Oscar Silva
@oscar-silva.bsky.social
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Oscar Silva
Cassandra Yang
3 days ago
How should models across scales be connected and evaluated? Who gets explanatory priority — the tissue or the cell? What challenges do imaging and sequencing techniques bring to data alignment? We are hosting a one-day philosophy of biology workshop in Cambridge to address exactly these questions:
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Oscar Silva
Timothy Fuqua
3 days ago
I’m excited to share the draft for our perspective piece on »Emergence Biases« that I wrote with
@vakirlis.bsky.social
on arxiv:
arxiv.org/abs/2604.20477
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Emergence biases in molecular evolution
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new funct...
https://arxiv.org/abs/2604.20477
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Oscar Silva
Matthew Sparkes
2 days ago
The latest New Scientist podcast, in which we talk about the current state of Chornobyl, the lingering contamination and also try some booze made from radioactive apples.
open.spotify.com/episode/2t1l...
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Chernobyl 40 Years On: Legacy of the World’s Worst Nuclear Disaster
Spotify video
https://open.spotify.com/episode/2t1lLo2EcDpleF8Rqt1L4N?si=lZwI_GVbRM-I-SSgtcNsPQ&pi=S0cs7GnBTpiqT&nd=1&dlsi=fc1f8dcd3afb4ce9
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Oscar Silva
Efrén Pérez
3 days ago
Me agreeing to a new project knowing full well it’s gonna add stress 🇲🇽
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“El periódico Milenio encontró que Jasso Ramírez era un seguidor de Hitler y llegó a publicar fotografías suyas haciendo el saludo nazi, lo que le aproxima a la ultraderecha fascista.”
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4 days ago
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Oscar Silva
Berta Verd
5 days ago
New Pre-Print Alert! Evolving initial conditions: an alternative developmental route to morphological diversity with Shannon Taylor and
@jamesehammond.bsky.social
www.biorxiv.org/content/10.6...
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Oscar Silva
El Pensador Sereno
5 days ago
"Lewontin (1970) argumenta que la evolución darwiniana por selección natural puede en principio aplicar a cualquier nivel de organización biológica, siempre que la variabilidad fenotípica heredable cause diferencias en la adecuación."
www.dialecticalsystems.eu/contribution...
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The Dialectics of Multi-Level Selection in Evolutionary Biology - Dialectical Systems
Introduction Dialectical thinking in biology has famously been put forward by the eponymous book of Levins and Lewontin (1985). Much of the book was dedicated to the interpenetration between organisms...
https://www.dialecticalsystems.eu/contributions/the-dialectics-of-multi-level-selection-in-evolutionary-biology/
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Oscar Silva
Daohan "Rex" Jiang
4 days ago
My first paper w/ Matt, about how mRNA and protein levels of the same genes should be expected to coevolve. It was carried over from my PhD at Michigan w/ George Zhang, but started too late to be in my thesis.
academic.oup.com/mbe/article/...
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On the Decoupling of Evolutionary Changes in mRNA and Protein Levels
Abstract. Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is close
https://academic.oup.com/mbe/article/doi/10.1093/molbev/msad169/7232263
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Oscar Silva
Animal Político
5 days ago
⭕️
#HoyEnAnimal
| Pemex indica que en México se han perforado más de 1,000 pozos de 2012 a 2026 y que el presupuesto a los proyectos de fracking aumentó 15.5% al inicio del gobierno de López Obrador.
grupoanimal.mx/explicacione...
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Pemex confirma fracking durante los gobiernos de López Obrador y Claudia Sheinbaum
Entre 2012 y 2026 se han perforado 1,095 pozos en Puebla y Veracruz mediante la técnica de fractura hidráulica convencional en un total de 2,164 ocasiones, respondió Pemex a una solicitud de informaci
https://grupoanimal.mx/explicaciones/pemex-fracking-obrador-sheinbaum
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Oscar Silva
Philip Ball
7 days ago
Feels like this paper on protein-templated DNA synthesis by a natural enzyme warrants some comment. So here's a 🧵. /1
www.science.org/doi/10.1126/...
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Science | AAAS
https://www.science.org/doi/10.1126/science.aed1656
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Olivia Guest · Ολίβια Γκεστ
7 days ago
oh wow... so honoured somebody did this!!
blog.informaticalibremx.net/carta-abiert...
Translation of our letter into Spanish! > Carta abierta: Frenemos la incorporación acrítica de las tecnologías de IA en la Academia
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“I will discuss the implications (all bad…) of this heterogeneous labeling history for recent efforts to train machine learning algorithms to discriminate different types of mutations.”
