#biorxiv — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #biorxiv, aggregated by home.social.
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🎉New preprint out today! We present rastair - an ultra-fast SNP and methylation caller for TAPS or 5-Base data. Rastair takes less than 1h to process e.g. a 50x 5-Base dataset, yet SNP call accuracy is nearly identical to GATK on WGS data 🔥
https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1
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PreprintToPaper dataset: connecting bioRxiv preprints with journal publications
#BiomedicalResearch #bioRxiv #ResearchData #ScientificCommunication
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Circlesquare: juggling DOIs when preprinting
https://quantixed.org/2026/02/17/circlesquare-juggling-dois-when-preprinting/
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Circlesquare: juggling DOIs when preprinting
https://quantixed.org/2026/02/17/circlesquare-juggling-dois-when-preprinting/
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My first #vibecoding applications. In my research life I struggle with keeping up with the literature and organizing my lab notebook.
I made a customizable automated literature search tool that performs weekly searches of #pubmed and #biorxiv then uses Claude to summarize and give a priority ranking based on my current #research
Also built an experiment management system to keep me on track and my data organized
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Otro pequeño orgullo de nuestro laboratorio del #iibce ya está en @biorxiv_neursci .
Un importante volumen de trabajo sobre las conexinas en la reparación de la médula espinal.
Gran equipo #MadeInUruguay lo hizo posible, gracias a financiación extranjera de #WingsForLife.#neuroscience #neuromastodon #medulaeespinal #conexinas #neurociencia #biology #biologia #investigacion #ciencia #Uruguay #spinalcordinjury #spinalcord #research #pedeciba @SocNeuroUy #preprint #biorxiv
https://www.biorxiv.org/content/10.64898/2026.01.16.699895v1.full.pdf+html
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Thank you #biorxiv staff for processing the pre-prints so quickly and nicely. Our latest manuscript addresses a rather specialized, albeit important, question in mRNA degradation in yeast. To what extent the Lsm1-7/Pat1 complex is involved in the degradation of mRNA by decapping activation ? By using a degron strain allowing rapid depletion of Lsm1, we find a slight impact of the complex on decapping, including changes in #NMD substrate levels.
https://www.biorxiv.org/content/10.64898/2025.12.17.694855v1
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#OpenRxiv just added an #AI #PeerReview feature for #preprints on #bioRxiv and #medRxiv. At the moment, they're using the #qedscience tool.
https://www.nature.com/articles/d41586-025-03909-5The bioRxiv announcement makes clear that AI review is optional for authors and that authors might be able to choose from other AI tools in the future.
https://connect.biorxiv.org/news/2025/11/04/qed_review_toolPS: My experiments lead me to think that AI isn't good enough to do peer review yet -- even if (1) it's getting better, (2) it can already help human reviewers, and (3) many human reviewers are worse. Journals that allow it too large a role are abdicating their responsibility and might be deceiving authors and readers. Referees who give it too large a role are abdicating their responsibility and might be deceiving journals, authors, and readers. If you lean in the same direction, let me suggest that these objections don't carry over to preprint servers making AI review an #FWIW option for authors. This kind of AI review doesn't pretend to be more than it is. When it happens, it's a voluntary decision by authors. Of course authors could have gotten AI feedback on their own, with the AI tools of their choice, and without the preprint-server mediation. But giving them another option for the same kind of feedback is harmless and convenient. Moreover, it creates a training ground to monitor the quality and improvement of the AI tools.
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Still doing #neuroscience.
Our #orbitofrontalcortex (#OFC) paper published in _Neuron_ today. (Also available in #biorxiv.)
Paul Cunningham, A. David Redish (2025) Opposing, multiplexed information in lateral and ventral orbitofrontal cortex guides sequential foraging decisions in rats Neuron.
https://www.cell.com/neuron/abstract/S0896-6273(25)00467-2
Key insights:
1. VO and LO are doing opposite things: LO is about immediate value, while VO is about opportunity costs.
2. OFC neurons are representing both task state (through which neurons are active) and value (as the total activity).
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Semantic search engine for ArXiv, biorxiv and medrxiv
#HackerNews #SemanticSearch #ArXiv #Biorxiv #Medrxiv #ResearchTools
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Vielleicht fragt ihr euch: Wie erkennen wir den Tumor z. B. in der IF-Aufnahme? Antwort: Über die Zelldichte – Tumorbereiche sind oft dichter gepackt, die Zellkerne liegen enger beieinander. #Histologie #H&E #CancerModels #Assembloids #Neuroonkologie #bioRxiv
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In the updated license selector, the most open Creative Commons licenses appear first, with refreshed accessible language for each license that centers the researcher and their choices. Thanks to the Chan Zuckerberg Initiative for supporting these efforts.
