Lightnews — Scholar-powered news

Manuel Lera-Ramirez

@manu-lera.bsky.social

140 followers 260 following 42 posts

Working on OpenCloning, an Open Source web application to plan and document cloning. https://opencloning.org/ Open Source in science enthusiast. Previously PomBase, yeast genetics, image analysis and cytoskeleton.

opencloning.org

Posts Media Videos Starter Packs

Pinned

Manuel Lera-Ramirez @manu-lera.bsky.social · Feb 6

🚀 #ShareYourCloning rebrands to #OpenCloning 🧫

An Open Source web application to plan and document molecular cloning 🧬 and genome engineering 🦠.

Latest version adds support for WekWikGene 🔍 as a plasmid source, and UI improvements.

👉 Check it out here: opencloning.org 🌍

4 6

Manuel Lera-Ramirez @manu-lera.bsky.social · 16d

✨ Last week at #ESSL2025 I presented a poster on #OpenCloning 🧬

🔥 Crowd favorite feature: pull gene sequences directly from NCBI — no copy-paste needed!

🎥 Here’s a quick demo

🔗 Visit opencloning.org

Reposted by Manuel Lera-Ramirez

LondonSynbioNetwork @londonsynbio.bsky.social · 21d

🎉 London SynBio Network is back! Join us on 25th of September.

🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski

💐 Open Flower: designer flowers for art and education
Nick Desnoyer

➡️ Register at: events.humanitix.com/london-synbi...

London SynBio Network 10

London SynBio afterwork talks and networking event on Thursday 25th of September

events.humanitix.com

1 4 6

Manuel Lera-Ramirez @manu-lera.bsky.social · 28d

Manuel Lera-Ramirez @manu-lera.bsky.social · Aug 13

🧬 Are you a wet lab scientist doing cloning or DNA engineering, or a bioinformatician curious about molecular biology? 🌱 Passionate about Open Source and Open Science?

Join the pydna hackathon: dtu.events/pydnahackath...

🌱 Whether you're new to Python or an expert, there's a place for you!

This link will take you to a page that’s not on LinkedIn

lnkd.in

1 4

Manuel Lera-Ramirez @manu-lera.bsky.social · Aug 7

🚀 OpenCloning now has a documentation page!

Whether you're getting started or diving deep, find everything you need to make the most of OpenCloning, including a powerful search function to quickly find exactly what you’re looking for.

#OpenCloning #OpenSource #SynBio

🔗 docs.opencloning.org

2 5

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 31

😍🚀🚀🚀🚀

Reposted by Manuel Lera-Ramirez

PomBase: The S. pombe knowledgebase @pombase.bsky.social · Jul 31

PomBase introduces two new interactive views for GO-CAM pathway models: Summary Maps (high-level, visual overview) and Mega-Models (connected models). Check them out here: lnkd.in/gfxNRdua

1 3 6

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 29

The kit is available from @addgene.bsky.social

www.addgene.org/kits/gasser-...

Addgene: GoldenPiCS Kit

www.addgene.org

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 29

🔬 I added a template for the #GoldenPiCS #MoClo kit to #OpenCloning!
⚡ Speed up your design when cloning in #Kphaffii!

🧪 Simulate plasmid assembly
🧬 …and integration into the genome!

👉 Check it out here: opencloning.org 🌍
🎥 youtu.be/BadWzLjojb4

GoldenPiCS with OpenCloning: Step-by-Step MoClo Cloning Tutorial

YouTube video by Genestorian

youtu.be

1 1 3

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 20

a man with a mustache wearing a hat and tie

ALT: a man with a mustache wearing a hat and tie

media.tenor.com

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 20

🧪 Maybe it's time to give #OpenCloning a try!

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
👨‍🔬 Built by a fellow researcher — for researchers!

👉 Check it out: bsky.app/profile/manu...

Manuel Lera-Ramirez @manu-lera.bsky.social · Mar 27

#OpenCloning now displays primer details! 🧬🔍 Minimal info is shown in the table, and the full #primer3 report when clicking the ℹ️ icon.

🧪 The values in parenthesis are for the full primer, the preceding ones for the annealing part.

🔗 Try it yourself: opencloning.org
🎥 Demo: youtu.be/-wjOY4i6mjg

1 1

Reposted by Manuel Lera-Ramirez

Ben Heineike @heineikeb.bsky.social · Jul 10

A paper I have been working on with Oliver Lemke in the Ralser lab has just come out: www.nature.com/articles/s41...

We used predicted structures to gain insight into the evolution of metabolic proteins in yeast.

A bit more in this linked-in post (www.linkedin.com/posts/benjam...).

