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zach cp

@zcpbx.bsky.social
1.1K followers 920 following 69 posts

Biochem, microbio, and protein science. Learning Rust for machine learning.

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Reposted by zach cp
Sean Carroll @seanmcarroll.bsky.social · 29/06/2026
Mindscape 359 | Solo: Theories of Dark Energy. Last week we heard about the cosmological constant; tune in this week for a dynamical conclusion! #MindscapePodcast www.preposterousuniverse.com/podcast/2026...
Title card for Mindscape episode -- Solo: Theories of Dark Energy.
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 23/04/2026
Come and study for a PhD with us on antibiotic-producing Streptomyces, trying to understand the roles of primary metabolic enzymes with additional cellular roles - Details below - please repost www.findaphd.com/phds/project...
findaphd.com
Primary metabolic enzymes in antibiotic-producing Streptomyces bacteria, but not as we know them! at University of Strathclyde on FindAPhD.com
PhD Project - Primary metabolic enzymes in antibiotic-producing Streptomyces bacteria, but not as we know them! at University of Strathclyde, listed on FindAPhD.com
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zach cp @zcpbx.bsky.social · 12/04/2026
Great episode. Although I might be in that Orwell-as-a-BS-detection-muse group that comes under a bit of David’s fire ….
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Past Present Future Podcast @ppfideas.bsky.social · 12/04/2026
NEW EPISODE OUT NOW! Today is the 1st in a new series about how the greatest political writer of the 20th century, George Orwell, responded in real time to the epochal events of WWII. What did he get right, what did he get wrong & what did he fail to understand at all? Find us at...🎧 ppfideas.com
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Sean Carroll @seanmcarroll.bsky.social · 30/03/2026
Mindscape 349 | Daniel Harlow on What Quantum Gravity Teaches Us About Quantum Mechanics. More real physicists thinking about the foundations of quantum mechanics! #MindscapePodcast www.preposterousuniverse.com/podcast/2026...
Title card for Mindscape podcast episode with Daniel Harlow.
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Yunha Hwang @microyunha.bsky.social · 18/03/2026
Applications for MIT Novo-Nordisk AI postdoc fellowships are due Apr 15. Focus area lists AI and Biology topics, apply to work on this exciting field with amazing peers! engineering.mit.edu/novo-nordisk
engineering.mit.edu
Novo Nordisk Fellowship
Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...
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Tami Lieberman @contaminatedsci.bsky.social · 18/03/2026
If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk
engineering.mit.edu
Novo Nordisk Fellowship
Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25/02/2026
We made FLIP2, a protein fitness benchmark spanning seven new datasets, including enzymes, protein-protein interactions, and light-sensitive proteins, as well as splits that measure generalization relevant to real-world protein engineering campaigns.
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Claire Berlinski @claireberlinski.bsky.social · 21/02/2026
The Logic of Catastrophe open.substack.com/pub/clairebe... Nuclear war isn't inevitable, but if we don't mitigate these risks, it approaches it. None of them will be fixed by optimism, fatalism, or denial. It will only be fixed if citizens get serious about this.
open.substack.com
The Logic of Catastrophe
Proliferation, launch-on-warning, and AI raise the risk of nuclear war far more than you think. This is what we must do to mitigate the risk.
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Eric Topol @erictopol.bsky.social · 09/02/2026
We used to think that the benefit of GLP-1 drugs (like Ozempic) was dependent on weight loss. Now we know so many health benefits have little to do with that! Today's report: www.sciencedirect.com/science/arti...
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Peter Kenny @pwk2024.bsky.social · 19/01/2026
Opportunity in chemical development at AstraZeneca (Dublin Ireland) closing: 27-Jan-2026 #SynChem #EUChemJobs #ChemJobs #chemsky 🧪 astrazeneca.eightfold.ai/careers/job/...
astrazeneca.eightfold.ai
Senior Scientist (Chemistry), Chemical Development | Blanchardstown Road North, Dublin, Ireland | AstraZeneca
- BSc/PhD level education in a relevant discipline and experience working within a Research & Development or Manufacturing environment, within the pharmaceutical industry. - Technical expertise and un...
