Dani León-Periñán 🇵🇸
@danilexn.bsky.social
Cells talk; I build tools to listen to them
Computational biologist • Occasional composer and pianist • he/him
Opinions are my own.
Computational biologist • Occasional composer and pianist • he/him
Opinions are my own.
Reposted by Dani León-Periñán 🇵🇸
Berlin’s senate invests >12 mio EUR for 3 NFL games in Berlin, at a time where they cut millions at the universities that are already underfunded, with collapsing buildings. They definitely seems to have priorities that are not mine.
www.tagesspiegel.de/berlin/senat...
www.tagesspiegel.de/berlin/senat...
Senat will 12,5 Millionen Euro investieren: NFL kommt 2025 für ein Spiel nach Berlin
Die nordamerikanische Football-Liga NFL wird 2025 ein Spiel in Berlin austragen. Bis 2029 könnten zwei weitere Folgen. Die Kosten dafür sind hoch. Das Land muss trotz Haushaltskrise Millionen investie...
www.tagesspiegel.de
November 6, 2025 at 7:50 PM
Berlin’s senate invests >12 mio EUR for 3 NFL games in Berlin, at a time where they cut millions at the universities that are already underfunded, with collapsing buildings. They definitely seems to have priorities that are not mine.
www.tagesspiegel.de/berlin/senat...
www.tagesspiegel.de/berlin/senat...
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
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
November 6, 2025 at 1:09 PM
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
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
Reposted by Dani León-Periñán 🇵🇸
🚨 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!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
October 30, 2025 at 5:50 PM
🚨 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!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
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...
Why don’t you invest a bit more on R&D and a little bit less on legal?
www.genomeweb.com/business-new...
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.
www.genomeweb.com
October 21, 2025 at 8:37 PM
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...
Why don’t you invest a bit more on R&D and a little bit less on legal?
www.genomeweb.com/business-new...
Reposted by Dani León-Periñán 🇵🇸
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.
October 15, 2025 at 9:27 AM
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.
Reposted by Dani León-Periñán 🇵🇸
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
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
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
YouTube video by Prof. Jean Fan
youtu.be
October 13, 2025 at 7:09 PM
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
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
Reposted by Dani León-Periñán 🇵🇸
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Dani León-Periñán 🇵🇸
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...
www.nature.com/articles/d41...
‘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.
www.nature.com
October 9, 2025 at 3:00 PM
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...
www.nature.com/articles/d41...
Reposted by Dani León-Periñán 🇵🇸
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
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
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...
www.biorxiv.org
October 7, 2025 at 7:43 PM
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
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
Reposted by Dani León-Periñán 🇵🇸
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.
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...
arxiv.org
October 5, 2025 at 5:45 PM
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.
Israel is a terrorist state.
“Vivimos humillaciones e injusticias que nunca imaginé, ni en mis peores pesadillas”: la vida al límite de la población gazatí social.elpais.com/biv5q4
October 5, 2025 at 8:32 PM
Israel is a terrorist state.
SQLite que no pase hambre
October 1, 2025 at 4:05 PM
SQLite que no pase hambre
Reposted by Dani León-Periñán 🇵🇸
We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
October 1, 2025 at 2:38 PM
We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
Reposted by Dani León-Periñán 🇵🇸
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.
Dropbox
tinyurl.com
June 12, 2025 at 11:26 AM
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.
Reposted by Dani León-Periñán 🇵🇸
🔴 ÚLTIMA HORA | La mayoría de los países abandonan la Asamblea General de la ONU a la llegada de Netanyahu social.elpais.com/njzv3
September 26, 2025 at 1:24 PM
🔴 ÚLTIMA HORA | La mayoría de los países abandonan la Asamblea General de la ONU a la llegada de Netanyahu social.elpais.com/njzv3
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.”
September 26, 2025 at 1:26 PM
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.”
Reposted by Dani León-Periñán 🇵🇸
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
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.
Open-ST (rajewsky-lab.github.io/openst) can generate that from a 1x3x4 mm piece of human tissue in two days.
IMSLP: Free Sheet Music PDF Download
imslp.org
September 22, 2025 at 11:31 AM
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.
Open-ST (rajewsky-lab.github.io/openst) can generate that from a 1x3x4 mm piece of human tissue in two days.
Reposted by Dani León-Periñán 🇵🇸
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.
🧵
A new article from ThinkingMachines explains why LLMs are nondeterministic, and it largely comes down to how parallelization and precision are handled.
🧵
September 13, 2025 at 10:16 PM
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.
🧵
A new article from ThinkingMachines explains why LLMs are nondeterministic, and it largely comes down to how parallelization and precision are handled.
🧵
Reposted by Dani León-Periñán 🇵🇸
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/...
August 28, 2025 at 6:18 PM
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/...
Reposted by Dani León-Periñán 🇵🇸
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
www.science.org/doi/10.1126/...
@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...
www.science.org
August 28, 2025 at 6:28 PM
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
www.science.org/doi/10.1126/...
@science.org
Reposted by Dani León-Periñán 🇵🇸
Adding layers of information to scRNA-seq data using pre-trained language models https://www.biorxiv.org/content/10.1101/2025.08.23.671699v1
August 28, 2025 at 5:47 AM
Adding layers of information to scRNA-seq data using pre-trained language models https://www.biorxiv.org/content/10.1101/2025.08.23.671699v1
Reposted by Dani León-Periñán 🇵🇸
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.
August 25, 2025 at 6:46 PM
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.
Reposted by Dani León-Periñán 🇵🇸
Deep-tissue transcriptomics and subcellular imaging at high spatial resolution🔓
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
Deep-tissue transcriptomics and subcellular imaging at high spatial resolution
Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycleHCR, a method that integrates multicycle DNA barcoding with Hy...
pmc.ncbi.nlm.nih.gov
August 24, 2025 at 1:01 PM
Deep-tissue transcriptomics and subcellular imaging at high spatial resolution🔓
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...