The role of metabolism in shaping enzyme structures over 400 million years - Nature

By combining structural biology and evolutionary genomics analyses, the evolution of enzymes over 400 million years is shown to be governed by catalytic function, metabolic network architecture, cost ...

www.nature.com

1 7 9

Manuel Lera-Ramirez @manu-lera.bsky.social · Jul 3

👏👏👏

Reposted by Manuel Lera-Ramirez

Melania D'Angiolo @melaniadangiolo.bsky.social · Jul 3

Superhappy to share the last paper from my PhD in @litinice.bsky.social lab. We evolved yeasts with humanized telomeric repeats and discovered that they adapt through amplification of telomere-binding proteins and inactivation of the DNA damage response.

www.biorxiv.org/content/10.1...

The adaptive molecular landscape of reprogrammed telomeric sequences

Telomeric sequences vary across the tree of life and intimately co-evolve with telomere-binding protein complexes. However, the molecular mechanisms allowing organisms to adapt to new telomeric sequen...

www.biorxiv.org

4 13 35

Reposted by Manuel Lera-Ramirez

Saccharomyces Genome Database @yeastgenome.bsky.social · Jun 9

FlyBase needs your help!

Because of recent changes to government funding, the NIH grant that supported FlyBase has been "terminated." flybase.org

23 19

Reposted by Manuel Lera-Ramirez

Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · May 30

PhD position available in Markus Ralser (Charite, Berlin), for a project about using spatially resolved metaproteomics to study microbial metabolic interactions 👇

1 4 4

Reposted by Manuel Lera-Ramirez

David Pfau @davidpfau.com · May 28

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

2 110 240

Reposted by Manuel Lera-Ramirez

Christophe 🔬 L @christlet.bsky.social · May 29

Reposting as I hear about a German Pubmed-like initiative: let's build on Europe PMC which is already great

Christophe 🔬 L @christlet.bsky.social · Jan 31

Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes *all* bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed

Prasad Jallepalli, MD, PhD @prasad.bsky.social · Jan 31

I’m very scared to see what happens to PubMed

2 12 41

Manuel Lera-Ramirez @manu-lera.bsky.social · May 19

Hi @retropz.bsky.social thanks! Happy to hear if you have any feedback, or if you would need some support for your users to get started.

Reposted by Manuel Lera-Ramirez

LondonSynbioNetwork @londonsynbio.bsky.social · May 9

Join us next week, 15th May, at UCL!

🧬 Using synthetic biology tools to optimise Cas9 expression in mosquito gene drives
Dr. Moeez Khan (Windbichler lab, ICL)

⚙️ Writing the future with synthetic DNA
Laurence Humphrey (Twist Biosciences)

events.humanitix.com/london-synbi...

London SynBio Network 9

London SynBio afterwork talks and networking event on Thursday 15th of May

events.humanitix.com

1 4 5

Reposted by Manuel Lera-Ramirez

Alex Fedorec @ajfedorec.bsky.social · May 12

Join us in London (12-13 November) for the 10th anniversary of SynBio UK, the premier conference for synthetic and engineering biology.

Organised this year by @biochemsoc.bsky.social and colleagues at @ucl.ac.uk.

www.eventsforce.net/biochemsoc/s...

#synbio

www.eventsforce.net

2 4

Reposted by Manuel Lera-Ramirez

Sebastian S. Cocioba @atinygreencell.bsky.social · May 2

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs.

Plant, Bacterial, Archaeal Non-model Bioeng
Custom Lab Hardware
Turn Key Genetic Design

Please repost for reach 💚

7 280 160

Manuel Lera-Ramirez @manu-lera.bsky.social · May 2

I built a database with mined gateway plasmids from addgene. Maybe it can be helpful.

bsky.app/profile/manu...

Manuel Lera-Ramirez @manu-lera.bsky.social · Feb 18

🧬🔬 Ever wondered if there’s a #GateWay plasmid in @addgene.bsky.social with GFP and the att sites you need? 🤔✨ Wonder no more!

🚀 Visit GateWayMine to search a database of #AddGene plasmids by feature or site type! 🧪🔍

🔗 gatewaymine.netlify.app

More context in the thread! 🧵👇

2 3

Manuel Lera-Ramirez @manu-lera.bsky.social · Apr 24

🚀 Just added support for Cre/Lox recombination to hashtag#OpenCloning! 🧬✨
👇 Check out an example showing excision of a plasmid from a locus and re-integration using classic LoxP sites.

👉 Try it here: opencloning.org
🎞️ Demo video: www.youtube.com/watch?v=n0he...

1 1 4

Manuel Lera-Ramirez @manu-lera.bsky.social · Apr 22

🧬 If you are in London and you want to learn about a free & Open Source SnapGene/Benchling alternative that also supports automation 🤖, come to our next London Synbio Network meeting this Thursday 24th in Imperial!🎓

🎤 I’ll be giving a talk about #OpenCloning!

events.humanitix.com/copy-of-lond...

London SynBio Network 8

London SynBio afterwork talks and networking event on Thursday 24th of April

events.humanitix.com

2 3