Ahmed Elfarargi
@ahmedelfarargi.bsky.social
Postdoc fellow @UT_AUSTIN | Evolutionary genomics | Local adaptation | Population genetics | Plant stress | Alumnus @MPIPZ_KÖLN @WUR
Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana
Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana
Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing ...
www.biorxiv.org
February 10, 2025 at 8:54 PM
Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana
Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae
Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae
As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which a...
www.biorxiv.org
February 9, 2025 at 4:54 PM
Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae
Quickdraws: a GWAS method to perform scalable association testing for quantiative and binary traits, without compromising computational efficiency
A scalable variational inference approach for increased mixed-model association power - Nature Genetics
Quickdraws is a mixed-model association tool with a noninfinitesimal prior for analyzing binary and quantitative traits, using a scalable variational inference that allows analysis of biobank-scale co...
www.nature.com
January 10, 2025 at 10:25 AM
Quickdraws: a GWAS method to perform scalable association testing for quantiative and binary traits, without compromising computational efficiency
Reposted by Ahmed Elfarargi
Very happy to see our work on deleterious mutations in #tomato published in @naturegenet.bsky.social 🧬🌱🍅! We identify deleterious mutations that were enriched during #domestication and apply #CRISPR to repair a mutation in cultivated tomato. #genetics #plantscience
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing - Nature Genetics
A deleterious mutation in the tomato transcription factor SSP2 was enriched during domestication. Repairing the deleterious mutation in cultivated tomato by base editing leads to compact growth and ea...
www.nature.com
January 4, 2025 at 11:29 AM
Very happy to see our work on deleterious mutations in #tomato published in @naturegenet.bsky.social 🧬🌱🍅! We identify deleterious mutations that were enriched during #domestication and apply #CRISPR to repair a mutation in cultivated tomato. #genetics #plantscience
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus
A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus
A rare dominant yellow SCC allele in B. napus was identified, which significantly increased SOC and decreased SLC simultaneously.
www.science.org
January 6, 2025 at 5:53 AM
A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - Nature Biotechnology
A language model predicts the effects of genetic variants in the human genome.
www.nature.com
January 6, 2025 at 2:24 AM
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants
The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum
The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum - Nature Genetics
A haplotype-resolved genome of hybrid sugarcane cultivar XTT22 and population analyses of Saccharum accessions highlight the genome evolution of allopolyploids and provide opportunities for sugarcane ...
www.nature.com
January 6, 2025 at 2:22 AM
The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum
RNAGenesis: Foundation Model for Enhanced RNA Sequence Generation and Structural Insights
RNAGenesis: Foundation Model for Enhanced RNA Sequence Generation and Structural Insights
RNA plays an essential role in a wide range of biological processes. Gaining a deeper understanding of their functions can significantly advance our knowledge of life's mechanisms and drive the develo...
www.biorxiv.org
January 6, 2025 at 2:15 AM
RNAGenesis: Foundation Model for Enhanced RNA Sequence Generation and Structural Insights
Orthology inference at scale with FastOMA
Orthology inference at scale with FastOMA - Nature Methods
FastOMA achieves fast and accurate orthology inference, with linear scalability.
www.nature.com
January 5, 2025 at 7:03 AM
Orthology inference at scale with FastOMA
Natural variation modifies centromere proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana
Natural variation modifies centromere proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana
Background: Centromeres mediate chromosome segregation during cell division. In plants, centromeres are loaded with CENH3-variant nucleosomes, which direct kinetochore formation and spindle microtubul...
www.biorxiv.org
January 5, 2025 at 6:59 AM
Natural variation modifies centromere proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana
Reposted by Ahmed Elfarargi
Really pleased to transition from 2024 to 2025 with Tatiana Vernie's work on the evolution of the common symbiosis pathway published @pnas.org 🔽
We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years!
www.pnas.org/doi/10.1073/...
We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years!
www.pnas.org/doi/10.1073/...
