Christophe Dessimoz

We’re hiring: Research Group Leader in computational biology.

Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI.

Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

#ScienceCareers @ewaldlab.org @embl.org

How to maximise the value of public investment, strengthen #OpenScience and international collaboration, and unlock the full potential of #FAIR www.nature.com/articles/s41... with colleagues from @sib.swiss & @elixir-europe.org

From @dessimoz.bsky.social and colleagues in @nature.com 's #Scientific #Data | The missing link in FAIR data policy: biodata resources in life sciences | #FAIR #Genomics #OpenScience #OpenSource #Proteomics 🧬 🖥️ 🧪 🔓
⬇️
www.nature.com/articles/s41...

Apply now! The 2026 call for the EMBO Young Investigator Programme is now open with a deadline of 1 April 12:00 midday CEST. 🧪

More info here:
https://www.embo.org/funding/fellowships-grants-and-career-support/young-investigator-programme/
#LifeSciences #research #funding

Robert Waterhouse — Earth BioGenome Project Rob Waterhouse has always been fascinated by life’s many interconnections, from his childhood on an isolated ranch in Swaziland to his current role leading a community of more than 1,100 researchers a...

Spotlight @ebpgenome.bsky.social www.earthbiogenome.org/newsletter-b... --- thanks to the fantastic #biodiversity #genomics @ergabiodiv.bsky.social #community!

(1/3) I am very happy to share that I’ll be moving to Aarhus University as an Assistant Professor in March. During these years, I’ve met so many great people who supported me on this path, and even if I can’t name everyone here, I’m truly grateful to all of you!

🧬 Just out in Bioinformatics Advances: "OMAnnotator: A novel approach to building an annotated consensus genome sequence". 

Full article available: https://doi.org/10.1093/bioadv/vbag015 

Authors include: @dessimoz.bsky.social, @whynevers.bsky.social

For each orthologous gene family, we constructed three MSAs: original, computed by applying sequence aligners directly to the input sequences; enriched, computed by aligning the combined set of orthologs and homologs identified by database search; and impoverished, obtained by removing the added homologs from the enriched MSA. We then used TCS to quantify congruence of the resulting trees against the known taxonomy. The normalized difference in congruence between the original and enriched trees captures the joint impact of sequence addition on alignment and tree inference. The normalized difference between the original and impoverished trees reflects the effect on alignment quality alone. The effect on tree inference can then be estimated by subtraction. We observed a positive impact of homolog enrichment on phylogenetic tree inference step, regardless of the sequence aligner used to build the alignments. Notably, the impact of sequence addition on alignments was marginal.

We devised a benchmark method to quantify the impact of homolog enrichment on phylogenetic inference, decomposing the effects on MSA quality, tree inference quality, and rooting. We show homolog enrichment improves tree inference, while effects on alignments remain marginal. 🧵2/n

Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n
📃 doi.org/10.64898/2026.01.26.701724

A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia Treponematosis, a bacterial infection caused by Treponema pallidum subspecies and T. carateum (yaws, bejel, syphilis, pinta), has afflicted humans for millennia. Despite paleopathological evidence and...

Treponemal diseases might have been with us much longer than previously thought! In our recent study, we used ancient DNA to reconstruct a 5,500-year-old 𝘛𝘳𝘦𝘱𝘰𝘯𝘦𝘮𝘢 𝘱𝘢𝘭𝘭𝘪𝘥𝘶𝘮 genome, revealing a previously unknown divergent subspecies.
You can check it out here:
www.science.org/doi/10.1126/...

🧬 Une découverte d'une équipe internationale, dont des scientifiques de l'Unil et du CHUV, apporte de nouveaux éléments attestant d'une grande #diversité de #pathogènes dans les Amériques bien avant l'arrivée des Européens.
👉 www.unil.ch/news/fr/1768...

@unil.bsky.social @sib.swiss #ADNancien #chuv

YouTube video by Département de Biologie Computationnelle - UNIL Millenia-old pathogen DNA shed light onto its evolution

👏 Congratulations on this new publication and the great video about the discovery www.youtube.com/watch?v=qewc...

