JavaScript is not available.

May 11

Building synthetic chromosomes from natural DNA doi.org/10.1101/2023.0

Institute for Protein Design

@UWproteindesign

May 11

Generative AI for protein design is now one click away. We've launched a new platform that puts powerful tools behind a simple web interface, making #proteindesign accessible to anyone. Try it here ➡️ huggingface.co/spaces/merle/P Learn more on YouTube ➡️ youtu.be/bS71K2U0amA

Sidney Lisanza and 3 others

187

588

Nature Conferences

@NatureConf

May 8

Our event exploring recent clinical and research developments of #NucleicAcid medicines is now open! Get your tix and submit abstracts at conferences.nature.com/CrackingCode In partnership with

UWChemE

@UWChemE

May 8

The 13th annual Distinguished Young Scholars Seminar #UWDYSS is coming up– will you be a part of it? Apply by May 15 to participate in a full day of mock faculty interviews and give a seminar in Seattle! depts.washington.edu/dyss/index.html #AcademicTwitter

pubs.acs.org/doi/10.1021/ac #microbiology #engineering #biotechnology #Biology #BIONICBACTERIA

Rob Lavigne

@RobLavigne1

Apr 28

Tailored #SynBio parts for #pseudomonas mined using our

@nanopore

-based ONT-cappable-seq, characterizing potent #terminator elements from #phage

@ERC_Research

#publication in

@ACSSynBio

Eveline-Marie Lammens and 5 others

synbiopapers

@synbio_papers

May 4

A Massively Parallel Double-Selection Workflow for the Evolution of Molecular Switches Based on Surface-Display in Escherichia coli dlvr.it/SnX6JF

are #hiring postdocs and technicians for multiple projects: -How "enabler" mutations drive evolution of #AMR -Microbiome of tracheobronchitis -Advancing

@evolvingstem

-Method dev for single-cell genomics & bioinformatics Join our #Pittsburgh evo-micro community!

May 2

Mapping the in vivo fitness landscape of a tethered ribosome science.org/doi/full/10.11

Harris Wang

@harriswangnyc

May 1

🧬 Excited to share our new paper published in

@NatureMethods

today! We introduce a faster, cheaper, & automated method for gene variant synthesis called MEGAA:

Fast and efficient template-mediated synthesis of genetic variants

Nature Methods - MEGAA, an efficient template-guided method to synthesize high-fidelity DNA variants

173

Mo Khalil

@MoKhalilLab

May 1

SO excited and proud of the program we've put together for the

@GordonConf

GRC Synthetic Biology conference this summer. This is your chance to apply -- spaces are filling very quickly!! Keynotes: Beth Sattely (

@Sattely_lab

), Jason Chin grc.org/synthetic-biol

107

Bugs as drugs!

GIF

read image description

ALT

Quote Tweet

Matthew Henn

@microbiologic

Apr 27

Today @SeresTx marked an important milestone in the development of drugs that leverage millions of years of coevolution between microbes and humans for the prevention or treatment of diseases. ir.serestherapeutics.com/news-releases/

Show this thread

Vega Shah

@dr_alphalyrae

Apr 26

De novo design of protein interactions with learned surface fingerprints | Nature

De novo design of protein interactions with learned surface fingerprints

Nature - A surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling the de novo design of protein interactions and of artificial proteins with...

281

Synthetic Biology Regulation in Europe: Containment, Release, and Beyond

Tom Ellis

@ProfTomEllis

Apr 26

As a synthetic biologist I get asked a lot if you could ever release an engineered microbe in the EU. This paper gives an important account of efforts to do so by a team at Cambridge, and describes the legal labyrinth that makes it possible yet impossible.

academic.oup.com

Abstract. While synthetic biology is hoped to hold promise and potential to address pressing global challenges, the issue of regulation is an under-appreciated

192

Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data doi.org/10.1101/2023.0

Pramod K. Jangir

@pramod_k_jangir

Excited to share our new paper on the evolution of colistin resistance and its unintended consequences

Quote Tweet

Craig MacLean

@CraigMacLean9

New #AMR paper with @pramod_k_jangir : Use of colistin in agriculture has driven the evolution of E.coli with increased resistance to immune effectors, including antimicrobial peptides and complement. elifesciences.org/articles/84395.

Show this thread

Christopher Voigt

@Geneticdesigner

It is only a bottleneck solved if the long DNA being synthesized can contain many active regulatory parts (e.g., promoters), repetitive sequences, multiple genes, and the like.

Quote Tweet

John Cumbers

@johncumbers

Apr 24

Has synthetic biology finally found the elixir to solve its biggest bottleneck? Read my latest piece in Forbes to find out how one company thinks they’ve cracked the code

forbes.com/sites/johncumb /1

Show this thread

Stanford Biochemistry and 5 others

Apr 24

Efficient evolution of human antibodies from general protein language models go.nature.com/40PRYMN

155

Apr 19

Research Highlight: Retrofitted E. coli genome confers phage resistance

Retrofitted E. coli genome confers phage resistance

Nature Biotechnology - Retrofitted E. coli genome confers phage resistance

Panos Poulis

@panos_poulis

The ribosome moves along the mRNA one codon at a time 🚂. Yes, but! Learn about the fascinating mechanics of the largest molecular machine of the cell and what happens when things go wrong in our latest review! 🗣 degruyter.com/document/doi/1

0:23

2.8K views

120

Henry Lee

@hhlee

Great story, let’s amplify more of those who have conviction, persistence, and laser focus on substance.

