Basile Wicky (@BasileWicky) header
Basile Wicky (@BasileWicky) profile picture

Basile Wicky

@BasileWicky

Protein design & synthetic biology • Asst. prof. @ETH_BSSE

 Basel, Switzerland
Joined July 2020
  • Tweets99
  • Following423
  • Followers1.8K
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Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)Photo by Basile Wicky (@BasileWicky)
Basile Wicky retweeted
D-BSSE, ETH Zurich (@ETH_BSSE) profile picture
D-BSSE, ETH Zurich@ETH_BSSEFeb 23
#JobAlert 🚀 Exciting opportunity for young scientists - please share: tinyurl.com/2rajyepc @ETH_en #BIIE @BaselStadt
Image from D-BSSE, ETH Zurich (@ETH_BSSE)
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Basile Wicky retweeted
Hannah Han (@Hannahlhan) profile picture
Hannah Han@Hannahlhan19 Mar 2024
Super excited to share our paper “Design of amyloidogenic peptide traps” is out now! 🧠 nature.com/articles/s41589-0… Special thanks to @eaandrzejewska , Danny Sahtoe and David Baker
Design of amyloidogenic peptide traps

Design of amyloidogenic peptide traps

Nature Chemical Biology - An approach to design proteins that can capture amyloidogenic protein regions present in, for example, tau and Aβ42 has now been developed. These designer proteins...

nature.com
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Short summary thread of our recent review on de novo protein design: (Poster-sized figure (36 x 48 inches) for printing: drive.google.com/file/d/1sG3…)
Image from Possu Huang Lab (@PossuHuangLab)
Nature Biotechnology (@NatureBiotech) profile pictureNature Biotechnology
@NatureBiotech21 Feb 2024
Sparks of function by de novo protein design go.nature.com/48jXz1z
Image from Nature Biotechnology (@NatureBiotech)
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I keep on preaching to my lab about the usefulness @ChatGPTapp for coding, but real-life demos might be more effective. A thread on a neural network we quickly developed to classify antibiotics sensitivity 🧵 (1/10)
Image from Amir Mitchell (@mitchell_sysbio)
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The commentary I wrote is now live at Nature Biotech: nature.com/articles/s41587-0… (free version rdcu.be/dwSSy).
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LigandMPNN preprint: biorxiv.org/content/10.1101/… LigandMPNN inference code + model weights (including ProteinMPNN, SolubleMPNN etc): github.com/dauparas/LigandMP…
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#openposition Exciting opportunity for a #postdoc: be part of the partnership @ETH_en and @Roche and become a Next-Gen Bioengineer > u.ethz.ch/m4Lwj Thanks for sharing!
Image from D-BSSE, ETH Zurich (@ETH_BSSE)
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Expanding protein pore palette beyond biology. Computational design of protein pores with various shapes and sizes. (Potential applications: Nanopore sensing, DNA/Protein sequencing, Custom pores for selective membranes and ligand-gated channels for cellular delivery.....)
Image from Sagardip Majumder (@sagardipm)
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We are hiring! Come join us for a PhD in Computational Language Evolution @ETH in Basel @ETH_BSSE and the National Research Program on Evolving Language @NCCR_Language. We are looking forward to receiving your application jobs.ethz.ch/job/view/JOPG_e…
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We're looking for a PhD student interesting in protein design and tech development. Exciting project interfacing protein @structbiolbxl and solid-state nanopores @imec_int. Computational design of hybrid nanopore sensors. Apply by December 15th! imec-int.com/en/work-at-imec…
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Basile Wicky retweeted
Chris Seymour (@iiSeymour) profile picture
Chris Seymour
@iiSeymour5 Dec 2023
Dorado v0.5 NCM release 🎉 - new simplex models - faster - higher accuracy - easier to use (auto model selection) - hemi-methylation (duplex mods) - primer & adapter trimming - custom barcodes #nanoporeconf github.com/nanoporetech/dora…
Release v0.5.0 · nanoporetech/dorado

Release v0.5.0 · nanoporetech/dorado

[0.5.0] (5 Dec 2023) This release of Dorado introduces new, more accurate, and faster v4.3 basecalling models. It also enables hemi-methylation basecalling of duplex reads. Dorado now supports DNA ...

github.com
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Is binarization of scATAC-seq data really necessary? The conclusion from our analysis is that a quantitative treatment is in fact beneficial. Now out in Nature Methods! @gagneurlab @fabian_theis nature.com/articles/s41592-0… Many additions since the preprint 👇(1/n)
Image from Laura Martens (@lauradmartens.bsky.social) (@lauradmartens)
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For anyone interested in generating publication-quality secondary structure diagrams from PDB files, SSDraw is available and now published by @ProteinSociety onlinelibrary.wiley.com/doi/…

SSDraw: Software for generating comparative protein secondary structure diagrams

The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein...

onlinelibrary.wiley.com
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Check out our latest work on a new algorithm for protein clustering and the discovery of new CRISPR systems! More on this soon. So grateful to have this work published by @ScienceMagazine !
Science Magazine (@ScienceMagazine) profile pictureScience Magazine
@ScienceMagazine23 Nov 2023
Using a new algorithm called FLSHclust, researchers have revealed rare and previously unknown #CRISPR-Cas systems. The approach and results provide novel opportunities for understanding the vast functional diversity of microbial proteins. scim.ag/4W6
Image from Science Magazine (@ScienceMagazine)
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I'm excited to share that I'll be joining @MITBiology as an Asst Prof. in Jan 2024! Come join us! 🤓🧪🖥️🧬
Image from Sergey Ovchinnikov (@sokrypton)
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Basile Wicky retweeted
antisense. (@razoralign) profile picture
antisense.@razoralign12 Feb 2023
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation nature.com/articles/s41586-0…
Image from antisense. (@razoralign)
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Evolutionary selection of proteins with two folds biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Promoting #Zinc staining which is as sensitive as that of #Silver staining and it takes ONLY 360 seconds!!! 1) Rince the gel with water 30 seconds 2) Shake the gel in 0.2 M imidazole 300 seconds 3) Soak the gel in 0.3 M Zinc Chloride 30 seconds!! And the magic happens 👇👇👇👇
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Protein sequence design is a very active field. However, people often use different validation sets, biologically-weak metrics, and no open-source code. We present PDBench, a manually curated benchmarking toolkit to solve these problems! #proteindesign academic.oup.com/bioinformat…
PDBench: evaluating computational methods for protein-sequence design

PDBench: evaluating computational methods for protein-sequence design

AbstractSummary. Ever increasing amounts of protein structure data, combined with advances in machine learning, have led to the rapid proliferation of meth

academic.oup.com
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Did you ever want to build your own transformer models from scratch? Well, now you can! We introduce Tracr to translate code written in RASP (a domain-specific language for transformers) into weights of a GPT-like model: arxiv.org/abs/2301.05062 Why you’d want to do this? 🧵👇
Tracr: Compiled Transformers as a Laboratory for Interpretability

Tracr: Compiled Transformers as a Laboratory for Interpretability

We show how to "compile" human-readable programs into standard decoder-only transformer models. Our compiler, Tracr, generates models with known structure. This structure can be used to design...

arxiv.org
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