Neuner-Jehle, Marco Molari, and Jacob Riina

🧬 Turning science into startups! A special session on launching #bioinformatics startups with insights on IP, legal, funding + case studies ( @bigomics.bsky.social, TrueYouOmics) from experts Swiss IP, Lenz&Staehelin, Innosuisse. Session chairs: @abxka.bsky.social, E. Özkırımlı, V. Zoete. #bc2basel

We love putting together [BC]² Basel Computational Biology Conference #bc2basel for you every two years.
And we do so much more! Come by our booth to find out about our vision for life-science data and all the services we offer academia and industry. #bc2basel

We now have plenary highlights of the latest research submitted in abstracts: from venom evolution & spatial lipidomics to deep learning, glioma cell states & rapid diagnostics for rare disease. Chaired by Katja Bärenfaller and @dgfeller.bsky.social.
#bc2basel #Bioinformatics #Omics #MachineLearning

Gavriilidou: proteins which are co-expressed in venom glands (work done with Giulia Zancolli @dee_unil) are also co-evolving
#bc2basel

Gavriilidou obtained ≈3k co-evolution networks between venoms and other protein families. E.g. dense cluster of 5 venom protein families co-evolving with each other and with many other protein families. The co-evolving proteins include venom-related functions as well as resistance-related […]

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes Author summary Genes that are involved in the same biological process tend to co-evolve. This property is exploited by the technique of phylogenetic profiling, which identifies co-evolving (and therefore likely functionally related) genes through patterns of correlated gene retention and loss in evolution and across species. However, conventional methods to computing and clustering these correlated genes do not scale with increasing numbers of genomes. HogProf is a novel phylogenetic profiling tool built on probabilistic data structures. It allows the user to construct searchable databases containing the evolutionary history of hundreds of thousands of protein families. Such fast detection of coevolution takes advantage of the rapidly increasing amount of genomic data publicly available, and can uncover unknown biological networks and guide in-vivo research and experimentation. We have applied our tool to describe the biological networks underpinning sexual reproduction in eukaryotes.

Gavriilidou investigates co-evolution of venomous predators and their preys by phylogenetic profiling, using HogProf https://doi.org/10.1371/journal.pcbi.1007553 #bc2basel

Athina Gavriilidou next, on a topic dear to my heart, evolution of venom 🕷️🐍 #bc2basel

Preprints and server from Craighero's work:
www.biorxiv.org/content/10.1101/2025.04....
www.biorxiv.org/content/10.1101/2024.04....
https://lts2.epfl.ch/ribotly/
#bc2basel

Craighero: "unfortunately I don't have an AI generated image for this, but imagine a ribosome made of cheese or whatever" 😁 #bc2basel

#bc2basel "Highlights - Top abstracts across all scientific themes", starting with Francesco Craighero @fcraighero.bsky.social, using deep learning to understand the regulation of translation elongation, i.e. ribosome stalling.

The 'Integrative Bioinformatics for Evolutionary and Environmental Processes' session at #bc2basel started with the amazing talk of #ElineLorenzen, starting with the Arctic Death Spiral, going to he lasting effects of whaling to sequencing data to model co-inhabitation of marine mammal species.

Lorenzen: from Arctic sedimentary DNA, reconstruct communities of (marine mammal) species. E.g., with opening of Nares straight at start of inter-glacial, we find DNA of temperate species such as seals. #bc2basel

In ‘Integrative Bioinformatics for Evolutionary and Environmental Processes’ our invited speaker is Eline Lorenzen from University of Copenhagen, Denmark. This session is chaired by Anne-Florence Bitbol and Anna-Sapfo Malaspinas. #bc2basel

Lorenzen: unlike polar bears, Bowhead whales had stable environment suitability and genomic population size until very recently. Then human hunting (whaling) arrived, leading to a demographic crash. Modeling predicts that population recovery will be very slow at best. #bc2basel