Emily Wissel, PhD

Excited to share our new Prosit-PTM paper is out! A deep learning model that predicts MS2 spectra and Retention time for modified peptides, using chemically informed encodings and data augmentation based on amino acid substitution to learn general rules for how PTMs affect spectra.

Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...

Ingénieur en bioinformatique pour le développement de la plateforme MicroScope - LABGeM Localisé au CEA/Genoscope, un centre de recherche scientifique dédié à la génomique environnementale, le Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme (LABGeM, UMR8030, l...

📢 Job opening — Bioinformatics Engineer
Join the MicroScope platform (LABGeM, CEA/Genoscope) to develop tools and pipelines for microbial genomics.

📍 Evry, France | ⏳ Fixed-term contract
🔗 bit.ly/3Z5WSXc

@ifb-elixir-fr.bsky.social

How to create a more accessible line chart – Nicola Rennie The default settings for chart software are not guaranteed to be accessible, and often need to be adapted for your own chart. In this blog post, we’ll transform a line chart to make it more accessible...

👀 New blog post! 👀

Ever made a *spaghetti* line chart and wondered how you can make it more accessible and more aesthetically pleasing at the same time? 📈

Read this blog post: nrennie.rbind.io/blog/accessi...

#DataViz #RStats

Thanks for writing and re-upping this. I think terminology is important, but I don't think regulating based on technical or statistical properties (e.g., "generative" or "transformer") is appropriate. I think the mode of interaction and epistemic function is more important for regulation.

Grading and googling hallucinated citations, as one does nowadays, and now that LLMs have been around for a while, I've discovered new horrors: hallucinated journals are now appearing in Google Scholar with dozens of citations bc so many people are citing these fake things

NEW: My Udemy course 'Propaganda & Disinformation for Beginners' has helped students in 26 countries worldwide strengthen their armour against disinformation since it launched 2 years ago. Techniques Cambridge Analytica used to secretly profile millions have become a vastly profitable industry.. /1

OpenAI denies liability in teen suicide lawsuit, cites ‘misuse’ of ChatGPT The case is ongoing.

Who says capitalism can't innovate when OpenAI is out here inventing consumer liability protection law from first principles

“There were no cervical cancer cases diagnosed in women aged <25 years in 2021 – the first time that this has occurred in data going back to 1982. This remarkable achievement is almost certainly due to the impact of HPV vaccination.” From report.cervicalcancercontrol.org.au

#vaccinationsaveslives

More people need to read "Why does he do that?" because a great deal of people are bullied and we don't turn into abusers. The narrative these people are victims is perverse to the goal of stopping abuse because it's not only false but contributes the cycle.

dn790007.ca.archive.org/0/items/Lund...

Koina: Democratizing machine learning for proteomics research - Nature Communications Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

Exited to share our latest work! Out now in @natcomms.nature.com

Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!

www.nature.com/articles/s41...

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

The amount of AI generated art in slides at this conference, primarily used by older scientists, is killing me. Scientists please. Don’t use these ai platforms to make your figures or slides. They look bad and I have yet to see them meaningfully improve the message of talks.

A reminder.

Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. ...

Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics!
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...

One throughline in all these AI promises is eliminating subjectivity. We don’t have to trust people’s accounts of their own experiences, because we can trust a magic machine’s *estimates* of those experiences. let ChatGPT write your memoir, act as “synthetic” interview respondents, choose yr dates..

For the avoidance of doubt, this is how the inventor of "vibe coding" actually writes code.

Can we all stop pretending now?

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...

Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social

One way of thinking about the AI bubble is that it's the final gasp of a grift based on specialized GPU's instead of tulips, a logical continuation from crypto and NFT's and the metaverse.

Like, there's nowhere else for it to go, no other magical use for this shit other than as electronic waste.

Large Language Muddle | The Editors The AI upheaval is unique in its ability to metabolize any number of dread-inducing transformations. The university is becoming more corporate, more politically oppressive, and all but hostile to the ...

"Our final defenses are more diffuse, working at a level of norms and attitudes. Stigmatization is a powerful force, and disgust and shame are among our greatest tools. Put plainly, you should feel bad for using AI." (finally reading this)

Microsoft Research AI for Science - Microsoft Research “Over the coming decade, deep learning looks set to have a transformational impact on the natural sciences. The consequences are potentially far-reaching and could dramatically improve our ability to ...

We have multiple senior scientist / engineer positions available across several geos in MSR AI for Science. Ping me or any of my colleagues if you have any questions!
www.microsoft.com/en-us/resear...

Preprint and the website by @dingdingpeng.the100.ci and @vincentab.bsky.social are great, and I got inspired to illustrate Bayesian workflow for model checking and comparison *before* model interpretation following their friendship importance example users.aalto.fi/~ave/casestu...

ecoevojobs.net 2025-26

The 2025-26 Eco-Evo job list is out. Good luck to those applying!

docs.google.com/spreadsheets...

If AI is so good at coding … where are the open source contributions? You can hardly get online these days without hearing some AI booster talk about how AI coding is going to replace human programmers. AI code is absolutely up to production quality! Also, you’re all…

A couple recent smart observations I've read bolster this intuition.

First is this piece by David Gerard from May asking where the AI contributions to pretty much any open code base are:

pivot-to-ai.com/2025/05/13/i...

AI: The New Aesthetics of Fascism It's embarrassing, destructive, and looks like shit: AI-generated art is the perfect aesthetic form for the far right.

Thanks @lukeplunkett.com for making me aware of this must-read piece by @garethwatkins.bsky.social:

newsocialist.org.uk/transmission...

Time to pick a lane.

CC @11bitstudios.bsky.social

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification. #HiFi #LongReads #Sequencing #Transcriptomics
@pacbio.bsky.social @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

The radicalization of the American right is THE story of US politics over the last four decades and political reporters are still not allowed to talk about it