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Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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Heng Li @lh3lh3.bsky.social · 14/01/2026
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
hlilab.github.io
HLi Lab - Vacancies
Openings
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zach cp @zcpbx.bsky.social · 11/01/2026
@ppfideas.bsky.social come do some live events in New York this year. We’d love to see you in person
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Laura Abbott @labbott.name · 20/11/2025
Oxide is hiring in the embedded space. If you enjoy baffling choices by hardware vendors and debugging performance issues come join me. oxide.computer/careers/sw-e...
oxide.computer
Embedded Systems Engineer / Oxide
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zach cp @zcpbx.bsky.social · 19/11/2025
Loved this pair of episodes. I was laughing at Chis’ unexpected jumps into accent.
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Aylwyn Scally @aylwyn-scally.bsky.social · 11/11/2025
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here. www.cam.ac.uk/jobs/faculty...
cam.ac.uk
Faculty Position in Computational Biology
Applications are invited for an Assistant/ Associate Professorship in Computational Biology to commence on 1 April 2026 or shortly thereafter. This is a joint post between the Department of Applied
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Albert Vilella, PhD. @albertvilella.bsky.social · 27/10/2025
BoltzGen now published and available as MIT licensed software
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Carlos Scheidegger @cscheid.net · 16/10/2025
Quarto friends! I need your help: We are implementing a new QMD parser in Quarto. It will be super nice. But it's a big change, and we want to minimize the impact. 1. Can you share a link to your Quarto project at github.com/quarto-dev/q... 2. repost this and let your Quarto friends know too?
github.com
Epic: are we production yet · Issue #63 · quarto-dev/quarto-markdown
We need to check against many large sites to get a good sense for the impact of this new syntax in practice. autogenerated qmd quartodoc-generated sites (tbd meet with @machow) sites quarto.org Shi...
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Ewan Birney @ewanbirney.bsky.social · 10/10/2025
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
embl.wd103.myworkdayjobs.com
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
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Anders Sejr Hansen @andersshansen.bsky.social · 17/09/2025
Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...
nature.com
Is enhancer-driven gene regulation all wrapped up? - Nature Reviews Genetics
In this Comment, Wendy Bickmore discusses mechanistic models of how 3D genome organization facilitates communication between distant enhancers and their target promoters to regulate gene expression.
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Conrad Hackett @conradhackett.bsky.social · 15/09/2025
Below is a clever visualization of the distribution of how land is used in the US. Cows roam over a lot of land! But this is not a map - for example, the 100 largest landowning families aren't confined to Florida.
This is a cartogram depicting the share of land associated with various purposes in the United States. 

From https://www.bloomberg.com/graphics/2018-us-land-use/#xj4y7vzkg
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Randall Munroe @xkcd.com · 09/09/2025
What if the Moon were made entirely of electrons? Watch the latest What If? video collaboration with @minuteearth.bsky.social! youtu.be/DiWFXv9N0Vs
youtu.be
What if the Moon were made entirely of electrons?
YouTube video by xkcd's What If?
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Lea Ypi @leaypi.bsky.social · 01/09/2025
Looking forward to discussing INDIGNITY with David Runciman @ppfideas.bsky.social at @waterstones.bsky.social in Cambridge THIS Wednesday! And I hope to see many of you there 🤩😍! For tickets: t.co/WY5iWDIUZ1
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Mitja M. Zdouc @mmzdouc.bsky.social · 21/08/2025
Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)
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Rabih Alameddine @rabihalameddine.bsky.social · 02/08/2025
The Mask of Sorrow is a monument located on a hill above Magadan, Russia, commemorating the many prisoners who suffered and died in the Gulag prison camps in the Kolyma region of the Soviet Union during the 1930s, 1940s, and 1950s.
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Eric Topol @erictopol.bsky.social · 21/07/2025
The anti-inflammatory power of semaglutide (Ozempic) seen by its normalization to healthy of a 72 protein signature tied to MASH liver disease nature.com/articles/s41...
