Davide Risso

EuroBioC2025 group photo on PRBB terrace with sea in background.

EuroBioC2025 welcome in PRBB auditorium by host Robert Castelo, showing slides with conference sticker and sponsor logos.

EuroBioC2025 hexwall banner with the hexwall creator Kevin Rue-Albrecht standing beside it.

EuroBioC2025 carved wooden keyring, a gift for all participants, created by Annekathrin Nedwed.

EuroBioC2025 is in full swing here in Barcelona!

Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!

#EuroBioC2025 #Bioconductor #OpenScience #Community

EuroBioC2025 late-breaking poster abstract submission Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

📣 Late-breaking poster call for #EuroBioC2025 is now open!

Submit by July 11 to present your work in Barcelona this September.
🔗 forms.gle/ewTGdKzB2xyE...
📅 Notifications by July 15

#Bioconductor #Bioinformatics

🤔Could quality control create more harm than good? We explore this question in the context of #SRT.

SpotSweeper is developed to combat implicit selection bias.

Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social

👉: bsky.app/profile/mict...

Everyone involved in trying to pass off that ChatGPT-extruded disinformation manifesto as a scientific report should be, at the very least, barred from public office for life. The MAHA report is dangerous criminal misconduct and an offence to the process of science.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

THREAD 🧵

Internal State Department records show that months of warnings have become a reality: The Trump administration’s sudden withdrawal of foreign humanitarian aid has brought about death, violence and unrest. 1/

Trump administration cancels plans to develop a bird flu vaccine The Department of Health and Human Services is ending a $766 million contract with the vaccine company Moderna to develop an mRNA vaccine for flu strains with pandemic potential, including bird flu.

22 years ago I pivoted from working on antibiotic resistance to pandemic viruses.

Since then, I've argued that if we care about saving US lives in expectation, advance capacity for producing bird flu vaccine offers by far the greatest expected return on investment.

...

We were so goddamn close.

This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.

I appreciate the offers from other scientists to help Harvard (students, labs, etc) through this attack, but what would be most helpful is for you to use your position to contact your elected representatives and make it clear this fight isn't just Harvard, it will affect you, and their districts too

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...

Fascinating talk by @andganna.bsky.social at #ds4hb A lot of food for thought on efficient data collection and fairness in AI for health!

Science Under Threat in the United States: How scientists and institutions should respond Individual researchers and university leaders need to make the case for science to their elected representatives and to the public at large.

Science is under threat in the US. @elife.bsky.social have commissioned a series of articles discussing the implications and what we can do. The first three articles are now live. More to follow:
elifesciences.org/articles/106...
elifesciences.org/articles/106...
elifesciences.org/articles/106...

Would you like to spend a #postdoctoral fellowship in the beautiful Italian Alps doing great science?

Apply for a MSCA Postdoctoral fellowship with us on #stats #biostats #genomics #epidemiology

Many infos here 👇 🧵

#StatsSky #rstats #popgen #nephsky

1/n

📣📣Are you looking for a postdoc? 📣📣

Does a EU or Horizon Europe assoc country (eg UK, S Korea) seem like a good destination?

These fellowships a great funding option for anyone in the 🌎

👀 Check them out - next call opens 8 May

🧪 👨‍🔬👩‍🔬
marie-sklodowska-curie-actions.ec.europa.eu/actions/post...

Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona.
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.

eurobioc2025.bioconductor.org

🎨 Reminder that EuroBioC2025 Sticker Contest is still open! Deadline Mar 10. Don't miss out on the chance to have your design featured at the conference and win free registration ✨
Submit buff.ly/42JiCLN

Abstracts are open for submission too!

#EuroBioC2025 #RStats #Bioinformatics #StickerContest

"Your AI can’t see gorillas!"
A few years ago we found that students are more likely to see the gorilla in their data if they are not also asked to test a specific hypothesis. In his blog Chiraag Gohel now shows that Chat-GPT can’t help you to find it either.
chiraaggohel.com/posts/llms-e...