#OpenScience #Preprints #CreativeCommons #bioRxiv #medRxiv #OpenAccess #Research #openRxiv
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Prépublications en sciences de la vie et de la santé : #bioRxiv et #medRxiv lancent #openRxiv une organisation indépendante à but non lucratif chargée de leur gouvernance
#Preprints #OpenAccess -
#Preprint sites #bioRxiv and #medRxiv launch new era of independence
The popular repositories, where life #scientists post research before #peerreview, will be managed by a new organization called #openRxiv.
Until now, they had been managed by Cold Spring Harbor Laboratory. The new organization, named openRxiv, will have a board of directors and a scientific and medical advisory board. It is supported by a fresh US$16M grant from Chan Zuckerberg Initiative (CZI).
https://www.nature.com/articles/d41586-025-00762-4 -
Bueno...
:googlefire: :googlefire: :googlefire: acaba de salir publicado el primer artículo del doctorado PEDECIBA de Cristina Parada.
Un pequeño paso para esta científica, pero un gran paso para su posgrado!https://onlinelibrary.wiley.com/doi/10.1002/arch.70048
#paywall mediante, pero está abierto en #biorxiv
#uruguay #ciencia #desarrollo #biologia #insectos #genetica #posgrado #pedeciba
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Everything is worrying at the moment but something I am wondering is if we should worry about the scientific publishers. Elsevier, Nature, #PLoS, maybe even #BiorXiv and others - is it possible that the US government forces them to either stop publishing, delete some or all of their published papers, or only accept papers that correspond to specific criteria?
Edited because I thought most of these were US-based but they are not.
Please tell me there is nothing to worry about on that front at least..
#Academia #Science #AcademicPublishing -
Precisely, the STEM community got it right with #arxiV , time for the rest of us to get on board with #medrxiV and #biorxiV. This will also save a lot of money from frivolous publication activities that only enrich the publishers but deprive everyone else of the benefits of publicly funded research
RE: https://bsky.app/profile/did:plc:7t2iueljk2bzxf6d2rcdhg7r/post/3licpt7lurs2q -
Our new #preprint on #ThreePhoton in vivo #imaging of #neurons and #glia 🔬 in the medial prefrontal cortex (#mPFC) 🧠 with sub-cellular resolution 🔍 is out! Check it out on #biorxiv:
🌍 https://www.biorxiv.org/content/10.1101/2024.08.28.610026v1
#Neuroscience #multiphoton #3p vs. #2p #twophoton #hippocampus #drosophila #MouseModel #DeepImaging #preprintalert #DZNE @dzne
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Our new #preprint on #ThreePhoton in vivo #imaging of #neurons and #glia 🔬 in the medial prefrontal cortex (#mPFC) 🧠 with sub-cellular resolution 🔍 is out! Check it out on #biorxiv:
🌍 https://www.biorxiv.org/content/10.1101/2024.08.28.610026v1
#Neuroscience #multiphoton #3p vs. #2p #twophoton #hippocampus #drosophila #MouseModel #DeepImaging #preprintalert #DZNE @dzne
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Our new #preprint on #ThreePhoton in vivo #imaging of #neurons and #glia 🔬 in the medial prefrontal cortex (#mPFC) 🧠 with sub-cellular resolution 🔍 is out! Check it out on #biorxiv:
🌍 https://www.biorxiv.org/content/10.1101/2024.08.28.610026v1
#Neuroscience #multiphoton #3p vs. #2p #twophoton #hippocampus #drosophila #MouseModel #DeepImaging #preprintalert #DZNE @dzne
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Our new #preprint on #ThreePhoton in vivo #imaging of #neurons and #glia 🔬 in the medial prefrontal cortex (#mPFC) 🧠 with sub-cellular resolution 🔍 is out! Check it out on #biorxiv:
🌍 https://www.biorxiv.org/content/10.1101/2024.08.28.610026v1
#Neuroscience #multiphoton #3p vs. #2p #twophoton #hippocampus #drosophila #MouseModel #DeepImaging #preprintalert #DZNE @dzne
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Our new #preprint on #ThreePhoton in vivo #imaging of #neurons and #glia 🔬 in the medial prefrontal cortex (#mPFC) 🧠 with sub-cellular resolution 🔍 is out! Check it out on #biorxiv:
🌍 https://www.biorxiv.org/content/10.1101/2024.08.28.610026v1
#Neuroscience #multiphoton #3p vs. #2p #twophoton #hippocampus #drosophila #MouseModel #DeepImaging #preprintalert #DZNE @dzne
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Bit late posting this here: Out now on #biorxiv: our grad student Katie took a deep dive into how different #IDRs affect the behaviour of #CBP #condensates in the nucleus. https://www.biorxiv.org/content/10.1101/2024.06.04.597392v2
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Updated #bioRxiv preprint:
Comparing representations of planning and habit in #hippocampus, #PrefrontalCortex, and dorsolateral #striatum as rats navigate complex and simple environments.