Quote Tweet

Angelos Georgakis

@angelosgeo

Biotech friends, I've spent the last couple of days reading everything I could find about Henri Termeer. Whenever you need a little motivation in your arduous journey, please read the story of this man. It will do your heart good. It will help you understand why you chose this… Show more

Show this thread

David Bikard

@dbikard

If like me you like to analyse genomics data in Jupyter notebooks I have something for you: dbikard.github.io/genomenotebook/

219

921

Deep flanking sequence engineering for efficient promoter design doi.org/10.1101/2023.0

GCE4ALL Research Center

@GCEcenter

Apr 19

We're excited to announce that we'll be hosting a 5 day intensive in-person workshop, Bioorthogonal Ligations - Clicking with GCE on Aug 8-12th 2023 in Corvallis OR. Open to all levels! Apply now! gceworkshops.org

Mar 15

A new E.coli strain is designed with an amino-acid swapped genetic code, making it resistant to viruses and also unable to replicate outside of a lab setting, preventing unwanted gene flow. #NBThighlight

A swapped genetic code prevents viral infections and gene transfer

Nature - A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its...

208

Albert-László Barabási

@barabasi

Apr 19

Excited to share our latest work, "Improving generalizability of protein-ligand binding predictions with AI-Bind," just out in

@NatureComms

rdcu.be/c9run. PDF at barabasilab.com/science/public 🧵. #AI #MachineLearning #TargetPrediction #Bioinformatics #NetSci

150

Tom Ellis

@ProfTomEllis

Apr 17

Very interesting use of up-scaled genome engineering to ask and answer big questions on evolution. Authors deleted various combinations of teh tRNA genes, tRNA modifying systems, and rRNA operons in E. coli to assess when redundancy in gene content is beneficial.

Quote Tweet

Apr 17

The layered costs and benefits of translational redundancy doi.org/10.7554/eLife.

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Michael Baym

@baym

Apr 17

Thrilled to share our latest preprint, in which

@KarelBrinda

(along with collaborators

@leandro_ishi

and

@ZaminIqbal

at EBI) introduces phylogenetic compression for storage and search of enormous microbial genome libraries: 1/

biorxiv.org

Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections makes it effectively...

138

308

Michael Fischbach

@mfgrp

Engineered skin bacteria induce antitumor T cell responses against melanoma

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent immune response against a distant tumor.

@yerinchen

led the charge w/ help from

1/26

A system to express tumor antigens in the skin commensal bacterium Staphylococcus epidermidis elicits T cells that treat local and systemic tumors.

523

1,497

Angewandte Chemie

@angew_chem

onlinelibrary.wiley.com/doi/10.1002/an

An Efficient Opal-Suppressor Tryptophanyl Pair Creates New Routes for Simultaneously Incorporating up to Three Distinct Noncanonical Amino Acids into Proteins in Mammalian Cells (Abhishek Chatterjee and co-workers)

@AchemSynBio

@ChemistryBC

Akos Nyerges

@AkosNyerges

💯 % can confirm.

Quote Tweet

Vega Shah

@dr_alphalyrae

Many bioinformatics programming tasks can be automated with ChatGPT

arxiv.org/abs/2303.13528

Roman Jerala

@rjerala

Apr 11

If you believe (like us) that #syntheticbiology will revolutionize gene and cell therapy & you are looking for a stimulative environment for your PhD, our group ki.si/en/departments may be right for you. Apply until May 15th ki.si/en/scientists4 or DM me. Please RT. 🧵

ki.si

Scientists4Future

Centre for Genomic Regulation (CRG) and 7 others

Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing go.nature.com/3ZH3eu8

122

373

Max Wilkinson

@maxewilkinson

How do LINE family retrotransposons jump around? Can we reprogram retrotransposons? What does this have to do with Rum and Raisin? Answers here and below!

0:30

82.2K views

450

1,584

De novo design of modular peptide binding proteins by superhelical matching

DeriveryLab

@DeriveryLab

Nov 17, 2022

Have you ever thought that there are not enough nanobodies against small peptide tags that also work in cells? If yes, have a look at our latest pre-print in collaboration with David Baker’s Lab (

@UWproteindesign

biorxiv.org

General approaches for designing sequence-specific peptide binding proteins would have wide utility in proteomics and synthetic biology. Although considerable progress has been made in designing...

241

Reza Kalhor

@kalhorlab

We are looking for new postdocs to join our team. Positions are fully funded and you can pursue your interest in technology development, biological questions, or understanding disease. jobrxiv.org/job/johns-hopk

Víctor de Lorenzo

@vdlorenzo_CNB

y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

35% of Escherichia coli genes lack experimental evidence of function 🤔

academic.oup.com

Abstract. Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated genes in cellular phenotypes. However, we lack a systematic unde

Amazing work from

showing how ribosomes translate mRNA differently in humans than bacteria, including structures with inhibitors. Significant implications for developing selective chemical inhibitors of translation!

mRNA decoding in human is kinetically and structurally distinct from bacteria

Nature - The reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower compared with bacteria due to eukaryote-specific...

Institute for Protein Design

@UWproteindesign

Apr 5

Today we report the design of proteins that bind to disordered targets. This design strategy focuses on features common to the peptide backbone and can be used to generate binders for disordered proteins.

De novo design of modular peptide-binding proteins by superhelical matching

Nature - A computational approach is used to design modular proteins that bind to synthetic peptides and disordered regions of human proteins with high affinity and specificity.

105

437

🚨New preprint alert!

shows that transfer learning works great for deep learning models of gene expression, allowing us to easily adapt trained models across contexts. Don't bin your models after use, recycle and refine!🤖+🦠 #ML #synbio doi.org/10.1101/2023.0