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Antoine Taly

@ataly.bsky.social
744 followers 590 following 196 posts

Researcher at CNRS interested in the biophysics of proteins. Modelling membrane proteins and their interaction with ligands. Working in Paris.

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Reposted by Antoine Taly
Elisa Frezza @elisafrezza.bsky.social · 25/09/2026
Happy to share our Application Note on RNA and chemical probing. MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data pubs.acs.org/jcisd8/artic...
pubs.acs.org
MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data
Abstract. Ribonucleic acid (RNA) molecules fold into complex, highly dynamic three-dimensional conformational structures that govern their biological activ
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Ulrich Hammes @uhammes.bsky.social · 24/09/2026
We’re looking for a new colleague in Würzburg! 🌱 W3 Professorship in Plant Metabolism 💊 Chair of Pharmaceutical Biology 🧪 Head of the Metabolomics Core Unit jobs.zeit.de/jobs/univers... Please spread the word! Questions? Feel free to contact me. www.biologie.uni-wuerzburg.de/en/about-the...
biologie.uni-wuerzburg.de
W3_Pflanzenmetabolismus - FACULTY OF BIOLOGY
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Valeria Venturini @valeriaventurini.bsky.social · 22/09/2026
In @pcusachs.bsky.social’s lab at @ibecbarcelona.eu we have a fully founded open PhD position! It’s a very nice working environment & can promise cool mechanobiology🔬🧫 Here all the info ibecbarcelona.eu/predoctoral-...
ibecbarcelona.eu
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Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026
The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions
career5.successfactors.eu
Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)
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Yann Ponty @yannponty.bsky.social · 08/09/2026
Yep, 100% this ⬇️ (and my lab is eligible for such positions 😜)
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Iris van Rooij 💭 @irisvanrooij.bsky.social · 05/09/2026
If you read closely, it is clear that @chess.com indeed was referring to the game tree complexity, and not the positions, since they say "possible chess games". I assume M*sk used and LLM to, which ofc is unable to get pragmatics.
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Jason Schadewald (He/Him) @jschadewald.bsky.social · 03/09/2026
If you want clear-headed and accessible reporting on AI incidents, this example is a gold standard.
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Elisa Fadda @elisafadda.bsky.social · 02/09/2026
I will be in Geneva at #ECCB2026 for a super #glycotime workshop in glyco-bioinformatics hosted by @glycoexpasy.bsky.social to present a hands-on guide to the new layout and features of @glycoshape.org If you want to hear all about it, just sign up! ⬇️ eccb2026.org/communities-... online and free
screenshot of the title slide of my talk showing a graphical representation of a cell surface in brown with glycans added dfrom structures in Glycoshape. the title of the talk reads 3D glyco-bioinformatics with GlycoShape
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 01/09/2026
En septembre sur #TOTProts, les protéines font leur rentrée à l'usine ! #Vulgarisation #Protéines topoftheprots.com/2024/11/25/r...
Carte postale ancienne montrant un atelier avec des artisans qui fabriquent des protéines.
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 27/08/2026
“Using research as an opportunity for learning-by-doing may produce seeming ‘inefficiencies,’ but that’s a feature, not a bug…the process of education is necessarily a productive struggle, and that the most important product of their education is not a GPA or a diploma but themselves“
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Palais de la découverte @palais-decouverte.fr · 30/08/2026
Dernier dimanche des vacances... Pourquoi ne pas le passer en science aux Étincelles Paris 15e ? Au programme : Physique Chimie Biologie Astronomie (Planétarium) Géosciences et Informatique ⤵️ billetterie-etincelles.palais-decouverte.fr
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Janani Durairaj (Jay) @ninjani.bsky.social · 28/08/2026
Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!
compare, predict, design
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Antoine Taly @ataly.bsky.social · 27/08/2026
🚨 🚨New preprint from the group 🚨🚨 "Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ? " E Reboul shows you can split SMILES into fragments that follow retrosynthetic analysis! with H Prabakaran J Waldispühl www.biorxiv.org/content/10.6...
biorxiv.org
Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ?
Molecules generated by deep learning models are often difficult to synthesize. Their synthetic accessibility can be improved with automated retrosynthetic analysis, which allows for identifying syntho...
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AI x Bio Discovery @aixbiobot.bsky.social · 27/08/2026
Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ? [new] SMILES sampling fragments molecules into ordered, concatenable blocks matching retrosynthons, improving break cov.
Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ?Figure 1Figure 2Figure 3
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Claudia Martinho @cssmartinho.bsky.social · 24/08/2026
Postdoc opportunity in my group! Please share! 🔁 Investigate the epigenetic mechanisms underlying stress memory in plants 🧬🌱 Looking for someone excited about computational genomics + plant molecular biology. 📍 Dundee, Scotland | 3 years 📅 Apply by 21 Sept www.dundee.ac.uk/work-for-us/...
