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Maddy Comerford

@maddycomerford.bsky.social
86 followers 160 following 5 posts

phd grad interested in human evolutionary genetics and archaic introgression @ SVIMR

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Reposted by Maddy Comerford
Paige Madison @fossilhistory.bsky.social · 8h
#OnThisDay in 1861, Charles Darwin wrote to his friend, "But I am very poorly today and very stupid and hate everybody and everything." 📜🧪
Sepia photograph of Charles Darwin in old age, seated in a chair and shown from the waist up in three-quarter profile facing right, against a plain backdrop. He is bald on top with white hair at the sides, a lined forehead, and a long, full white beard. He wears a dark, heavy overcoat with wide lapels over a waistcoat, his hands resting in his lap at the lower right.A line of Charles Darwin's handwriting in brown ink on cream paper, with faint writing showing through from the other side of the page. It reads: "But I am very poorly today & very stupid & hate everybody & everything."
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Bat1K Genome Project @bat1kgenomes.bsky.social · 23/09/2026
Where did bats come from?🦇🌍 After decades of debate, the biggest bat genome + fossil study ever done has an answer - and it’s not where anyone expected! 🤩OUR PHASE 1 FLAGSHIP is out today in nature! doi.org/10.1038/s415... A thread 🧵
doi.org
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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David Gokhman @david-gokhman.bsky.social · 23/09/2026
Humans are remarkably prone to degenerative skeletal diseases. Other apes, much less so, even in old age. In our new paper in @nature.com , we map the genetic changes that shaped our skeleton and uncover a major clue to why it is so vulnerable to degeneration.🧵👇 www.nature.com/articles/s41...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 11/09/2026
Massively parallel characterization reveals context-dependent and non-additive regulatory effects of closely spaced variant pairs www.biorxiv.org/content/10.64898/20…
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Nature Reviews Genetics @natrevgenet.nature.com · 11/09/2026
New online! Genomic insights into natural selection in recent human history
dlvr.it
Genomic insights into natural selection in recent human history
Nature Reviews Genetics, Published online: 11 September 2026; doi:10.1038/s41576-026-01010-9Advances in genome-wide selection scans and ancient DNA have greatly expanded our ability to study human evolution. This Review discusses the conceptual and statistical challenges in identifying and interpreting selection signals, and how recent approaches are reshaping our understanding of human evolution over the past 10,000 years.
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Philip Ball @philipcball.bsky.social · 11/09/2026
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1 www.science.org/doi/10.1126/...
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the ...
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Nature @nature.com · 09/09/2026
An abandoned quarry in southwestern China has given scientists an unprecedented glimpse into the lives and abilities of the mysterious ancient humans called Denisovans go.nature.com/46NsuVp
go.nature.com
Who were the Denisovans? Rich trove of fossils and tools paints new picture
Objects found in a cave in southwestern China suggest that these enigmatic ancient humans were accomplished hunters.
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Yun S. Song @yun-s-song.bsky.social · 09/09/2026
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
doi.org
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
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Nature @nature.com · 08/09/2026
AI model AlphaGenome forecasts the consequences of altering every single DNA letter in the human genome go.nature.com/4xQ7ZDK
go.nature.com
DeepMind’s new genome ‘atlas’ charts effects of all 9 billion human gene mutations
AI model AlphaGenome forecasts the consequences of altering every single DNA letter in the human genome.
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Cecilia Padilla-Iglesias @ceciliapad.bsky.social · 07/09/2026
Since they are not on Bluesky, here sharing the fantastic new paper by the Archaeo- and Paleogenetics group here in Tübingen on the settlement history of western Remote Oceania.🧬 www.cell.com/cell/fulltex...
cell.com
Ancient genomes reveal distinct human dispersals and social stratification in the settlement history of western Remote Oceania
The peopling of Remote Oceania involved some of humanity’s greatest expansions into the open ocean. Ancient DNA spanning the last 3,000 years from the Solomon Islands, Vanuatu, Fiji, and Tonga reveals...
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Marco Capodiferro @marcocapo.bsky.social · 04/09/2026
Our paper on archaic introgression in imputed ancient genomes is out. Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable. doi.org/10.1038/s414...
doi.org
Archaic ancestry inference in imputed ancient human genomes - Nature Communications
Genotype imputation enables accurate detection of Neanderthal and Denisovan ancestry in low-coverage ancient genomes and allows the identification of introgressed haplotypes as well as candidate genes...
