iiinova — where your digital self keeps evolving

Andrew Severin @andrewseverin.bsky.social · 18/12/2025

Problem solving is by far the best part of being a manager of a bioinformatics core. I’ll be at PAG33 in San Diego this January. If you have an experiment you want to run by me or a tricky analysis you’re stuck on, let's meet up! 🧬 🖥️ hashtag#PAG33. Send me an gifhelp@iastate.edu!

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Andrew Severin @andrewseverin.bsky.social · 17/12/2025

Genome annotation is an unsolved problem. All the current tools struggle predicting gene models due to the limitations of short reads. With long read data, annotation will improve but still limited to RNA expression under many conditions. Functional Annotation is similarly challenging 🧬 🖥️ #PAG33

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Andrew Severin @andrewseverin.bsky.social · 16/12/2025

Data analysis/discovery is the fun part but documentation is super important if not more important in bioinformatics. We use Github as our version controlled, searchable and sharable lab notebook to keep track of each project. The key to good project management adoption is a low barrier to entry.

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Andrew Severin @andrewseverin.bsky.social · 15/12/2025

Bioinformatics rests on three pillars of knowledge: Biology, Sequencing Technology and Software. Not understanding the assumptions and limitations of these pillars as they relate to your project will reduce your ability to explore your data. 🧬 🖥️ #PAG33

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Andrew Severin @andrewseverin.bsky.social · 12/12/2025

When I first started learning Unix commands, learning how to explore file contents was very important. Now that I teach bioinformatics, I came up with a fun way to remember these commands: A `cat` has a `head` and a `tail`, `more` or `less`. 🧬 🖥️ #PAG33

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Germán Bonilla-Rosso @germusthermophilus.bsky.social · 04/06/2025

🖥️🧬♀️I overheard a conversation guilty of youth and arrogance, saying there were not many women in bioinformatics besides Margaret Dayhoff (PAM). That is not only stupid but also wrong. Since my foundation years bioinformatics was always very female: #WomenInBioinformatics #WomenInStem

Ruth NUSSINOV (RNA folding), Barbara McClintock (transposons), Tomoko Ohta (neutral theory), Jorja Henikoff (BLOSUM), Christine Orengo (CATH), Janet Thornton (CATH), Julie Thompson (CLUSTAL), Theresa Attwood (PRINTS), Tracy Heath (Bayesian), Bonnie Berger (ARACHNE), Kim Pruitt (RefSeq), Tatiana Tatusova (Entrez), Kira Makarova (COGs), Claire Fraiser (TIGR)

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Earlham Institute @earlhaminst.bsky.social · 12/05/2025

A study from the Earlham Institute and @ox.ac.uk has generated ultra #longread @nanoporetech.com reads, to reveal the majority of the human #genome is replicated from dispersed initiation sites, with around 80% of the sites never reported before. 🖥️🧬 @conradn.bsky.social @drkarimgharbi.bsky.social

buff.ly

Starting point of DNA replication mystery solved

The question of where DNA replication starts in the human genome has finally been addressed, with the conclusion it is largely random.

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naturepoker @binomicalabs.org · 09/05/2025

Whoa iqtree is finally up to version 3. It's setup in a separate github repo so if you rely on automated setup scripts (like I do) you'll have to make minor changes. Time to run some tests to see if recent results remain consistent 💻🧬 github.com/iqtree/iqtree3

github.com

GitHub - iqtree/iqtree3: IQ-TREE version 3: software for phylogenetics

IQ-TREE version 3: software for phylogenetics. Contribute to iqtree/iqtree3 development by creating an account on GitHub.

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Plenty of Room - Newsletter @plenty-of-room.bsky.social · 06/05/2025

Are you looking for something cool to read? 😎 What about using AI to improve protein sequencing? It's an exciting one! 🧪🧬🖥️ plentyofroom.beehiiv.com/p/ai-protein...

plentyofroom.beehiiv.com

AI Protein Sequencing Breakthrough: Decoding Peptides Faster!

AI-powered protein sequencing: Instanovo uses advanced machine learning to decipher peptide structures, revolutionizing proteomics and biomedical research.