dundee.ac.uk
Postdoctoral Research Assistant - UOD2369
Closing date: Monday 21 September 2026, 23:59
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Jessica Andreani @jessicaandreani.bsky.social · 21/08/2026
🚨📣 Hiring a postdoc in bioinformatics 🧬🧑‍💻 Join our team at @i2bcparissaclay.bsky.social to explore biomolecular interactions and improve protein function prediction in bacteriophages! 📍 Gif-sur-Yvette, France ⏳ 13 months (+ possible extension) 📅 Apply here: emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Job offer - Post-doctoral researcher in bioinformatics (M/F): exploring biomolecular interactions for bacteriophage protein function prediction
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 18/08/2026
MEM-CALVADOS: A Residue-Level Model for Flexible Proteins at Membrane Interfaces www.biorxiv.org/content/10.64898/20…
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Anja Geitmann @geitmannlab.bsky.social · 17/08/2026
Postdoc Opportunity at McGill University, Montreal, Canada You have worked with Arabidopsis / other plant model systems & are trained in high-end imaging? Details: www.plantbiomechanics.net/joining-the-... #plants, #Arabidopsis, #postdoc, #jobs, #microscopy, #confocal, #molecularbiology
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Debbie Gale Mitchell @heydebigale.bsky.social · 16/08/2026
Do any #chemchat #chemsky folks have resources around best practices for ALT text for chemical structures?
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Chenxin Li, PhD @chenxinli2.bsky.social · 15/08/2026
Arabidopsis Col-0 is not one thing "Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s". #PlantScience From: www.biorxiv.org/content/10.6...
biorxiv.org
Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s
The model plant Arabidopsis thaliana has been a workhorse of plant biology since the 1950s, when the Columbia-0 (Col-0) accession was widely adopted by the research community as a reference genotype. ...
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Palais de la découverte @palais-decouverte.fr · 15/08/2026
🐸 🐜 🪳 Pour les enfants dès 6 ans aux Étincelles du Palais, vous avez aujourd'hui un exposé sur les grenouilles à 10h20 et un atelier "dessine-moi les fourmis" à 11h40. Demain dimanche en plus : les insectes et les fourmis 😉 ➡️ billetterie-etincelles.palais-decouverte.fr
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vincentholst.bsky.social @vincentholst.bsky.social · 14/08/2026
As promised, we now share some details why it took 32 months to get this Matters Arising published, and, since many asked, share some comments on the reply to our critique. All details can be found in this small FAQ vincentholst.github.io/the_curious_.... Below is a summary 🧵
vincentholst.github.io
The Curious Case of the Declining Disruption’s Disappearance
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Franck Ramus @franckramus.bsky.social · 10/08/2026
Pour l'été je vous offre un best-of de mes articles et chroniques, sous forme de feuilleton. Aujourd'hui: ramus-meninges.fr/television-e...
ramus-meninges.fr
L’exposition à la télévision et le test du bonhomme
par Magali Lavielle-Guida, Jonathan Bernard et Franck Ramus Synthèse grand public d’un article publié dans ANAE : Lavielle-Guida, M., Bernard, J. Y., & Ramus, F. (2022). Effets des écrans sur l…
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Dr Elodie Chabrol @eloscicomm.bsky.social · 24/07/2026
🏆Les Ig Nobel s'installent en Europe et vous pouvez vivre la cérémonie officielle depuis Paris ! @psl-univ.bsky.social 📅 Jeudi 3 septembre 2026 🕠 À partir de 17 h 45 📍 Université Paris Dauphine – PSL, Paris 🎟️ Événement gratuit sur inscription - 100% en anglais 👉 my.weezevent.com/ig-nobel-36t...
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Juan Carlos De la Concepcion @delaconcepcionjc.bsky.social · 05/08/2026
PLEASE SHARE! New job openings in my lab @zmbp-tuebingen.bsky.social. We have a broad interest into the mechanistic basis of how molecular complexes are rewired during cellular development in plants and during invasion by pathogens. 🌱🍄🔬 See details below 👇 #PlantSciJobs
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Palais de la découverte @palais-decouverte.fr · 04/08/2026
Aujourd'hui aux Étincelles riche offre en Biologie. ➡️ billetterie-etincelles.palais-decouverte.fr Deux ateliers (avec observation au microscope) : - secrets de fleurs à 10h20 - microbservations à 14h20. Mais aussi ⤵️
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Tristan Bereau @tbereau.bsky.social · 03/08/2026
PhD position in Heidelberg: generating amorphous molecular thin films with diffusion models rather than waiting for MD to equilibrate them — free energies from the same model. With U. Köthe. 3 years, funded. Physics degree required. tristanbereau.com/positions/ge...
tristanbereau.com
Generative machine learning for molecular thin films – Tristan Bereau
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Ketan Joshi @ketanjoshi.co · 31/07/2026
Absolutely nuts: Google Earth now has a feature that lets you convincingly fabricate satellite imagery www.digitaldigging.org/p/how-to-pla...
a fakje satellite image of a craterWe take misinformation seriously - every image created with Nano Banana in Google Earth includes the SynthID digital watermark, so if someone is unsure about an image, they can ask the Gemini app or use Lens in Search to see if the image was Al-generated. In addition, we prevent image creation on harmful topics and are continually updating our protections.