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Quanyu Chen @yeezus-chen.bsky.social · 02/09/2026
cool
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Maddy Comerford @maddycomerford.bsky.social · 03/09/2026
Very pleased to be sharing this one! Understanding the consequences of Denisovan introgression remains challenging given the poor representation of global introgression in functional genomics resources. We wanted to know if, and how, AlphaGenome could help us navigate that gap 🧭 ⬇️
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Irene Gallego Romero @ee-reh-neh.bsky.social · 03/09/2026
Here's something a bit different that we've been noodling around with! Nearly 10y ago we established a panel of cell lines from Papuan donors, which let us check predictions from AlphaGenome against experimental data. If you've followed the field you'll know that expression prediction is very tough
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Andrew Curry @andrewcurry.com · 02/09/2026
Ancient parchments, covered in ancient disease DNA! Researchers led by @ucddublin.bsky.social's @gingerhowley.bsky.social recover the genes of a deadly animal pathogen from medieval manuscripts. @science.org
science.org
Ancient sheep virus found hiding in medieval parchment
Newly recovered sheeppox sequences reveal when and how the virus emerged
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Science Magazine @science.org · 31/08/2026
This is what a Jurassic forest may have sounded like. By combining exquisitely preserved fossil wings with experiments on living insects, computer simulations, and machine learning, scientists have re-created what they say is a partial Middle Jurassic soundscape. scim.ag/4cirWKy
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Riley Mangan @rimangan.bsky.social · 28/08/2026
I'm very excited to share the preprint of the central project of my postdoc, titled "Sequence-to-function deep learning decodes human cis-regulatory evolution" available today on BioRxiv. Preprint: www.biorxiv.org/content/10.6...
Figure 1: Sequence-based deep learning prediction of lineage-specific cis-regulatory elements in human evolution  (a) Identification of lineage-specific cis-regulatory elements (linCREs). We generated diploid personalized genomes across 17 hominin and great ape short read sequencing libraries through reference-guided assembly. We used Enformer22 to predict genome-wide chromatin accessibility profiles across 100 epigenomic contexts across all 34 haplotypes. We compared chromatin accessibility at open chromatin elements to identify linCREs. (b) Six classes of linCREs, defined by the lineage and direction of differential accessibility. Schematics at top illustrate accessibility profiles defining each class. Total linCRE instances and the number of distinct loci are reported for each class. Predicted accessibility across all 34 haplotypes in a 3kb window centered on a representative example element of each class are shown below, colored by lineage.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 19/08/2026
Agwamba et al. identify the western Iberian Peninsula as the primary source of American populations of house mice; divergence dates are consistent with post-15th-century European maritime expansion and settlement in the Americas 🔗 academic.oup.com/gbe/article/... #societyjournal #evolution #genome
GBE | New Country for Old Mice: The Recent Colonization History of Mus musculus domesticus in the Americas
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svimedicalresearch.bsky.social @svimedicalresearch.bsky.social · 21/08/2026
A new international study, led by Associate Professor Irene Gallego Romero, has revealed gaps in how human diversity is represented and reported in some of the world’s largest public genomics databases. Find out more: www.svi.edu.au/news-events/...
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Irene Gallego Romero @ee-reh-neh.bsky.social · 18/08/2026
maybe this is my new lab photo?
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Irene Gallego Romero @ee-reh-neh.bsky.social · 14/08/2026
Don't let the title mislead you - we parsed through 700,000 SRA record so you don't have to! We looked at who's doing research, where, who they're including, and how they're describing them. In brief: knowledge generation is concentrated in HICs, and heavily features people who live in said HICs.
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Pai Kusuma @paikusuma.bsky.social · 14/08/2026
New preprint out! The Punan of Borneo offer rare windows into what happens molecularly when a hunter-gatherers transitions to a settled lifestyle, and the answer is: a lot and fast. Deep gratitude to the communities for their trust & participation. Feedback welcome 🙏 www.biorxiv.org/content/10.6...
biorxiv.org
Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers
The transition from hunter-gatherer to agricultural lifestyles is one of the landmarks in the history of human societies, but its phenotypic and immediate molecular consequences remain poorly understo...
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Irene Gallego Romero @ee-reh-neh.bsky.social · 14/08/2026
Old lady in first author paper shocker! 🧪🧬🖥️ (ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!) www.cell.com/cell-genomic...
cell.com
Reporting and representation of population descriptors in public RNA-seq databases
By combining repository metadata, genotype-inferred ancestry, and manual curation of publications, Gallego Romero et al. demonstrate that public RNA-seq datasets are dominated by samples from high-inc...
