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Nicholas Southern

@neuroscinikolai.bsky.social
818 followers 1.8K following 65 posts

PhD Student @ niopeklab.de Engineering switchable proteins💡 Views and opinions are my own 🇺🇸 in 🇩🇪

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Reposted by Nicholas Southern
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 13/10/2026
Computational design of protein conformational landscapes for metamorphic behavior www.biorxiv.org/content/10.64898/20…
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Nicholas Southern @neuroscinikolai.bsky.social · 05/10/2026
I'm a bit biased, but this is certainly well deserved :)
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Reposted by Nicholas Southern
Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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Reposted by Nicholas Southern
Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Reposted by Nicholas Southern
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 03/09/2026
Unbiased and scalable reduction of diverse bacterial genomes www.biorxiv.org/content/10.64898/20…
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Reposted by Nicholas Southern
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 06/08/2026
Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli www.biorxiv.org/content/10.64898/20…
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Nicholas Southern @neuroscinikolai.bsky.social · 20/07/2026
Nice method analogous to our RAMPhaGE system but applied to conjugation instead of phages for gene evolution
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Magnus Bauer @kinasekid.bsky.social · 14/07/2026
Can we program a kinase like a switch? Inspired by natural autoinhibitory complexes, we designed miniproteins against active- and inactive-like conformations of Focal Adhesion Kinase. Depending on the targeted state, the resulting binders either activated or inhibited the kinase.
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Reposted by Nicholas Southern
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 04/07/2026
Protein Surface Site Determines the Evolutionary Accessibility of Allosteric Regulation www.biorxiv.org/content/10.64898/20…
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Nicholas Southern @neuroscinikolai.bsky.social · 05/07/2026
New preprint! We used protein domain insertion to tighten the editing window of the TadA8e adenine base editor. Bulky domain insertions concentrated editing around position A5, maintained robust on-target activity, and reduced Cas-independent off-target editing. 🧬 doi.org/10.64898/202...
biorxiv.org
Domain Insertion Improves the Precision of a CRISPR Adenine Base Editor
Adenine base editors (ABEs) enable efficient A:T to G:C conversion, but their broad activity windows frequently cause unintended bystander edits. We hypothesized that insertion of a bulky, inert prote...
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Reposted by Nicholas Southern
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13/05/2026
If you missed the preprint, now is a good time to read the journal version of @grocklin.bsky.social et al’s fantastic paper on multiplexed HDX measurements Large-scale discovery, analysis and design of protein energy landscapes doi.org/10.1038/s415...
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Reposted by Nicholas Southern
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 30/04/2026
Bridge recombinase enables versatile rewriting of bacterial genomes www.biorxiv.org/content/10.64898/20…
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Reposted by Nicholas Southern
Shinya Tsukiji @shinyatsukiji.bsky.social · 23/04/2026
Excited to share that our AzoTag paper is now out in @natchem.nature.com! 🥳 We demonstrate de novo chemo-optogenetics through the rational design of photoresponsive small molecules and selection of their artificial protein binding pairs. www.nature.com/articles/s41...
nature.com
De novo chemo-optogenetics through the rational design of photoresponsive molecules and selection of their artificial protein binding pairs - Nature Chemistry
Optical manipulation of proteins is central to modulating and characterizing biomolecular functions in cell biology, but tools based on natural proteins are difficult to reconfigure for desired photoc...
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Reposted by Nicholas Southern
Seth Shipman @seth-shipman.bsky.social · 23/04/2026
Out now in Nature Biotechnology! Alejandro González-Delgado and a fantastic team of collaborators worked across nine labs to get retron recombineering up-and-running in fifteen bacterial species. Molecular parts on addgene: www.addgene.org/browse/artic... Happy editing!
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Reposted by Nicholas Southern
bioRxiv Bioengineering @biorxiv-bioeng.bsky.social · 19/04/2026
GROQ-seq Datasets Across Transcription Factors (LacI, RamR, VanR), T7 RNA Polymerase and TEV Protease www.biorxiv.org/content/10.64898/20…
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Pujuan Poppy Deng @poppy-pujuan-deng.bsky.social · 16/04/2026
I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...
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Raphael Laurenceau @raphael-microb.bsky.social · 16/04/2026
🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...
nature.com
Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology
Diversity-generating retroelements are engineered for directed evolution in E.coli.
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Reposted by Nicholas Southern
Dominik Niopek @dominikniopek.bsky.social · 15/04/2026
New paper from the lab on phage-assisted evolution of allosteric light-switches now out in Nature Comms. Congratulations to Nick and all co-authors! www.nature.com/articles/s41...
nature.com
Phage-assisted evolution of allosteric protein switches - Nature Communications
Allostery enables proteins to respond to signals but remains difficult to engineer. Here, Southern et al. developed a phage-assisted evolution framework for allosteric protein switches yielding high-p...
