10 courses for my dream bioinformatics curriculum: 1. Unix Commands with Greg Wilson www.youtube.com/watch?v=U3i... 2. statistics and R with Rafael Irizarry rafalab.dfci.harvard.edu/pages/harva...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

📢 18-month PostDoc Fellowship – University of Montpellier (France) 🦠🦋 Interested in insect pathology, immunity, microbiome, or genomics? We’re looking for a motivated candidate (<2 years post-PhD by mid-2026). 🧪 📩 Contact me ASAP for details! ⏳ Application deadline: 16/01/26 🔁 Please RT / Repost

PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social

🧬 PhD Position: Evolutionary & Comparative Genomics 🕷️ Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13). We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes! More infos 👇 and s.gwdg.de/eDrAAY #Evolution #Genomics #Bioinformatics

Full paper now out in GENETICS: The relationship between sexual dimorphism and intersex correlation: do models support intuition? 🔗 academic.oup.com/genetics/art... #Evolution #QuantGenetics @GeneticsGSA

1/ a single job opening receives >1000 applications. (I am not kidding). How to stand out? Most bioinformatics CVs look the same: Python, R, RNA-seq, pipelines. But hiring managers don’t care about skills on paper. They care about proof. 🧵

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4

Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social. Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n

Massive thanks to @tegangaetano.bsky.social and @fmanfredini.bsky.social for impecably hosting while I was over - fantastic to hear about all the exciting research going on in Aberdeen🏴󠁧󠁢󠁳󠁣󠁴󠁿, meeting great people🍻, as well as seeing the wildlife🦭🦭🦭

Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...

Simplify and elevate your data visualization with GGally, an R package designed to extend ggplot2. Visualization: https://ggobi.github.io/ggally/ Details: https://statisticsglobe.com/online-course-data-visualization-ggplot2-r #tidyverse #datavisualization #datasciencecourse #data #package

🐝Great to have this out @molbioevol.bsky.social and well done Hongfei Xu (not on BlueSky) for all the hard work

Review: Transcriptomics in the era of long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/efBjP) 🧬🖥️🧪

Using my Tidyverse local synteny visualization tools first time in 3 months. This a biosynthetic gene cluster with 2 P450s and a O-methyltransferase. Visualized across assemblies for 4 cultivars. GitHub: github.com/cxli233/Tidy...

Our review on k-mers + pop gen is now published! doi.org/10.1093/molb...

Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments @stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao doi.org/10.1101/gr.2...

Resulting from an @snsf-ch.bsky.social SPARK grant this took some time to mature, but the outcome is very imformative and builds a foundation for where to head next - how to liberate facts/information locked in the published literature www.biorxiv.org/content/10.1... #textmining #biodiversity

Bitte am Sonntag wählen gehen! Noch nie war eine Wahl so wichtig für Deutschlands Zukunft. #Btw2025

Wow. This is sooo good. Echoing @urbanevol.bsky.social this user’s manual for Ne should be required reading for popgen and conservation genetics folks. onlinelibrary.wiley.com/doi/10.1111/...

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...

Finally ready to see the world! Theories of balancing selection - past, present and future: www.biorxiv.org/content/10.1... A true collaborative effort that brought together theoreticians and empiricists, models, data, and fresh perspectives on how balancing selection can shape genetic variation.

Olá, Brasil! 🇧🇷 Interested in a research stay in Germany? Are you currently a postdoc at a uni or research institution in Brazil? Our CAPES #Fellowship offers you funding for a #research stay for 6-24 mth! Join our info event on 18 Feb! www.humboldt-foundation.de/en/connect/i...

Principled PCA separates signal from noise in omics count data www.biorxiv.org/content/10....

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity 🧬🖥️🧪 Paper: https://www.biorxiv.org/content/10.1101/2025.02.06.636847v1 #Rstats Code: https://github.com/Yunuuuu/ggalign Docs: https://yunuuuu.github.io/ggalign/ Book (Quarto): https://yunuuuu.github.io/ggalign-book/

New paper with Sarthak Mishra! Maybe it will bring you some joy given all this (waves arms around). "Estimating recombination using only the allele frequency spectrum" 1/2 www.biorxiv.org/content/10.1...