Conservation of symbiotic signaling since the most recent common ancestor of land plants | PNAS
Plants have colonized lands 450 million years ago. This terrestrialization was facilitated
by developmental and functional innovations. Recent evo-...
www.pnas.org
January 1, 2025 at 12:05 PM
Really pleased to transition from 2024 to 2025 with Tatiana Vernie's work on the evolution of the common symbiosis pathway published @pnas.org 🔽
We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years!
www.pnas.org/doi/10.1073/...
We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years!
www.pnas.org/doi/10.1073/...
Reposted by Ahmed Elfarargi
Paper #2 - we generated 10 new chr-level genomes for hornworts covering all families and most genera. Also the first look into their U/V sex chromosomes! 3/4 www.nature.com/articles/s41...
Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes - Nature Plants
This study presents 11 new hornwort (Anthocerotophyta) genomes that clarify the structure and evolution of sex and accessory chromosomes in bryophytes and shed new light on the early evolution of land...
www.nature.com
January 3, 2025 at 11:11 AM
Paper #2 - we generated 10 new chr-level genomes for hornworts covering all families and most genera. Also the first look into their U/V sex chromosomes! 3/4 www.nature.com/articles/s41...
Reposted by Ahmed Elfarargi
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...
Increasing aridity may threaten the maintenance of a plant defence polymorphism
Increasing Aridity May Threaten the Maintenance of a Plant Defence Polymorphism
It is unclear how environmental change influences standing genetic variation in wild populations. Here, we characterised environmental conditions that protect versus erode polymorphic chemical defenc...
onlinelibrary.wiley.com
January 4, 2025 at 7:49 PM
Increasing aridity may threaten the maintenance of a plant defence polymorphism
The role of pangenomics in orphan crop improvement
The role of pangenomics in orphan crop improvement - Nature Communications
A single reference genome is not enough to harness the full genetic variation of a species. Here, the authors review pangenomics principles, construction and applications for orphan crop improvement, ...
www.nature.com
January 4, 2025 at 12:47 PM
The role of pangenomics in orphan crop improvement
The genomic secrets of invasive plants
The genomic secrets of invasive plants
Genomics has revolutionised the study of invasive species, allowing evolutionary biologists to dissect mechanisms of invasion in unprecedented detail. Botanical research has played an important role ...
nph.onlinelibrary.wiley.com
January 4, 2025 at 3:47 AM
The genomic secrets of invasive plants
Reposted by Ahmed Elfarargi
Gabriele's paper is out in PNAS! He found a large number of genes with repeated sweeps in multiple plant species. Most interestingly: they tend to be peripheral in co-expression networks (low pleiotropy), consistent with mig-sel theory!! @gabnocgenomics.bsky.social www.pnas.org/doi/10.1073/...
January 2, 2025 at 9:31 PM
Gabriele's paper is out in PNAS! He found a large number of genes with repeated sweeps in multiple plant species. Most interestingly: they tend to be peripheral in co-expression networks (low pleiotropy), consistent with mig-sel theory!! @gabnocgenomics.bsky.social www.pnas.org/doi/10.1073/...
Reposted by Ahmed Elfarargi
We may have cut our last Canu release in 2024, but we are starting off 2025 with Verkko2! 🎉 Not only is it 4x faster than Verkko1, this version integrates Hi-C data for both phasing and scaffolding, enabling the automated assembly of acrocentric chromosomes! Preprint: www.biorxiv.org/content/10.1...
January 2, 2025 at 3:27 PM
We may have cut our last Canu release in 2024, but we are starting off 2025 with Verkko2! 🎉 Not only is it 4x faster than Verkko1, this version integrates Hi-C data for both phasing and scaffolding, enabling the automated assembly of acrocentric chromosomes! Preprint: www.biorxiv.org/content/10.1...
Reposted by Ahmed Elfarargi
Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
January 2, 2025 at 9:49 PM
Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...