Gilberto Alvarez
@gilb-alvarez.bsky.social
Computational biologist at the Gompel Lab, Uni Bonn
PhD EMBL
My interests: Evo Devo, Gene regulation and Quantitative biology
PhD EMBL
My interests: Evo Devo, Gene regulation and Quantitative biology
Reposted by Gilberto Alvarez
First hours of embryonic zebrafish development. Credit to Mona Wellhäusser, Timo Schreiber, & @lennarthilbert.bsky.social. #ZebrafishZunday 🧪
January 4, 2026 at 2:02 PM
First hours of embryonic zebrafish development. Credit to Mona Wellhäusser, Timo Schreiber, & @lennarthilbert.bsky.social. #ZebrafishZunday 🧪
Reposted by Gilberto Alvarez
In October, the International Society for Artificial Life recognized several SFI researchers and co-authors with the ISAL Award for Outstanding Publication of 2024.
The award celebrates the paper “Fundamental constraints to the logic of living systems," which was published last fall.
The award celebrates the paper “Fundamental constraints to the logic of living systems," which was published last fall.
Fundamental logic of life paper receives Outstanding Publication award
In October, the International Society for Artificial Life recognized several SFI researchers and co-authors with the ISAL Award for Outstanding Publication of 2024. The award celebrates the paper “Fun...
www.santafe.edu
December 18, 2025 at 10:03 PM
In October, the International Society for Artificial Life recognized several SFI researchers and co-authors with the ISAL Award for Outstanding Publication of 2024.
The award celebrates the paper “Fundamental constraints to the logic of living systems," which was published last fall.
The award celebrates the paper “Fundamental constraints to the logic of living systems," which was published last fall.
Reposted by Gilberto Alvarez
Well well. The standard model for how frequencies of recessive disease genes are established doesn't work. And that seems to be because recessive variants are visible to selection due to pleiotropy. (But still we teach Mendelian genetics...)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 16, 2025 at 2:20 PM
Well well. The standard model for how frequencies of recessive disease genes are established doesn't work. And that seems to be because recessive variants are visible to selection due to pleiotropy. (But still we teach Mendelian genetics...)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Gilberto Alvarez
Read more here www.dpag.ox.ac.uk/named-lectur...
December 13, 2025 at 7:03 AM
Read more here www.dpag.ox.ac.uk/named-lectur...
Reposted by Gilberto Alvarez
Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...
Generative epigenetic landscapes map the topology and topography of cell fates | PNAS
Epigenetic landscapes were proposed by Waddington as the central concept to describe
cell fate dynamics in a locally low-dimensional space. In mode...
www.pnas.org
December 10, 2025 at 1:27 PM
Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...
Reposted by Gilberto Alvarez
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
Reposted by Gilberto Alvarez
During host cell invasion, Toxoplasma mimics the FFAT motif and repurposes it to associate its parasitophorous vacuole to the endoplasmic reticulum!
I'm happy to have been part of this work! Congratulations to Chahat Mehra and Lena Pernas for all the hard work!
www.nature.com/articles/s41...
I'm happy to have been part of this work! Congratulations to Chahat Mehra and Lena Pernas for all the hard work!
www.nature.com/articles/s41...
Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection - Nature Microbiology
The Toxoplasma gondii effector TgROP1 mimics host factors to bind VAPA/B, thereby establishing parasite–host ER contact sites.
www.nature.com
December 8, 2025 at 2:38 PM
During host cell invasion, Toxoplasma mimics the FFAT motif and repurposes it to associate its parasitophorous vacuole to the endoplasmic reticulum!
I'm happy to have been part of this work! Congratulations to Chahat Mehra and Lena Pernas for all the hard work!
www.nature.com/articles/s41...
I'm happy to have been part of this work! Congratulations to Chahat Mehra and Lena Pernas for all the hard work!
www.nature.com/articles/s41...
Reposted by Gilberto Alvarez
Verrückter Fakt des Tages: #vfdt
Das größte Tier, das jemals auf der Erde flog, war vermutlich Quetzacoatlus, der in der Endphase der Dinosaurier-Ära im heutigen Nordamerika lebte. Das Tier war ungefähr so groß wie eine Giraffe, mit einer Flügelspannweite von ca. 10m. Und so etwas konnte fliegen!
