sinamajidian.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

The PAN-GO paper is a remarkable milestone. It not only provides the most comprehensive picture of human gene function to date, but also carefully maps this knowledge across the tree of life! Congratulations @marcfeuermann.bsky.social, Pascale Gaudet & collaborators! www.sib.swiss/news/sib-hel...

submitted 14 hours ago • 0 comments

We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).

submitted 19 hours ago • 1 comment

Very cool framework for haplotype assembly

submitted 20 hours ago • 0 comments

Just extended the deadline to March 21 for this position in the Plant Phylogenomics group at the University of Vienna. It is sort of a "post doc plus" position funded for up to six years. Please reach out if you want to chat - I'd love to talk to you about it! jobs.univie.ac.at/job/Universi...

submitted 1 day ago • 0 comments

A mathematical theory of evolution: phylogenetic models dating back 100 years—a new #PhilTransB theme issue describes recent developments in models of #evolutionary trees and networks, and in #phylogenetic modeling for applications in biology: https://buff.ly/41r1wkR @tanjastadler.bsky.social

submitted 6 days ago • 2 comments

Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.

submitted 2 days ago • 0 comments

📢 Don’t miss the deadline ⚠️ 27 February ⚠️ to submit your abstract to the [BC]2 Basel #ComputationalBiology Conference. From #GeneExpression to #evolution or #biomedicine - we are waiting to learn more on your research projects at #bc2basel! 👉Submit your abstract now: tinyurl.com/49w6wthj

submitted 13 days ago • 2 comments

New round of the Lise Meitner Excellence Program for tenure track group leaders in @maxplanck.de institutes opened today -- please consider applying! The program aims to recruit and promote exceptionally qualified female scientists. Because diversity increases excellence! www.mpg.de/lise-meitner...

submitted 15 days ago • 0 comments

This is a small but very nice meeting on phylogenomics in Granada, Spain. The registration deadline has been just extended to March 3rd, and there is still room for contributed talks! Please fwd to anyone interested. I'll also be there for a few days! mceb2025.sciencesconf.org

submitted 6 days ago • 0 comments

Delighted to see our new paper out, led by PhD student Asia Hoile. We explored new genes that emerged during the early evolution of Lepidoptera 🦋 Many cool insights which we think open up new questions to explore. Get in touch if you have thoughts/want to discuss more! 🔗: tinyurl.com/48rx72es

submitted 7 days ago • 1 comment

🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!

submitted 26 days ago • 1 comment

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff... genome.cshlp.org/content/35/2...

submitted 12 days ago • 1 comment

#Pangenome graphs from sets of high-quality genomes help reduce representation bias by incorporating data from multiple #genomes within a population, species, or genus 🧬 Join the #ERGAPlenary on Monday to learn more about their applications ➡️ www.erga-biodiversity.eu/post/pangeno...

submitted 13 days ago • 0 comments

Aneuploidy is the leading cause of pregnancy loss. In our latest study (www.biorxiv.org/content/10.1...) led by undergrad Angela Yang, we used a simulation framework to infer rates of both meiotic (39-43%) and mitotic errors (1-3% per division) that best explain data from human IVF embryo biopsies.

submitted 79 days ago • 1 comment

🧬🖥️ We are hosting free bioinformatics office hours on Feb 19th at 10am-noon PST. Bring your bioinformatics career or technical questions, and @robert.bio and I will try to answer them. Sign up here: tally.so/r/mOb6dM Please share especially with students and early career scientists!

submitted 16 days ago • 1 comment

Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).

submitted 21 days ago • 0 comments

The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss

submitted 23 days ago • 0 comments

🚀Exciting PhD Opportunity🚀 Are you passionate about: 🧬 Graph algorithms for real-world genome sequencing? 💻 Writing efficient, reusable code & libraries? 🌲 Exploring stunning Nordic nature? This PhD position is for YOU! 🎓✨ 📅 Apply by March 2 #PhD #ComputerScience #Bioinformatics #GraphAlgorithms

submitted 20 days ago • 1 comment

We are now accepting applications for scholarships to the @cshlaboratory.bsky.social Biology of Genomes meeting from the @jxtxfoundation.bsky.social. Open to students worldwide in support of open science. Please help spread the word! jxtxfoundation.org/news/2025-2-...

submitted 21 days ago • 0 comments

We are looking for a postdoc in bioinformatics interested in broad questions about the ecology and evolution of host-associated microbiomes using social bees as model. Please share with potential candidates and if interested apply here: career5.successfactors.eu/career?caree...

submitted 22 days ago • 0 comments

📣Second #call for proposals: NRP 84 “Plant Breeding Innovation” seeks interdisciplinary #research projects on the #humanities and social sciences. 📆 Submission deadline: 7 May 2025 📌 For more info ➡

submitted 24 days ago • 0 comments

Zenodo vs Open Science Framework

submitted 26 days ago • 0 comments

Excited to share our latest work, published this morning in Nature Biotechnology! 🎉 We developed a hybrid quantum computing-enhanced generative model to design KRAS inhibitors. Check it out here: rdcu.be/d68Fs. Some fascinating insights along the way:

submitted 35 days ago • 3 comments

We are excited to share our work on molar #EvoDevo 🦷 in mouse and hamster 🐁, led by the amazing team of Marie Sémon and Sophie Pantalacci. We find an inverted hourglass pattern, with a maximum of evolutionary divergence at the bell stage. www.biorxiv.org/content/10.1... @lbmcinlyon.bsky.social

submitted 31 days ago • 2 comments

We are recruiting a Bioinformatics PostDoctoral Research to join our team @ibb-botanic.bsky.social @csic.es. Reach out if you have questions! #transposons #Drosophila bioinformaticsbarcelona.eu/job/bioinfor...