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7 days ago
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Oscar Silva
Andy Mascola
7 days ago
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Gregory Kohn
10 days ago
Pinker’s shtick is eloquently projecting mischaracterizations of topics that knows nothing about into the public sphere. He masquerades as an expert, despite never seriously engaging with the fields he critiques. He’s the Trump of popular science writing.
www.currentaffairs.org/news/steven-...
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Steven Pinker Doesn’t Know Anything About Marxism
Bill Gates’ favorite writer keeps spewing out lazy clichés about Marxism being a “disaster” whenever it’s “implemented.” But he’s way off-base, and Marx deserves better critics.
https://www.currentaffairs.org/news/steven-pinker-doesnt-know-anything-about-marxism
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Oscar Silva
Alexis Verger 🧬🧫🧪
26 days ago
Within the field of transcription, the distinctive style of Mark Ptashne and Kevin Struhl stands out. At his best, Kevin Struhl provides a valuable clarification of the relationship between promoters and enhancers in the regulation of transcription.
www.annualreviews.org/content/jour...
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The Semantics and Mechanisms of Enhancers and Promoters: “What Is True for E. coli Is True for the Elephant, Only More So”
Three fundamental classes of gene regulatory elements were identified in Escherichia coli in the 1960s: operators bound by repressor proteins, promoters bound by the basic transcription machinery, and...
https://www.annualreviews.org/content/journals/10.1146/annurev-biochem-080125-014150
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Oscar Silva
New Phytologist
12 days ago
Somatic genome-doubling is the most parsimonious route to allopolyploidy
#TansleyInsight
by Burns et al.
@robinburns.bsky.social
@alisondawnscott.bsky.social
@pnovik.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
#plantscience
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Oscar Silva
Lior Pachter
14 days ago
On Martin Nowak, the evolution of cooperation, Jeffrey Epstein, and the corruption of mathematicians.
liorpachter.wordpress.com/2026/04/10/n...
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Oscar Silva
bioRxiv Evolutionary Biology
16 days ago
Gene-level complexity explains genome-wide variation in the distribution of fitness effects
https://www.biorxiv.org/content/10.64898/2026.04.08.717178v1
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Oscar Silva
Will Ratcliff
19 days ago
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
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The fitness costs of reproductive specialization scale inversely with organismal size
https://www.pnas.org/doi/epdf/10.1073/pnas.2536055123
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Oscar Silva
Haoran Cai
21 days ago
🚨 New Paper 🚨 Thrilled to share new work with
@evodaveo.bsky.social
eo.bsky.social
! We dive into the evolution of gene duplicates and demonstrate how expression variability might contribute to retention following duplication. Read the full article here:
academic.oup.com/gbe/article/...
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Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates
Abstract. Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. Nevertheless,
https://academic.oup.com/gbe/article/doi/10.1093/gbe/evag077/8566041
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"In the past when environments changed rapidly, biological diversity plummeted, and we live at a time when environmental change is unusually fast."
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22 days ago
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Oscar Silva
Pijus Magnificus
23 days ago
Hoy se conmemora la muerte de Brian de Nazareth, también conocido como Brian al que llaman Brian. Vendedor de snacks romanos hasta que entró en el Frente Popular de Judea. No murió por nuestros pecados ni era el Mesías pero era majete.
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Paul Smaldino
23 days ago
I've been thinking a lot about the foundations of cultural evolutionary theory. While there's been a lot of work on transmission mechanisms, there has been far less work on cultural *selection*. Here's a new working paper presenting a taxonomy of cultural selection processes.
osf.io/preprints/so...
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Oscar Silva
Simon Fisher
24 days ago
Nature: Hallucinated citations generated by AI are polluting the scientific literature. What on earth can be done? Also Nature: Our revolutionary AI-powered research assistant saves you from investing time & effort in reading, understanding & writing.
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"The quest to reconstruct the ancestral protein alphabet has often been structured as a contest between competing lines of evidence. Our view is that we should stop asking which model...
