Oscar Silva
@oscar-silva.bsky.social
📤 419
📥 455
📝 237
reposted by
Oscar Silva
Simon Fisher
about 17 hours ago
🤯 Evo 2, a model trained on 9 trillion DNA letters from curated genomic atlas across all domains of life “learns to accurately predict functional impact of gene variation...Model parameters, training code, inference code etc = fully open, to accelerate exploration & design of biological complexity”🧪
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Genome modelling and design across all domains of life with Evo 2 - Nature
Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and p...
https://www.nature.com/articles/s41586-026-10176-5
1
34
13
reposted by
Oscar Silva
Botanical Society of America
about 18 hours ago
From the upcoming
#AppsPlantSci
special issue "Branching out: Resolving
#PlantEvolution
through
#Phylogenetic
Networks" Introducing ghostbuster: a new tool to detect cryptic ghost lineage introgression in genomic datasets (by Forsythe et al)
bsapubs.onlinelibrary.wiley.com/doi/full/10....
#botany
0
8
2
reposted by
Oscar Silva
bioRxiv Evolutionary Biology
6 days ago
A mathematical synthesis of genetics, development, and evolution
https://www.biorxiv.org/content/10.64898/2026.02.25.707927v1
0
7
2
reposted by
Oscar Silva
Laura Dee
9 days ago
Excited to share our new paper in
@natcomms.nature.com
We synthesize causal discovery & inference approaches across traditions (regression adjustment, quasi-expts, SEMs, Granger causality, convergent cross-mapping, and more) into a unified workflow for ecologists.
www.nature.com/articles/s41...
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Best practices for moving from correlation to causation in ecological research - Nature Communications
Different scientific traditions offer seemingly disparate approaches to inferring causal relationships in ecological systems. This Perspective unifies the causal assumptions and methods from...
https://www.nature.com/articles/s41467-026-69878-z
3
159
69
reposted by
Oscar Silva
Mart Krupovic
2 days ago
With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome.
arxiv.org/abs/2602.23268
5
221
107
reposted by
Oscar Silva
Journal of the Marine Biological Association
5 months ago
"Why sequence the
#genome
of every species? A view from evolutionary biology" Did you catch this amazing new review in our journal by
@peterhox.bsky.social
? REad it for FREE here now:
www.cambridge.org/core/journal...
@thembauk.bsky.social
#dnasequencing
#chromosome
#mutation
#evolution
0
13
8
reposted by
Oscar Silva
The Associated Press
3 days ago
Oil prices are up sharply as the widening Iran war disrupted tanker traffic through the Strait of Hormuz, highlighting how important the passageway is to the world's oil supply.
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What to know about the Strait of Hormuz, a key passageway essential for global energy supply
Oil prices are up sharply as the widening Iran war disrupted tanker traffic through the Strait of Hormuz, highlighting how important the passageway is to the world’s oil supply.
https://bit.ly/3OFXnpf
8
75
34
reposted by
Oscar Silva
Lilly Cummins
3 days ago
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!
rdcu.be/e6pHY
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Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
https://rdcu.be/e6pHY
4
83
40
reposted by
Oscar Silva
Molecular Biology and Evolution
3 days ago
For a new MBE Review, Presgraves et al. argue that many features of genome evolution, content, and organization seemingly inexplicable by adaptation or nearly neutral processes are instead best accounted for by meiotic drive. 🔗
academic.oup.com/mbe/article/...
#evobio
#molbio
1
21
13
reposted by
Oscar Silva
Stephen Turner
4 days ago
Pangenome-guided sequence assembly via binary optimization
academic.oup.com/bib/article/...
🧬💻🧪
github.com/jkbonfield/qpg
0
9
3
Parece ser que la ejecución ya ha sido confirmada por medios iraníes.
add a skeleton here at some point
4 days ago
1
0
0
¿Soy yo o aún hay bastante incertidumbre respecto a la ejecución de Khamenei? Parece ser que la única fuente proviene de Israel; pero yo esperaría a tener otras fuentes.
5 days ago
1
1
1
reposted by
Oscar Silva
Christian Landry
5 days ago
New paper alert: Paralog interference contributes to the preservation of genetic redundancy
www.cell.com/current-biol...