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Updated #bioRxiv preprint:
Comparing representations of planning and habit in #hippocampus, #PrefrontalCortex, and dorsolateral #striatum as rats navigate complex and simple environments.
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Updated #bioRxiv preprint:
Comparing representations of planning and habit in #hippocampus, #PrefrontalCortex, and dorsolateral #striatum as rats navigate complex and simple environments.
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Updated #bioRxiv preprint:
Comparing representations of planning and habit in #hippocampus, #PrefrontalCortex, and dorsolateral #striatum as rats navigate complex and simple environments.
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Updated #bioRxiv preprint:
Comparing representations of planning and habit in #hippocampus, #PrefrontalCortex, and dorsolateral #striatum as rats navigate complex and simple environments.
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Looking forward to spending some time with this new #biorxiv #preprint "Causal inference with observational data and unobserved confounding variables," by Jarrett Byrnes and Laura Dee. It looks like an very useful work-through of practical issues in applying modern causal techniques to the kind of study design issues ecologists deal with.
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The #COAR (@coar_ev) #Notify project has created exciting new levels of #interoperability between #OpenAccess #preprint #repositories and other pieces of #OpenInfrastructure.
https://www.coar-repositories.org/news-updates/whats-new-with-coar-notify/Notify now supports:
* One-click requests for peer review (from #Prereview, @prereview) for #preprints in #bioRxiv (@biorxivpreprint) and #SciELO (@redescielo)
* One-click submissions to OA journals (from #Episciences, @episciences) for preprints in #HAL (@hal_fr)
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Talking about #arXiv #bioRxiv, one weakness is that there is no "flag" to indicate whether PDF is a #preprint or the post- #peerReview #postprint. I am surprised at the lack of attention on this.
Although I have my reservations on the quality of #peerReviewing in general, I believe it should be a point of attention of an institutional archive to make sure the file is post-peer review, or, if that version is under paywall only (which is a problem), state it at least.
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bioRxiv just turned 10 years old and medRxiv is now 4! 🎉 If you are a preprint reader and/or author, please fill out the bioRxiv & medRxiv survey now!
https://bit.ly/biomedrxivsurvey
Deadline: December 10th, 11:59 PM EST
Length: 15-20 mins
Thank you!
#biorxiv #medrxiv #preprints -
bioRxiv is almost 10 years old and medRxiv just turned 4! 🎉 Tell us how we’ve done so far & how to keep improving by answering the bioRxiv & medRxiv survey!
Deadline: December 10th, 11:59 PM EST
Length: 15-20 mins
Thank you!
🔗 https://bit.ly/biomedrxivsurvey
#biorxivmedrxivsurvey #biorxiv #medrxiv #preprints -
@steveroyle Done!
IMHO it would be nice if @biorxivpreprint and @medrxivpreprint would accept theoretical / conceptual preprints (as far as I know they are rejected on screening, unless it changed recently). So I made that suggestion on the survey.#biorxiv #medrxiv #biology #science #research #academicchater
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The bioRxiv/medRxiv crew are running a survey to understand how the community uses these preprint servers. If you have a few minutes to spare:
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New #preprint on “#Engram cell connectivity as a mechanism for #InformationEncoding and #memory function” by Clara Ortega-de San Luis et al.: https://doi.org/10.1101/2023.09.21.558774
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Cadherins differentiate between two populations of L5 projection neurons, are instrumental in organizing perisomatic inhibition by PV-Basket vs CCK-Basket cells. Fits well with the "cadherins = neuronal barcoding" hypothesis.
