Guillermo Parada
@geparada.bsky.social
Postdoctoral researcher at Blencowe’s lab, University of Toronto 🇨🇦. PhD, University of Cambridge - Wellcome Sanger Institute 🇬🇧. Alternative splicing and Bioinformatics 🧬💻🦾
https://scholar.google.cl/citations?user=PTLeXysAAAAJ&hl=en
https://scholar.google.cl/citations?user=PTLeXysAAAAJ&hl=en
Reposted by Guillermo Parada
Interesting new @medrxivpreprint.bsky.social study, bearing on the interpretation of GWAS results:
“Common and rare genetic variants show network convergence for a majority of human traits” 🧪🧬
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Common and rare genetic variants show network convergence for a majority of human traits
While both common and rare variants contribute to the genetic etiology of complex traits, whether their impacts manifest through the same effector genes and molecular mechanisms is not well understood...
www.medrxiv.org
June 29, 2025 at 7:49 AM
Interesting new @medrxivpreprint.bsky.social study, bearing on the interpretation of GWAS results:
“Common and rare genetic variants show network convergence for a majority of human traits” 🧪🧬
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Guillermo Parada
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Reposted by Guillermo Parada
Machine learning (ML) is revolutionizing genomics, but common pitfalls can lead to misleading results. Here's a thread on how to avoid them 🧵
January 24, 2025 at 2:45 PM
Machine learning (ML) is revolutionizing genomics, but common pitfalls can lead to misleading results. Here's a thread on how to avoid them 🧵
Reposted by Guillermo Parada
What DNA variants alter transcription factor (TF) binding affinity? Here, we describe a new workflow baal-nf. We used it to trawl through 6017 ChIP-Seq data sets for 558 TFs and 46 genotyped cell lines, finding 298,783 allele-specific binding sites (ASBs).
www.biorxiv.org/content/10.1...
1/2
www.biorxiv.org/content/10.1...
1/2
January 21, 2025 at 8:02 PM
What DNA variants alter transcription factor (TF) binding affinity? Here, we describe a new workflow baal-nf. We used it to trawl through 6017 ChIP-Seq data sets for 558 TFs and 46 genotyped cell lines, finding 298,783 allele-specific binding sites (ASBs).
www.biorxiv.org/content/10.1...
1/2
www.biorxiv.org/content/10.1...
1/2
Reposted by Guillermo Parada
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Guillermo Parada
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Guillermo Parada
New brain aging study is out today in Nature
The largest single-cell RNA seq dataset of mouse brain aging reveals incredible insights and could pave the way for future therapies to slow or manage the impacts of the aging process. 🧵 #studyBRAIN
The largest single-cell RNA seq dataset of mouse brain aging reveals incredible insights and could pave the way for future therapies to slow or manage the impacts of the aging process. 🧵 #studyBRAIN
January 1, 2025 at 5:07 PM
New brain aging study is out today in Nature
The largest single-cell RNA seq dataset of mouse brain aging reveals incredible insights and could pave the way for future therapies to slow or manage the impacts of the aging process. 🧵 #studyBRAIN
The largest single-cell RNA seq dataset of mouse brain aging reveals incredible insights and could pave the way for future therapies to slow or manage the impacts of the aging process. 🧵 #studyBRAIN
Reposted by Guillermo Parada
Method of moments framework for differential expression analysis of single-cell RNA sequencing data: Cell
www.cell.com/cell/fullte...
www.cell.com/cell/fullte...
December 21, 2024 at 2:45 PM
Method of moments framework for differential expression analysis of single-cell RNA sequencing data: Cell
www.cell.com/cell/fullte...
www.cell.com/cell/fullte...
Reposted by Guillermo Parada
The most complete collection of uniformly processed ChIP-seq data on identification of transcription factor binding sites for human and mouse. Convenient web interface with advanced search, browsing and genome browser based on the BioUML platform. gtrd.biouml.org/
December 20, 2024 at 6:00 PM
The most complete collection of uniformly processed ChIP-seq data on identification of transcription factor binding sites for human and mouse. Convenient web interface with advanced search, browsing and genome browser based on the BioUML platform. gtrd.biouml.org/
Reposted by Guillermo Parada
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements www.nature.com/articles/s4...
December 19, 2024 at 3:15 PM
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements www.nature.com/articles/s4...
