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Nat Walker-Hale (@phylonatworks) profile picture

Nat Walker-Hale

@phylonatworks

🇳🇿 PDRA with @Chomicki_G @DurBiol @durham_uni. Mostly phylo stuff, sometimes NZ pol, sometime just pol

 Durham, England
Joined October 2017
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Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)Photo by Nat Walker-Hale (@phylonatworks)
Nat Walker-Hale retweeted
Lior Pachter (@lpachter) profile picture
Lior Pachter@lpachterOct 8
Update: Hundreds of papers published (the package) ✅ The author list is "the consortium" ✅ Raw data not released ✅ Within days errors found in multiple publications ✅ One person claims credit for all the work of the consortium and compares himself to Newton ✅
Lior Pachter (@lpachter) profile pictureLior Pachter@lpachterSep 9
Mathematics has now fully morphed into biology: Project costs millions $ ✅ Put out paper that nobody has read ✅ Massive paper supplement nobody will read ✅ Advertise with pretty art ✅ Vicious authorship fight ✅ Say you're curing cancer ✅
Image from Lior Pachter (@lpachter)
Image from Lior Pachter (@lpachter)
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Ryo Yokoyama (@yokoyama_ryo) profile picture
Ryo Yokoyama@yokoyama_ryoOct 8
Machine learning–assisted directed evolution of plant Rubisco | Science Advances science.org/doi/10.1126/scia… @ScienceAdvances
Machine learning–assisted directed evolution of plant Rubisco

Machine learning–assisted directed evolution of plant Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is foundational to life on Earth, catalyzing carbon dioxide (CO2) fixation to generate biomass. However, Rubisco is a slow and inefficient...

science.org
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Nat Walker-Hale retweeted
Rasmus Nielsen (@ras_nielsen) profile picture
Rasmus Nielsen@ras_nielsenOct 8
Forensic likelihood ratios for shotgun sequencing data from DNA mixtures biorxiv.org/content/10.64898…
Forensic likelihood ratios for shotgun sequencing data from DNA mixtures

Forensic likelihood ratios for shotgun sequencing data from DNA mixtures

Shotgun sequencing of DNA mixtures has the potential to become an important tool in forensic genetics, particularly for degraded samples or complex mixtures. However, the analysis of shotgun-sequen...

biorxiv.org
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Nicolò Cesa-Bianchi (@NicoloCB) profile picture
Nicolò Cesa-Bianchi@NicoloCBOct 7
My dream had always been to prove beautiful theorems as the AI agents unloaded my dishwasher. Well, it went the wrong way... 😂
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Mar Albà (@maralbasoler) profile picture
Mar Albà@maralbasolerOct 4
We are recruiting!! EU-funded PhD position to study the evolution of recently emerged small proteins - from noise to function apply before Oct 22! albagroup.researchmar.net/po… orfeus-dn.eu @GRIB_Barcelona @the_prbb
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Macroevolutionary Rates of Species Interactions: Approximate Bayesian Inference from Cophylogenies academic.oup.com/sysbio/adva… @systbiol
Macroevolutionary Rates of Species Interactions: Approximate Bayesian Inference from Cophylogenies

Macroevolutionary Rates of Species Interactions: Approximate Bayesian Inference from Cophylogenies

Abstract. Understanding the macroevolutionary dynamics of species interactions such as parasitisms, commensalisms, and mutualisms is an important goal in e

academic.oup.com
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John Ganz (@lionel_trolling) profile picture
John Ganz@lionel_trollingOct 2
I found a Soviet primer on dialectical materialism, and this was the note of a previous owner inside
Image from John Ganz (@lionel_trolling)
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Jakob Heinz (@JakobHeinz9) profile picture
Jakob Heinz@JakobHeinz9Oct 1
I’m excited to share our new preprint introducing HipHap (HIgh-Performance HAPlotype assigner), a tool for assigning long reads to haplotype-resolved diploid reference assemblies! With Max Marin, Matthew Meyerson, @lh3lh3 Preprint: biorxiv.org/content/10.64898… 🧵1/6
HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes

HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes

Diploid genome assemblies are now routinely available, but most read aligners were designed for haploid references, which have long been the gold standard. When reads are aligned to a diploid...