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dave @daveliepmann.com · 20/07/2025
Software history nerds don't miss Casey Muratori's long-ass talk tracing the origins of OOP www.youtube.com/clip/Ugkx9Di...
youtube.com
YouTube
Share your videos with friends, family, and the world
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Natural Product Reports @natprodreports.rsc.org · 08/07/2025
🔓Read a #OpenAccess review by @drlaurasanchez.bsky.social‬ et al. from @ucsantacruz.bsky.social‬ in our MS Metabolomics themed collection covering mass spectrometry approaches for high-throughput directed evolution screening of natural product enzymes #secmet #natprod
pubs.rsc.org
‘Need for speed: high throughput’ – mass spectrometry approaches for high-throughput directed evolution screening of natural product enzymes
Covering: 2015 to 2024 Mass spectrometry (MS)-based methods have been implemented extensively for enzyme engineering due to their label-free nature, making them suitable for screening a wide range of…
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Stephen Turner @stephenturner.us · 07/07/2025
ggplot2 4.0.0 is coming soon, and is moving some of the internals from S3 to the new S7 OOP system. This is worth a read if you're developing packages with ggplot2 (bioconductor or otherwise) blog.bioconductor.org/posts/2025-0... #Rstats
blog.bioconductor.org
Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog
Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do
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zach cp @zcpbx.bsky.social · 02/07/2025
Beautiful. I really like the speed changes as emphasis
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Janet Iwasa @jiwasa.bsky.social · 02/07/2025
Check out this new review (with animations, natch) of mechanisms of licensing origins of DNA replication - a wonderful (and continuing!) collaboration with Bruce Stillman @cshlnews.bsky.social and John Diffley @crick.ac.uk! www.nature.com/articles/s41...
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Digital Discovery @digital-discovery.rsc.org · 01/07/2025
In today's featured article, Kerackian, Romero-Laboureur et al. use high-throughput experimentation to construct a high-quality dataset on nitration reactions and use it to develop a predictive machine learning tool. Find out more in this open access Communication: doi.org/10.1039/D5DD...
A graphical summary of the method.
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Mathew Kiang @mathewkiang.com · 25/06/2025
Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages. ki.se/en/about-ki/...
ki.se
Call for 20 Assistant Professor positions
Karolinska Institutet is a world-leading medical university with a long and proud history of ground-breaking research. We are now recruiting outstanding early-career researchers with particularly exce...
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Derek Lowe @dereklowe.bsky.social · 24/06/2025
Journalists keep asking me, baffled, “What’s the Trump administration really trying to do to the science agencies?” So I say “They are trying to destroy them. Cut off their funding, ruin their facilities, harass their staff into leaving.” It’s not reform, and it never was. It’s destruction.
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Nature Chemical Biology @natchembio.nature.com · 13/06/2025
A new paper reports the genomic discovery and biochemical characterization of a widely distributed gene cluster family for briarane diterpenoid biosynthesis in metazoans www.nature.com/articles/s41...
nature.com
A widespread metabolic gene cluster family in metazoans - Nature Chemical Biology
Grayson et al. report the genomic discovery and biochemical characterization of a widely distributed gene cluster family for briarane diterpenoid biosynthesis in metazoans. This study expands our unde...
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Brian O. Bachmann @brianobachmann.bsky.social · 13/06/2025
Dracomicins, Hybrid Oligosaccharide–Nonribosomal Peptide Antibiotics from Amycolatopsis Species pubs.acs.org/doi/10.1021/...
On the left, a picture of a Petri dish showing an amycalotopsis from which comes in the center, a cartoon dragon and under the dragon the molecules called Dracomycins, which are drawn in the shape of the dragon. On the right a petri dish showing a cartoon of zones of inhibition.
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Ed Sherer @hartreefocker.bsky.social · 07/06/2025
Very excited to be recruiting for an Associate Principal Scientist: Molecular Modeling, Analytical Research & Develop. Our Digital Sciences team is seeing many requests related to influencing formulation design, especially for biologics. #chemjobs #compchem #chemsky jobs.merck.com/us/en/job/R3...
jobs.merck.com
Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job in Rahway, New Jersey, United States of America | jobs at Merck migration
Apply for Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job with Merck migration in Rahway, New Jersey, United States of America. Browse and apply for the jobs a...