Das größte Tier, das jemals auf der Erde flog, war vermutlich Quetzacoatlus, der in der Endphase der Dinosaurier-Ära im heutigen Nordamerika lebte. Das Tier war ungefähr so groß wie eine Giraffe, mit einer Flügelspannweite von ca. 10m. Und so etwas konnte fliegen!
November 18, 2025 at 7:05 PM
Verrückter Fakt des Tages: #vfdt
Das größte Tier, das jemals auf der Erde flog, war vermutlich Quetzacoatlus, der in der Endphase der Dinosaurier-Ära im heutigen Nordamerika lebte. Das Tier war ungefähr so groß wie eine Giraffe, mit einer Flügelspannweite von ca. 10m. Und so etwas konnte fliegen!
Das größte Tier, das jemals auf der Erde flog, war vermutlich Quetzacoatlus, der in der Endphase der Dinosaurier-Ära im heutigen Nordamerika lebte. Das Tier war ungefähr so groß wie eine Giraffe, mit einer Flügelspannweite von ca. 10m. Und so etwas konnte fliegen!
Reposted by Gilberto Alvarez
Really old illustrations, but Megatherium looks nice in black with a white stripe.
November 15, 2025 at 10:43 AM
Really old illustrations, but Megatherium looks nice in black with a white stripe.
Reposted by Gilberto Alvarez
This week's #FluorescenceFriday, we'll be treated with one of the classical models of #devbio, the neural crest cells. Here is a beautiful video of neural crest cells with GFP-tagged focal adhesion kinase (🔵) and LifeAct-RFP (🟣) migrating on a Fibronectin matrix.
📹: Adam Shellard
📹: Adam Shellard
November 14, 2025 at 5:45 PM
This week's #FluorescenceFriday, we'll be treated with one of the classical models of #devbio, the neural crest cells. Here is a beautiful video of neural crest cells with GFP-tagged focal adhesion kinase (🔵) and LifeAct-RFP (🟣) migrating on a Fibronectin matrix.
📹: Adam Shellard
📹: Adam Shellard
Reposted by Gilberto Alvarez
Mechanical constraints disrupt gastruloid polarisation without changing gene expression - uncouples morphogenesis & patterning
Gregor & co use tunable hydrogels to show cell motility, not gene expression, drives axis formation in gastruloids
journals.biologists.com/dev/article/...
Gregor & co use tunable hydrogels to show cell motility, not gene expression, drives axis formation in gastruloids
journals.biologists.com/dev/article/...
Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids
Highlighted Article: A bioinert confinement system enables dissection of how stiffness and timing shape gastruloid development, revealing uncoupling between polarization and transcriptional programs.
journals.biologists.com
October 3, 2025 at 9:54 AM
Mechanical constraints disrupt gastruloid polarisation without changing gene expression - uncouples morphogenesis & patterning
Gregor & co use tunable hydrogels to show cell motility, not gene expression, drives axis formation in gastruloids
journals.biologists.com/dev/article/...
Gregor & co use tunable hydrogels to show cell motility, not gene expression, drives axis formation in gastruloids
journals.biologists.com/dev/article/...
Reposted by Gilberto Alvarez
Love #protists? Then you'd love this! Beautiful collection of hand-drawn critters represented here at the Oxford-Japan symposium on ethological dynamics in diorama environments sites.google.com/view/oxford-... #ciliates #testateamoeba #diatoms
September 24, 2025 at 3:14 PM
Love #protists? Then you'd love this! Beautiful collection of hand-drawn critters represented here at the Oxford-Japan symposium on ethological dynamics in diorama environments sites.google.com/view/oxford-... #ciliates #testateamoeba #diatoms
Reposted by Gilberto Alvarez
@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting!
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
September 11, 2025 at 2:34 PM
@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting!
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...
Reposted by Gilberto Alvarez
For anyone wanting to follow up on my brief mention at the Helgoland meeting of how spacetime might be an emergent property of quantum entanglement, here's a nice but pretty high-level essay on it.
journals.aps.org/prl/abstract...
journals.aps.org/prl/abstract...
Essay: Emergent Holographic Spacetime from Quantum Information
In a new forward-looking PRL Essay, Tadashi Takayanagi explores the intersection of quantum information theory with quantum gravity within the framework of holographic duality, and its potential to he...
journals.aps.org
June 23, 2025 at 9:54 AM
For anyone wanting to follow up on my brief mention at the Helgoland meeting of how spacetime might be an emergent property of quantum entanglement, here's a nice but pretty high-level essay on it.
journals.aps.org/prl/abstract...
journals.aps.org/prl/abstract...