biorxiv.org
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Nature Methods (@naturemethods) profile picture
Nature Methods@naturemethodsOct 2
ResolVI: error and batch correction for spatial transcriptomics data. nature.com/articles/s41592-0…
Image from Nature Methods (@naturemethods)
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Nature Methods (@naturemethods) profile picture
Nature Methods@naturemethodsOct 2
Spatial Hi-C allows the study of chromatin in a spatially resolved manner, as applied to adult and developing mouse brains. nature.com/articles/s41592-0…
Image from Nature Methods (@naturemethods)
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Early-diverging lineages provide little information about ancestors academic.oup.com/sysbio/adva… @systbiol
'Early-Diverging' Lineages Provide Little Information about Ancestors

'Early-Diverging' Lineages Provide Little Information about Ancestors

Abstract. Large phylogenetic trees are often unbalanced near the root, with a species-depauperate lineage sister to a far more species-rich clade. The spec

academic.oup.com
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Chenxu Zhu (@chenxuzhu) profile picture
Chenxu Zhu@chenxuzhuOct 2
How do our genomes tolerate millions of non-coding mutations without changing gene expression? This new preprint introduces Nanopore-HiChIP, which maps multi-way enhancer hubs at haplotype resolution. biorxiv.org/content/10.64898…
High-order enhancer hubs buffer allelic regulatory variation through kinetic compensation

High-order enhancer hubs buffer allelic regulatory variation through kinetic compensation

Diploid genomes carry millions of heterozygous variants in cis-regulatory DNA, yet most genes produce similar RNA output from two parental alleles. How this balance is maintained is unclear. We...

biorxiv.org
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Daniel Tabin (@DanTabin) profile picture
Daniel Tabin
@DanTabinSep 29
New preprint on rescaling in forward in time simulations like SLiM from Takahiro Sakamoto. Not only does the preprint nicely quantify the biases involved in rescaling, but they also provide a less biased way of doing so. Find the preprint here: biorxiv.org/content/10.64898…
Image from Daniel Tabin (@DanTabin)
Image from Daniel Tabin (@DanTabin)
Image from Daniel Tabin (@DanTabin)
Image from Daniel Tabin (@DanTabin)
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New Phytologist (@NewPhyt) profile picture
New Phytologist@NewPhytSep 30
Linking genomic variation to floral trait adaptation across species boundaries #TansleyReview by Acoca-Pidolle et al. nph.onlinelibrary.wiley.com/… #plantscience
Linking genomic variation to floral trait adaptation across species boundaries

Linking genomic variation to floral trait adaptation across species boundaries

Examples of floral trait divergences between sister species adapted to different pollination modes.

nph.onlinelibrary.wiley.com
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Iñaki Ruiz-Trillo (@multicellgenome) profile picture
Iñaki Ruiz-Trillo@multicellgenomeOct 1
Evolution can innovate without inventing. Cell type families retain ancient regulatory “vocabularies”, while individual cell types evolve by reshuffling how those motifs are combined. New cell types from old regulatory words. We like this! @NatureEcoEvo doi.org/10.1038/s41559-026-0…
Image from Iñaki Ruiz-Trillo (@multicellgenome)
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Cameron Thrash (@jcamthrash) profile picture
Cameron Thrash@jcamthrashSep 29
Mutational bias and local genome context constrain adaptive paths in experimental evolution academic.oup.com/genetics/ad…
Mutational bias and local genome context constrain adaptive paths in experimental evolution

Mutational bias and local genome context constrain adaptive paths in experimental evolution

Abstract. Experimental evolution provides a reproducible testing ground for the study of adaptive evolution where the numerous degrees of freedom impacting

academic.oup.com
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Adam Bentham (@AdamRBentham) profile picture
Adam Bentham@AdamRBenthamSep 30
🚨 Please share! 🚨 I'm recruiting a fully funded 4-year Gatsby Sainsbury PhD studentship at Durham! 🌱🤖 Designing plant immune receptors from scratch, combining AI protein design with structural biology and plant immunity. benthamlab.org shorturl.at/U2PdV
Bentham Lab — Durham University

Bentham Lab — Durham University

Bentham Lab, Centre for Programmable Biological Matter, Durham University. Structural biology and de novo protein design applied to host-pathogen interactions, plant immunity, and neglected tropical...

benthamlab.org
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Ethan Linck (@ethanblinck) profile picture
Ethan Linck@ethanblinckSep 30
I'm hiring a postdoc as part of NSF-funded work on inferring complex speciation histories from genomic data. looking for strong computational skills or a willingness to learn. details flexible—please reach out with questions! (ad follows)
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Ryo Yokoyama (@yokoyama_ryo) profile picture
Ryo Yokoyama@yokoyama_ryoSep 29
Metabolic engineering of Saccharomyces cerevisiae for the biosynthesis of indole-derived compounds: Trends in Biotechnology cell.com/trends/biotechnolog…
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