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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026
We have a new preprint out :D www.biorxiv.org/content/10.6... Did Denisovans inherit their AMBN gene from Homo erectus? We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social ~Summary below~
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bioRxivpreprint @biorxivpreprint.bsky.social · 08/08/2026
Denisovan leg bones from Taiwan reveal large body size www.biorxiv.org/content/10.64898/20…
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Jonathan Pritchard @jkpritch.bsky.social · 09/08/2026
Must-know numbers in human genetics -- As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties. jkpritchard.substack.com/p/on-fermi-p...
jkpritchard.substack.com
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
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Nature Portfolio @natureportfolio.nature.com · 24/06/2026
Some of the last surviving Neanderthals of northwestern Europe may have lived in large, well-connected groups, separate from other Neanderthals and early humans, according to research in Nature. go.nature.com/4ahgsWF 🧬🏺🧪
This is figure 1, which shows temporal and geographical overview of the analysed Neanderthal remains.
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David Grimm @david-grimm.bsky.social · 24/06/2026
The 12 souls aboard will drift for a long 8 months, mostly without seeing the Sun, through one of the most inhospitable and least explored regions on Earth. Fun story by Richard Stone for @science.org
science.org
A dozen people will spend 8 months trapped in Arctic ice—for science
Battling darkness and cold, researchers on a drifting laboratory will probe the biology of the Arctic Ocean
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ellie_ancient @elenaessel.bsky.social · 23/06/2026
So happy and proud to see this paper out in @natcomms.nature.com today! We show that traces of human DNA can persist on cave walls for thousands of years. Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team! www.nature.com/articles/s41...
nature.com
Investigating ancient human DNA preservation on cave walls and in rock art - Nature Communications
Ancient DNA can be preserved on materials from archaeological floor deposits such as bones, sediments and artifacts. Here, the authors investigate whether Palaeolithic wall art can preserve human DNA ...
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Cedric Boeckx @cedricboeckx.bsky.social · 11/06/2026
Important new work on introgression, by E. Eichler & colleagues, out in @science.org 🧪🧬💀 “A global map for introgressed structural variation and selection in humans” www.science.org/doi/10.1126/...
science.org
A global map for introgressed structural variation and selection in humans
Genetic introgression from Neanderthals and Denisovans shaped modern human genomes; however, introgressed structural variants (SVs ≥ 50 base pairs) remain challenging to discover. We integrated high-q...
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Navya Shukla @navya-shukla.bsky.social · 09/06/2026
Lift&Add is live 🙂 suprised that trying to the answer the simple problem - how do I get more marsupials in my alignments? - has let to a method paper, but happy nonetheless. academic.oup.com/bioinformati...
academic.oup.com
Lift&Add—rapid and robust addition of new species to alignments of conserved non-coding sequences
AbstractMotivation. Identifying sequence constraint across long evolutionary distances is a powerful method for the discovery of functional genomic sequenc
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Maddy Comerford @maddycomerford.bsky.social · 31/03/2026
devastating scenes. trying to be like the honey badger and not care but it's hard... 🥺😭
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V Pellicer- looking for work! @veppart.bsky.social · 26/03/2026
#2026MMM #SweetSixteen #BoneyardDivision #TeamHoneyBadger Art by Valeria Pellicer @veppart.bsky.social
A portrait of a snarling honey badger against a black background with red lightning in the back
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svimedicalresearch.bsky.social @svimedicalresearch.bsky.social · 25/03/2026
Researchers from the Human Genomics & Evolution Lab have helped uncover how DNA inherited from extinct human relatives continues to influence our biology today. Find out more: www.svi.edu.au/news-events/...
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 23/03/2026
The 9th Annual Mutational Scanning Symposium starts tomorrow. We can't wait to see you for an action-packed 3 days of insightful presentations and posters and stimulating discussions. www.mss2026.org #VariantEffect26 #MAVE #Genomics #PrecisionMedicine #Symposium #AVEAlliance #AtlasOfVariantEffect
mss2026.org
MSS26
Mutational Scanning Symposium 2026, 25-27 March, Melbourne
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Digital Media Creatives @creativesatbc.bsky.social · 19/03/2026
Fun developments, but I'm glad it won! - Creative Amir #2026MMM #bcVAMMM #2026mmm
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Gwen C. Katz @gwenckatz.bsky.social · 13/03/2026
History is written BY the victors but ON the losers #2026MMM
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Patrick Gibbs @patrickgibbs.bsky.social · 28/02/2026
Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...