One clause in there is checkable tonight, so I checked it. Google prevents image creation on harmful topics. Refugees at a border. A nuclear plant in Iran. A fatal crash on an Amsterdam street. A hospital with a bomb crater in Gaza.

Nothing was refused. No warning, no softened output, no suggestion to try a different prompt.

Now look at the rest of the answer. The watermark is Google’s. The app that reads the watermark is Google’s. The search that reads it is Google’s. Every road out of the problem runs back through the company that built it.

I understand that Google has Google products to run Google checks. Planet Earth is bigger than Google.

I put one of tonight’s clips on X and asked nobody to check it. Hive, one of th
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Michael Sieber @michaelsieber.bsky.social · 01/07/2026
Have ideas for your own, independent research program in Theoretical Biology? Then come and join us as a Group Leader at the @mpi-evolbio.bsky.social in Plön, Germany!
mpg.de
Group Leader in Theoretical Biology (m/f/d)
Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics
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Jeff Groh @jeffgroh.bsky.social · 28/07/2026
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
pnas.org
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
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AI x Bio Discovery @aixbiobot.bsky.social · 27/07/2026
Deep-learning predictions of biomolecular structures : persistent limitations and new horizons extended by explicit ion addition [new]
Deep-learning predictions of biomolecular structures : persistent limitations and new horizons extended by explicit ion additionFigure 1Figure 3Figure 2
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Antoine Taly @ataly.bsky.social · 27/07/2026
Latest preprint on AlphaFold potential and limitations. We look in particular at the addition of ions to models.
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 27/07/2026
Deep-learning predictions of biomolecular structures : persistent limitations and new horizons extended by explicit ion addition www.biorxiv.org/content/10.64898/20…
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Mickaël Correia @mickacorreia.bsky.social · 26/07/2026
Je repense à cette Une du Figaro Magazine de mai 2026.
Une du Figaro Magazine : "Lanceurs d'alerte ou faux prophète ? Enquête sur les écolo-alarmistes".
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Marc Somssich @somssich.bsky.social · 21/02/2024
Ok, so #ExpansionMicroscopy has now reached the #PlantScience field 🔬🌾 Preprints from two labs out today on @biorxiv-plants.bsky.social #1, Magali S. Grison et al. bsky.app/profile/soms... #2: Michelle Gallei, Sven Truckenbrodt, et al. bsky.app/profile/soms... #PlantMicroscopy #PlantCellBiology
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Dr. Jules Marien @marienj.bsky.social · 24/07/2026
New publication with Chantal Prévost and @sacquin-mo.eurosky.social is out in JPCB ! We show with all-atom MD simulations that disordered alpha-tubulin C-terminal tails wrap around the proline-rich region of the Tau protein, but not so much around its repeat domains pubs.acs.org/doi/10.1021/...
pubs.acs.org
Simulations of an Extended Tau/Tubulins Interface Reveal a Complex Disorder–Disorder Interplay Mediated by the C-Terminal Tails
Building on a complex between a tubulin protofilament (PF) and a fragment of the Tau protein containing residues 169 to 367, we investigate the dynamics of the disordered elements of the system, namely the tubulin C-terminal tails (CTTs) and the Tau protein, using classical all-atom molecular dynamics simulations. Our results show that CTTs adopt a hook-like dynamic pattern on the bare PF while remaining highly mobile. The binding of Tau on the PF surface alters the dynamics of the αI-CTTs in a sequence-dependent manner. While the repeat domains of Tau are mostly maintained on the PF by weak and strong binding patches with the tubulin cores, the Proline-Rich Region (PRR) relies on the wrapping phenomenon of αI-CTTs to fuzzily stabilize its interaction with the PF. Our study thus provides a deep dive into the dynamic interplay between the Tau protein and the CTTs of microtubules, the latter being characterized extensively using a variety of disorder-adapted metrics.
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Emily M. Bender @emilymbender.bsky.social · 21/07/2026
This is very well done, I think: leidendeclaration.ai A few choice quotes, that should be of interest well beyond mathematics: >>
leidendeclaration.ai
Leiden Declaration on Artificial Intelligence and Mathematics
This declaration calls for action to address the challenges posed by the use of artificial intelligence within mathematics research.
