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...
02.12.2025 15:15 β π 8 π 3 π¬ 1 π 0
Intro to Bedder β The Quinlan Lab
We are thrilled to announce the first official release (v0.1.8) of #π―π²π±π±π²πΏ, the successor to one of our flagship tool, #π―π²π±ππΌπΌπΉπ! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
02.12.2025 02:28 β π 281 π 139 π¬ 5 π 10
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
11.11.2025 09:00 β π 43 π 54 π¬ 4 π 2
Posnien - Georg-August-UniversitΓ€t GΓΆttingen
Webseiten der Georg-August-UniversitΓ€t GΓΆttingen
𧬠PhD Position: Evolutionary & Comparative Genomics π·οΈ
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 π and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
18.11.2025 07:04 β π 23 π 29 π¬ 2 π 0
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 donβt care about skills on paper.
They care about proof. π§΅
22.08.2025 13:15 β π 4 π 1 π¬ 1 π 0
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...
FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms π¦ππͺ±π§¬ππͺ²
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
15.08.2025 00:05 β π 58 π 30 π¬ 2 π 1
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
π§¬π₯οΈ 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
21.08.2025 19:24 β π 39 π 9 π¬ 2 π 1
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...
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
27.05.2025 19:35 β π 27 π 15 π¬ 1 π 2
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 Aberdeenπ΄σ §σ ’σ ³σ £σ ΄σ Ώ, meeting great peopleπ», as well as seeing the wildlifeπ¦π¦π¦
23.05.2025 15:22 β π 2 π 0 π¬ 0 π 0
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
13.01.2025 15:23 β π 3 π 1 π¬ 0 π 0
πGreat to have this out @molbioevol.bsky.social and well done Hongfei Xu (not on BlueSky) for all the hard work
16.04.2025 15:53 β π 5 π 3 π¬ 0 π 0
A local synteny visualization with 3 genes across 4 genotypes.
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...
19.03.2025 15:25 β π 17 π 3 π¬ 0 π 1
Our review on k-mers + pop gen is now published!
doi.org/10.1093/molb...
05.03.2025 17:43 β π 40 π 29 π¬ 0 π 0
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
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...
03.03.2025 14:24 β π 32 π 15 π¬ 1 π 0
Bitte am Sonntag wΓ€hlen gehen! Noch nie war eine Wahl so wichtig fΓΌr Deutschlands Zukunft.
#Btw2025
22.02.2025 10:49 β π 15 π 6 π¬ 1 π 0
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...
14.02.2025 22:20 β π 68 π 35 π¬ 1 π 1
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 (...
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.
14.02.2025 16:49 β π 29 π 15 π¬ 2 π 1
OlΓ‘, Brasil! π§π· 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...
13.02.2025 15:08 β π 26 π 10 π¬ 0 π 1
Principled PCA separates signal from noise in omics count data www.biorxiv.org/content/10....
13.02.2025 15:15 β π 12 π 2 π¬ 0 π 0
ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity π§¬π₯οΈπ§ͺ
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/
08.02.2025 12:14 β π 61 π 30 π¬ 0 π 0
vcfsim: flexible simulation of all-sites VCFs with missing data
VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invari...
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...
04.02.2025 02:50 β π 50 π 18 π¬ 2 π 0
CASTER: Direct species tree inference from whole-genome alignments https://www.science.org/doi/10.1126/science.adk9688 π§¬π₯οΈπ§ͺ https://github.com/chaoszhang/ASTER
31.01.2025 21:00 β π 15 π 6 π¬ 0 π 0
Origins and consequences of genome mutation; software for genomic discovery.
Prof. and Chair of Human Genetics at U. of Utah.
https://www.genetics.utah.edu/
http://quinlanlab.org
The Earth BioGenome Project (EBP), a moonshot for biology, aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of ten years.
π²Keep up with all EBP updates: https://linktr.ee/earthbiogenomeproject
Bioinformatics Scientist / Next Generation Sequencing, Single Cell and Spatial Biology, Next Generation Proteomics, Liquid Biopsy, SynBio, AI/ML in biotech // http://albertvilella.substack.com
May contain ants
http://evolution.vnehring.de | Behaviour, Evolution, Ecology | Assistant Prof@Uni Freiburg, Germany | AE @PlosONE | Secretary Central European IUSSI
Postdoc at IST Austria, population genetics
Curating and cataloging the world's data for the fruit fly Drosophila melanogaster into our database at http://flybase.org. Aiding discovery since 1992.
Evolutionary biologist, Inst. Evol. Biol. (CSIC, Barcelona). Invertebrate genomics, trying to understand how animals colonised land (and also caves). www.metazomics.com
Evolutionary Applications. Scientific journal. Evolutionary approaches to environmental, biomedical and socio-economic issues. Tweets by Social Media Editor
https://onlinelibrary.wiley.com/journal/17524571
PhD candidate | JGU Mainz | Palaeogenetics Group | Palaeo-epigenomics | aDNA | πͺπ¬
The goal of the Canadian BioGenome Project is to produce high-quality reference genomes 𧬠for all Canadian species π
Sequencing Canada's Biodiversity πΏπ¦ππ§¬π’π¦πΈπ³πΏππ¦π¦¦
Learn more: https://linktr.ee/canadianbiogenome
Associate Professor @ UC-Davis | Former Senior Director @ Exai Bio | Computational Biology, ML/AI, Genomics, RNA, Cancer
EvoDevo, Spider enthusiast, Drosophila, biologist, side cut, punk&hardcore, dog owner
working on sexually deceptive pollinationπͺ»π PhD student at University of Hohenheim
Securing tomorrowβs resources: The JKI is the Federal Research Center for Cultivated Plants in Germany and one of four departmental research institutes of the Federal Ministry of Food and Agriculture (#BMLEH). www.julius-kuehn.de/en/
Incoming Group Leader at Max Planck Institute for Biology TΓΌbingen @mpi-bio-fml.bsky.social.
EvoDevo, Sex determination, Haplodiploidy π π π and occasionally, sex chromosomesπ‘ π¦
theoretical evolutionary biologist, working on transitions between genetic systems.
Genome annotation geek at University of Greifswald, always interested in friendly scientific collaboration. Developer of BRAKER, GALBA, MakeHub and other Gaius-Augustus tools.
Scientific lab head at a natural history museum (LIB / Museum KΓΆnig Bonn, Germany). Research in animal genomics & evolution (insects, fish), teaching bioinformatics. Enjoying literature & history, 50/60s Jazz and arthouse movies.
