Andrew Hogan

🍁 Newfie ⚓ via Manitoba 🌾now a Postdoc at EMBL Heidelberg 🇩🇪 Working on phage-bacteria-protozoa interactions 🦠
Typas and van Gestel groups

[bioRxiv Microbiology @biorxiv_micrbio]

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://t.co/GOFjNi2HNR #biorxiv_micrbio

[Jordi van Gestel @jordivangestel]

Super excited to share our latest study on Bacillus subtilis in defense mode against protistan predation! https://t.co/YfPgyItWpL

[bioRxiv Microbiology @biorxiv_micrbio]

Burkholderia Genes Involved in Extracellular Bioplastic Degradation Revealed by Tn-seq and CRISPR-Cas https://t.co/fk4D4GLx6G #biorxiv_micrbio

[bioRxiv Microbiology @biorxiv_micrbio]

Novel origin of replication for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and ... https://t.co/YJAxyueL11 #biorxiv_micrbio

[Glen D'Souza @nonresidentdesi]

We have openings for motivated and curious individuals to join our team https://t.co/9VvSMEajPZ

[EMBL Events @EMBLEvents]

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
➡️ https://t.co/McRP8XgGuk
📩 Application deadline: 2 April

[Prof. Dr. Kenneth Dumack @KDumack]

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!

[Jordi van Gestel @jordivangestel]

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! https://t.co/4GQrkWEG9E

[Biology+AI Daily @BiologyAIDaily]

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: https://t.co/xSVlnU7xWr
📜Paper: https://t.co/CzeruToqne

#StructuralBiology #AlphaFold #MachineLearning #ProteinFolding #DeepLearning #Bioinformatics #ComputationalBiology

[Brun Lab @BrunLabCaulo]

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 @ [email protected]. See
https://t.co/2DjrErxpqw

[bioRxiv Microbiology @biorxiv_micrbio]

TXA11114: Discovery of an in vivo efficacious efflux pump inhibitor in Pseudomonas aeruginosa https://t.co/drewKDRFIr #biorxiv_micrbio

[Andrew Hogan @MicrobeAndrew]

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

[Jordi van Gestel @jordivangestel]

Are you excited about microbial predation and have a background in microscopy/microfluidics? Please apply to join our team @EMBL! Retweet please
https://t.co/gjoYQX38ZK
https://t.co/HLEqszftBS

[EMBL @embl]

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:
https://t.co/wlj1i614ey

[bioRxiv Microbiology @biorxiv_micrbio]

Cross-linked agarose-gelatine beads as a substrate for investigating biofilms of bacterial pathogens https://t.co/N4f7rH9QWL #biorxiv_micrbio

[Andrew Hogan @MicrobeAndrew]

A really cool step forward in data transparency and reproducible science publishing!

A publishing platform that places code front and centre
https://t.co/7rCZ3CX47Z

[Andrew Hogan @MicrobeAndrew]

For the inducible promoter nerds among us:
Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors
https://t.co/RkbTwBV332

[Jordi van Gestel @jordivangestel]

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

[bioRxiv Microbiology @biorxiv_micrbio]

Inducible transposon mutagenesis for genome-scale forward genetics https://t.co/wr4SqO4C3I #biorxiv_micrbio

[Dr. Mason McNair (he/him) @SarraceniaMason]

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 https://t.co/A7TGFunIL8

[Silvia Cardona @cardona_lab]

📣new from our lab: essential antibacterial targets served in a single test tube! Thanks to the work of
@zisanurrahman @J_Novomisky @ArchitDevarajan in collaboration with @UIC_BioS Yuri Polikanov and Egor Syroegin
#CRISPRi #antibiotics #burkholderia #AMR