Andrew Hogan

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales biorxiv.org/content/10.110… #biorxiv_micrbio

Super excited to share our latest study on Bacillus subtilis in defense mode against protistan predation! pnas.org/doi/10.1073/pn…

Burkholderia Genes Involved in Extracellular Bioplastic Degradation Revealed by Tn-seq and CRISPR-Cas biorxiv.org/content/10.110… #biorxiv_micrbio

Novel origin of replication for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and ... biorxiv.org/content/10.110… #biorxiv_micrbio

We have openings for motivated and curious individuals to join our team microbialeco.systems

Are you working on biological transitions in fundamental developmental processes? 🔎 Get ready to deep dive into the theoretical knowledge of biological transitions and get hands-on training using state-of-the-art methods applied in-depth in different model systems. ⏰ Hurry up and apply for #EMBLDevBio ➡️ s.embl.org/ptd25-01-x 📩 Application deadline: 2 April

I'm starting my group in Koblenz on April 1st (no April Fools' joke!) - advertising soon two postdoc positions in #protist #ecology & genomics. If you're a (soon-to-be?) postdoc-level #protistologist looking for a job, get in touch! One position on wastewater, the other flexible!

Super excited to share our new selection-free CRISPR-Cas9 editing protocol for Dictyostelids, generating 80% KO and 30% KI efficiencies without selection in D. discoideum, and being effective in Dictyostelid species that diverged millions of years ago! biorxiv.org/content/10.110…

ABCFold: Easier Running and Comparison of AlphaFold 3, Boltz-1, and Chai-1 - Structural biology has seen a revolution with deep learning-based protein structure predictors like AlphaFold 3, Boltz-1, and Chai-1. However, running and comparing these models efficiently remains a challenge. - ABCFold is a new tool that simplifies the process of running and benchmarking AlphaFold 3, Boltz-1, and Chai-1, allowing users to generate structure predictions with a standardized input format. - The tool converts AlphaFold 3 JSON inputs into compatible formats for Boltz-1 and Chai-1, enabling seamless execution of all three models from a single input. - ABCFold provides automated multiple sequence alignment (MSA) handling, supporting both JackHMMER-based searches and the MMseqs2 API. Users can also supply custom MSAs and template structures. - The software includes a unified output visualization framework, allowing side-by-side comparison of model predictions, pLDDT scores, and predicted aligned error (PAE) values. Structural clashes are also highlighted for better assessment. - One of the key benefits of ABCFold is its ability to automate installation and version management of Boltz-1 and Chai-1, reducing setup complexity for researchers. - By providing standardized evaluation metrics and interactive visualization tools, ABCFold enhances reproducibility and helps researchers assess the relative strengths of different structure prediction methods. - This tool is an important step toward better benchmarking of next-generation protein structure predictors, enabling broader adoption and more effective model selection for specific biological applications. 💻Code: github.com/rigdenlab/ABCF… 📜Paper: biorxiv.org/content/10.110… #StructuralBiology #AlphaFold #MachineLearning #ProteinFolding #DeepLearning #Bioinformatics #ComputationalBiology

Please repost: Postdoc position in antibiotic discovery in a multidisciplinary project w. high-throughput approaches, microscopy, AI, and hit-to-lead optimization @UMontreal @med_umontreal @Mila_Quebec @IRIC_umontreal. Apply @ ML.Antibiotics@gmail.com. See lnkd.in/dVVk4N3s

TXA11114: Discovery of an in vivo efficacious efflux pump inhibitor in Pseudomonas aeruginosa biorxiv.org/content/10.110… #biorxiv_micrbio

Come join our lab! Exciting ideas, cutting edge equipment, and a beautiful campus in Heidelberg, Germany 🇩🇪🦠

Applications for the EMBL International PhD Programme are open! 👀 The programme offers fully funded PhD positions at EMBL’s six sites across Europe 🌍 Have a look at this opportunity to start your career in the life sciences here: embl.org/about/info/emb…

Cross-linked agarose-gelatine beads as a substrate for investigating biofilms of bacterial pathogens biorxiv.org/cgi/content/sh… #biorxiv_micrbio

A really cool step forward in data transparency and reproducible science publishing! A publishing platform that places code front and centre nature.com/articles/d4158…

For the inducible promoter nerds among us: Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors pubs.acs.org/doi/10.1021/ac…

Only few more spots available with an extended deadline! Make sure not to miss out!!

Inducible transposon mutagenesis for genome-scale forward genetics biorxiv.org/cgi/content/sh… #biorxiv_micrbio

Interested in 3D printable lab equipment? Check out our designs! Every like, download, and make helps get the word out on these FREE & Open Source designs @printablescom by @ATinyGreenCell @PeterPietrzyk @TrevorRife and myself printables.com/model/45750-co…