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Nicholas Southern @neuroscinikolai.bsky.social · 15/04/2026
1/28 How do you optimize a dynamic protein property that emerges from multiple states? Our finally published paper in @NatureComms takes on one of the hardest problems in protein engineering with phage assisted evolution: evolving allosteric switches🧵
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Reposted by Nicholas Southern
Deni Szokoli @szokoli.bsky.social · 06/03/2026
Check out this incredible new method for the directed evolution of protein ON/OFF switches!!! www.cell.com/cell/fulltex...
cell.com
Light-directed evolution of dynamic, multi-state, and computational protein functionalities
Optovolution leverages optogenetics and the yeast cell cycle to impose rapid, tunable selection, enabling the continuous evolution of light-responsive regulators, logic gates, and other complex protei...
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Nicholas Southern @neuroscinikolai.bsky.social · 04/03/2026
Fantastic opportunity!
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Nicholas Southern @neuroscinikolai.bsky.social · 24/02/2026
Wow congrats to the authors this is truly impressive
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Sophien Kamoun @kamounlab.bsky.social · 13/02/2026
Vorholt Lab re-created endosymbiosis in the lab: injected bacteria into a fungus and evolved a heritable partnership. Evolution, fast-forwarded. doi.org/10.1038/s415...
doi.org
Inducing novel endosymbioses by implanting bacteria in fungi - Nature
A study presents an approach to establish and track a new endosymbiotic partnership by implanting bacteria in a non-host fungus and shows that stable inheritance of the implanted bacteria is possible ...
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Reposted by Nicholas Southern
Jan Mathony @jmathony.bsky.social · 12/02/2026
🎉🎉 Our paper on temperature-dependent protein control using AsLOV2 variants is now published at @natchembio.nature.com: www.nature.com/articles/s41... including some new insights from extend variant characterizations.
nature.com
Modular engineering of thermoresponsive allosteric proteins - Nature Chemical Biology
Thermogenetics enables spatiotemporal control of protein activity using temperature. Now, engineering of a compact, insertable thermoresponsive protein module diversifies the classes of proteins amena...
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Reposted by Nicholas Southern
Gabriel Abrahams @gabriel-abrahams.bsky.social · 21/01/2026
Our research on magneto-sensitive fluorescent proteins and some of their applications has now been published! Huge thank you to the many many people involved in making this happen. 🧪 www.nature.com/articles/s41...
nature.com
Quantum spin resonance in engineered proteins for multimodal sensing - Nature
A recently developed class of magneto-sensitive fluorescent proteins are engineered to alter the properties of their response to magnetic fields and radio frequencies, enabling multimodal sensing of b...
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Reposted by Nicholas Southern
Rezwan Siddiquee @rezwansiddiquee.bsky.social · 14/01/2026
Nature has a trick to evolve multimeric proteins via gene duplication. 🧬One copy compensates, the other explores.🧬 Although this has only been a theory so far. Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication. www.biorxiv.org/content/10.6...
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Nicholas Southern @neuroscinikolai.bsky.social · 01/03/2025
With the state of biomedical science in the U.S. becoming increasingly uncertain, definitely consider these options if you’re a student. I’ve had a great experience doing my PhD in Germany—strong research, supportive environment, and a reasonable cost of living. Happy to share advice if interested!
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CIBSS – Centre for Integrative Biological Signalling Studies @cibss.bsky.social · 09/01/2026
Join us for a 📢 #CIBSS / SFB 1381 Joint Seminar 🗓 13 Jan 2026 | 12:00–13:00 👉 @jmathony.bsky.social (#uniheidelberg) 🎙 Engineering stimulus-controlled proteins through modular domain recombination 📍 Lecture Hall, Institute of Biology I, Hauptstr. 1 🔗 kurzlinks.de/4mlv #SynBio #ProteinEngineering
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Bryan Dickinson @chembiobryan.bsky.social · 26/12/2025
1/ Check out our newest paper where we ask: How fast can we experimentally discover binders from scratch? And we mean scratch: a blinded study. TLDR: 26 days. And the binders work…and led to new cancer biology. We’re coming for you AI…. chemrxiv.org/engage/chemr...
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Aude Bernheim @audeber.bsky.social · 15/12/2025
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...
biorxiv.org
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
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Ed Boyden @eboyden3.bsky.social · 12/12/2025
We are hiring a lab manager, for our research group, the Synthetic Neurobiology group (aka Boyden Lab) at MIT/HHMI (on the MIT campus, Cambridge, MA)! Please apply if you're qualified and interested, and spread the word! hhmi.wd1.myworkdayjobs.com/External/job...
hhmi.wd1.myworkdayjobs.com
Laboratory Manager II - Boyden Lab
Primary Work Address: 77 Massachusetts Avenue, Cambridge, MA, 02139 Current HHMI Employees, click here to apply via your Workday account. The Synthetic Neurobiology Group (Boyden Lab) at the MIT McGov...