A little poster promoting the event indicating its date and time (10 March, 2 pm, campus San Giobbe Venice, Room 6)

In two weeks (10th March) John Burn-Murdoch will be holding a Conversation at the San Giobbe campus, Room 6A (2pm). Everyone is very welcome to join (and thanks @crisvarin.bsky.social for making this happen)!

New #rstats pkg gander is now on CRAN!

gander is a coding assistant that knows how describe the objects in your global R environment. So, when you're working with data, LLMs will know the names, types, and distributions of data columns, resulting in much more effective completions.

European Bioconductor Conference 2025 EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…

📣 EuroBioC2025: Abstract Submissions Open!

Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.

➡️ Submit https://buff.ly/3EN9w6P

#EuroBioC2025 #Bioinformatics #RStats #DataScience

The package is general and can be used with any distribution of the exponential dispersion family, which includes the Gaussian, Poisson, negative binomial, and many others.

More to come soon, including a @bioconductor.bsky.social wrapper to make it easier to work with single-cell RNA-seq data.

The sgdGMF #rstats package is now officially on CRAN:
cran.r-project.org/package=sgdGMF

Please give it a try and let us know if you have any feedback!

🎨 EuroBioC2025 Sticker Contest!
Unleash your creativity for the European Bioconductor Conference in Barcelona! The winning sticker will be featured on our website and handed out at the event.
🗓 Deadline: Mar 10, 2025
🏆 Prize: Free reg to EuroBioC2025 for winning design!
Abstract call coming soon!

Trump & Musk are making massive cuts to the National Institutes of Health.

I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.

INTRODUCTION

Modern-Day Oracles or Bullshit Machines?

Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take.

thebullshitmachines.com

8. It is difficult to overstate what a catastrophe this will be for the US research and education systems, particular in biomedical fields.

It is deliberate and wanton devastation entirely out of scale with any concern about DEI activities on campuses.

The goal is destroy US universities.

1. Today the NIH director issued a new directive slashing overhead rates to 15%.

I want to provide some context on what that means and why it matters.

grants.nih.gov/grants/guide...

Shoutout to all of the exceptional Black scientists who have contributed to and are currently contributing to virology research! Your work is vitally important to understanding basic virology controlling viral diseases worldwide! #BlackHistoryMonth

The statement reads: We are disappointed in the rapid capitulation by some U.S. institutions and organizations to recent attacks on diversity, equity, inclusion, and access. At their core, these weak arguments are fueled by the familiar underlying assumption that people from Black, Indigenous, and other marginalized identities cannot be excellent and therefore have not ‘earned’ our place in public intellectual life. However, we have always been competent, hardworking, and creative people who have contributed positively to society at large, across sectors but especially in science. We reject these attempts at silencing and erasure and will continue to be a place of respite and community in these turbulent times. To our members, your talent, skills, and safety are important! To our friends and allies, you may be feeling like everything happening is out of your control, but we want you to know that your voice and actions can make a difference. We want to point you towards some immediate actions that you can take. These are the top 3 issues we are concerned about and what you can do about it if you mirror our concerns. Freezing of federal funding and cutting grant programs for scientific research that have any connotation of being “DEI.” The potential confirmation of RFK Jr., a vocal anti-vaccination proponent, as the head of HHS. The American Society for Microbiology (ASM) removed their ABRCMS and IDEAAS webpages in addition to some scientist spotlights and written articles highlighting the current and historic contributions of microbiologists who are a part of marginalized communities including LGBTQIA+, Women, Indigenous and Black, as well as others page that could be considered “‘DEI”. Many have now been reinstated with changes to language (i.e. removing terms like “equity” and “marginalized”), and the statements released by ASM did not acknowledge the harm that they have caused to their members and showed no remorse for their actions.

A statement from the BMA Board Members to the BMA Community and Beyond.

Additional alt text to follow due to the character limit.