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

Shocking and very sad news. Peer Bork passed away much too soon. Our thoughts are with his family, friends, and the entire EMBL community. www.embl.org/news/embl-an...

Three further SIB knowledgebases gain prestigious European recognition A total of eight expertly curated knowledgebases developed by SIB scientists are now designated as ELIXIR Core Data Resources (CDRs) – with the three new additions representing half of those sel...

🎉 Congratulations to Bgee and the two complementary SwissOrthology knowledgebases, OMA and OrthoDB, for being selected as ELIXIR Core Data Resources! See more👇

@bgee.org @marcrr.bsky.social @dessimoz.bsky.social @elixir-europe.org

This needs boosting.
How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps.
Having one place control it all - is dangerous.

#OpenScience

Fresh conflicts erupt around giant database for flu and COVID-19 sequences Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic

“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪

We are pleased to welcome 3 new Group Leaders to SIB as of 1 January 2026.
Nadine Fournier leads the Biomedical Data Science Facility at UNIGE
Tim Roloff-Handschin and Helena Seth-Smith (UZH) join SIB’s microbial genomics community.
These appointments strengthen SIB’s network and expertise.

#TAIR is a key reference tool #plantscience. That's why nearly 100 volunteers chose to contribute to the soon-to-be-released reannotation of the #Arabidopsis genome. 🧪

Meet one of those volunteers: Emmanuel Boutet: bit.ly/4p6FagQ

#plantbiology #genomics #TAIR12 #plantbiology #scisky

👉 Point your friends, family and connections to our new video 📹 on the point of bioinformatics!

The 90-second video is available in:

🇬🇧 youtu.be/yjbv1WZcM2M
🇫🇷 youtu.be/BG-h_nxwSE4
🇩🇪 youtu.be/e4S4m1IhfiU
🇮🇹 youtu.be/V4QcZHjnsGo

Full Stack Web Developer for Life Science Research

We are hiring for a web developer position, ideally with some experience in bioinformatics. This position is aimed at helping us turn our research in human genetics into useful tools. A background in either bioinformatics or web development is required.

jobs.ethz.ch/job/view/JOP...

Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

🔬 Call to create junior research groups at the Institut Pasteur

Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies

📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD

Apply now 📝 research.pasteur.fr/en/call/crea...

#JobOpportunity #Research

Amos Bairoch, Swiss pioneer of bioinformatics, passes away We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...

We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We honour his legacy by continuing to build the future of bioinformatics.

I will be giving several talks this coming week at universities in Switzerland: Lausanne, Neuchâtel, Basel, and Bern. Hope to see some of you there!

Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? I’m hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed.

Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...

🚀 Partner with ECCB 2026 in Geneva (31 Aug–4 Sept), gathering 1,000+ experts in compbio, bioinformatics, AI, biodiversity & data-driven health, to:
🔹Showcase your innovations
🔹Increase your visibility in Europe
🔹Recruit top talents
👉 Explore our packages: eccb2026.org/become-partner

PhyloWeaver – Interactive phylogenetic tree editor Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.

I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/

Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

Interested in the newest developments in orthology? Check out the last Quest for Orthologs (QfO9) meeting report:
link.springer.com/article/10.1...
#orthology #function #domains #AI #paralogy
Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.

Building a continuous benchmarking ecosystem in bioinformatics Benchmarking, which involves collecting reference datasets and demonstrating method performance, is a requirement for the development of new computational tools, but also becomes a domain of its own t...

From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓  
⬇️
journals.plos.org/ploscompbiol...

A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision.

A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...

Join our upcoming @fidelis-project.bsky.social network training event, organized by SIB, to explore: AI for Digital Repositories: Opportunities and Challenges, on 2 December 2025, 15:00–16:30 CET. eden-fidelis.eu/events/ai-di...

@sduvaud.bsky.social @geertvangeest.bsky.social