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Will Freyman

@willfreyman.bsky.social
532 followers 483 following 15 posts

computational population genetics and phylogenetics. willfreyman.org into oakland, bikes, synths, mountains, cities, bayesian stuff he/him

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Will Freyman @willfreyman.bsky.social · 12h
Bike Lane Uprising is awesome but doesn't submit to Oakland's 311
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Will Freyman @willfreyman.bsky.social · 20h
This app reports directly to Oakland's 311 system and is quick to use: loudbicycle.com/bb/
loudbicycle.com
Bike Bureau — report blocked bike lanes
Your frustration has a submit button now.
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Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Joe Hanly @hanliconius.bsky.social · 22/09/2026
I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:
chromosome synteny riparian plot in which every chromosome has crossing lineschromosome synteny plot in which no chromosomes have crossing lines. The underlying structure is identical.
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April Wei @aprilwei.bsky.social · 14/09/2026
New preprint from our collaborators @giulsguidi.bsky.social, and her PhD students Yifan Li and Qingyao Sun, which enabled GRG-based statistical genetics across different computer architecture🔥. So the practical win for GRG users: you can pick the matvec backend to best leverage your machine &task.
biorxiv.org
Sparse Linear Algebra Accelerates Genotype Representation Graph Computation at Biobank Scale
Biobank-scale genomic analyses are increasingly constrained by computational costs, as hundreds of thousands to millions of samples and variants must be analyzed together. The genotype representation ...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 06/08/2026
Regular reminder that the first thing you should do if you're interested in population structure of some samples is not PCA, NJ tree, or STRUCTURE. Just build a dang kinship matrix and look at it.
kinship matrix of a number of Tripsacum individuals based on whole genome sequencing
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alex ioannidis @alexgioannidis.bsky.social · 16/07/2026
Scaling genetic clustering (ADMIXTURE/STRUCTURE-style unsupervised clustering) is now easy. Out in Bioinformatics, our ADAMIXTURE method clusters all of UK Biobank (500k genomes) in just over a hour with likelihoods as good as ADMIXTURE, which would take weeks. doi.org/10.1093/bioi...
doi.org
ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering
AbstractMotivation. Estimating genetic clusters from sequencing data is a fundamental task in population and medical genetics, enabling demographic inferen
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David Ho @davidho.bsky.social · 23/06/2026
This amount would fund the US National Science Foundation for a decade. 🧪
apnews.com
Pentagon seeks $80 billion from Congress for Iran war
The Pentagon has told lawmakers it needs roughly $80 billion, mostly to cover the cost of the war in Iran.
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Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
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Eric Topol @erictopol.bsky.social · 14/06/2026
Discovery of a 14-protein biomarker that predicts lung cancer 5.6 years before it is diagnosed, even in non-smokers, and an anti-inflammatory medicine that prevents its progression. And, challenging dogma, the proteins are not coming from cancerous cells!
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MU-Peter Shimon 🀄 @mu-peter.bsky.social · 01/06/2026
Ok, this is cool... Treemble: A graphical tool to generate Newick strings from phylogenetic tree images🧪 academic.oup.com/bioinformati... Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org.
Treemble views and performance.
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Carl T. Bergstrom @carlbergstrom.com · 29/05/2026
Of all the harm this administration has done to US science, today's proposed changes to the way federal grants are awarded and administered is the most damaging yet. The text of the federal register document is impenetrably tedious by design, so here's an excellent summary of what it says.
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Gideon Bradburd @gbradburd.bsky.social · 29/05/2026
postdoc alert 🚨! NIH-funded postdoc in my lab to work on Ancestral Recombination Graphs in space. Please spread the word widely in your networks, and please reach out if you're interested! (2-3yr position, start date flexible, pay/benefits good!). details here: careers.umich.edu/job_detail/2...
genescape.org
recruitment
Multiple positions available: ​ Postdoc PhD students
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Eric Turkheimer @ent3c.bsky.social · 18/05/2026
With @remyfurrer.bsky.social, a new piece in Nature Human Behavior. The standard description of a polygenic score as a "genetic predisposition" essentializes a statistical construct. It's not language policing: PGS are a new kind of entity; now is the time to think carefully about what they are.
nature.com
Polygenic risk scores are not genetic predispositions - Nature Human Behaviour
Nature Human Behaviour - Polygenic risk scores are not genetic predispositions
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William DeWitt @wsdewitt.github.io · 09/05/2026
A nice finding on phylodynamic identifiability: Louca-Pennell congruence classes collapse to a unique model in settings where mutation is associated with birth events (e.g. cell division).
arxiv.org
Information on hidden birth events restores identifiability in phylodynamic inference
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. H...
