Joe Colgan
LightNews LightNews
banner
hibernogruppe.bsky.social
Joe Colgan
@hibernogruppe.bsky.social
97 followers 180 following 3 posts
Asst. Prof. JGU Mainz 🇩🇪 (he/him)| 🐝🧬 wild bee evolution | 🐟💻 salmonid genomics | https://github.com/joscolgan
Posts Replies Media Videos
Reposted by Joe Colgan
vbsdoublet.bsky.social
📢 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
November 21, 2025 at 9:13 AM
Reposted by Joe Colgan
hoehna.bsky.social
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
hoehnalab.github.io
November 11, 2025 at 9:00 AM
Reposted by Joe Colgan
posnienlab.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
Posnien - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
s.gwdg.de
November 18, 2025 at 7:04 AM
Reposted by Joe Colgan
lkhayward.bsky.social
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
The relationship between sexual dimorphism and intersex correlation: do models support intuition?
Abstract. The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by
academic.oup.com
August 23, 2025 at 11:16 PM
Reposted by Joe Colgan
tommytang.bsky.social
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. 🧵
August 22, 2025 at 1:15 PM
Reposted by Joe Colgan
rosafernandez.bsky.social
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...
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...
www.nature.com
August 15, 2025 at 12:05 AM
Reposted by Joe Colgan
robp.bsky.social
🧬🖥️ 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
Tree-based differential testing using inferential uncertainty for RNA-seq
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
August 21, 2025 at 7:24 PM
Reposted by Joe Colgan
vikramshivakumar.bsky.social
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
Partitioned Multi-MUM finding for scalable pangenomics
Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...
www.biorxiv.org
May 27, 2025 at 7:35 PM
hibernogruppe.bsky.social
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🦭🦭🦭
tegangaetano.bsky.social Tegan Gaetano @tegangaetano.bsky.social · May 23
A million thanks to @hibernogruppe.bsky.social for coming all the way to Aberdeen to share your research with us.
🐝 🧬 🐝 🧬

@fmanfredini.bsky.social
May 23, 2025 at 3:22 PM
Reposted by Joe Colgan
katharinahoff.bsky.social
Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...
Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...
www.biorxiv.org
April 21, 2025 at 5:37 AM
Reposted by Joe Colgan
joachimschork.bsky.social
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
January 13, 2025 at 3:23 PM
hibernogruppe.bsky.social
🐝Great to have this out @molbioevol.bsky.social and well done Hongfei Xu (not on BlueSky) for all the hard work
April 16, 2025 at 3:53 PM
Reposted by Joe Colgan
stephenturner.us
Review: Transcriptomics in the era of long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/efBjP) 🧬🖥️🧪
March 29, 2025 at 8:57 AM
Reposted by Joe Colgan
chenxinli2.bsky.social
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...
A local synteny visualization with 3 genes across 4 genotypes.
March 19, 2025 at 3:25 PM
Reposted by Joe Colgan
milesroberts.bsky.social
Our review on k-mers + pop gen is now published!

doi.org/10.1093/molb...
March 5, 2025 at 5:43 PM
Reposted by Joe Colgan
kuanhaochao.bsky.social
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...
Combining DNA and protein alignments to improve genome annotation with LiftOn
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
doi.org
March 3, 2025 at 2:24 PM
Reposted by Joe Colgan
rmwaterhouse.bsky.social
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
From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning
The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...
www.biorxiv.org
February 25, 2025 at 7:31 PM
Reposted by Joe Colgan
wkhuber.bsky.social
Bitte am Sonntag wählen gehen! Noch nie war eine Wahl so wichtig für Deutschlands Zukunft.
#Btw2025
February 22, 2025 at 10:49 AM
Reposted by Joe Colgan
jrossibarra.bsky.social
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/...
The Idiot's Guide to Effective Population Size
This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...
onlinelibrary.wiley.com
February 17, 2025 at 6:26 PM
Reposted by Joe Colgan
kamilsjaron.bsky.social
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...
February 14, 2025 at 10:20 PM
Reposted by Joe Colgan
martynazwoinska.bsky.social
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.
A century of theories of balancing selection
Traits that affect organismal fitness are often very genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that nature (...
www.biorxiv.org
February 14, 2025 at 4:49 PM
Reposted by Joe Colgan
humboldt-foundation.de
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...
February 13, 2025 at 3:08 PM
Reposted by Joe Colgan
tommytang.bsky.social
Principled PCA separates signal from noise in omics count data www.biorxiv.org/content/10....
February 13, 2025 at 3:15 PM
Reposted by Joe Colgan
stephenturner.us
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/
February 8, 2025 at 12:14 PM
Reposted by Joe Colgan
3rdreviewer.bsky.social
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...
Estimating recombination using only the allele frequency spectrum
Standard methods for estimating the population recombination parameter, rho, are dependent on sampling individual genotypes and calculating various types of disequilibria. However, recent machine lear...
www.biorxiv.org
February 6, 2025 at 4:29 PM