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Paralog interference contributes to the preservation of genetic redundancy
Duplicated self-interacting proteins can interact and interfere with each other’s function. Cisneros, Mattenberger, et al. show that selection against interfering loss-of-function alleles extends the ...
https://www.cell.com/current-biology/abstract/S0960-9822(26)00145-4
0
45
28
www.pnas.org/doi/10.1073/...
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From peptides to DNA: All required steps can be catalyzed | PNAS
Ensuring information flow (heredity) and metabolic processes (catalysis) are two important prerequisites for early evolution. The widely accepted “...
https://www.pnas.org/doi/10.1073/pnas.2534387123
5 days ago
0
0
0
reposted by
Oscar Silva
PutoMikel
6 days ago
NUEVO VÍDEO: ¿Hemos vuelto al fascismo? LINK:
youtu.be/56YZf-ye8y0?...
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¿Hemos vuelto al fascismo?
YouTube video by PutoMikel
https://youtu.be/56YZf-ye8y0?si=EML1acqORZVbvLup
8
307
114
reposted by
Oscar Silva
Robin Pranter
6 days ago
How does development affect the evolutionary process? Join our symposium at
www.evodevoconference26.com
in Glasgow this June. We have a strong lineup of invited speakers, chaired by me and
@milocco.bsky.social
Submit your abstract before Thursday! ⏰
0
7
8
reposted by
Oscar Silva
Centro Prodh
6 days ago
Los avances en el rescate a dos décadas del siniestro en la mina Pasta de Conchos representan pasos de justicia que demuestran que, cuando hay voluntad política, se pueden mover toneladas de tierra y romper con décadas de impunidad. 1/2
1
0
1
reposted by
Oscar Silva
bioRxiv Evolutionary Biology
6 days ago
Parallel evolution of industrial melanism in the peppered moth: one locus, many alleles
https://www.biorxiv.org/content/10.64898/2026.02.26.707722v1
0
15
11
reposted by
Oscar Silva
Sergi Valverde
3 months ago
Debates like “programming is dead,” “AI will automate X,” or the latest “vibe coding” trend all miss the point. They treat complexity as something we can engineer away—instead of recognizing the ecological forces shaping software.
1
3
2
reposted by
Oscar Silva
James McInerney
6 days ago
New paper out in MBE! 🧵 "Genomic Perplexity and the Evolution of Context-Dependent Function" The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this.
academic.oup.com/mbe/article/...
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Genomic Perplexity and the Evolution of Context-Dependent Function
Abstract. The fundamental principle that selection acts on a gene’s function often assumes implicitly that this function is fixed and intrinsic. However, e
https://academic.oup.com/mbe/article/doi/10.1093/molbev/msag041/8497498
2
60
17
reposted by
Oscar Silva
Josef Uyeda
7 days ago
This post is about biologists' obligation to speak up for trans rights, in case I need to spell it out directly.
add a skeleton here at some point
0
11
4
reposted by
Oscar Silva
Chenxin Li, PhD
7 days ago
"Friends don't let friends make bad graphs" repo has reached 7000 stars on GitHub! When I created it back in 2022, I'd never imagine it will become this popular.
#DataVis
github.com/cxli233/Frie...
1
38
8
reposted by
Oscar Silva
Juliet Turner
15 days ago
I'm very happy to share that a paper from my DPhil thesis has been selected as the Editor's Choice article in Evolution. 😊 You can read it here:
lnkd.in/eCnAQfzT
🐜
@journal-evo.bsky.social
#EvolutionaryBiology
#SocialEvolution
#Insects
1
69
7
reposted by
Oscar Silva
Evgenii Protasov
11 days ago
On the nature of the earliest known lifeforms
#evolution
#microbiology
@elife.bsky.social
doi.org/10.7554/eLif...
0
16
5
reposted by
Oscar Silva
The Ramsey Lab
10 days ago
New Element in the
#PhilBio
series by Silvia De Cesare—free to download until March 2! De Cesare examines the thorny issue of 'evolutionary progress,' recounting the arguments against and in favor of cashing out this contested notion 👇📕
www.cambridge.org/core/element...
#evosky
#HPS
#philsky
0
39
21
reposted by
Oscar Silva
Stephen Turner
12 days ago
Evolutionary causes and consequences of gene duplication
www.nature.com/articles/s41...
🧬💻🧪 (🔓
rdcu.be/e4CYK
)
0
31
9
reposted by
Oscar Silva
Will Ratcliff
30 days ago
New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects.
www.nature.com/articles/s44...
