Jaime A Castro-Mondragon
@jaimicore.bsky.social
Computational biologist (and baker)
Interested in gene expression regulation, stats, and data visualisation.
Living in the limbo of automating processes on the computer and crafting stuff in the material world.
https://jaimicore.github.io/
Interested in gene expression regulation, stats, and data visualisation.
Living in the limbo of automating processes on the computer and crafting stuff in the material world.
https://jaimicore.github.io/
Reposted by Jaime A Castro-Mondragon
📣 Calling Bioconductor users and developers! 🧬 ✨
Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!
Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!
November 14, 2025 at 4:50 PM
📣 Calling Bioconductor users and developers! 🧬 ✨
Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!
Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!
Reposted by Jaime A Castro-Mondragon
Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42...
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
November 17, 2025 at 10:44 AM
Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42...
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
Reposted by Jaime A Castro-Mondragon
Halloween logicals, still the best 10/31 venn
October 31, 2025 at 10:52 PM
Halloween logicals, still the best 10/31 venn
Reposted by Jaime A Castro-Mondragon
just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters
October 20, 2025 at 3:22 PM
just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters
Reposted by Jaime A Castro-Mondragon
(TPCPA), a proteomic resource that provides proteome-scale quantifications of 999 tumors across 22 cancer types in a unified manner, for discovering tumor biology, biomarkers, and therapeutic targets. hgserver1.amc.nl/cgi-bin/r2/...
September 25, 2025 at 2:15 PM
(TPCPA), a proteomic resource that provides proteome-scale quantifications of 999 tumors across 22 cancer types in a unified manner, for discovering tumor biology, biomarkers, and therapeutic targets. hgserver1.amc.nl/cgi-bin/r2/...
Reposted by Jaime A Castro-Mondragon
I keep stumbling when, in biological data analysis, someone uses the word "noise" as if it represented an objectively existing, tangible thing.
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
September 14, 2025 at 10:11 AM
I keep stumbling when, in biological data analysis, someone uses the word "noise" as if it represented an objectively existing, tangible thing.
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)
Reposted by Jaime A Castro-Mondragon
Reposted by Jaime A Castro-Mondragon
I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: www.nature.com/articles/d41...
Beyond AlphaFold: how AI is decoding the grammar of the genome
Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.
www.nature.com
August 19, 2025 at 6:26 PM
I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: www.nature.com/articles/d41...
Reposted by Jaime A Castro-Mondragon
solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
August 12, 2025 at 2:15 PM
solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
Reposted by Jaime A Castro-Mondragon
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
June 11, 2025 at 10:40 PM
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Reposted by Jaime A Castro-Mondragon
I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Tomtom-lite: Accelerating Tomtom enables large-scale and real-time motif similarity scoring
Summary Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete characters. With the growing prevalence of machine lear...
www.biorxiv.org
June 3, 2025 at 6:02 PM
I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jaime A Castro-Mondragon
Bonjour, nous sommes le
May 25, 2025 at 4:29 AM
Bonjour, nous sommes le
Reposted by Jaime A Castro-Mondragon
Reposted by Jaime A Castro-Mondragon
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Perspective on recent developments and challenges in regulatory and systems genomics
Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul
doi.org
May 13, 2025 at 4:59 PM
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Reposted by Jaime A Castro-Mondragon
Reposted by Jaime A Castro-Mondragon
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Reposted by Jaime A Castro-Mondragon
We have a new preprint out! Led by brilliant PhD student @estefvazquez.bsky.social. here we investigate through transcriptomics and proteomics the microenvironment of ulcerated #acral #melanoma 👇🏾
The microenvironment of ulcerated acral melanoma is characterised by an inflammatory milieu and an enhanced humoral immune response https://www.medrxiv.org/content/10.1101/2025.05.05.25325616v1
May 8, 2025 at 6:34 AM
We have a new preprint out! Led by brilliant PhD student @estefvazquez.bsky.social. here we investigate through transcriptomics and proteomics the microenvironment of ulcerated #acral #melanoma 👇🏾
Reposted by Jaime A Castro-Mondragon
Thrilled to celebrate 9 rewarding years since founding my group @ncmbm.bsky.social , @uio.no, @nordicembl.bsky.social. Proud of our achievements and honored to now serve as Ass. Director. Deep gratitude to all fantastic team members past & present, collaborators, colleagues. Excited for what's next!
May 5, 2025 at 6:42 PM
Thrilled to celebrate 9 rewarding years since founding my group @ncmbm.bsky.social , @uio.no, @nordicembl.bsky.social. Proud of our achievements and honored to now serve as Ass. Director. Deep gratitude to all fantastic team members past & present, collaborators, colleagues. Excited for what's next!
Reposted by Jaime A Castro-Mondragon
many well-known alternative TF isoforms function as negative regulators of their cognate reference isoforms (e.g. STAT3b), leading us to wonder how widespread this phenomenon may be. we used our data to classify alt TF isoforms into two categories: negative regulators & rewirers
March 26, 2025 at 6:09 PM
many well-known alternative TF isoforms function as negative regulators of their cognate reference isoforms (e.g. STAT3b), leading us to wonder how widespread this phenomenon may be. we used our data to classify alt TF isoforms into two categories: negative regulators & rewirers
Reposted by Jaime A Castro-Mondragon
📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... 👇
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... 👇
March 14, 2025 at 10:34 AM
📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... 👇
We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks.
doi.org/10.1101/2024... 👇
Reposted by Jaime A Castro-Mondragon
1/At the #HoffmanLab lab meeting, we often have tech talks describing useful tools for other lab members. Since they might also prove useful for others, we've been posting almost every #HoffmanLabTechTalk for years. 🧪🧬💻
June 11, 2024 at 9:24 PM
1/At the #HoffmanLab lab meeting, we often have tech talks describing useful tools for other lab members. Since they might also prove useful for others, we've been posting almost every #HoffmanLabTechTalk for years. 🧪🧬💻
Reposted by Jaime A Castro-Mondragon
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Reposted by Jaime A Castro-Mondragon
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
February 27, 2025 at 8:01 AM
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
Reposted by Jaime A Castro-Mondragon
🚀 Introducing #Nextflow Training Week!
A free, self-paced online training designed to help beginners get started with Nextflow.
📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum
Learn more and join us: hubs.la/Q038kTQm0
A free, self-paced online training designed to help beginners get started with Nextflow.
📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum
Learn more and join us: hubs.la/Q038kTQm0
Nextflow Training Week (2025-Q1)
🚀 Nextflow Training Week is a new quarterly self-paced online training designed for accessibility and flexibility. Featuring on-demand walkthrough videos and near real-time support via the community f...
community.seqera.io
February 26, 2025 at 8:22 AM
🚀 Introducing #Nextflow Training Week!
A free, self-paced online training designed to help beginners get started with Nextflow.
📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum
Learn more and join us: hubs.la/Q038kTQm0
A free, self-paced online training designed to help beginners get started with Nextflow.
📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum
Learn more and join us: hubs.la/Q038kTQm0