iiinova — where your digital self keeps evolving

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Frank Hochholdinger @hochholdingerf.bsky.social · 07/03/2025

Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting: - The chair of the meeting - The winner of the most prestigious McClintock award - A plenary speaker - Two short talk presenters - 22 scientists presenting posters. #MGM2025

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Matt Hufford @mbhufford.bsky.social · 26/01/2025

The latest preprint from the PanAnd project, led by @mcstitzer.bsky.social is out today. We look at genome evolution in the Andropogoneae tribe of grasses. Interesting to see how processes occurring in #maize after #polyploidy may not be a general phenomenon. www.biorxiv.org/content/10.1...

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 27/01/2025

I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...

mcstitzer.github.io

Panand Genomes

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Michelle Stitzer @mcstitzer.bsky.social · 27/01/2025

New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...

On top, five Andropogoneae grass species, from left to right Zea mays subsp. mays, Hemarthria uncinata, Miscanthus sinensis, Sorghum bicolor, Andropogon gerardi. On bottom, a map of the world, with collection sites of Andropogoneae grasses in points. A green background shows the distribution of Andropogoneae grasses throughout tropical and temperate latitudes

On left, a phylogeny of Andropogoneae species, with 14 independent polyploidy origins noted. On right, genome size and repeat content of each assembly. Across all assemblies, average assembly size is 1.9 Gb, and average repeat size is 1.5 Gb.

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Joachim Goedhart @joachimgoedhart.bsky.social · 16/12/2024

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

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Marc Somssich @somssich.bsky.social · 02/01/2024

I have written a couple of threads 🧵 on "classic" #PlantScience papers. I always tag them with #PlantScienceClassics , but will also compile them here in this thread: 👇

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Aanchal Choudhary @aanchal12.bsky.social · 08/12/2024

🎉I am really excited to share that our paper is out. We present PHILO ChIP-seq, a user-friendly and cost-effective platform for high-throughput, low-input chromatin profiling in plants! From Mark Zander group academic.oup.com/nar/advance-...

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Christa Buecker @chribue.bsky.social · 02/12/2024

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

doi.org

Redirecting

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 08/12/2024

Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations. www.biorxiv.org/content/10.1101/202…

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Jan Broder Engler @jbengler.de · 06/12/2024

Hey educators, tidyplots.org is great for teaching students data visualization because it is 🕊️ Free and open-source 🚀 Easy, intuitive and fast 💾 Loaded with demo datasets 🏆 Embracing best practices 🌈 Beautiful #rstats #phd #dataviz #education

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Kevin Bird @stairwaytokevin.bsky.social · 06/12/2024

Cool preprint! How do polyploids lose genes during fractionation/diploidization? Old work in maize pointed to recombination-driven deletions (journals.plos.org/plosbiology/...) but generality was unclear. New evidence this is the more common deletion mechanism! www.researchsquare.com/article/rs-4...

researchsquare.com

The Subordinate Role of Pseudogenization over Recombinative Deletion Following Polyploidization in Angiosperms

Extensive gene loss is a key feature of the rediploidization process following polyploidization. Despites this, the molecular mechanisms behind such gene loss are unclear, whether it is through pseudo...

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Stephen Turner @stephenturner.us · 05/12/2024

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/dietvin/pod5...

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Javier Santoyo @jsantoyo.bsky.social · 05/12/2024

Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning. #Nanopore #Sequencing #XenoNucleicAcids #XNAs #genomics #bioinformatics @nanoporetech.com 🧬🖥️ www.biorxiv.org/content/10.1...

Source:
https://www.biorxiv.org/content/10.1101/2024.12.02.625113v1.full

High throughput nanopore sequencing of synthetic xeno-nucleic acids (XNAs)

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RCAC Bioinformatics @ Purdue University @rcac-bioinfo.bsky.social · 04/12/2024

🚨 Summer '25 Paid Internships! Join Purdue’s Anvil Research Experience for Undergraduates for hands-on experience in AI, bioinformatics, & data centers. $680/week + housing. Apply now: purdue.ca1.qualtrics.com/jfe/form/SV_... 🌟

purdue.ca1.qualtrics.com

Anvil REU Applications

Application submission for the Purdue Anvil REU program.

