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Dani León-Periñán

@danilexn.bsky.social
561 followers 661 following 100 posts

Cells talk; I build tools to listen to them @mdc-berlin.bsky.social Computational biologist • Occasional composer and pianist • he/him Opinions are my own.

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Dani León-Periñán @danilexn.bsky.social · 28/09/2026
Reading fully-AI-generated manuscripts is extremely frustrating.
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Dani León-Periñán @danilexn.bsky.social · 26/08/2026
Under the hood, Malva is a k-mer method. In the last years, this field has seen lots of *great* ideas and applications, and we are happy to contribute a small part to this. You can find out all details in the paper!
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Dani León-Periñán @danilexn.bsky.social · 26/08/2026
Malva out in Nature! 🚀 RNA sequences make cells different from each other. Single-cell data captures much of this, but most stays in the dark because we reduce it to gene counts. We introduce Malva to make the world's single-cell data searchable. What took days is now one query in seconds.
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Dani León-Periñán @danilexn.bsky.social · 27/02/2026
This is such an exciting project, join us!
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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026
🚀 We're looking for people to join Malva! 🧬 @danilexn.bsky.social Malva is the first search engine for single-cell genomics: we process massive amounts of sequencing data to enable ultrafast analysis of millions of cells. (1/4)
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Nature Methods @natmethods.nature.com · 14/01/2026
SpatialZ generates virtual single-cell transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues. www.nature.com/articles/s41...
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Damian Carrington @dpcarrington.bsky.social · 13/01/2026
‘A bombshell’: doubt cast on discoveries of #microplastics throughout human body, from brain to blood, arteries to testes Exclusive: Some scientists say many detections are most likely error, with one high-profile study called a ‘joke’ Story by me www.theguardian.com/environment/...
theguardian.com
‘A bombshell’: doubt cast on discovery of microplastics throughout human body
Exclusive: Some scientists say many detections are most likely error, with one high-profile study called a ‘joke’
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Martin Pacesa @martinpacesa.bsky.social · 26/12/2025
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
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Kris Willis @kawillis.bsky.social · 18/12/2025
Today is a big day. After many years of work, I’m excited to finally share a paper describing a novel approach to identifying potential breakthroughs in biomedical research, up to twelve years before the breakthrough itself occurs. 1/15
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Bioinformatics Advances @bioinfoadv.bsky.social · 05/12/2025
🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)”  Full article available: doi.org/10.1093/bioadv/vbaf290  Authors include: @pavelvesely.bsky.social, @brinda.eu
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Nature Biotechnology @natbiotech.nature.com · 28/10/2025
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - @distefanolab.bsky.social @brumbaugh-lab.bsky.social go.nature.com/3X215du
go.nature.com
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
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Dani León-Periñán @danilexn.bsky.social · 06/11/2025
This is pure bullshit. You don’t need to run 200 LLM agents for >8 hours to do DE, GSEA and generate a couple of heatmaps. And if you do, just spend 2 weeks learning bioinformatics and you won’t need to give money to a company selling snake oil. arxiv.org/pdf/2511.02824
arxiv.org
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Champi @jpascualanaya.bsky.social · 30/10/2025
🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch! 📅 Starting date early 2026, with some flexibility. 🙏Please, RT!
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Dani León-Periñán @danilexn.bsky.social · 21/10/2025
My humble advice to 10X: Why don’t you invest a bit more on R&D and a little bit less on legal? www.genomeweb.com/business-new...
genomeweb.com
10x Genomics to Sue Illumina Alleging Infringement of Single-Cell, Spatial Patents
The lawsuits are the latest IP battle for 10x, which has sued just about every competitor it has faced in both the single-cell and spatial transcriptomics markets.
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Sam Gershman @gershbrain.bsky.social · 15/10/2025
When I was an undergrad, I saw a talk by Oliver Sacks about music. During the Q&A, someone asked Sacks if he thought science would reveal the deepest mysteries of art. Sacks (a rare humanist among scientists) said that he doubted it, at which Eric Kandel (the host) leaped up and grabbed the mic.