What is a differentially expressed gene? https://www.biorxiv.org/content/10.1101/2025.01.31.635902v1 🧬🖥️🧪 https://github.com/Morris-Research-Group/bayexpress

A new tool, vcfsim, developed by Paimon Goulart, a stellar undergraduate researcher in my lab! vcfsim allows for the quick and easy simulation (via parameterized msprime simulations) of "all-sites" vcfs, with arbitrary ploidy and amounts of missing data. www.biorxiv.org/content/10.1...

CASTER: Direct species tree inference from whole-genome alignments https://www.science.org/doi/10.1126/science.adk9688 🧬🖥️🧪 https://github.com/chaoszhang/ASTER

locuszoomr: an R package for visualising publication-ready regional gene locus plots https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf006/7958574 🧬🖥️🧪 #Rstats https://github.com/myles-lewis/locuszoomr

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications https://pubmed.ncbi.nlm.nih.gov/39862387/ 🧬🖥️🧪 #Rstats https://github.com/almeidasilvaf/doubletrouble

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:

🐝 3-year Postdoc position 🐝 Join us @bristolbiosci.bsky.social to study the impacts of parasitic bees on tropical bee communities using eDNA, SNPs & field-based surveys. 📅 Deadline: 23 Feb 2025 💃Vibrant city 🌎 Collaboration with USP 🇧🇷 🐝 Details here: tinyurl.com/586u7vau @leverhulme.bsky.social

Fantastic having @tegangaetano.bsky.social visit @unimainz.bsky.social and a nice experience to develop scientific links between my adopted homeland 🇩🇪 and the country I get most mistaken for 🏴󠁧󠁢󠁳󠁣󠁴󠁿 🐝

The maintenance of genetic polymorphism underlying sexually antagonistic traits doi.org/10.1093/evle... Now in @evolletters.bsky.social by Ewan Flintham et al.

eyedroppeR, a package to automatically extract color palettes from images. github.com/doehm/eyedro...

Join us next week Thursday at 14:00 UTC for another seminar of the Internal Conflicts and Organismal Adaptation STN! John Werren and Bengt Bengtsson will discuss the early days of studying internal conflicts and selfish genetic elements. See internalconflictsstn.wordpress.com/seminars for more info.

SAMURAI: Shallow Analysis of copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline https://www.biorxiv.org/content/10.1101/2024.09.30.615766v2 🧬🖥️🧪 Nextflow pipeline https://github.com/DIncalciLab/samurai

I made a "gene info" custom GPT. Paste in a list of human gene symbols. It'll run some python code against a custom knowledge base to provide information about those genes (from RefSeq) https://chatgpt.com/g/g-677277d002608191887af1a9c0a9e832-gene-info 🧵 1/4 🧬🖥️🧪

NCBI RefSeq: reference sequence standards through 25 years of curation and annotation academic.oup.com/nar/advance...

My Tidyverse local synteny visualizer is up on GitHub: github.com/cxli233/Tidy... GitHub page contains 2 example datasets, as well as step-by-step instruction & explanations on how it works. Details on required input data are discussed in the GitHub page. Let me know if you run into issues.

In the mean time, @ctitusbrown.bsky.social --- the fastest parser I've seen is RabbitFX, and they have a QC control tool too (github.com/RabbitBio/Ra...). But make *sure* that you use the Intel i-sal library for gzip decompression if you can, makes a huge difference.

Return to this for teaching etc every few years bsky.app/profile/jros...

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

📜 Did you ever wonder why females and males are of different size in many species? We tested if sexual selection could drive the evolution of sexual size dimorphism (SSD) synthesizing the results of 77 comparative studies. #OpenAccess in Ecology Letters: onlinelibrary.wiley.com/doi/10.1111/...

Create simple, beautiful personal websites and landing pages using only R Markdown https://github.com/seankross/postcards