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Fabricio Almeida-Silva @almeidasilvaf.bsky.social · 24/11/2024

Thrilled to see this paper out! 🎉 We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.

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Mike Vella @vellamike.bsky.social · 27/11/2024

Exciting news! The latest hifiasm release from Haoyu Cheng and Heng Li adds beta support for @nanoporetech.com simplex R10 reads. Initial results look very promising. 🚀 Check it out: github.com/chhylp123/hi...

github.com

Release Hifiasm-0.21.0-r686 · chhylp123/hifiasm

Since Hifiasm-0.20.0 (r639): New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below: hifiasm -t64 --ont -o...

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Camille Marchet ⚡ @camillemrcht.bsky.social · 28/11/2024

If you've missed hyper-k-mers, this joint work with Lucas who's presenting, @imartayan.bsky.social Antoine Limasset and Yoshihiro Shibuya. They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.

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Oxford Nanopore @nanoporetech.com · 27/11/2024

We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them. Read more: nanoporetech.com/news/oxford-...

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Stephen Turner @stephenturner.us · 26/11/2024

bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 #rstats github.com/trichelab/bamSliceR from @timtriche.bsky.social lab

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Arun Seetharam @arnstrm.bsky.social · 26/11/2024

annoy a bioinformatician with these simple phrases: "Can't you just use Excel?" "Isn't BLAST basically Google for DNA?" "But did you annotate it?"

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Mike Barker @barkerms.bsky.social · 26/11/2024

Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience @uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...

A photo of the Sonoran Desert at night with a saguaro cactus in the foreground with the top glowing from the moonlight. A field of stars is visible in the sky behind the cactus.

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Emily Liu @emilyliu.me · 25/11/2024

By popular request, here's how to add Bluesky replies as your blog's comment section! This requires some technical know-how for now, but I'm hoping that we see some no-code solutions for this pop up soon, like Ghost or Wordpress plugins. emilyliu.me/blog/comments

emilyliu.me

Using Bluesky posts as blog comments

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MultiQC @multiqc.info · 23/11/2024

Just out: @multiqc.info v1.25.2 🎉 This patch release fixes a whole host of bugs, the most important one being for #bcl2fastq 🐛 There are also a host of small additions sneaking in for #ngsbits, #picard, #Nanostat, #Samtools and more - so well worth the update! github.com/MultiQC/Mult...

github.com

Release v1.25.2 · MultiQC/MultiQC

MultiQC v1.25.2 - 2024-11-20 Multiple bug fixes and minor updates. Updates Add natural sort for sample sorting (#2959) Custom content: for plot_type: image, support custom_data config with section...

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Craig P. Burrows @cpburrowsphoto.bsky.social · 23/11/2024

Hello! I've made it to bluesky. I never liked Twitter but we'll give this a go! Starting with Sarcodes sanguinea, aka Snow Plant fungal parasite associated with conifers. Recorded in UVIVF, I hypothesize that the blue fluorescence is intended to attract bees! #botany #photography #uvivf

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Florian Wünnemann @flowuenne.bsky.social · 21/11/2024

@linathekim.bsky.social too bad we missed you, but don't worry, help desks happen every Tuesday 2pm Eastern and Thursday 10 AM central European nf-co.re/blog/2024/he...

nf-co.re

Announcing: Weekly Helpdesk

A weekly drop-in sessions to connect and work together.

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Ryan Layer @ryanlayer.bsky.social · 21/11/2024

We have a method for fast GWAS data access. STABIX adds a p-value index that with a position index (what TABIX has) allows you to quickly retrieve, eg. all significant SNPs in a target gene. Also column compression to reduce the size. www.biorxiv.org/content/10.1... github.com/kristen-schn...

biorxiv.org

STABIX: Summary statistic-based GWAS indexing and compression

Genome-Wide Association Studies (GWAS) are widely used to investigate the role of genetics in disease traits, but the resulting file sizes from these studies are large, posing barriers to efficient st...