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Dr. Jean Fan @jef.works · 13/10/2025
What is RNA velocity in situ? ChatGPT kept getting it wrong... So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0 #AcademicSky
youtu.be
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
YouTube video by Prof. Jean Fan
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Robert Aboukhalil @robert.bio · 09/10/2025
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
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Camille Marchet ⚡ @camillemrcht.bsky.social · 09/10/2025
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ? www.nature.com/articles/d41...
nature.com
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
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Sheila Teves @sheilateves.bsky.social · 07/10/2025
How does a “universal” transcription factor evolve to do species-specific jobs? Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes. Read it here 👉 www.biorxiv.org/content/10.1... #MolecularEvolution #Transcription
biorxiv.org
Molecular determinants underlying functional divergence of TBP homologs
The TATA-box binding protein (TBP) is a highly conserved basal transcription factor and a core component of the pre-initiation complex (PIC) for all three eukaryotic RNA polymerases (RNA Pols). Despit...
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Dr. Damien P. Williams, dread portent down from a mountain cave @wolven.blacksky.app · 05/10/2025
Preliminary results show that the current framework of "AI" makes ppl less likely to help or seek help from other humans, or to seek to soothe conflict, and that people actively prefer that framework to any others, literally serving to make them more dependent on it.
arxiv.org
Sycophantic AI Decreases Prosocial Intentions and Promotes Dependence
Both the general public and academic communities have raised concerns about sycophancy, the phenomenon of artificial intelligence (AI) excessively agreeing with or flattering users. Yet, beyond isolat...
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Dani León-Periñán @danilexn.bsky.social · 05/10/2025
Israel is a terrorist state.
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Dani León-Periñán @danilexn.bsky.social · 01/10/2025
SQLite que no pase hambre
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Merriam-Webster @merriam-webster.com · 01/10/2025
We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
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Paul Medvedev @pashadag.bsky.social · 12/06/2025
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
tinyurl.com
Dropbox
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EL PAÍS @elpais.com · 26/09/2025
🔴 ÚLTIMA HORA | La mayoría de los países abandonan la Asamblea General de la ONU a la llegada de Netanyahu social.elpais.com/njzv3
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Dani León-Periñán @danilexn.bsky.social · 26/09/2025
Mr. Big Ears said at the UN today, “Thanks to the efforts of our intelligence service, this message is being streamed to every Gazan’s phone.”
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)
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Dani León-Periñán @danilexn.bsky.social · 22/09/2025
IMSLP (imslp.org; the biggest public library for classical music) generated >4 TB of data over the last 20 years. Open-ST (rajewsky-lab.github.io/openst) can generate that from a 1x3x4 mm piece of human tissue in two days.
imslp.org
IMSLP: Free Sheet Music PDF Download
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 13/09/2025
How come different people giving the same prompt to ChatGPT get different answers? A new article from ThinkingMachines explains why LLMs are nondeterministic, and it largely comes down to how parallelization and precision are handled. 🧵
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Dani León-Periñán @danilexn.bsky.social · 08/09/2025
elpais.com/espana/2025-...
elpais.com
Sánchez anuncia un decreto para legalizar el embargo total de armas a Israel y habla por primera vez de “genocidio” de los palestinos
España llama a consultas a su embajadora en Israel tras prohibir Netanyahu la entrada en el país de las ministras Yolanda Díaz y Sira Rego
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Proceedings of the National Academy of Sciences @pnas.org · 28/08/2025
A machine learning model can sort people with myalgic encephalomyelitis/chronic fatigue syndrome from healthy controls with 77% accuracy by sequencing the cell-free RNA in their plasma, suggesting a test for the condition may be on the horizon. In PNAS: www.pnas.org/doi/10.1073/...
Biological pathway analysis of myalgic encephalomyelitis/chronic fatigue syndrome. Heatmap of activated (blue) and inhibited (red) pathway marker genes for the selected pathways (n = 69 genes).
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Eric Topol @erictopol.bsky.social · 28/08/2025
This is how generative A.I. could be used to design far better, more potent mRNAs (linear and circular) for the future for genome editing, engineered T cells, cancer therapy, vaccines www.science.org/doi/10.1126/... @science.org
science.org
Deep generative models design mRNA sequences with enhanced translational capacity and stability
Despite the success of mRNA COVID-19 vaccines, extending this modality to more diseases necessitates substantial enhancements. We present GEMORNA, a generative RNA model that utilizes Transformer arch...
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bioRxivpreprint @biorxivpreprint.bsky.social · 28/08/2025
Adding layers of information to scRNA-seq data using pre-trained language models www.biorxiv.org/content/10.1101/202…
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Manuel Álvarez @manuelalvarez.bsky.social · 25/08/2025
el futuro está siendo lo que siempre soñé que sería: que al buscar algo en google te salga arriba del todo una puta chorrada de mierda de los cojones.