Reposted by Guillermo Parada
Real science:
1. Is not correlated with the amount of funding
2. Progresses slowly, usually taking many years
3. Leads to more questions than it answers
4. Advances when we disengage & in improvisational discussions
5. Is too important a thing to be done in a non-playful way
1. Is not correlated with the amount of funding
2. Progresses slowly, usually taking many years
3. Leads to more questions than it answers
4. Advances when we disengage & in improvisational discussions
5. Is too important a thing to be done in a non-playful way
December 20, 2024 at 3:38 AM
Real science:
1. Is not correlated with the amount of funding
2. Progresses slowly, usually taking many years
3. Leads to more questions than it answers
4. Advances when we disengage & in improvisational discussions
5. Is too important a thing to be done in a non-playful way
1. Is not correlated with the amount of funding
2. Progresses slowly, usually taking many years
3. Leads to more questions than it answers
4. Advances when we disengage & in improvisational discussions
5. Is too important a thing to be done in a non-playful way
Reposted by Guillermo Parada
🌟 Thrilled to announce that our project, Deep Immune Receptor Modeling (#DIRM), has been awarded funding under the (@novo-nordisk.bsky.social) Nordisk Foundation Data Science Collaborative Research Programme! 🎉
December 19, 2024 at 4:04 PM
🌟 Thrilled to announce that our project, Deep Immune Receptor Modeling (#DIRM), has been awarded funding under the (@novo-nordisk.bsky.social) Nordisk Foundation Data Science Collaborative Research Programme! 🎉
Reposted by Guillermo Parada
Our novel tool for finding recent TE invasions without repeat library - great work by amazing student Riccardo (not yet on bsky) genomebiology.biomedcentral.com/articles/10....
GenomeDelta: detecting recent transposable element invasions without repeat library - Genome Biology
We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-qualit...
genomebiology.biomedcentral.com
December 19, 2024 at 8:25 AM
Our novel tool for finding recent TE invasions without repeat library - great work by amazing student Riccardo (not yet on bsky) genomebiology.biomedcentral.com/articles/10....
Reposted by Guillermo Parada
We applied Squidiff to model blood vessel #organoids using single-cell RNA sequencing to examine their response to neutron irradiation and pro-regenerative G-CSF treatment, simulating cosmic irradiation anticipated in #deepspace missions🧑🚀. 5/🦑
December 9, 2024 at 2:13 PM
We applied Squidiff to model blood vessel #organoids using single-cell RNA sequencing to examine their response to neutron irradiation and pro-regenerative G-CSF treatment, simulating cosmic irradiation anticipated in #deepspace missions🧑🚀. 5/🦑
Reposted by Guillermo Parada
Proud of this work spearheaded by the phenomenal @jlfan.bsky.social and @mingxz.bsky.social in collaboration w/ Ben Izar! The past 3 years we've worked hard to unravel how #CNVs shape #tumor phenotypic plasticity seen in #singlecell #RNAseq data ➡️ #Echidna 🦔
December 18, 2024 at 2:08 PM
Proud of this work spearheaded by the phenomenal @jlfan.bsky.social and @mingxz.bsky.social in collaboration w/ Ben Izar! The past 3 years we've worked hard to unravel how #CNVs shape #tumor phenotypic plasticity seen in #singlecell #RNAseq data ➡️ #Echidna 🦔
Reposted by Guillermo Parada
Today we published a new paradigm to do CRISPR screens in complex model systems such as in vivo but also e.g. in organoids. The publication came out in Nature Biotechnology.
1/
www.nature.com/articles/s41...
1/
www.nature.com/articles/s41...
CRISPR-StAR enables high-resolution genetic screening in complex in vivo models - Nature Biotechnology
Pooled genetic CRISPR screening is improved in complex models through leveraging internal controls.
www.nature.com
December 16, 2024 at 12:02 PM
Today we published a new paradigm to do CRISPR screens in complex model systems such as in vivo but also e.g. in organoids. The publication came out in Nature Biotechnology.
1/
www.nature.com/articles/s41...
1/
www.nature.com/articles/s41...
Reposted by Guillermo Parada
This is huge. Mis-splicing of a 24nt-long micro-exon in the CPEB4 #RNA binding protein leads to formation of irreversible aggregates, which normally would dissolve after depolarization, and consequent deregulation of genes associated with autism spectrum disorders www.nature.com/articles/s41...
Mis-splicing of a neuronal microexon promotes CPEB4 aggregation in ASD - Nature
The molecular mechanisms of how small changes in the degree of inclusion of a neuron-specific microexon in CPEB4 lead to dominant-negative effects in the expression of genes associated with autism spe...
www.nature.com
December 9, 2024 at 12:13 AM
This is huge. Mis-splicing of a 24nt-long micro-exon in the CPEB4 #RNA binding protein leads to formation of irreversible aggregates, which normally would dissolve after depolarization, and consequent deregulation of genes associated with autism spectrum disorders www.nature.com/articles/s41...