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Stephen Turner @stephenturner.us · 22/11/2024

Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python academic.oup.com/bioinformatics/adv… 🧬🖥️🧪 github.com/complextissue/pytximport

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Stephen Turner @stephenturner.us · 22/11/2024

New weekly recap: Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ... blog.stephenturner.us/p/weekly-reca… 🧬🖥️🧪

blog.stephenturner.us

Weekly Recap (Nov 2024, part 3)

Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ...

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Alasdair Hubbard @dralhubb.bsky.social · 22/11/2024

I've used EasyFig before, its a little more basic compared to clinker but does what it says on the tin: mjsull.github.io/Easyfig/

mjsull.github.io

Easyfig - home

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Sébastien Guizard @bioinformaticus.bsky.social · 22/11/2024

Need to download reads from Box.com on your HPC and the box client is not installed? Just build a container! Here is the singulaity recipe: github.com/sguizard/bio... #Bioinformatics

github.com

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Dr. Arun Sethuraman @arunsethuraman.bsky.social · 17/11/2024

New pub out from my lab today in MBE, led by my PhD student Tamsen. We develop a forward time polyploid genome simulator, build an inference model, test it on empirical datasets to show that a majority of plant genomes are of allopolyploid origin. Do check it out! doi.org/10.1093/molb...

doi.org

Accurate Inference of the Polyploid Continuum using Forward-time Simulations

Abstract. Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Mu

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Erin Sparks @erinsparks.bsky.social · 20/11/2024

ahhh love love love all the defectors coming to Bluesky!!! 😍

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Sunil Kenchanmane Raju @kenchanmane.bsky.social · 20/11/2024

Honored to have Marissa from #ASBMBToday feature our work on rhythmic lipid and gene expression change under chilling! 🌱 tinyurl.com/lipid-rhythm Huge thanks to @rebeccaroston.bsky.social @szintri.bsky.social & Frank Harmon #UCBerkeley for this fantastic collaboration tinyurl.com/Jxbmillet

tinyurl.com

From lab to land: Crop modifications are fortifying our food supply against climate change

Scientists explore genetic and biochemical innovations fueling future-proofing agriculture

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 21/11/2024

Slide I put together for a Darwin Day talk I'm giving next year. Unconscious selection = Natural selection. Leaf angle in maize has not been directly selected on by breeders but shows huge change! A meta-analysis of natural & wild pops suggests selection under domestication is, if anything is weaker

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Stephen Turner @stephenturner.us · 21/11/2024

Tidyplots empowers life scientists with easy code-based data visualization www.biorxiv.org/content/10.1101/202… #rstats

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Adam Phillippy @aphillippy.bsky.social · 21/11/2024

Long-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data! 📄 genome.cshlp.org/content/34/1... 📖 genome.cshlp.org/content/34/1...

genome.cshlp.org

Table of Contents — November 2024, 34 (11)

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

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Frank Hochholdinger @hochholdingerf.bsky.social · 20/11/2024

#OTD 15 years ago the draft sequence of the maize 🌽 inbred line B73 was published. @maizegdb.bsky.social

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Stephen Turner @stephenturner.us · 19/11/2024

Blackbird: structural variant detection using synthetic and low-coverage long-reads www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 github.com/1dayac/Blackbird

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Stephen Turner @stephenturner.us · 19/11/2024

MultiOmicsIntegrator-MOI: A nextflow pipeline for integrated omics analyses academic.oup.com/bioinformaticsadva…

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Stephen Turner @stephenturner.us · 20/11/2024

Expand your Bluesky network with R: Find people followed by the people you follow, but who you don't follow, using R and the atrrr package blog.stephenturner.us/p/expand-you... #Rstats

blog.stephenturner.us

Expand your Bluesky network with R

Find people followed by the people you follow, but who you don't follow, using R and the atrrr package

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Jennifer McHenry, PhD @jennmchenry.bsky.social · 15/11/2024

Pinning the EcoEvo job board so I’ll no longer have a reason to revisit the blue bird website. 🚨📌 docs.google.com/spreadsheets...

docs.google.com

ecoevojobs.net 2024-25

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 20/11/2024

I can never remember to put in the appropriate tags. Well here #PlantScience for the corn facts you never knew you needed. bsky.app/profile/jros...

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