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!

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

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.

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

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

🖥️🧬♀️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

From #OUP 's @bioinfoadv.bsky.social journal | Mars: simplifying #bioinformatics #workflows through a containerized approach to tool integration and management | #OpenScience #Singularity #Container 🧬 🖥️ 🧪 🔓 ⬇️ academic.oup.com/bioinformati...

Mars: simplifying bioinformatics workflows through a containerized approach to tool integration and management

AbstractSummary. Bioinformatics is a rapidly evolving field with numerous specialized tools developed for essential genomic analysis tasks, such as read si

academic.oup.com

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

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.

buff.ly

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 - 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.

github.com

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...

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.

plentyofroom.beehiiv.com

The tutorial for how to assemble organellar genomes from nuclear-targeted long reads is ready to be used. Please check it out bioinformaticsworkbook.org/dataAnalysis... #Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria

Extracting and Assembling a Mitochondrial and Chloroplast Genome from Nuclear-targeted Nanopore Reads

A workbook to help scientists working on bioinformatics projects

bioinformaticsworkbook.org

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

Complete Genome of the iconic Pacific Banana Slug 🧬🧬 ✅ A total of 2.3 Gb (Human Genome is 3.4 Gb) ✅ As part of California Conservation #Genomics Project (CCGP), this project will inform conservation policies #genome #biodiversity #climatechange

Scientists produce first complete genome of a banana slug

Scientists at UC Santa Cruz have completed the first end-to-end genome of the iconic Pacific banana slug, a species synonymous with California's coastal redwood forests and the university's beloved ma...

phys.org

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...

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

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

doi.org

@science.org 🧪🧬💻 @evolutionaryscale.bsky.social @arcinstitute.org

Eric Topol@erictopol.bsky.social · 2y ago

Whoa! When a large language of life model generates a protein equivalent to ~500 million years of evolution. @science.org science.org/doi/10.1126/...

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

Should you learn R or Python first?

YouTube video by OMGenomics

youtu.be

Hornwort Genomes Provide Clues On How Plants Moved From Water To Land On Earth astrobiology.com/2025/01/horn... #astrobiology #genomics #evolution

Hornwort Genomes Provide Clues On How Plants Moved From Water To Land On Earth - Astrobiology

Over 450 million years ago, plants began the epic transition from water to dry land. Among the first pioneers were the ancestors of humble hornworts

astrobiology.com

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

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes https://academic.oup.com/bib/article/26/1/bbae680/7941744 🧬🖥️🧪 https://github.com/gdefazio/kMetaShot

Two resources to learn bioinformatics yourself: 1. Path to a free self-taught education in Bioinformatics! github.com/ossu/bioinf... #bioinformatics

GitHub - ossu/bioinformatics: :microscope: Path to a free self-taught education in Bioinformatics!

:microscope: Path to a free self-taught education in Bioinformatics! - ossu/bioinformatics

github.com

Simply Statistics: Biologists, stop putting UMAP plots in your papers https://simplystatistics.org/posts/2024-12-23-biologists-stop-including-umap-plots-in-your-papers/ from @rafalab.bsky.social 🧬🖥️🧪

🧬🖥️

Travis Wheeler@wheelerlab.org · 2y ago

Version 0.3.0 of nail is out. nail (github.com/TravisWheele...) is a tool for protein sequence annotation. It bridges most of the sensitivity gap between the two excellent tools MMSeqs2 (fast) and HMMER3 (very sensitive), and is >20x faster than HMMER3. Search with profile HMMs or single sequences.

Genetic ancestry and population structure in the All of Us Research Program cohort https://www.biorxiv.org/content/10.1101/2024.12.21.629909v1 🧬🖥️🧪

An Emirati pangenome incorporating a diploid telomere-to-telomere reference https://www.biorxiv.org/content/10.1101/2024.12.16.628631v1 🧬🖥️🧪

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 🙌

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.*

Ming Tommy Tang@tommytang.bsky.social · 2y ago

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

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

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

Well written article in Quanta Magazine on a new paper led by @rebeccavarney.bsky.social that dropped today on path dependent evolution of chiton visual systems www.quantamagazine.org/mollusk-eyes...

Mollusk Eyes Reveal How Future Evolution Depends on the Past | Quanta Magazine

The visual systems of an obscure group of mollusks provide a rare natural example of path-dependent evolution, in which a critical fork in the creatures’ past determined their evolutionary futures.

quantamagazine.org