24 days ago
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Oscar Silva
Plant Cell Atlas
about 1 month ago
PCA's Computation, Modeling, & AI Committee is happy to announce their two-part speaker series, highlighting recent advances in AI-driven tools for single-cell datasets happening May 4 and May 11, 2026 (12:00pm ET / 11:00am CT / 9:00am PT)! Learn More:
bit.ly/4cTuGPH
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Oscar Silva
Josué Daniel Sánchez Tapetillo
25 days ago
Y así estamos, bien entrados en la 3ra década del siglo XXI, dependiendo aún de tinacos y, como ahora, señalando y responsabilizando a la gente por no lavarlos. Es desesperanzador ver tan lejos el necesario cambio hacia un sistema en el que podamos beber agua del grifo. (6/6)
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Oscar Silva
Royal Society Publishing
26 days ago
#BiologyLetters
in
@theconversation.com
| Faster speciating cacti have faster evolving flowers:
doi.org/10.1098/rsbl...
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Cacti may help explain a centuries-old mystery of evolution
Deserts seem unforgiving. However, the fragile flowers of cacti are evolving quickly.
https://theconversation.com/cacti-may-help-explain-a-centuries-old-mystery-of-evolution-278227
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Oscar Silva
The Plant Cell
26 days ago
Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy (Le-Han Rössner , Clemens Rössner , Doudou Kong , et alr)
doi.org/10.1093/plce...
#PlantScience
@aspbofficial
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Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy
The analysis of the California poppy genome sequence and expression atlas reveals contrasting histories of duplication and loss for metabolic pathway and f
https://doi.org/10.1093/plcell/koag039
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Oscar Silva
PLOS Biology
25 days ago
What selective forces first enabled protocells to evolve functional coding sequences?
@andrewpom.bsky.social
&co show that genetic
#heredity
could only originate once
#protocells
achieved sufficient metabolic capacity, so growth had to precede information
@plosbiology.org
🧪
plos.io/3Py9uFl
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Oscar Silva
Marc Robinson-Rechavi
25 days ago
This! AlphaFold is PDB + UniProt + Deep learning. No data sharing, no curation, no data standards, no AlphaFold.
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Oscar Silva
Santa Fe Institute
26 days ago
The world around us is full of examples of diversity from small, incremental evolutionary changes. But sometimes, something entirely new appears. In his new book, The Origins of the New, SFI's Doug Erwin asks how radically different entities come to be, and how the world produces true novelty.
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How novelty arrives: Review of “Origins of the New”
The built and natural worlds around us are full of examples of diversity from small, incremental evolutionary changes. Keyboard designs offer slightly different key spacing and press stiffness; two sp...
https://www.santafe.edu/news-center/news/how-novelty-arrives-review-of-origins-of-the-new
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Oscar Silva
Olivia Ghosh
26 days ago
Really excited that this major work from my PhD is finally published in
@plosbiology.org
! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n)
journals.plos.org/plosbiology/...
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Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003618
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El "DNA basura" es real y no un producto de la ignorancia de la genética evolutiva del siglo pasado.
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27 days ago
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Oscar Silva
Roli Roberts
29 days ago
Really neat piece of work in
@plosbiology.org
, inferring the hidden layer of "fitnotypes" that link genotypes to fitness, and finding surprisingly low dimensionality. From
@oliviamghosh.bsky.social
@grantkinsler.bsky.social
@benjaminhgood.bsky.social
&
@petrovadmitri.bsky.social
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Oscar Silva
Enrico Sandro Colizzi
about 1 month ago
How common is multicellularity in bacteria? And archaea? And how does it evolve? We wrote a short review "On the architecture and evolution of prokaryotic multicellularity". Preprint link:
bit.ly/4ta06Gq
Sharing and comments are much appreciated. 1/4
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"En su lógica profunda —aunque no siempre en su funcionamiento cotidiano—, el método científico recompensa la refutación y la revisión. La crítica no es un fallo del sistema; es su combustible."
elpais.com/ciencia/2026...
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¿Está realmente corrompida la ciencia?
Cada escándalo científico alimenta una narrativa ya conocida: la investigación no es diferente del resto de ámbitos de poder, también responde a intereses y también puede manipularse
https://elpais.com/ciencia/2026-03-25/esta-realmente-corrompida-la-ciencia.html
about 1 month ago
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Oscar Silva
Li Zhao
about 1 month ago
We wrote a review on using machine learning to study evolutionary genetics and molecular evolution in Trends in Genetics. It is open access—please take a look if you are interested in this topic
www.sciencedirect.com/science/arti...
@cp-trendsgenetics.bsky.social
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Machine learning for evolutionary genetics and molecular evolution
Over the past decade, the rapid expansion of large-scale data and advances in computational power have allowed machine learning (ML), especially deep …
https://www.sciencedirect.com/science/article/pii/S0168952526000326
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Oscar Silva
Cuaderno de Cultura Científica
about 1 month ago
El teorema central del límite permite detectar trampas: si un resultado es extremadamente raro, probablemente algo no cuadra. Una herramienta clave para entender el azar.
