Joseph Guhlin
(he/him) Genomics Researcher. The Kākāpō Genomics Guy. Theoretical Genomicist. Annotation Artist. #Conservation #Bioinformatics #Rust #CompBio 🦀 #genomics #fedi22 #CompBio #popgen #Annotation #Stats #MachineLearning 🏳️🌈
- Reposted by Joseph GuhlinNew review! Theory & a practical guide to structural variants in popgen🧬 Many thanks to my co-authors: @rebekahoomen.bsky.social @annatigano.bsky.social @marenwellenreuther.bsky.social @janawold.bsky.social @dlfield.bsky.social @clairemerot.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
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- Reposted by Joseph GuhlinExploring #PAG33 and San Diego for the first time! If you're interested in knowing more about why bird microchromosomes are so hard to sequence, come by poster 287 this afternoon!
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Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.- Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986
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- Reposted by Joseph GuhlinI'm delighted to share that our publication 'Nest survival models and genomics illuminate hybridisation attempts, guiding culturally informed management to recover a critically endangered seabird' is out now in Animal Conservation @animalconserv.bsky.social! doi.org/10.1111/acv.... 🧵 1/9
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- Reposted by Joseph GuhlinBig bluestem has been a lovely and complex system to work with for the majority of my PhD and will always have a piece of my heart! Very excited to share this work with the community.
- Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.
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- Reposting for other time zones! Check this out and please give us a boost! :)
- 🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all! www.biorxiv.org/content/10.1... #hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature
- 🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all! www.biorxiv.org/content/10.1... #hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature
- Population genomics reveal three divergent subspecies with urgent #conservation implications. #popgen
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- Reposted by Joseph GuhlinWe did a penguin GWAS! Turns out that yellow-eyed penguins (or hoiho) are actually three very divergent groups, which we are calling subspecies www.biorxiv.org/content/10.1... @josephguhlin.bsky.social @peterkdearden.bsky.social @annasanture.bsky.social @cegrueber.bsky.social
- Reposted by Joseph GuhlinNew Zealand’s invasive starlings on the cover of Molecular Ecology! 🐦🧬 This collaborative project unpacks the invasion history of starlings in Aotearoa New Zealand, combining population genomics with historical records of human-mediated translocations. onlinelibrary.wiley.com/doi/10.1111/...
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- Reposted by Joseph GuhlinGenetic load, fitness and conservation in the Seychelles warbler. A wonderful PhD opportunity - spanning important evolutionary and conservation-relevant concepts. Come work with us lnkd.in/dtGaEJV2
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- Reposted by Joseph GuhlinExcited to begin the search for the next (6th) Burpee Post-Doctoral Fellow in Botany here in my lab at Bucknell! Funded research and teacher-scholar training embedded in the primarily undergraduate institution (#PUI) environment. #iamabotanist Details (+ application portal) here: lnkd.in/eVsbe7K5
- Reposted by Joseph GuhlinNow published in Cell! We found that ~15% of SNPs from divergent refs did not liftover as SNPs in the gray fox ref—half mapped to monomorphic sites, half failed to map. Co-authored with Matthew Genchev, @elliecat.bsky.social, and @jazlynmooney.bsky.social www.sciencedirect.com/science/arti...
- 1/7 🧬 New Preprint Alert: Our study highlights the risks of using divergent reference genomes in population genomics. The choice of reference genome can skew key inferences about demography, diversity, and selection. Read on for insights! www.biorxiv.org/content/10.1...
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- Reposted by Joseph GuhlinGenomic imputation can boost dataset quality and benefit research on wild populations. In hihi, we found high #imputation accuracies despite a small reference panel of high-fecundity individuals. Imputation improves downstream #ConservationGenomics analyses. onlinelibrary.wiley.com/doi/10.1111/...
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- Reposted by Joseph GuhlinBreaking genetics news‼️🌱🌽 A natural DNA trick triples recombination in maize. What we first saw in Arabidopsis (@hendersi lab) a decade ago is now confirmed in crops—opening new doors for plant breeding. Published today in Nature Plants! More details 👉 www.nature.com/articles/s41...
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- Reposted by Joseph GuhlinLong runs of homozygosity are reliable genomic markers of inbreeding depression 🧬 www.cell.com/trends/ecolo...
- Reposted by Joseph Guhlinstarting to suspect my neighbor is a large language model
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- Who chose this color scheme?
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- Reposted by Joseph Guhlin*ALERT! GLOBAL GENETIC DIVERSITY TREND RE-ANALYSIS* "Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis" doi.org/10.1101/2025...
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- Reposted by Joseph GuhlinHuge news! Having spent a while studying #kiwi pukupuku, this got me very excited. Finding a remnant mainland population of LSK is probably more significant than finding more #kakapo. Huge respect to those involved and particularly the hunter who found them. www.doc.govt.nz/news/media-r...
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