doi.org
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs
The phenotypic effects of germline variants are often mediated through gene regulation. Expression quantitative trait loci (eQTLs) are genetic variants associated with changes in gene expression. Understanding how eQTLs vary across populations is essential for characterising the genetic and regulatory drivers of trait diversity. Meta-analysing eQTL studies from multiple populations enables more robust detection of eQTLs and can reveal regulatory mechanisms shaped by population-specific environmental or ancestry-related factors. However, across the multi-ancestry eQTL literature, a wide range of methods have been used to quantify eQTL portability across ancestry groups. Because different studies employ different portability metrics, it is challenging to form a coherent view of the regulatory landscape across populations. In this work, we analyse eQTL summary statistics from ten datasets matched on tissue type and sequencing technology. We compare portability metrics used previously and show that they can yield markedly different patterns of apparent regulatory conservation or divergence. We then examine the statistical determinants of portability across metrics and demonstrate that sample size, minor allele frequency, and linkage disequilibrium are major drivers of the observed differences in eQTL portability across studies. These findings highlight that differences in statistical power stemming from factors such as population size and allele frequency must be accounted for when evaluating eQTL portability. To address this issue, we introduce a new approach designed to correct for these factors when calling eQTL portability. Finally, we show that empirical Bayes multivariate adaptive shrinkage provides a powerful framework for meta-analysing multiple eQTL studies, with the ability to pool signals across populations to produce more robust effect-size estimates within each population. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council, https://ror.org/011kf5r70, Ideas Grant 2020501, Investigator Grant 1195595
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 28/02/2026
Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs www.biorxiv.org/content/10.64898/20…
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Pai Kusuma @paikusuma.bsky.social · 24/02/2026
We posted a preprint on Zenodo: “The important role of community engagement in genetic research: Lessons from the study of Bornean contemporary hunter–gatherers” (zenodo.org/records/1875...). We present a practical, field-tested approach to doing genomics with Indigenous communities. 1/
zenodo.org
The important role of community engagement and equal collaboration in population genetic research: Lessons from Bornean contemporary hunter-gatherers
Abstract - Population and medical genetics can provide valuable information about human history and health. However, research involving Indigenous and vulnerable communities often raises ethical issue...
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Katie Hinde @mammalssuck.bsky.social · 19/02/2026
BRACKET DROP DAY!!!! Get yours now at the LibGuide! libguides.asu.edu/MarchMammalM... Pick your portal: Players, Learners, or Educator! #2026MMM
Decorative Image Array of the Bracket Guide, the Combatant Logo and the 2026 Bracket. Screen-reader materials available at the LibGuide.
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svimedicalresearch.bsky.social @svimedicalresearch.bsky.social · 17/12/2025
Congratulations to all our SVI PhD students who completed their seminars this year: Navya Shukla, David De George, Angela (Yi) Wang, Pongsakorn Sukonthamarn, Laura Sanz Villanueva, Yali Deng, Aaron Kwok, Lara Abbouche, Maddy Comerford, Jenny Lam, Stephanie Rowe, Dhruti Parikh and Luke Spencer.
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Hadley Wickham @hadley.nz · 06/11/2025
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
github.com
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
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Cell Press @cellpress.bsky.social · 24/10/2025
DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social
Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 20/10/2025
A high-coverage genome from a 200,000-year-old Denisovan www.biorxiv.org/content/10.1101/202…
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Janet Kelso @janetk.bsky.social · 20/10/2025
In a new paper led by Jiaqi Yang we trace the distribution of Denisovan introgressed DNA in ancient modern human genomes over time. www.cell.com/current-biol...
cell.com
An early East Asian lineage with unexpectedly low Denisovan ancestry
Yang et al. study Denisovan ancestry in ancient and present-day humans. In contrast to other East Asians, genomic comparisons suggest that the Jomon derived most of their ancestry from a deep lineage ...
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Navya Shukla @navya-shukla.bsky.social · 15/10/2025
My non-MPRA phd work! 😄
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R-Ladies Melbourne @rladiesmelb.bsky.social · 25/07/2025
Just discovered {ggcats} and yes, it does exactly what you think: adds cats to your ggplots. 🐈📈 Because sometimes your data visualisation needs a little more purr-sonality. 👉 github.com/R-CoderDotCo... #RStats #ggplot2 #dataviz #catsinstats
github.com
GitHub - R-CoderDotCom/ggcats: The geom you always wished for adding cats to ggplot2
The geom you always wished for adding cats to ggplot2 - R-CoderDotCom/ggcats
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Trends in Genetics @cp-trendsgenetics.bsky.social · 23/07/2025
"Decoding Genomic Landscapes of Introgression" by Martin Kuhlwilm (@kuhlwilm.bsky.social) & co "The detection of introgressed loci has evolved into a diverse methodological field encompassing summary statistics, probabilistic modeling, and supervised learning." authors.elsevier.com/sd/article/S...
Figure 1. Introgression and its genomic landscapes.
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Irene Gallego Romero @ee-reh-neh.bsky.social · 11/07/2025
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere! Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
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