Oscar Silva
@oscar-silva.bsky.social
Reposted by Oscar Silva
We suggest that a combination of traditional and machine learning methods make measuring selection on the transcriptome an achievable task-- even in the field, at manageable sample sizes.
paper link: academic.oup.com/gbe/article/...
paper link: academic.oup.com/gbe/article/...
Predicting Fitness-Related Traits Using Gene Expression and Machine Learning
Abstract. Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenoty
academic.oup.com
March 25, 2025 at 1:00 PM
We suggest that a combination of traditional and machine learning methods make measuring selection on the transcriptome an achievable task-- even in the field, at manageable sample sizes.
paper link: academic.oup.com/gbe/article/...
paper link: academic.oup.com/gbe/article/...
Reposted by Oscar Silva
Gentle reminder that John Odling-Smee, who is now in his 90s (!) published his big update on #NicheConstruction last year.
It's open access and can be downloaded here: direct.mit.edu/books/oa-mon...
( #pleasecite )
It's open access and can be downloaded here: direct.mit.edu/books/oa-mon...
( #pleasecite )
Niche Construction: How Life Contributes to Its Own Evolution
How niche construction theory extends evolutionary theory beyond natural selection to a more general theory about the coevolution of organisms with their e
direct.mit.edu
December 10, 2025 at 3:10 PM
Gentle reminder that John Odling-Smee, who is now in his 90s (!) published his big update on #NicheConstruction last year.
It's open access and can be downloaded here: direct.mit.edu/books/oa-mon...
( #pleasecite )
It's open access and can be downloaded here: direct.mit.edu/books/oa-mon...
( #pleasecite )
Reposted by Oscar Silva
Researchers use partitioned local depth (PaLD) to search for patterns within time series transcriptome data
academic.oup.com/insilicoplan...
#Arabidopsis #GRN #PlantScience
academic.oup.com/insilicoplan...
#Arabidopsis #GRN #PlantScience
December 10, 2025 at 4:10 PM
Researchers use partitioned local depth (PaLD) to search for patterns within time series transcriptome data
academic.oup.com/insilicoplan...
#Arabidopsis #GRN #PlantScience
academic.oup.com/insilicoplan...
#Arabidopsis #GRN #PlantScience
Reposted by Oscar Silva
SMBE2026 Symposium 12 | Reconstructing the deep Tree of Life: challenges and new approaches
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
December 10, 2025 at 2:10 PM
SMBE2026 Symposium 12 | Reconstructing the deep Tree of Life: challenges and new approaches
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
Reposted by Oscar Silva
1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
The fitness costs of reproductive specialization scale inversely with organismal size
The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...
www.biorxiv.org
December 9, 2025 at 7:44 PM
1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Oscar Silva
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
December 9, 2025 at 1:58 PM
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
Un artículo de revisión del 2000 que concluye en que el glifosato no representa un riesgo para humanos ha sido retirado recientemente.
El artículo sí debía ser retirado y espero que se más esfuerzos se enfoquen en revisar los aspectos metodológicos de estudios con claro conflicto de interés.
El artículo sí debía ser retirado y espero que se más esfuerzos se enfoquen en revisar los aspectos metodológicos de estudios con claro conflicto de interés.
A review article concluding the weed killer Roundup--aka glyphosate--“does not pose a health risk to humans” has been retracted 8 years after documents released in a court case revealed employees of Monsanto, the company that developed it, wrote the article but were not named as coauthors.
Glyphosate safety article retracted eight years after Monsanto ghostwriting revealed in court
Credit: Mike Mozart/Flickr (CC BY 2.0) A review article concluding the weed killer Roundup “does not pose a health risk to humans” has been retracted eight years after documents released in a court…
retractionwatch.com
December 8, 2025 at 10:40 PM
Un artículo de revisión del 2000 que concluye en que el glifosato no representa un riesgo para humanos ha sido retirado recientemente.
El artículo sí debía ser retirado y espero que se más esfuerzos se enfoquen en revisar los aspectos metodológicos de estudios con claro conflicto de interés.
El artículo sí debía ser retirado y espero que se más esfuerzos se enfoquen en revisar los aspectos metodológicos de estudios con claro conflicto de interés.
Reposted by Oscar Silva
"...enhance models, highlighting opportunities such as incorporating time-varying connections, adaptive topologies, and multilayer structures to better represent the temporal dynamics and multilevel interactions characteristic of biological systems."
www.sciencedirect.com/science/arti...
🧪 #EvoBio
www.sciencedirect.com/science/arti...