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Joshua G. Schraiber @jgschraiber.bsky.social · 10/05/2026
I was told that some college students getting mad at racists speaking at their schools were the real threat to free speech and scholarship at universities
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 02/05/2026
Highly efficient genotype compression leveraging genealogical relatedness www.biorxiv.org/content/10.64898/20…
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Evolution Letters @evolletters.bsky.social · 27/04/2026
Choosing the right tree matters. Phylograms outperform chronograms for neutral traits but not for detecting selection. By @phylogenetrips.bsky.social et al. doi.org/10.1093/evle...
doi.org
Phylograms better fit neutrally evolving traits than chronograms
Many species are characterized by trait differences between each other. For example, the brain size of different primate and human lineages varies. The que
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telescyote 🔭 @cosmicyote.bsky.social · 01/05/2026
Less than 800 NSF grants awarded over the first half of the fiscal year for the entire country. Previous years were already over 2-3k awards by now. It is not particularly overdramatic to say we are seeing the death of federally funded science research in the United States.
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Graham Coop @gcbias.bsky.social · 17/04/2026
Reposting this old thread on the "Pervasive findings of directional selection" from ancient DNA. While the authors extended their results in various ways, I think many of these points still stand.
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Carl Zimmer @carlzimmer.com · 15/04/2026
Until now, scientists have identified only a few dozen variants that went through natural selection in humans in the past 10,000 years. A new study claims to find hundreds--maybe thousands. Here's my story on the provocative research, and the mixed reception it's getting. Gift link: nyti.ms/4tSJH9G
A scientist drills a skull in search of ancient human DNA
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Matthew Hahn @3rdreviewer.bsky.social · 10/04/2026
Whoa—machine learning strikes again (in a good way) www.pnas.org/doi/10.1073/...
pnas.org
Coalescence and translation: A language model for population genetics | PNAS
Probabilistic models such as the sequentially Markovian coalescent have long provided a powerful framework for population genetic inference, enabli...
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 08/04/2026
Graph transformer for ancient ancestry inference www.biorxiv.org/content/10.64898/20…
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Adam Auton @adamauton.bsky.social · 08/04/2026
By running a GWAS on data we collected from an online survey about GLP-1 medication, we found a missense variant in GLP1R that predicts treatment success. This makes sense! GLP1R is the target of the GLP-1 medications!
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David Roberts @volts.wtf · 12/03/2026
"We started a war of aggression for no reason & commenced it by accidentally bombing an elementary school & killing over 100 kids." That simple fact is so horrific that it's just kind of bouncing on the surface of our collective consciousness. We can't absorb its full implications & significance.
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David Ho @davidho.bsky.social · 12/03/2026
The 2026 National Science Foundation budget is $8.75 Billion.
nytimes.com
First 6 Days of Iran War Cost U.S. $11.3 Billion, Pentagon Says
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/03/2026
This looks neat, actually does a formal analysis of what I've suspected for a long time -- ΔK is an odd way to decide number of pops. H/T @biologyjoe87.bsky.social for the paper. (Personally I think K=0) www.biorxiv.org/content/10.6...
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Dr. Jey McCreight 🏳️‍⚧️🧬 @jeymccreight.bsky.social · 27/02/2026
Major thanks to @melodyschreiber.com for interviewing me about what biology actually says about sex & gender Unscientific attacks on trans rights are fueled by fascism, not science, and harm all of us - cis or trans Excellent reporting 🧬🏳️‍⚧️ www.theguardian.com/us-news/2026...
theguardian.com
Science of sex and gender being misrepresented by Trump officials, experts warn
Scientists say crackdown on gender-affirming care could have impact on healthcare of all Americans
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Jeremy Berg @jeremymberg.bsky.social · 01/03/2026
NSF Update (Awards through 2/27/26) Directorates to follow 1/10
A line graph showing NSF grant awards made through 2/27/26 for fiscal year 2026 compared with grant awards for fiscal years 2021-2025.