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Priority effects inhibit the repeated evolution of phototrophy - npj Complexity
npj Complexity - Priority effects inhibit the repeated evolution of phototrophy
https://www.nature.com/articles/s44260-026-00069-z
3
137
59
reposted by
Oscar Silva
Jon Norberg
13 days ago
Please help me spread this postdoc position with me at Stockholm University, Sweden!!!!
su.varbi.com/en/what:job/...
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Postdoctoral Fellow in Eco-evolutionary Modelling and Machine Learning
The Department of Ecology, Environment and Plant Sciences (DEEP) at Stockholm University is located in the Arrhenius Laboratories on the Frescati campus. Currently, approximately 100 people, including
https://su.varbi.com/en/what:job/jobID:902750/
1
26
31
reposted by
Oscar Silva
New Phytologist
14 days ago
Breaking and making
#genes
: the genesis of novel traits in
#plants
A
#ResearchReview
by Fiza Hamid, Simran Arora & Shailesh Kumar 👇 📖
nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue
0
4
3
reposted by
Oscar Silva
El Pensador Sereno
14 days ago
¿Dónde estarán los adalides de la libertad académica y de opinión? ¿Esos que nos contaban en The War On Science que la izquierda woke y la teoría crítica generaban ambientes de censura en las universidades? Supongo que tendrán mucho que decir al respecto de esto.
add a skeleton here at some point
0
8
3
reposted by
Oscar Silva
Luisa F. Pallares
15 days ago
New Perspective!🔥It's fascinating how scientists from different fields but interested in the same question [e.g. genotype-phenoytpe relationship] can have such different perspectives. Here we put in our 2 cents wrt genetic effects being context-dependent, and pheno variation being mostly polygenic
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Beyond Mendel: a call to revisit the genotype–phenotype map through new experimental paradigms
Abstract. The long-standing notion that genotypes map to phenotypes through simple one gene–one trait relationships continues to shape both research in the
https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyag024/8488818?utm_source=authortollfreelink&utm_campaign=genetics&utm_medium=email
0
32
20
"Our analysis of 5,678 species, across all insect groups, finds no evidence that haplodiploidy has driven an increased rate of eusocial evolution."
add a skeleton here at some point
16 days ago
1
1
0
reposted by
Oscar Silva
PZ Myers
16 days ago
If you can't understand gene duplication, you're never going to understand evolution.
freethoughtblogs.com/pharyngula/2...
1
29
4
reposted by
Oscar Silva
Wide Hybridization Group
16 days ago
Latest work from our group together with
@jsharbro.bsky.social
This review synthesizes insights into cytonuclear incompatibility in plant hybrids and allopolyploids, highlighting maternal bias, evolutionary consequences, and applications such as cytoplasmic male sterility in seed production.
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Causes and Consequences of Cytonuclear Incompatibility in Hybrids of Flowering Plants
Abstract. Hybridization and polyploidization combine divergent nuclear genomes with maternally inherited organelles, often disrupting cytonuclear coadaptat
https://academic.oup.com/jxb/article/doi/10.1093/jxb/erag075/8475166
0
9
6
reposted by
Oscar Silva
Edoardo Gianni
20 days ago
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in
@science.org
on a new small polymerase. 1/n
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A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
https://www.science.org/doi/10.1126/science.adt2760
10
497
237
reposted by
Oscar Silva
Ricard Solé
19 days ago
Could life have begun with simpler molecules than we once thought? A new paper in
@science.org
by
@edogia.bsky.social
shows that a tiny RNA catalyst can self-replicate itself, suggesting that life may have been easier to emerge than expected. Getting closer.
www.biorxiv.org/content/10.1...
1
47
19
reposted by
Oscar Silva
Siobhan Guerrero
19 days ago
Han arrestado a Victoria Sámano!!! El responsable es el gobierno de CDMX! Exigimos su liberación!!
1
20
22
reposted by
Oscar Silva
Big Biology | A Science Podcast
21 days ago
Episode 145 "Evolution at the speed of life" is out now! In this episode, David Reznick, talks about studying adaptation in the wild, eco-evolutionary dynamics, and placental evolution in live-bearing fish.