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The Matter Lab @thematterlab.bsky.social · 21/08/2025
We're excited to present our latest article in Nature Machine Intelligence - Boosting the predictive power of protein representations with a corpus of text annotations. Link: www.nature.com/articles/s42... [1/4]
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/08/2025
SpatialFinder: A Human-in-the-Loop Vision-Language Framework for Prioritizing High-Value Regions in Spatial Transcriptomics www.biorxiv.org/content/10.1101/202…
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Nature Biotechnology @natbiotech.nature.com · 22/08/2025
Stereo-cell is a DNA nanoball array-based method that enables scalable, spatially resolved single-cell sequencing across diverse cell types and sizes with multimodal integration capabilities. #NBThighlight www.science.org/doi/10.1126/...
science.org
Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arrays
Single-cell sequencing technologies have advanced our understanding of cellular heterogeneity and biological complexity. However, existing methods face limitations in throughput, capture uniformity, c...
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Lucien Hinderling @lhinderling.bsky.social · 21/08/2025
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
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AI x Bio Discovery @aixbiobot.bsky.social · 20/08/2025
Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learning [new] AI maps 3D genes from 2D data. Modeling enables isotropic resolution, revealing gradients.
Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learningFigure 2Figure 4
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bioRxiv Pathology @biorxiv-pathology.bsky.social · 16/08/2025
Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS) www.biorxiv.org/content/10.1101/202…
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Greg Gloor @ggloor.bsky.social · 14/08/2025
for the love of all that you hold dear, no. A lot of bioinformatics is already blind plug-in play and making this easier is just going to lead to even shittier analysis.
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Jamie Heather @jamieheather.bsky.social · 14/08/2025
My generation had to deal with datasets where Excel had autocorrected gene names to dates. Future generations are going to have to deal with the hallucinations of slopbots.
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Markus Landthaler @landthalerm.bsky.social · 14/08/2025
www.biorxiv.org/content/10.1...
biorxiv.org
The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo
Cell-fate commitment in metazoan development relies on precise gene regulatory programs. This study presents a comprehensive single-cell atlas of gene expression (scRNA-seq), nascent transcription (sc...
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The Transmitter @thetransmitter.bsky.social · 13/08/2025
FlyBase, a Drosophila database, will lose a third of its team in early October because the Harvard grant that covered the employees’ salaries was canceled. Scientists warn that losing FlyBase could devastate fly research. By @claudia-lopez.bsky.social www.thetransmitter.org/community/ha...
thetransmitter.org
Harvard University lays off fly database team
The layoffs jeopardize this resource, which has served more than 4,000 labs for about three decades.
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Dani León-Periñán @danilexn.bsky.social · 13/08/2025
“Nobody with intellectual integrity should still believe that pure scaling will get us to AGI.” Amazing piece by @garymarcus.bsky.social (IMO, also applies to the FM for biology bs) garymarcus.substack.com/p/gpt-5-over...
garymarcus.substack.com
GPT-5: Overdue, overhyped and underwhelming. And that’s not the worst of it.
A new release botched … and a breaking research new paper that spells trouble
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Katie Mack @astrokatie.com · 10/08/2025
"PhD-level experts in your back pocket" is a completely nonsensical description of AI but a pretty good description of social media if you follow the right people
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Olivia Guest · Ολίβια Γκεστ @olivia.science · 09/08/2025
Likening PhD holders to a (non-functional) algorithm is a form of dehumanisation & anti-intellectualism that is a bellwether for contemporary fascism. Essentially it's a typical — if not the archetypal — first step towards fascism: to dehumanise, deskill, defund, and, ultimately, fire the academics.
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Keith Robison @omicsomics.bsky.social · 07/08/2025
www.genengnews.com/topics/omics...
genengnews.com
10x Genomics Scales Up, Agrees to Acquire Scale Biosciences
An exclusive interview with Serge Saxonov of 10x Genomics and Giovanna Prout of Scale Biosciences on what the acquisition means for single cell genomics.
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Manuel Irimia @mirimiam.bsky.social · 06/08/2025
🧬🧬🧬 New review from the lab: Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks authors.elsevier.com/sd/article/S... By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.
Three major trends in comparative transcriptomics
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