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Will Freyman @willfreyman.bsky.social · 01/03/2026
💯
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Eric Topol @erictopol.bsky.social · 26/02/2026
This week's cover @thelancet.com
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𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻 @basantakhakurel.bsky.social · 25/02/2026
Our new paper 'A covarion model for phylogenetic estimation using discrete morphological datasets,' is out in SysBio! We introduce the "covariomorph" model in RevBayes to capture character and lineage specific rates of morphological traits. 🔗 doi.org/10.1093/sysb...
doi.org
A covarion model for phylogenetic estimation using discrete morphological datasets
Abstract. The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morp
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John Paul Helveston @jhelvy.bsky.social · 28/01/2026
Incredible self own for the US. The damage being done to the US scientific enterprise is generational. We will look back on this as a tipping point where the US chose all on its own to stop leading the world in science. www.science.org/content/arti...
science.org
U.S. government has lost more than 10,000 STEM Ph.D.s since Trump took office
A Science analysis reveals how many were fired, retired, or quit across 14 agencies
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Dr. Jey McCreight 🏳️‍⚧️🧬 @jeymccreight.bsky.social · 28/01/2026
🚨 Requesting help: I am looking for an agent who can facilitate more speaking gigs, podcast appearances, and interviews with journalists I want to more widely share my story and expertise as a trans geneticist who understands the reality and complexity of "biological sex" 🏳️‍⚧️🧬 Please signal boost?
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Dr. Jey McCreight 🏳️‍⚧️🧬 @jeymccreight.bsky.social · 28/01/2026
I also welcome any direct connections people may have to podcasts who need a guest, or organizations who need a speaker (it's about that time to start planning for Trans Day of Visibility!) If you have questions or ideas, DM me or email me at jey (at) beyondxandy (dot) org @beyondxandy.bsky.social
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Ilhan Omar @ilhanmn.bsky.social · 25/01/2026
Voting NO on the DHS funding bill is the bare minimum. Backing Kristi Noem’s impeachment is the bare minimum. Holding law-breaking ICE agents legally accountable is the bare minimum. ICE is beyond reform. Abolish it.
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Brandon Friedman @brandonfriedman.bsky.social · 24/01/2026
This is courage. Looking a masked, government fascist dead in the eye, face to face, knowing full well that your life is on the line. If elected officials had 1/10th of Alex Pretti's resolve, we would have far fewer troubles.
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Dimitri Drekonja, MD, MS @dimitridrekonja.bsky.social · 24/01/2026
Alex Pretti was a colleague at the VA. We hired him to recruit for our trial. He became an ICU nurse- I lover working with him. He was a good kind person who lived to help and these fuckers executed him. White. Hot. Rage.
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Kevin Bird @stairwaytokevin.bsky.social · 24/01/2026
An excellent, bone-chilling story about a cadre of online racists who stole genetic data from studies on children so they could make specious arguments for the innate inferiority of non-white people, it's embrace by Elon Musk/twitter & how the Trump administration might make it easier to do again.
nytimes.com
Genetic Data From Over 20,000 U.S. Children Misused for ‘Race Science’
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Matthew Hahn @3rdreviewer.bsky.social · 23/01/2026
New paper with @smishra677.bsky.social! How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process. 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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Will Freyman @willfreyman.bsky.social · 23/01/2026
Minneapolis ❤️
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David Ho @davidho.bsky.social · 20/01/2026
This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...
This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.
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phy_papers @phypapers.bsky.social · 15/01/2026
Unifying phylogenetic traversal and deep learning to guide tree exploration www.biorxiv.org/content/10.64898/20…
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Bryan Culbertson 🥄 @bryanculbertson.com · 15/01/2026
ICE will continue to murder us until we abolish them
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Joshua G. Schraiber @jgschraiber.bsky.social · 13/01/2026
Minneapolis is literally occupied by its own federal government, this is an abomination, an act of civil war by the federal government against the sovereign states.
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Ilhan Omar @ilhanmn.bsky.social · 13/01/2026
Kristi Noem must be impeached.
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 12/01/2026
Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs www.biorxiv.org/content/10.64898/20…
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Matthew Hahn @3rdreviewer.bsky.social · 08/01/2026
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS! academic.oup.com/genetics/art...
academic.oup.com
Estimating recombination using only the allele frequency spectrum
Abstract. Standard methods for estimating the population recombination parameter, ρ, are dependent on sampling individual genotypes and calculating various
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Ilhan Omar @ilhanmn.bsky.social · 08/01/2026
It was not "domestic terrorism.” It was state sanctioned violence. A family will forever live with the pain caused by the admin's reckless and deadly actions. Abolishing ICE is not enough. They must be held accountable.
cnn.com
Rep. Omar: Trump admin’s take on MN shooting is ‘delusional,’ ‘we’ve all seen the video’ | CNN
Minnesota Rep. Ilhan Omar joins The Lead.
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Alfred Twu @alfredtwu.com · 07/01/2026
Bay Resistance has an anti-war organizing call tonight as well as many local organizing meetings in the East, West, and South Bay coming up - get the details at www.bayresistance.org/events
bayresistance.org
Events — Bay Resistance
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