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Dmitri Petrov @petrovadmitri.bsky.social · 03/06/2025
Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...
philanthropy.cam.ac.uk
Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
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Simon Willison @simonwillison.net · 25/05/2025
I put together an annotated version of the new Claude 4 system prompt, covering both the prompt Anthropic published and the missing, leaked sections that describe its various tools It's basically the secret missing manual for Claude 4, it's fascinating! simonwillison.net/2025/May/25/...
Introducing Claude
Establishing the model’s personality
Model safety
More points on style
Be cognizant of red flags
Is the knowledge cutoff date January or March?
election_info
Don’t be a sycophant!
Differences between Opus 4 and Sonnet 4
The missing prompts for tools
Thinking blocks
Search instructions
Seriously, don’t regurgitate copyrighted content
More on search, and research queries
Artifacts: the missing manual
Styles
This is all really great documentation
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Matt Hutchings @matthutchings.bsky.social · 15/05/2025
A clever new system for the introduction and heterologous expression of biosynthetic gene clusters into genome-optimised Streptomyces coelicolor: microbialcellfactories.biomedcentral.com/articles/10....
microbialcellfactories.biomedcentral.com
A highly efficient heterologous expression platform to facilitate the production of microbial natural products in Streptomyces - Microbial Cell Factories
Background Heterologous expression in Streptomyces provides a platform for mining natural products (NPs) encoded by cryptic biosynthetic gene clusters (BGCs) of bacteria. The BGCs are first engineered...
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Past Present Future Podcast @ppfideas.bsky.social · 04/05/2025
NEW EPISODE OUT NOW! David talks to historian Gary Gerstle about the last time the Republican party got caught up in a tariffs disaster and how it changed American politics. The Smoot-Hawley Act of 1930 brought tariffs back and helped bring down the global economy. Find us at...🎧 ppfideas.com
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Simon Fisher @profsimonfisher.bsky.social · 02/05/2025
Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n
Four images to illustrate some prominent single-gene myths. Top left shows a photograph of a person deftly rolling their tongue into a U-shape. Top right shows a photograph of a person’s ear, highlighting the shape and features of the earlobe and cartilage. Bottom left shows a close-up photograph of a person’s eye, with a vivid blue colouration. Bottom right shows a photograph of a person poised to write with their left hand on the blank white page of a spiral-bound notebook.
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Molly Przeworski @mollyprz.bsky.social · 24/04/2025
Posting on behalf of Shamil Sunyaev: Eimear(Vice Chair) and I (Chair) are organizing the 2025 Gordon Research Conference (GRC) on Human Genetics and Genomics, which will be held on July 6-11, 2025 in beautiful University of Southern Maine, Portland, Maine.
grc.org
2025 Human Genetics and Genomics Conference GRC
The 2025 Gordon Research Conference on Human Genetics and Genomics will be held in Portland, Maine. Apply today to reserve your spot.
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Adam Phillippy @aphillippy.bsky.social · 09/04/2025
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.
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Past Present Future Podcast @ppfideas.bsky.social · 04/04/2025
“Podcast University” A little something by David ⬇️ www.theideasletter.org/essay/podcas...
theideasletter.org
Podcast University - The Ideas Letter
The popularity of podcasts evinces a strong public appetite for traditional academic content—belying concerns that universities’ pedagogical methods are outdated. Runciman contends that podcasting pre...
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CompBioPhys @compbiophys.bsky.social · 01/04/2025
🧐 Are you a computational physicist and expert in probability theory? 👉 Contribute to our project "Theory and Algorithms for Structure Determination from Single Molecule X-Ray Scattering Images" as PhD student or Postdoc! 🔗 Check our job advert for more details www.mpinat.mpg.de/4988122/09-2...
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Matt Hutchings @matthutchings.bsky.social · 31/03/2025
New Microbe Profile: Streptomyces venezuelae, a model species for the genus. Genetically tractable and completes its life cycle in liquid culture in 24 hours. www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Microbe Profile: Streptomyces venezuelae – a model species to study morphology and differentiation in filamentous bacteria
Streptomyces bacteria are renowned for their multicellular lifestyle and production of bioactive molecules (natural products) with important applications in medicine, agriculture and industry. Studies...
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