🧪 #EvoBio
December 7, 2025 at 11:41 PM
"...enhance models, highlighting opportunities such as incorporating time-varying connections, adaptive topologies, and multilayer structures to better represent the temporal dynamics and multilevel interactions characteristic of biological systems."
www.sciencedirect.com/science/arti...
🧪 #EvoBio
www.sciencedirect.com/science/arti...
🧪 #EvoBio
Reposted by Oscar Silva
Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed https://www.biorxiv.org/content/10.1101/2025.09.09.675213v1
September 10, 2025 at 4:32 AM
Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed https://www.biorxiv.org/content/10.1101/2025.09.09.675213v1
Reposted by Oscar Silva
Lineage-specific evolution of regulatory landscapes in polyploid plant and its diploid progenitors https://www.biorxiv.org/content/10.64898/2025.12.04.692133v1
December 5, 2025 at 9:31 PM
Lineage-specific evolution of regulatory landscapes in polyploid plant and its diploid progenitors https://www.biorxiv.org/content/10.64898/2025.12.04.692133v1
Reposted by Oscar Silva
Check out this new #AJB On the Nature of Things essay!
#Pangenomes as a framework for adaptive radiation, speciation & adaptation
By @nicolo-tellini.bsky.social , Ole Tørresen, David Edwards, Loren Rieseberg, Kjetill Jakobsen & José Cerca
doi.org/10.1002/ajb2... #botany #plantscience #evolution
#Pangenomes as a framework for adaptive radiation, speciation & adaptation
By @nicolo-tellini.bsky.social , Ole Tørresen, David Edwards, Loren Rieseberg, Kjetill Jakobsen & José Cerca
doi.org/10.1002/ajb2... #botany #plantscience #evolution
December 5, 2025 at 2:51 PM
Check out this new #AJB On the Nature of Things essay!
#Pangenomes as a framework for adaptive radiation, speciation & adaptation
By @nicolo-tellini.bsky.social , Ole Tørresen, David Edwards, Loren Rieseberg, Kjetill Jakobsen & José Cerca
doi.org/10.1002/ajb2... #botany #plantscience #evolution
#Pangenomes as a framework for adaptive radiation, speciation & adaptation
By @nicolo-tellini.bsky.social , Ole Tørresen, David Edwards, Loren Rieseberg, Kjetill Jakobsen & José Cerca
doi.org/10.1002/ajb2... #botany #plantscience #evolution
Reposted by Oscar Silva
Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Reconstructing Waddington’s landscape from data | PNAS
The development of a zygote into a functional organism requires that this single progenitor
cell gives rise to numerous distinct cell types. Attemp...
www.pnas.org
December 4, 2025 at 6:29 AM
Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Reposted by Oscar Silva
I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making!
Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃
https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution
Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃
https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution
December 3, 2025 at 2:09 PM
I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making!
Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃
https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution
Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃
https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution
Reposted by Oscar Silva
Submit an abstract to our symposium "S20 Mapping fitness landscapes with mechanistic models, machine learning and experiments" 🧬 - organised with @meikewortel.bsky.social
Abstract submission & Award applications for SMBE 2026 are now open!
Submit your research and apply for SMBE awards via the submission portal.
📝 Read more & submit here: smbe2026.org/abstracts
And symposium selection is now finalized!
👉 See all accepted symposia: smbe2026.org/programme
#SMBE2026
Submit your research and apply for SMBE awards via the submission portal.
📝 Read more & submit here: smbe2026.org/abstracts
And symposium selection is now finalized!
👉 See all accepted symposia: smbe2026.org/programme
#SMBE2026
December 1, 2025 at 2:35 PM
Submit an abstract to our symposium "S20 Mapping fitness landscapes with mechanistic models, machine learning and experiments" 🧬 - organised with @meikewortel.bsky.social
Reposted by Oscar Silva
Reposted by Oscar Silva
And while I'm at it, just because a genomic loci is transcribed, it does not follow that it is a gene! (yes, I'm looking at you lncRNA people!)
THANK YOU.
THANK YOU.
November 28, 2025 at 3:08 PM
And while I'm at it, just because a genomic loci is transcribed, it does not follow that it is a gene! (yes, I'm looking at you lncRNA people!)
THANK YOU.
THANK YOU.
Reposted by Oscar Silva
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 4:21 PM
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Reposted by Oscar Silva
An inspirational example of 𝐬𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐜𝐫𝐞𝐚𝐭𝐢𝐯𝐢𝐭𝐲, 𝐨𝐫𝐢𝐠𝐢𝐧𝐚𝐥𝐢𝐭𝐲 𝐚𝐧𝐝 𝐫𝐢𝐠𝐨𝐫:
Chemiosmosis remains one of the most striking examples of originality in modern biology. At a time when biochemical dogma insisted on high-energy intermediates, Peter Mitchell proposed & rigorously articulated the radical ...