Reposted by Gilberto Alvarez
Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
June 22, 2025 at 12:15 AM
Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
Reposted by Gilberto Alvarez
How did evolution drive massive genome contraction during oceanic island colonization? A new paper from our lab.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 19, 2025 at 4:58 PM
How did evolution drive massive genome contraction during oceanic island colonization? A new paper from our lab.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Gilberto Alvarez
Wow - one of the largest coronal holes of solar cycle 25! This coronal hole has survived for over NINE MONTHS, one of the most persistent coronal holes I have ever seen. We are seeing the high speed solar wind at Earth now which may intensify in the coming days.
#heliophysics
#heliophysics
June 15, 2025 at 2:33 AM
Wow - one of the largest coronal holes of solar cycle 25! This coronal hole has survived for over NINE MONTHS, one of the most persistent coronal holes I have ever seen. We are seeing the high speed solar wind at Earth now which may intensify in the coming days.
#heliophysics
#heliophysics
Reposted by Gilberto Alvarez
Of course there's also the answer that Twitter/X got shit and is run by a neo-Nazi ket-head but this is still genuinely interesting.
Happy to share this paper. Full thread coming soon!
June 2, 2025 at 1:37 PM
Of course there's also the answer that Twitter/X got shit and is run by a neo-Nazi ket-head but this is still genuinely interesting.
Reposted by Gilberto Alvarez
In 1984, Francis Crick described a biological conundrum: Memories last years, while most molecules degrade in days or weeks. “How then is memory stored in the brain so that its trace is relatively immune to molecular turnover?” he wrote in Nature. www.quantamagazine.org/the-molecula...
May 11, 2025 at 8:04 PM
In 1984, Francis Crick described a biological conundrum: Memories last years, while most molecules degrade in days or weeks. “How then is memory stored in the brain so that its trace is relatively immune to molecular turnover?” he wrote in Nature. www.quantamagazine.org/the-molecula...
Reposted by Gilberto Alvarez
Happy to share my new article on how morphological diversification proceeds during evolutionary radiations: "The diffused evolutionary dynamics of morphological novelty" www.pnas.org/doi/10.1073/... 🧵 1/12
The diffused evolutionary dynamics of morphological novelty | PNAS
Rates of evolution are fundamental to understand the processes that shaped the history
of life. The predominant view holds that high rates of pheno...
www.pnas.org
May 2, 2025 at 8:46 AM
Happy to share my new article on how morphological diversification proceeds during evolutionary radiations: "The diffused evolutionary dynamics of morphological novelty" www.pnas.org/doi/10.1073/... 🧵 1/12
Reposted by Gilberto Alvarez
Our BAT paper is accepted in Nature Ecology & Evolution! Single cell, gene regulation, TADs and key TFs that shape the bat wing. Genomics goes Evodevo 😍
May 6, 2025 at 8:34 AM
Our BAT paper is accepted in Nature Ecology & Evolution! Single cell, gene regulation, TADs and key TFs that shape the bat wing. Genomics goes Evodevo 😍
Reposted by Gilberto Alvarez
ICYMI: Modelling and design of transcriptional enhancers
Modelling and design of transcriptional enhancers
Nature Reviews Bioengineering, Published online: 28 February 2025; doi:10.1038/s44222-025-00280-yEnhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to…
www.nature.com
March 1, 2025 at 6:54 PM
ICYMI: Modelling and design of transcriptional enhancers
Reposted by Gilberto Alvarez
🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!
Solanum pan-genetics reveals paralogues as contingencies in crop engineering - Nature
Gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability.
nature.com
March 5, 2025 at 4:43 PM
🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!
Reposted by Gilberto Alvarez
New #preprint: "A model for boundary-driven tissue morphogenesis" arxiv.org/abs/2503.03688.
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
March 6, 2025 at 9:52 AM
New #preprint: "A model for boundary-driven tissue morphogenesis" arxiv.org/abs/2503.03688.
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
A must read :D
Should biology put complexity first?
Thought it might be worth sending this round again, as it seems to be resonating with some. This link should give free access until 1 April.
authors.elsevier.com/a/1karS8YyDfuZ5m
Thought it might be worth sending this round again, as it seems to be resonating with some. This link should give free access until 1 April.
authors.elsevier.com/a/1karS8YyDfuZ5m
authors.elsevier.com
February 21, 2025 at 10:34 PM
A must read :D