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Shicheng Guo @shihcheng.bsky.social · 18/01/2025

Unveiling the Yadong trout (Salmo trutta) genome! 🐟 A near-complete 2.49 Gb assembly with 96.87% anchored to 40 chromosomes. Key insights await! #Genomics PMID:39814780, Sci Data 2025, @ScientificData doi.org/10.1038/s415...

doi.org

Near complete genome assembly of Yadong trout (Salmo trutta) - Scientific Data

Scientific Data - Near complete genome assembly of Yadong trout (Salmo trutta)

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Robert Aboukhalil @robert.bio · 10/01/2025

Should you learn R or Python first for bioinformatics? 🤔 🧬 🖥️ ➡️ youtu.be/-XU5Jxe4LpE

youtu.be

Should you learn R or Python first?

YouTube video by OMGenomics

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Andrew Severin @andrewseverin.bsky.social · 07/01/2025

I have been working on a new project for teaching bioinformatics to beginners that involves an integrated holistic and project based approach to learning. As a bioinformatician with over 15 years of experience, I am humbled by how fast this field evolves as I go back to the basics! #bioinformatics

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Stephen Turner @stephenturner.us · 03/01/2025

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes academic.oup.com/bib/article/26/1/b… 🧬🖥️🧪 github.com/gdefazio/kMetaShot

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Stephen Turner @stephenturner.us · 31/12/2024

Simply Statistics: Biologists, stop putting UMAP plots in your papers simplystatistics.org/posts/2024-12-… from @rafalab.bsky.social 🧬🖥️🧪

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Travis Wheeler @wheelerlab.org · 27/12/2024

🧬🖥️

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Stephen Turner @stephenturner.us · 24/12/2024

Genetic ancestry and population structure in the All of Us Research Program cohort www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪

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Stephen Turner @stephenturner.us · 20/12/2024

An Emirati pangenome incorporating a diploid telomere-to-telomere reference www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪

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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 08/12/2024

Have questions about #bioinformatics, #genomics, #evolution or stuck on a project? 🧬💻 I want to help! Happy to discuss data, figures, writing, academia/industry or chatting just for kicks—no strings attached Drop questions below, DM, or schedule a meeting Science together is better than alone 🙌

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

Seconded. I use the postcards #Rstats package from @seankross.com for my personal website. Just a few lines of RMarkdown and you get a very nice-looking website. GitHub README has several examples github.com/seankross/po.... Trainee? Job-hunting? Have a public website/portfolio. *Take up space.*

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Andrew Steele @statto.bsky.social · 21/11/2024

There’s more to rainbows than the human eye can see: here’s how a rainbow extends into the infrared and ultraviolet. Photos: 1. Infrared 2. Visible (obviously) 3. Ultraviolet, and 4. A composite showing how UV is beyond the violet in a rainbow, and IR beyond the red end. 🧪 #photography

An infrared photo of a rainbow: a strange, ghostly-looking rainbow in a mostly black and white photo, with a faintly red outer edge and a cyan inner edge, and what look like a few even fainter ‘echo’ bows inside

A regular visible-light pic of a rainbow

An ultraviolet picture of a rainbow: a dark, foreboding landscape with a deep purple stripe emanating from it, and a grey stripe inside

A composite of the three preceding photos, showing that the infrared bow is ‘outside’ the visible light rainbow, and the ultraviolet bow ‘inside’

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Bluesky @bsky.app · 16/11/2024

Another day, another million new people have joined Bluesky! 18M users? 🙂‍↔️ 18M friends 🙂‍↕️

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Stephen Turner @stephenturner.us · 28/02/2024

A harmonized public resource of deeply sequenced diverse human genomes www.biorxiv.org/content/10.1... gnomad.broadinstitute.org/news/2020-10...

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Stephen Turner @stephenturner.us · 29/02/2024

This app just got a lot more useful

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Andrew Severin @andrewseverin.bsky.social · 28/02/2024

I spoke at the 2024 Innovate Iowa State P&S conference about what I learned about ChatGPT and how to use it in academia to reduce the time to do mundane tasks and improve the output. I made my book free today until midnight at www.amazon.com/dp/B0C9F9M8FN/ #AI #ChatGPT. Check it out!

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Andrew Severin @andrewseverin.bsky.social · 16/01/2024

It feels like screaming into the void when you start on a new platform. But if you see this message and want to learn how to create prompts effectively using #ChatGPT, my book is free today. I encourage you to check it out! www.amazon.com//dp/B0C9F9M8...

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Andrew Severin @andrewseverin.bsky.social · 15/01/2024

#PAG31 Poster Session today. Stop by my poster on ChatGPT. Let me know how you are using ChatGPT in your research in the comments.

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