Chemiosmosis remains one of the most striking examples of originality in modern biology. At a time when biochemical dogma insisted on high-energy intermediates, Peter Mitchell proposed & rigorously articulated the radical ...
November 27, 2025 at 1:45 PM
An inspirational example of 𝐬𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐜𝐫𝐞𝐚𝐭𝐢𝐯𝐢𝐭𝐲, 𝐨𝐫𝐢𝐠𝐢𝐧𝐚𝐥𝐢𝐭𝐲 𝐚𝐧𝐝 𝐫𝐢𝐠𝐨𝐫:
Chemiosmosis remains one of the most striking examples of originality in modern biology. At a time when biochemical dogma insisted on high-energy intermediates, Peter Mitchell proposed & rigorously articulated the radical ...
Chemiosmosis remains one of the most striking examples of originality in modern biology. At a time when biochemical dogma insisted on high-energy intermediates, Peter Mitchell proposed & rigorously articulated the radical ...
Miss Universo nunca me había parecido tan interesante, hasta el día de hoy.
De lo kitsch al crimen organizado: la polémica de Miss Universo destapa una red de tráfico de drogas, armas y huachicol
Raúl Rocha ha pasado de ser acusado de amañar el premio a favor de la ganadora mexicana a ser perseguido por liderar una red criminal dozz.es/0b2qz16
Raúl Rocha ha pasado de ser acusado de amañar el premio a favor de la ganadora mexicana a ser perseguido por liderar una red criminal dozz.es/0b2qz16
De lo kitsch al crimen organizado: la polémica de Miss Universo destapa una red de tráfico de drogas, armas y huachicol
Raúl Rocha, el dueño del certamen de belleza, ha pasado en una semana de ser acusado de amañar el premio a favor de la ganadora mexicana a ser perseguido por liderar una red criminal con vínculos dentro de la propia fiscalía federal
dozz.es
November 27, 2025 at 8:53 PM
Miss Universo nunca me había parecido tan interesante, hasta el día de hoy.
"We review the highly expanded range of departures from the standard genetic code, highlighting previously unanticipated code forms and their molecular underpinnings."
Natural and artificial variations of the standard genetic code
Great new review by Julius Lukes & colleagues 👇
www.cell.com/current-biol...
Great new review by Julius Lukes & colleagues 👇
www.cell.com/current-biol...
November 27, 2025 at 12:34 AM
"We review the highly expanded range of departures from the standard genetic code, highlighting previously unanticipated code forms and their molecular underpinnings."
Reposted by Oscar Silva
Our friend Kunihiko Kaneko published his new amazing book!
"Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle"
An insights into biology from physics perspective providing picture of the universal characteristics of living systems across scales
"Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle"
An insights into biology from physics perspective providing picture of the universal characteristics of living systems across scales
Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle
Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle : Kaneko, Kunihiko: Amazon.de: Books
www.amazon.de
November 26, 2025 at 10:43 AM
Our friend Kunihiko Kaneko published his new amazing book!
"Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle"
An insights into biology from physics perspective providing picture of the universal characteristics of living systems across scales
"Universal Biology: The Physics of Life through the Macro-Micro Consistency Principle"
An insights into biology from physics perspective providing picture of the universal characteristics of living systems across scales
Reposted by Oscar Silva
Treating emergent traits of the microbiome like quantitative genetic traits of the host reveals how environmentally acquired symbionts can contribute to hosts' adaptation
Quantitative genetics of microbiome-mediated traits
Microbiomes, the complex communities of microorganisms associated with multicellular hosts, play a vital role in shaping host traits and fitness. But how d
buff.ly
November 24, 2025 at 3:19 PM
Treating emergent traits of the microbiome like quantitative genetic traits of the host reveals how environmentally acquired symbionts can contribute to hosts' adaptation
Reposted by Oscar Silva
"The discovery pushes the boundaries of our knowledge of just how small and simple cellular life can become, as it evolves even into forms that are barely alive."
Genome sequencing technology is introducing biologists to a world of quasi-life forms that they’ve never met before. @jakebuehler.bsky.social reports: www.quantamagazine.org/a-cell-so-mi...
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
www.quantamagazine.org
November 24, 2025 at 4:07 PM
"The discovery pushes the boundaries of our knowledge of just how small and simple cellular life can become, as it evolves even into forms that are barely alive."
Reposted by Oscar Silva
#OnThisDay in 1859, Charles Darwin's On the Origin of Species was first published.
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
November 24, 2025 at 11:26 AM
#OnThisDay in 1859, Charles Darwin's On the Origin of Species was first published.
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)