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Timnit Gebru @timnitgebru.blacksky.app · 21/07/2026
Weeks ago, @chanda.blacksky.app sent me this declaration, written and signed by a bunch of mathematicians. But I only had time to read it yesterday, which ended up being right on time given a new round of hype falling exactly under the patterns this document notes.🧵 leidendeclaration.ai
leidendeclaration.ai
Leiden Declaration on Artificial Intelligence and Mathematics
This declaration calls for action to address the challenges posed by the use of artificial intelligence within mathematics research.
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Extreme Temperatures Around the World @extremetemps.bsky.social · 19/07/2026
50 AGAIN IN CENTRAL ASIA ! 🇹🇲 50.0 Bagtiyarlyk 48.6 Kerki 47.8 Turkmenbat 46.2 BurdalykM 🇰🇿 49 Konyrolen 48.9 Arys 48.5 Shardara 46.5 ToleBi 45.2 Shkymkent 44.5 Bakanas 🇰🇬 44.6 Jhagy Jer NATIONAL RECORD AGAIN 43.5 Bishkek 40.1 Talas 🇹🇯 43.8 DushanbeM 42.5 Pendzhikent 🇺🇿 43.9 Dzizak 43.6 Samarkhand
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Mara Wilson @marawilson.bsky.social · 18/07/2026
Thinking about how so many people I know said Don’t Look Up was so stupid and over the top and ridiculous but my environmental scientist brother was like “Nope, that’s exactly how it feels”
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Maëlle Fouquenet @fouquenet.eurosky.social · 15/07/2026
Jusqu'à dimanche inclus, répondez à notre enquête sur les usages et besoins de l'IA dans les TPE et PME. On a besoin des points de vue des salarié•es, représentant·es des syndicats et/ou du personnel, c'est rapide et anonyme forms.fillout.com/t/jeREW6XcFhus #IA #TPE #PME
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Structural Biology and Chemistry Dpt - Institut Pasteur @ipdbsc.bsky.social · 15/07/2026
Job Opportunity: #CNRS Chemistry - #InstitutPasteur Mid-Career Group Leader (Chemistry for Health) is open in Paris, France. This is a fantastic opportunity for a standout chemist to establish themselves in a world-class environment. research.pasteur.fr/en/call/mid-...
research.pasteur.fr
Mid-career Group Leader position in Chemistry for Health at Institut Pasteur, Paris - Research
Institut Pasteur and the CNRS are launching a joint call for a mid-career group leader position in Medicinal Chemistry and Chemistry for Health. We are looking for an experienced researcher (typically...
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Volker Lipka @volkerlipka.bsky.social · 14/07/2026
We are currently recruiting an Independent Junior Research Group Leader in the field of biotic and/or abiotic stress biology in plants at the University of Göttingen (starting in January 2027). www.uni-goettingen.de/de/644546.ht... Best, Salma Balazadeh & Volker Lipka
uni-goettingen.de
Stellenanzeigen - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
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Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 13/07/2026
If you have a background in #philosophy with relevant modeling skills, or a master's in climate science with interest in #philsci, consider applying to this PhD vacancy (@clpskuleuven.bsky.social)! Sylvia Wenmackers is an excellent mentor and one of the brightest & kindest scholars I know! #philsky
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Baptiste Coulmont @coulmont.bsky.social · 14/07/2026
Un contrat post-doctoral sciencespo-career.talent-soft.com/Pages/Offre/... "réaliser une enquête qualitative sur les pratiques éditoriales d’anonymisation ou de recueil des consentements dans la publication d’articles de revues de sciences sociales"
sciencespo-career.talent-soft.com
SCIENCES PO - Chercheur ou Chercheuse H/F
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Palais de la découverte @palais-decouverte.fr · 10/07/2026
❓️Selon Paracelse, tout est poison, seule la dose importe. Comment la pharmacie a-t-elle pu utiliser les pires toxines pour soigner ? 𝐏𝐨𝐢𝐬𝐨𝐧𝐬 : 𝐝𝐮 𝐯𝐞𝐧𝐢𝐧 𝐚𝐮 𝐦𝐞́𝐝𝐢𝐜𝐚𝐦𝐞𝐧𝐭 à 14h20 aux Étincelles. Un exposé de Biologie pour un public 12 ans et + billetterie-etincelles.palais-decouverte.fr/etincelles.h...
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Djamé 🟥 @zehavoc.bsky.social · 09/07/2026
Super urgent, I'm desperately trying to find two emergency reviewers for Neurips on a super interesting paper that study how LLM alignements evaluation depends on many different geopolitical factors. Seriously, I've been trying for a week, no one answered.
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Ralf Reski @reskilab.bsky.social · 09/07/2026
Professorship Plant Biochemistry. Bielefeld, Germany. #plantscijobs #plantscijob #plantsciencejob www.uni-bielefeld.de/uni/karriere...
uni-bielefeld.de
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