iiinova — where your digital self keeps evolving

Reposted by Renard Lab

Ferdous Nasri @ferbsx.bsky.social · 10/06/2026

Use of AI agents is becoming more prevalent in science. But in an outbreak, a single wrong sequence can shift what we think a virus came from, or if a treatment still works. We ask, can a deterministic retrieval layer fix the unreliability of AI agents querying NCBI Virus? 🧵

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Reposted by Renard Lab

Ferdous Nasri @ferbsx.bsky.social · 10/06/2026

"Using AI agents to navigate biological data infrastructure is like driving through an old city that was designed before cars." Laura Luebbert in the @anthropic.com blog post about our work. Adding highway tunnels, like gget virus, is the fix! www.anthropic.com/research/age...

anthropic.com

Paving the way for agents in biology

Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

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Renard Lab @renardlab.bsky.social · 19/03/2026

In under 2 days, we construct a PTM-specific dataset of nearly 11 million spectra and used it to retrain a phosphorylation classifier. The retrained model matched the performance of the original model on an independent test set, showing the power of scalable, automated data generation. 🧵 6/7

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Renard Lab @renardlab.bsky.social · 19/03/2026

Within 49 hours we parsed over 800 million PSMs from over 1,200 projects on PRIDE and made them filterable through their metadata, allowing the curation of task-specific datasets. 🧵 5/7

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Renard Lab @renardlab.bsky.social · 19/03/2026

usiGrabber 🏗️ to the rescue! A scalable framework for assembling large proteomic datasets. It extracts spectra identification, stores project-level metadata, indexes raw spectra using USIs, and offers download utilities to retrieve spectra data at scale. 🧵 4/7

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Renard Lab @renardlab.bsky.social · 19/03/2026

Curating a task-specific proteomics dataset requires deep domain expertise. In a time consuming step, researchers have to manually select relevant spectra from accessible repositories, potentially missing out important data and projects. 🧵 3/7

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Renard Lab @renardlab.bsky.social · 19/03/2026

G. Auge, M. Clausen, K. Ketterer, J. Schaefer, N. Schmitt, T. Altenburg, @yhartmaring.bsky.social, @hendraet.bsky.social, C.N. Schlaffner & B.Y. Renard turned what started as a fun hackathon 💻 into this project, huge thanks to everyone who brainstormed, coded, and experimented along the way!🙌 🧵 2/7

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Renard Lab @renardlab.bsky.social · 19/03/2026

We are excited to present 🏗️ 'usiGrabber: Automating the curation of proteomics spectra data at scale, making large datasets ready for use in machine learning systems' now available on bioRxiv: doi.org/10.64898/202... #proteomics #machine-learning #mass-spec #dataset-curation 🧵 1/7

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Reposted by Renard Lab

Pascal Iversen @pascivers.bsky.social · 03/06/2025

Despite hundreds of published models for cancer drug response prediction, none are used in clinical practice. Why? In our preprint, we outline key challenges and introduce a living benchmark to help the field move forward. Check out the thread by my co–first author @judith-bernett.bsky.social:

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Renard Lab @renardlab.bsky.social · 30/05/2025

What a run! 🏃‍♀️🏃‍♂️ Last week, our group took part in the Berlin #Firmenlauf, and we had an amazing time out there, running, cheering each other on, and just enjoying the energy of the event! #TeamVibes Thanks to everyone who made it such a memorable day 🤗 #ScienceInSneakers @hpi.bsky.social

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Reposted by Renard Lab

Helene Kretzmer @helenekretzmer.bsky.social · 02/03/2025

We’re excited to share that our paper on rapid molecular classification of brain tumors has just been published in Nature Medicine!

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Renard Lab @renardlab.bsky.social · 06/03/2025

In his project in collaboration with the Icahn School of Medicine at Mount Sinai @hpims.bsky.social, he is exploring the effect of biological administration timing on treatment outcomes in patients with Inflammatory Bowel Disease. Supervised by Dr. Susanne Ibing @sibing.bsky.social.