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Reposted by Nicholas Southern
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 12/12/2025
Anti-CRISPR-mediated continuous directed evolution of CRISPR-Cas9 in human cells www.biorxiv.org/content/10.64898/20…
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 01/12/2025
An ultra-low background far-red light-responsive optogenetic tool based on an engineered biliverdin-binding domain www.biorxiv.org/content/10.1101/202…
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Nicholas Southern @neuroscinikolai.bsky.social · 18/10/2025
Especially today, as the administration sidelines evidence-based policy decisions and pressures scientific institutions, this bears repeating: A strong, well-funded, and politically independent scientific ecosystem is vital to innovation, national security, and public health. The stakes are clear.
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Nico Claassens @nicoc-micsynmet.bsky.social · 17/10/2025
Great to see our MOSAIC story about an easy, cloning-free efficient protocol for mutating plasmids using recombineering is out now officially and the cover story of ASC Synthetic Biology pubs.acs.org/toc/asbcd6/1... ! Great shoutout to Marijn van den Brink, Tim Althuis and Christophe Danelon!
pubs.acs.org
ACS Synthetic Biology
We introduce MOSAIC, a highly efficient protocol for the editing of plasmids and generation of combinatorial plasmid libraries. This quick protocol employs the single-stranded DNA annealing protein Cs...
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Sternberg Lab @sternberglab.bsky.social · 17/10/2025
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...
biorxiv.org
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 15/10/2025
Mapping the diverse topologies of protein-protein interaction fitness landscapes www.biorxiv.org/content/10.1101/202…
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Keri Martinowich @martinowk.bsky.social · 30/09/2025
New Hot Topics piece from @rphillips3.bsky.social and Stephanie Page in @npp-journal.bsky.social describing emerging insights on roles of molecularly-defined cell types in the lateral septum, which serves as a hub for coordinating diverse social behaviors. www.nature.com/articles/s41...
nature.com
Role of molecularly defined lateral septum cell types and circuits in social behaviors - Neuropsychopharmacology
Neuropsychopharmacology - Role of molecularly defined lateral septum cell types and circuits in social behaviors
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Keri Martinowich @martinowk.bsky.social · 24/09/2025
In the early years of my PhD I remember being asked if we'd ever treat or cure diseases like HIV or Huntington's. I remember saying maybe, but not knowing if I believed. Seeing research pay off as real impact on human lives is - incredible. www.bbc.com/news/article... www.bbc.com/news/article...
bbc.com
Huntington's disease successfully treated for first time
One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.
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Jörg Vogel @jorg-vogel-lab.bsky.social · 10/09/2025
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
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Nicholas Southern @neuroscinikolai.bsky.social · 08/09/2025
Been having a lot of fun lately listening to the Night Science Podcast after stumbling on it from the article series by @itaiyanai.bsky.social and Martin Lercher, definitely recommend it if you have a passing interest in the creative aspects of how the scientific process is conducted 😄
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Constantinos Patinios @copabio.bsky.social · 04/09/2025
🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...
doi.org
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology
Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.
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Sorek Lab @soreklab.bsky.social · 02/09/2025
Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵
biorxiv.org
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 30/08/2025
Growth, dissolution and segregation of genetically encoded RNA droplets by ribozyme catalysis www.biorxiv.org/content/10.1101/202…
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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...
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John Skiles Skinner @skiles.blue · 17/08/2025
A terrorist targeted federal workers last week. There wasn’t much reporting on it. But I’m not finished thinking about it! 🧵 An anti-vaxxer fired more than 500 gunshots into CDC Atlanta, shattering 150 “blast-proof” windows on 6 buildings. Employees were pinned down in terror.
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 13/08/2025
De novo design of light-regulated dynamic proteins using deep learning www.biorxiv.org/content/10.1101/202…
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Jeremy Berg @jeremymberg.bsky.social · 07/08/2025
Well, this is a huge Executive Order power grab... www.whitehouse.gov/presidential... 1/3
whitehouse.gov
Improving Oversight of Federal Grantmaking
By the authority vested in me as President by the Constitution and the laws of the United States of America, and to improve the process of Federal
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Nature Methods @natmethods.nature.com · 06/08/2025
PANCS-Binders (phage-assisted noncontinuous selection of protein binders) screens multiple high-diversity protein libraries against a panel of dozens of targets for high-throughput binder discovery. @chembiobryan.bsky.social @mstyles-chembiol.bsky.social www.nature.com/articles/s41...
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