Alexey Sergushichev

Role play in question: "You are an experienced software engineer. Write a program that ..."

CATS: Canine Airport Therapy Squad

Bioinformatics is in shambles at the Denver airport’s acronym game

Technically correct, the best kind of correct

I find the lack of reference to Star Wars with this name disturbing

Motherfucking Rex in the motherfucking park

📢 We are announcing the Adaptive Immune Profiling Challenge 2025!
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
🗓️ Launches Nov 5 on @kaggle.com
More Info: uio-bmi.github.io/adaptive_imm...

Does anyone have a high-res version of NCBI GEO logo (www.ncbi.nlm.nih.gov/geo/img/geo_...)? I hate putting their low-res version in the slides/figures. I've tried to use AI tools for upscaling, but the results aren't perfect (colors are off). Anyone want to take a shot at it? Here is my best take:

Somatic mutation and selection at population scale - Nature A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.

ohhhhhhhh wow
www.nature.com/articles/s41...

Postdoc Description.docx Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution @cellcellpress.bsky.social @sstevenwang.bsky.social @yalepress.bsky.social
www.cell.com/cell/fulltex...

Redid this thanks to @james-gagnon.bsky.social reminding me about NIH Databook. R01 applications numbers are dropping greatly at NIGMS but success rates (after being flat) dropped greatly last year. Suspect this will be even more drastic in 2025

I see... I assumed it's the same for ESI and established

I believe you can submit multiple grants to NIGMS in parallel, you just had to withdraw other applications to get awarded, no? Which doesn't sound too bad, because it means you are getting a grant.

One of them should be 5e-324. Another - maybe 1e-300 as a rounding of that? And maybe 1e-200 as another capping threshold?

An array of 9 purple discs on a blue background. Figure from Hinnerk Schulz-Hildebrandt.

A nice shift in perceived colour between central and peripheral vision. The fixated disc looks purple while the others look blue.

The effect presumably comes from the absence of S-cones in the fovea.

From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

I'm in the `sed -n 2~4p` camp

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

github.com/assaron

Oh, fun: Someone did some personal science to evaluate if _they personally_ benefit from "AI", and this is what they found:

«Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]

Thank you, Mike!

It's artificial as in artificial leather—in other words, fake.

Stealth genomics startup focused on non-cancer diagnostic applications Senior Deep Learning Engineer • Ph.D. in relevant field with 3+ years practical experience in deep learning for biology • Demonstrated proficiency in building DL architectures using Pytorch or TensorFlow+Keras. • Substantial expertise in training lightweight deep learning models and tuning large foundation models. • Substantial expertise with developing efficient data loaders for large datasets and optimizing training workflows. • Deep expertise training and deploying models in Cloud-based compute environments and local hardware. • Sufficient knowledge of the genomics of gene regulation to ask the right questions for the specific information to be gained. • Expertise in developing models of gene regulation and sequence-to-function models is a plus. • Interactive team player in highly collaborative small setting. Experience collaborating and communicating with biologists. Interested candidates can send their CV to anshul @ kundaje . net

Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.

Download statistics for the top 75 Bioconductor packages

An important milestone for me and my lab: fgsea has passed DESeq2 on the list of most downloaded Bioconductor packages. It started as a side project during my PhD, back when DESeq2 was already a staple of RNA-seq analysis. I never even thought it could go this far — but here we are!

1. Make an Excel file with your author information
2. Drag and drop
3. Copy a nicely formatted author list into Word

🐶 slowkow.com/authorbud

I almost wrote "what did you expect from a Frontiers journal", but it turned out to be different Frontiers :)

A screenshot of a graph of water levels from a station in Hawaii as the tsunami impacted the region.

Does water always recede prior to the arrival of a tsunami?

I was asked this yesterday after posting a graph of observed water levels at a station in Hawaii, which shows water levels first *increasing,* contrary to what many have heard about tsunamis.

The answer: no, not always! A thread... 🧵 1/9

It even looks much more Manhattanish compared to a GWAS Manhattan plot

Hot and Dense Nuclear Matter Proceedings of the NATO Advanced Study Institute on [title], held in Bodrum, Turkey, Sept.-Oct. 1993. Leading researchers present new material and new results with regard to hot and dense nuclear matt...

Using google ngrams I found a book that has a Manhattan plot from 1994 (not related to genetics): www.google.com/books/editio...