KC Maharana

So you want to work on a new pathogen: a self-onboarding checklist Imagine, you are a bioinformatician but you go into a new lab or go into a new project. You know your basics: genome assembly, genome annotation, SNPs, MLST, the usual toolkits. So you’re mostly good...

Day 1 in a new lab:
“You’ll be working on this organism now.”

Me: cool cool cool
(has never heard of it)

I wrote the checklist I use to survive that situation:

👉 self-onboarding a new pathogen
lskatz.github.io/posts/2026/0...

GenDiS3 database: census on prevalence of protein domain superfamilies of known structure in the entire sequence database https://www.biorxiv.org/content/10.1101/2025.03.14.643262v1

A simple way to find related sequences with position-specific probabilities One way to understand biology is by finding genetic sequences that are related to each other. Often, a family of related sequences has position-varying probabilities of substitutions, insertions, and ...

Anyone else having issues actually accessing the pdfs on @biorxivpreprint.bsky.social ? E.g. this one : www.biorxiv.org/content/10.1...

Slice'N'Dice: maximizing the value of predicted models for structural biologists Recent advancements in computational structural modelling have provided structural biologists with access to high-quality predictions that can be used to aid experimental structure determination. Slic...

Pleased to see our latest paper out in Acta Cryst D (journals.iucr.org/d/issues/202...). It describes Slice'N'Dice, software for splitting up an AlphaFold model (or any structure actually) in a variety of ways, and then placing it with Molecular Replacement or directly into a cryo-EM map.

AI as an accelerator for defining new problems that transcends boundaries - BioData Mining Interdisciplinary, transdisciplinary, convergence, and No-Boundary Thinking (NBT) research are methodology and technology-agnostic approaches to problem solving. The focus is on defining problems info...

AI as an accelerator for defining new problems that transcends boundaries biodatamining.biomedcentral.com/articles/10.... #science #research #artificialintelligence

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...

Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy The 16S ribosomal RNA (rRNA) gene is frequently sequenced to classify prokaryotes and identify new taxa. If sequences from two strains share less than ~99% identity, the strains are usually classified...

Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.biorxiv.org/content/10.1... #jcampubs

A batch of cowpea seeds — better known as lobia in Hindi or thattapayaru in Tamil — have successfully sprouted in space, days after they were taken into orbit by an Indian Space Research Organisation mission.
www.thehindu.com/sci-tech/sci...

We added another 100 citations (total 577) in the latest version of our review on LLMs and agents in chemistry. Take a look!

arxiv.org/abs/2407.01603

Complete genomes of 152 root commensal bacteria from the model legume Lotus japonicus https://www.biorxiv.org/content/10.1101/2025.01.02.630998v1

Happy new year

1³+2³+3³+4³+5³+6³+7³+8³+9³

CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants https://www.biorxiv.org/content/10.1101/2024.12.29.630569v1

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs Motivation Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ab...

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. #VCF #VariantFiltering #RUST @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

Like ‘old Twitter’: The scientific community finds a new home on Bluesky After recent changes to Elon Musk’s X, a gradual migration turns into a stampede

#science ♥️ #bluesky
www.science.org/content/arti...

Protein structure prediction from the AlphaFold Database

Prediction confidence scores help #AlphaFold users gauge the reliability of protein structure predictions. 🖥️🧬

But things get more challenging for protein families.

A new method helps improve low confidence predictions within protein families.

academic.oup.com/bioinformati...

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...