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El teorema central del límite
El teorema central del límite empezó como un truco de bar para los jugadores del siglo XVIII. Hoy los científicos recurren a él a diario.
https://culturacientifica.com/2026/03/24/campanas-de-gauss/
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Oscar Silva
Trends in Plant Science
about 1 month ago
Modeling of gene regulatory networks: an annotated glossary
#plantscience
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Modeling of gene regulatory networks: an annotated glossary
Biological processes are complex. Their behavior cannot be understood from the sum of their parts. Modeling, which allows for articulating hypotheses as equations and rules, has become indispensable for studying biological complexities. When written as computer code, mathematical models can be evaluated to test multiple potential outcomes. Modeling is useful for identifying essential system components and revealing new interactions. However, implementing models in biological research requires a solid understanding of computational and mathematical vocabulary, which typically requires formal training. Furthermore, communication barriers often hinder collaborations with computational modelers. To address this, we present an annotated glossary of terms associated with modeling gene regulatory networks. Aimed at biologists, we explain common computational modeling terms and frameworks using examples from published studies.
http://dlvr.it/TRhQwH
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Oscar Silva
Dmitri Petrov
about 1 month ago
A question for biologists: we often talk about evolutionary novelty. What does “novelty” mean for you? What’s your favorite definition if any? Or just a rule of thumb for what is and isn’t novel.
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Oscar Silva
Torrico
about 1 month ago
Hoy se cumplen 50 años de la última dictadura militar de Argentina Por más que milei y todo el bloque de La Libertad Avanza niegue y célebre los hechos de las dictadura,ni olvido ni perdón Fueron 30000
#NuncaMas
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Oscar Silva
Robin Pranter
about 1 month ago
How do cell lineages evolve, and how does that shape trait evolution? Join our symposium Tracing Evolution Through Cell Lineages (Plön, 12–14 October). Hear perspectives from leading scientists and contribute with your own. Read more at:
bit.ly/3PCSkpQ
#EvoDevo
#DevBio
#StemCell
#evolution
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Oscar Silva
Christian Landry
about 1 month ago
For those interested, the papers associated with my talk:
pubmed.ncbi.nlm.nih.gov/39146405/
pubmed.ncbi.nlm.nih.gov/41699381/
pubmed.ncbi.nlm.nih.gov/36735790/
pubmed.ncbi.nlm.nih.gov/36050399/
pubmed.ncbi.nlm.nih.gov/41763210/
pubmed.ncbi.nlm.nih.gov/31454312/
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Oscar Silva
Kate (Kathryn) Lawrence
about 1 month ago
It's out! I hope this work encourages folks to move beyond a standard "one variant, one gene" QTL paradigm and consider proxitropic variant effects. Big thanks to the reviewers and editors at
@ajhgnews.bsky.social
for their help!
@sbmontgom.bsky.social
www.sciencedirect.com/science/arti...
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Oscar Silva
Roli Roberts
about 1 month ago
Back in the noughties when I was an academic, my lab did quite a bit of work on (conserved) alternative transcripts. This study in
@plosbiology.org
presents compelling evidence that most alternative transcripts are deleterious noise
journals.plos.org/plosbiology/...
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Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans
Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003671
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La verdad es que muchas bases de datos solamente requieren un análisis de regresión lineal simple.
add a skeleton here at some point
about 1 month ago
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Oscar Silva
Richard McElreath 🐈⬛
about 1 month ago
Statistical Rethinking 2026 is done: 20 new lectures emphasizing logical and critical statistical workflow, from basics of probability theory to causal inference to reliable computation to sensitivity. It's all free, made just for you. Lecture list and links:
github.com/rmcelreath/s...
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Oscar Silva
Society for Molecular Biology and Evolution
about 1 month ago
🧬 EvolCompGen presents: Christian Landry on the Evolution of gene duplication, from redundancy to dependency
@christianlandry.bsky.social
🗓️ Join us on Monday, March 23 at 11:00 AM EDT 📌 Register here:
us02web.zoom.us/webinar/regi...
#society
#compbio
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Oscar Silva
Stephen Turner
about 1 month ago
Nature Genetics: The polygenic, omnigenic and stratagenic models of complex disease risk
www.nature.com/articles/s41...
🧬💻🧪 read free:
rdcu.be/eZ2AE
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