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Renard Lab @renardlab.bsky.social · 06/03/2025

We're proud to have Akin present his ongoing master's thesis project at the European Crohn's and Colitis Organisation (ECCO) Congress 2025!

Akin joyously standing in front of his poster titled “Morning administration of biological therapy is associated with decreased risk of treatment failure in patients with Inflammatory Bowel Disease” at the European Crohn’s and Colitis Organisation (ECCO) congress!

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Renard Lab @renardlab.bsky.social · 11/02/2025

Check out the awesome opportunity to join the group of one of the brilliant minds at our chair!

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Renard Lab @renardlab.bsky.social · 07/02/2025

Her work produces daily immunity indices for each regional location, given vaccination and infection data for different infectious diseases, which in turn can be used to, e.g., predict the spread of disease 🧬🤧🌐

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Renard Lab @renardlab.bsky.social · 07/02/2025

Ferdous Nasri presenting her work on the 'Spatio-temporal immunity index tool for infectious diseases' at the Digital Health Summit at University of Cape Town in South Africa!

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Renard Lab @renardlab.bsky.social · 31/01/2025

She has published numerous papers and presented her work at various conferences. Her next step will focus on her research collaborations across the atlantic. 🚀

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Renard Lab @renardlab.bsky.social · 31/01/2025

Her achievements are outstanding and we are very proud to be celebrating this day with her!💐 She started her PhD as a part of the Böttinger Lab, spent some time working with Mount Sinai in NY and switched to our Lab later. She led projects with many students, one of which won the DMEA Sparks Award🏆

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Renard Lab @renardlab.bsky.social · 31/01/2025

💐Congratulations to ✨ Dr. Susanne Ibing! 🎓 Susanne, @sibing.bsky.social, successfully defended her doctoral dissertation @hpi.bsky.social this month on “Computational Strategies for Chronic Disease Characterization and Treatment by Leveraging Electronic Health Records and Omics Data” 🩻🧬👩🏼‍💻

Dr. Susanne Ibing joyously shaking hands with Prof. Bernhard Renard!

Susanne defends her dissertation in front of the fully-packed room.

Dr. Susanne standing proudly wearing her graduation hat and robe in front of the HPI Digital Health building smiling with all the people that participated in her dissertation defence.

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Renard Lab @renardlab.bsky.social · 02/01/2025

With an ablation study, we demonstrated the added value of information derived from clinical notes not only for the computable phenotyping, but also the disease prediction task. 🧵 6/6

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Renard Lab @renardlab.bsky.social · 02/01/2025

When comparing coded conditions between identified cases and controls, we saw significant overrepresentation of GI-related conditions in cases, indicating the diagnostic delay of the disease. 🧵 5/6

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Renard Lab @renardlab.bsky.social · 02/01/2025

We found that adding information on age at diagnosis extracted from the clinical notes improves the phenotyping performance and allows to better distinguish between referral and incident cases, compared phenotyping mainly relying on structured clinical data. 🧵 4/6

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Renard Lab @renardlab.bsky.social · 02/01/2025

For automated cohort identification, we compared two computable phenotyping approaches with different levels of NLP and information extracted from clinical notes incorporated. 🧵 3/6

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Renard Lab @renardlab.bsky.social · 02/01/2025

Diagnostic delay is a common problem in Crohn’s disease, and with delayed treatment induction leading to overall worsened outcomes. This study aimed to automatically identify newly diagnosed patients to use pre-diagnostic EHR for data disease prediction. 🧵 2/6

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Renard Lab @renardlab.bsky.social · 02/01/2025

New paper: Electronic Health Records-Based Identification of Newly Diagnosed Crohn’s Disease Cases By Susanne Ibing @sibing.bsky.social , Julian Hugo, et al., now available in Artificial Intelligence in Medicine. authors.elsevier.com/a/1kA113KEGa... 🧵 1/6 Thread below:

authors.elsevier.com

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Renard Lab @renardlab.bsky.social · 02/01/2025

Happy New Year and a warm hello world from our group! 🥳😄

Picture of the group members smiling standing in a meeting room facing the camera.

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