submitted 30 days ago • 0 comments

In a new Science study, researchers present CASTER, a tool that uses arrangements in DNA sequences known as site patterns to infer “species trees,” which are diagrams that depict the evolutionary relationships among species. Learn more:

submitted 32 days ago • 4 comments

🚨 Keynotes at RECOMB-seq 2025! 🚨 🌟 Alicia Oshlack – computational transcriptomics @aliciao.bsky.social 🌟 Rayan Chikhi – sequencing data structures @rayanchikhi.bsky.social 🗓️ Dates: April 24–25, 2025 📍 Seoul, South Korea recomb-seq.github.io/speakers/

submitted 34 days ago • 0 comments

🚨 UPCOMING DEADLINES 🚨 ⭐️Highlights: January 27, 2025 📋Posters: January 27, 2025 RECOMB-Seq: January 31 (abstracts) RECOMB-Microbiome: January 31 RECOMB-P&E: February 5 RECOMB-CG: February 7 RECOMB-CCB: February 7 (abstracts) RECOMB-Genetics: February 14 #RECOMB2025 #deadlines

submitted 34 days ago • 0 comments

Review: Diversity and consequences of structural variation in the human genome https://www.nature.com/articles/s41576-024-00808-9 (read free: https://rdcu.be/d64zN) 🧬🖥️🧪

submitted 36 days ago • 0 comments

Call for abstract: "Pangenome graphs and their applications in biodiversity genomics" A symposium of the SMBE 2025 Annual Meeting of the Society for Molecular Biology July 2025, China

submitted 36 days ago • 0 comments

🚨 We also have a "Scientist" position in my lab at St. Jude. The position is financially stable and with a very competitive salary range. 📝 If you have Postdoctoral experience and want to develop a steady research career this one is for you! ➡️ Apply here: talent.stjude.org/careers/jobs...

submitted 37 days ago • 0 comments

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

submitted 40 days ago • 11 comments

So long San Diego! Here’s my opinionated meeting report from #PAG2025 | #PAG32. What else did I miss???

submitted 42 days ago • 5 comments

The next Alliance webinar is scheduled for this Thursday January 16, at noon ET. This month's webinar is on Literature Tools, and will be presented by Kimberly Van Auken. Register by Wednesday January 15 to receive the Zoom link forms.gle/GzMnmwK23SzP...

submitted 44 days ago • 1 comment

From #BMCGenomics | BenchAMRking: a @galaxyproject.bsky.social -based platform for illustrating the major issues associated with current antimicrobial resistance (#AMR) gene prediction #workflows | 🧬 🖥️ 🧪 #UseGalaxy | bmcgenomics.biomedcentral.com/articles/10....

submitted 45 days ago • 0 comments

"Bridging Wright–Fisher and Moran models" for allele frequency evolution doi.org/10.1016/j.jtbi.2024.112030 Moran: overlapping generations, one birth/death. WF: nonoverlapping generations via binomial sampling. Proposed model replaces 𝑀 out of N individuals via binomial sampling 𝑀=𝑁:WF, 𝑀=1:Moran💯💯

submitted 46 days ago • 0 comments

Super excited to see that this work @drpintothe2nd.bsky.social and I collaborated on with some super smart people at NIST for the Genome in a Bottle Benchmarking project is out! A benchmark for X and Y chromosome small variants! www.nature.com/articles/s41...

submitted 46 days ago • 0 comments

Good morning San Diego! Looking forward to all the great talks at #PAG2025 this week. Here are a few that I can recommend: Amazing plants, long reads, genome editing, microbiomes, bioifx education, DNA/RNA-mods, and assembly, annotation, & more! Make sure to stop by to say hi! 👋

submitted 47 days ago • 1 comment

Are you at #PAG32? Don’t miss the talk by Lars Gabriel on our new gene finder Tiberius on Tue at 11:50 in Pacific A! He also presents 2 posters on Tiberius. P102 is on diatom genome annotation.

submitted 47 days ago • 2 comments

Review: Pangenome graphs and their applications in biodiversity genomics https://www.nature.com/articles/s41588-024-02029-6 (read free: https://rdcu.be/d5Bv7) 🧬🖥️🧪

submitted 49 days ago • 0 comments

🚨🚨🚨 We are hiring 🚨🚨🚨 After the creation of logan-search (see: bsky.app/profile/pier...) we propose a 2-years engineer position for continuing the development and optimizations. With @rayanchikhi.bsky.social and @tlemane.bsky.social Details + applications: recrutement.inria.fr/public/class...

submitted 76 days ago • 1 comment

Have you checked out our behind-the-paper blog post on FastOMA? Read it here go.nature.com/4a3V9q3 I’ll give you a quick intro to orthology, a bit of history of orthology methods, and the story of how FastOMA came to life—and how it works!

submitted 49 days ago • 0 comments

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

submitted 51 days ago • 1 comment

Postdoc opportunities! The Johns Hopkins Data Science and AI Institute has a new postdoc program! We’re looking for candidates across data science and AI, including science, health, medicine, the humanities, engineering, policy, and ethics. Spread the word and apply! ai.jhu.edu/postdoctoral...

submitted 102 days ago • 0 comments