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Evolution at the speed of life (Ep 145)
What are eco‑evolutionary dynamics and how can we study them in the wild?
https://bigbiology.substack.com/p/evolution-at-the-speed-of-life-ep
1
4
3
reposted by
Oscar Silva
Ele Willoughby
21 days ago
For
#printerSolstice2526
prompt 2: my
#linocut
of trailblazing
#microbiologist
Esther Lederberg (née Zimmer, 1922-2007) 🧪🐡👩🏼🔬
#histsci
who made discoveries fundamental to modern understanding of bacterial gene regulation, recombination & exchange, but her work was both overshadowed by & sometimes 🧵
4
21
8
reposted by
Oscar Silva
Simon Fisher
21 days ago
One of my favourite things about this figure (sketched by Charles Darwin in one of his notebooks in 1837) is the “I think” at the top. Beyond an illustration of his evolving thoughts on descent with modification, the image somehow captures the essence of scientific curiosity.
#DarwinDay
2026
5
48
11
reposted by
Oscar Silva
Young Modellers in Ecology
22 days ago
Great opportunity to interact with the French Community of Ecological Theory: "Biodiversity in Equations" Conference in Montpellier, France on April 9 and 10, 2026, organized by GDR TheoMoDive and SFE2. Registration is free! Find more info here:
biodiveq.sciencesconf.org?forward-acti...
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Biodiversity in equations - Sciencesconf.org
Welcome
https://biodiveq.sciencesconf.org/?forward-action=index&forward-controller=index&lang=en
0
13
7
reposted by
Oscar Silva
PLOS Biology
22 days ago
#DeepMutationalScanning
(DMS) experiments are limited by gene size due to library complexity & costs.
@christianlandry.bsky.social
&co develop an efficient & cost-effective barcoded cloning strategy for plasmid-based DMS libraries that enables study of large genes
@plosbiology.org
🧪
plos.io/4abhyUf
0
14
11
reposted by
Oscar Silva
Cameron Thrash
22 days ago
Recent microbial evolutionary insights from metagenomics
academic.oup.com/gbe/advance-...
#jcampubs
0
16
5
reposted by
Oscar Silva
EcoEvoRxiv
23 days ago
'Modeling evolutionary rescue'
doi.org/10.32942/X25...
0
21
12
reposted by
Oscar Silva
bioRxiv SysBio
23 days ago
Existence of Causation without Correlation in Transcriptional Networks
https://www.biorxiv.org/content/10.64898/2026.02.09.704821v1
0
2
3
reposted by
Oscar Silva
the Node
24 days ago
Nivedita Mukherjee and Mateus de Oliveira Lisboa reflect on
@biologists.bsky.social
Workshop titled ‘Decoding Whole Genome Doubling: Insights From Evolution, Development and Disease’. ⬇️
thenode.biologists.com/decoding-who...
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Whole-Genome Doubling and Polyploidy: Cells, Cancer, and Evolution
Discover how whole-genome doubling and polyploidy drive cellular adaptations, shape cancer progression, and fuel evolutionary innovation across species.
https://thenode.biologists.com/decoding-whole-genome-doubling-insights-from-evolution-development-and-disease/uncategorized/
0
4
3
reposted by
Oscar Silva
bioRxiv Evolutionary Biology
26 days ago
Deconstructing empirical fitness seascapes across scales of granularity
https://www.biorxiv.org/content/10.64898/2026.02.04.703871v1
0
2
2
Me pregunto qué pensaría Susumu Ohno de que los eventos más antiguos que podemos rastrear mediante métodos filogenéticos sean procesos de duplicación génica.
add a skeleton here at some point
26 days ago
0
4
2
reposted by
Oscar Silva
Kaçar Lab at UW-Madison
27 days ago
What happened before the last universal common ancestor? Pre-LUCA evolution is hard to study. In our new Cell Genomics Perspective we spotlight how paralogous proteins open a window onto the deepest chapters of evolution. 🧬🌍 Out today! -->
www.cell.com/cell-genomic...
@cellpress.bsky.social
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Universal paralogs provide a window into evolution before the last universal common ancestor
Universal paralog protein families form due to gene duplications that occurred prior to the last universal common ancestor of life. This perspective describes how these protein families offer valuable...
https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00002-9
1
35
15
reposted by
Oscar Silva
Genetics Society of America
28 days ago
In
#GENETICS
, a new model developed by
@christianlandry.bsky.social
and colleagues examines how molecular dominance determines total protein activity and contributes to phenotypic dominance.
buff.ly/CfaTDp7
1
10
8
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