Cadherins orchestrate specific patterns of perisomatic inhibition onto distinct pyramidal cell populations
Jezequel et al., #preprint at #biorxiv 2023
https://www.biorxiv.org/content/10.1101/2023.09.28.559922v1 -
A new #preprint #OpenScience #PeerReview by @PCIEvolBiol: Florian Benitiere, Anamaria Necsulea, Laurent Duret (2023) Random genetic drift sets an upper limit on mRNA splicing accuracy in #metazoans. #biorxiv, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology https://doi.org/10.1101/2022.12.09.519597 🔽
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Clearly, there is still much to learn about this corner of the dark genome defined by HEATR5 proteins and their co-factors.
#Biorxiv #Preprint #MembraneTraffic #DarkGenome #DarkProteome #RareDisease #AlphaFold #AlphaFold2 #ProteinPrediction #Golgi #Clathrin #CellBiology #biochemistry #Bioscience
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A new #preprint #OpenScience #PeerReview by @PCI_forestWSci: Laurent Bouffier, Sandrine Debille, Pierre Alazard, Annie Raffin, Patrick Pastuszka, Jean-François Trontin (2023) #Pollen contamination and mating structure in #maritimepine (Pinus pinaster Ait.) clonal seed orchards revealed by #SNPmarkers. #bioRxiv https://doi.org/10.1101/2022.09.27.509769 🔽
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Ever wondered why your #TRIS-buffered solutions turn turbid on the shelf so quickly? Look no further, it’s #pseudomonas. new study from our lab out as a preprint describing a complete TRIS degradation pathway in #bacteria https://www.biorxiv.org/content/10.1101/2023.08.01.551466v1.abstract?%3Fcollection= #microbiology #HGT #biorxiv
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Ever wondered why your #TRIS-buffered solutions turn turbid on the shelf so quickly? Look no further, it’s #pseudomonas. new study from our lab out as a preprint describing a complete TRIS degradation pathway in #bacteria https://www.biorxiv.org/content/10.1101/2023.08.01.551466v1.abstract?%3Fcollection= #microbiology #HGT #biorxiv
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Ever wondered why your #TRIS-buffered solutions turn turbid on the shelf so quickly? Look no further, it’s #pseudomonas. new study from our lab out as a preprint describing a complete TRIS degradation pathway in #bacteria https://www.biorxiv.org/content/10.1101/2023.08.01.551466v1.abstract?%3Fcollection= #microbiology #HGT #biorxiv
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Ever wondered why your #TRIS-buffered solutions turn turbid on the shelf so quickly? Look no further, it’s #pseudomonas. new study from our lab out as a preprint describing a complete TRIS degradation pathway in #bacteria https://www.biorxiv.org/content/10.1101/2023.08.01.551466v1.abstract?%3Fcollection= #microbiology #HGT #biorxiv
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Ever wondered why your #TRIS-buffered solutions turn turbid on the shelf so quickly? Look no further, it’s #pseudomonas. new study from our lab out as a preprint describing a complete TRIS degradation pathway in #bacteria https://www.biorxiv.org/content/10.1101/2023.08.01.551466v1.abstract?%3Fcollection= #microbiology #HGT #biorxiv
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Our work on fragment ion intensity prediction for the analysis of timsTOF #immunopeptidomics data is now online on #bioRxiv: https://www.biorxiv.org/content/10.1101/2023.07.17.549401v1
Check out this great effort by Charlotte Adams, who basically learned #DeepLearning/#MachineLearning from scratch for this project.
Thread. 👇
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" Instead, #Hepatoblastoma #tumors contain a large suppressive #myeloid compartment which poses opportunities for targeting. Specifically, therapeutic antibodies
targeting the #tumor antigen #GPC3 to induce ADCP by #macrophages, in combination with myeloid
#ImmuneCheckpointBlockade (#CD47/SIRPa, or VISTA) could be a feasible strategy to explore in future studies"Krijgsman et al. from Vercoulen lab in the #UMCUtrecht, on #bioRXiv:
https://www.biorxiv.org/content/10.1101/2023.06.28.546852v1 -
A new #preprint #OpenScience #PeerReview by @PCIgenomics: G. Aubert et al. #SNP discovery by #exome capture and resequencing in a #pea genetic resource collection. #bioRxiv https://doi.org/10.1101/2022.08.03.502586 🔽
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A new #preprint #OpenScience #PeerReview by @PCIgenomics: G. Aubert et al. #SNP discovery by #exome capture and resequencing in a #pea genetic resource collection. #bioRxiv https://doi.org/10.1101/2022.08.03.502586 🔽
