Pranavathiyani G

AI-built ‘scientists’ get the job done quickly In Virtual Lab project, CZ Biohub San Francisco researchers and collaborators assemble team of interdisciplinary AI agents that can solve complex research questions

Virtual Lab #AI
www.czbiohub.org/news/with-no...

PhyloScape: interactive and scalable visualization platform for phylogenetic trees. r#PhylogeneticTees #Visualization #Bioinformatics #BMCbioinformatics
bmcbioinformatics.biomedcentral.com/articles/10....

Genomic reproducibility in the bioinformatics era genomebiology.biomedcentral.com/articles/10.... 🧬🖥️

Exploring R and Rust in Bioinformatics - online developer forum blog.bioconductor.org/posts/2025-0... #Rstats #rustlang

AlphaGenome: AI for better understanding the genome Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.

#AlphaGenome: #AI for better understanding the #genome
deepmind.google/discover/blo...

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature Biotechnology Protein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource.

Tissue specific protein-protein associations

#atlas #ppi #disesse

Candida auris is emerging as a prevalent urinary pathogen Urinary tract infections (UTIs) are one of the most common infections, with a subgroup of these infections, catheter-associated UTIs (CAUTIs), accounting for 40% of nosocomial infections. While the ma...

#Candida auris - emerging pathogen of #UTI

The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health - Genome Medicine Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; ...

🧬 Out today 🧬 - our TyphiNET
#AMR surveillance dashboard for #typhoid

Use TyphiNET to view genome-derived data on global and national annual trends in AMR and circulating pathogen genotypes via any standard web browser.

genomemedicine.biomedcentral.com/articles/10....

Which programming language should I use? A guide for early-career researchers Computer scientists and bioinformaticians address four key questions to help rookie coders to make the right choice.

#Programming for research

Margaret Dayhoff! #Bioinformatics

www.nature.com/articles/s43...

Genome modeling and design across all domains of life with Evo 2 All of life encodes information with DNA. While tools for sequencing, synthesis, and editing of genomic code have transformed biological research, intelligently composing new biological systems would ...

Genome modeling and design across all domains of life with Evo 2 | bioRxiv www.biorxiv.org/content/10.1...

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview).
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
🐍 available in bioconda

KlebPhaCol

www.klebphacol.org

KlebPhaCol: A community-driven resource for Klebsiella research identified a novel gut phage order associated with the human gut The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite incr...

#KlebPhaCol
www.biorxiv.org/content/10.1...

#klebsiella #phage

Bacteria’s Stress Strategy: Slow Down to Avoid the Crowd Computer simulations highlight how bacteria slow their growth to avoid overcrowding, a behavior that may inform pathogen control.

Bacteria’s Stress Strategy: Slow Down to Avoid the Crowd www.the-scientist.com/bacteria-s-s...

#bacteria #stress #simulation

Introducing RFpeptides - Institute for Protein Design Generative AI based on RFdiffusion designs cyclic peptides with atomic accuracy.

www.ipd.uw.edu/2024/11/intr...

#peptidedesign #diffusion

What’s the secret to living to 100? Centenarian stem cells could offer clues A bank of cells from people more than 100 years old gives scientists a new resource for studying longevity.

www.nature.com/articles/d41...

#longevity #aging

Language Models for Molecular Dynamics Molecular Dynamics (MD) simulations provide accurate descriptions of the motions of molecular systems, yet their computational demands pose significant challenges in applications in molecular biology ...

Language Models for Molecular Dynamics
www.biorxiv.org/content/10.1...

#languagemodel #moleculardynamics

EasyPubPlot: a shiny web application for rapid omics data exploration and visualization https://www.biorxiv.org/content/10.1101/2024.11.26.625339v1 Computational toolkits for data exploration and visualization from widely used omics platforms often

EasyPubPlot: a shiny web application for rapid omics data exploration and visualization https://www.biorxiv.org/content/10.1101/2024.11.26.625339v1

GitHub - jwohlwend/boltz: Official repository for the Boltz-1 biomolecular interaction model Official repository for the Boltz-1 biomolecular interaction model - jwohlwend/boltz

We’re excited to release a major update to the Boltz repo: v0.3.0. This release contains several important new features, including our confidence model and memory-efficient inference. Give it a try! github.com/jwohlwend/bo...

Promotional logo for MMseqs2 16 with the MMseqs2 Rocket mascot as a smart phone like App logo

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

networkcommons.readthedocs.io/en/main/

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrast...

#NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological #networks
www.biorxiv.org/content/10.1...

UniProt: the Universal Protein Knowledgebase in 2025 Abstract. The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely acce

UniProt: the Universal Protein Knowledgebase in 2025 academic.oup.com/nar/advance-... #jcampubs

WhatIsMyGene: Back to the Basics of Gene Enrichment Since its inception over 20 years ago, gene enrichment has been largely associated with curated gene lists (e.g. GO) that are constructed to represent various biological concepts; the cell cycle, canc...

#WhatIsMyGene: Back to the Basics of Gene Enrichment

www.biorxiv.org/content/10.1...

#enrichment #genes

PanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs Microbes are omnipresent, thriving in a range of habitats from oceans to soils and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting t...

#PanTax: Strain-level taxonomic classification of metagenomic data using #pangenome graphs
www.biorxiv.org/content/10.1...

#microbiome #metagenomics #taxonomy

Your friends shape your microbiome — and so do their friends
Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.
www.nature.com/articles/d41...

Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources Abstract. By processing and abstracting diverse omics datasets into associations between genes and their attributes, the Harmonizome database enables resea

#Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources
academic.oup.com/nar/advance-...

#knowledgegraph #multiomics #genes #data #llm

Gaia: A Context-Aware Sequence Search and Discovery Tool for Microbial Proteins Protein sequence similarity search is fundamental to genomics research, but current methods are typically not able to consider crucial genomic context information that can be indicative of protein fun...

#Gaia: A Context-Aware #Sequence Search and Discovery Tool for Microbial #Proteins
www.biorxiv.org/content/10.1...

#languagemodel #llm

CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models https://www.biorxiv.org/content/10.1101/2024.11.20.619750v1 In recent years, advances in cell segmentation techniques have played a critical role in the analysi

CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models https://www.biorxiv.org/content/10.1101/2024.11.20.619750v1