Redish Lab2d ago

We're still doing science! New preprint dropped: *Hippocampal representations differentiate reactive and anticipatory responses during foraging under threat* (Damphousse et al. bioRxiv).

*** Fleeing from a predator is represented fundamentally differently than retreat from anxiety about that predator.

On our "run the gauntlet" version of the "robogator" task, the dorsal hippocampus represents the attack (behind it as it flees) more during retreat from an actual attack than when it retreats from an anxiety-related pause (no actual attack).

*** Note that this means representation during theta can be about the thing behind the rat that it is running from, not just goals ahead of it.

We also found that when rats pause (presumably out of anxious concern about being attacked), aborting the journey (mid-track aborts) represented the attack more than continuing the journey (mid-track continue on).

https://www.biorxiv.org/content/10.64898/2026.04.17.719234v1.full.pdf+html

#neuroscience #bioRxiv

Bérénice A. Benayoun, PhDApr 11
🚨 New lab preprint alert! 🚨 A study 6 years in the making, made possible by @[email protected] support : "A multi-omic atlas in the African turquoise killifish reveals increased glucocorticoid signaling as a hallmark of brain aging" now on #biorXiv: www.biorxiv.org/content/10.6... A 🧵 1/11 🧪🖥️🧬
Benjamin S-B Mar 24

🎉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

#biorxiv #epigenetics #bioinformatics #science #preprint

Rastair: an integrated variant and methylation caller

Cytosine methylation is a crucial epigenetic mark that impact tissue-specific chromatin conformation and gene expression. For many years, bisulfite sequencing (BS-seq), which converts all non-methylated cytosine (C) to thymine (T), remained the only approach to measure cytosine methylation at base resolution. Recently, however, several new methods that convert only methylated cytosines to thymine (mC→T) have become widely available. Here we present rastair, an integrated software toolkit for simultaneous SNP detection and methylation calling from mC→T sequencing data such as those created with Watchmaker's TAPS+ and Illumina's 5-Base chemistries. Rastair combines machine-learning-based variant detection with genotype-aware methylation estimation. Using NA12878 benchmark datasets, we show that rastair outperforms existing methylation-aware SNP callers and achieves F1 scores exceeding 0.99 for datasets above 30x depth, matching the accuracy of state-of-the-art tools run on whole-genome sequencing data. At the same time, rastair is significantly faster than other genetic variant callers, processing a 30x depth file takes less than 30 minutes given 32 CPU cores on an Intel Xeon, and half as long when a GPU is available. By integrating genotyping with methylation calling, rastair reports an additional 500,000 positions in NA12878 where a SNP turns a non-CpG reference position into a "de-novo" CpG. Vice-versa, rastair also identifies positions where a variant disrupts a CpG and corrects their reported methylation levels. Rastair produces standard-compliant outputs in vcf, bam and bed formats, facilitating integration into downstream analyses pipelines. Rastair is open-source and available via conda, Dockerhub, and as pre-compiled binaries from https://www.rastair.com. ### Competing Interest Statement Pascal Hertleif is a employee and owner of Softleif AB, a software development company. All other authors declare no competing financial interests. Ludwig Institute For Cancer Research

bioRxiv
Geert AartsMar 17

Did you know bioRxiv, thé preprint server for biology requires "submissions to be associated with an organization that can provide oversight of research activities"? So if you lost your job as scientist because your research institute has been dismantled by the government since it doesn't fit with its political agenda, you can no longer place preprints on bioRxiv?

#openscience #openaccess #OpenAccess #science #biorxiv @biorxivpreprint

Infodoc MicroVeilleMar 2

PreprintToPaper dataset: connecting bioRxiv preprints with journal publications

https://microblogging.infodocs.eu/2026/03/02/preprinttopaper-dataset-connecting-biorxiv-preprints-with-journal-publications/

#BiomedicalResearch #bioRxiv #ResearchData #ScientificCommunication

PreprintToPaper dataset: connecting bioRxiv preprints with journal publications – InfoDoc MicroVeille

Stephen RoyleFeb 17

Circlesquare: juggling DOIs when preprinting

https://quantixed.org/2026/02/17/circlesquare-juggling-dois-when-preprinting/

#computing #publishing #bioRxiv #DOI #github #zenodo

Circlesquare: juggling DOIs when preprinting – quantixed

HazletokJan 25

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

Thanks for the inspiration @kevin and @Casey

https://hazletonlab.com/software.html

Software - Hazleton Lab | Research Tools

Open-source research software tools developed by the Hazleton Lab, including automated literature monitoring, lab data management, and paper management systems.

Daniel PrietoJan 20

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.

@constanzasilvera

#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

Show threadJocelyn EtienneJan 5

@jonmsterling

They explain that there are simply too many ultra-low quality reviews posted.

#bioRxiv has not been accepting to archive reviews for years already (at least since 2017). Their FAQ says it's irrelevant as #preprint because they're not novel in themselves, but I believe part of the reason is also that there's a flooding of dodgy reviews.

#arXiv

https://www.nature.com/articles/d41586-025-03664-7

https://web.archive.org/web/20170419045045/https://www.biorxiv.org/about/FAQ

Preprint site arXiv is banning computer-science reviews: here’s why

The repository is taking steps to tackle a surge in low quality, AI-generated content.

Cosmin SaveanuDec 19

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

#RNA #decapping