Colin Jackson
@cjjackson.bsky.social
Reposted by Colin Jackson
Keen to use an open source workflow for nanobody discovery? Check out Alpseq 🦙
Alpseq’s diversity analysis, enrichment counts & clustering allow different approaches for nanobody selection
Great collab with bioinformaticians @qgouil.bsky.social Kathleen Zeglinski
www.biorxiv.org/content/10.1...
Alpseq’s diversity analysis, enrichment counts & clustering allow different approaches for nanobody selection
Great collab with bioinformaticians @qgouil.bsky.social Kathleen Zeglinski
www.biorxiv.org/content/10.1...
alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing
Nanobodies have emerged as promising tools for many biotechnological applications due to their small size, high stability, and remarkable binding specificity. Next-Generation Sequencing (NGS) enables ...
www.biorxiv.org
October 27, 2025 at 3:18 AM
Keen to use an open source workflow for nanobody discovery? Check out Alpseq 🦙
Alpseq’s diversity analysis, enrichment counts & clustering allow different approaches for nanobody selection
Great collab with bioinformaticians @qgouil.bsky.social Kathleen Zeglinski
www.biorxiv.org/content/10.1...
Alpseq’s diversity analysis, enrichment counts & clustering allow different approaches for nanobody selection
Great collab with bioinformaticians @qgouil.bsky.social Kathleen Zeglinski
www.biorxiv.org/content/10.1...
Reposted by Colin Jackson
Pomfret Vermont
📸 Ngoc Minh
📸 Ngoc Minh
October 9, 2025 at 9:27 AM
Pomfret Vermont
📸 Ngoc Minh
📸 Ngoc Minh
Reposted by Colin Jackson
H.M. Saffer II (American, b.1942) :
Moon Waters, 2023
Oil on canvas
30 × 30 in | 76.2 × 76.2 cm
Further description & bio in the alt text 👇
Moon Waters, 2023
Oil on canvas
30 × 30 in | 76.2 × 76.2 cm
Further description & bio in the alt text 👇
September 25, 2025 at 3:28 AM
H.M. Saffer II (American, b.1942) :
Moon Waters, 2023
Oil on canvas
30 × 30 in | 76.2 × 76.2 cm
Further description & bio in the alt text 👇
Moon Waters, 2023
Oil on canvas
30 × 30 in | 76.2 × 76.2 cm
Further description & bio in the alt text 👇
Reposted by Colin Jackson
‘Protein evolution as a complex system’ – A new Comment discusses protein evolution in terms of complex systems theory and machine learning approaches to model the dynamics of protein evolution
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Protein evolution as a complex system - Nature Chemical Biology
Viewing protein evolution through the lens of complex systems theory may offer new insights into the principles driving biological adaptation. In this Comment we explore how characteristics such as se...
www.nature.com
August 18, 2025 at 5:02 PM
‘Protein evolution as a complex system’ – A new Comment discusses protein evolution in terms of complex systems theory and machine learning approaches to model the dynamics of protein evolution
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Colin Jackson
Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions:
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
July 29, 2025 at 6:01 PM
Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions:
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
Reposted by Colin Jackson
Protein-ligand complexes are all the rage with OpenBind+other efforts launching
3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org
A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more
fraserlab.com/2025/07/29/E...
3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org
A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more
fraserlab.com/2025/07/29/E...
Embrace the Mess
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
July 29, 2025 at 8:38 PM
Protein-ligand complexes are all the rage with OpenBind+other efforts launching
3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org
A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more
fraserlab.com/2025/07/29/E...
3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org
A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more
fraserlab.com/2025/07/29/E...
Reposted by Colin Jackson
Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!
July 19, 2025 at 8:46 PM
Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!
Reposted by Colin Jackson
nothing would make me happier than US science returning to the amazing and transformational legacy of success and dominance
but if that's not possible, we need other places with the vision to take over as the pacesetter
humanity's long term success demands no less
but if that's not possible, we need other places with the vision to take over as the pacesetter
humanity's long term success demands no less
Are you a top US-based scientist wanting to relocate to Australia? We are now calling for formal applications from both Australian and non-Australian citizens based in the US whose work is internationally recognised as exceptional.
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
📅 Applications close: Aug 29, 2025
🔗 science.org.au/gtap/?utm_so...
July 12, 2025 at 2:30 AM
nothing would make me happier than US science returning to the amazing and transformational legacy of success and dominance
but if that's not possible, we need other places with the vision to take over as the pacesetter
humanity's long term success demands no less
but if that's not possible, we need other places with the vision to take over as the pacesetter
humanity's long term success demands no less
Pleased to announce I have been promoted to the rank of GRANDMASTER thank you for your attention to this matter
July 11, 2025 at 2:19 PM
Pleased to announce I have been promoted to the rank of GRANDMASTER thank you for your attention to this matter
Reposted by Colin Jackson
Proud to share our work where we resolved a longstanding question regarding the existence of a human telomerase dimer and provided insights into its function. Led by 3 amazing lab members in collaboration with @yiliangding.bsky.social and @rdaslab.bsky.social.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization
Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work showe...
www.science.org
July 10, 2025 at 9:26 PM
Proud to share our work where we resolved a longstanding question regarding the existence of a human telomerase dimer and provided insights into its function. Led by 3 amazing lab members in collaboration with @yiliangding.bsky.social and @rdaslab.bsky.social.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
This paper started probably 20 years ago when I was working with John Oakeshott, a long time in the making and I think a nice summary of a complex real world evolutionary process
How predictable are the evolutionary pathways leading to insecticide resistance? Why do some species gain resistance while others do not? We explore these questions in our latest preprint. A huge effort from Rebecca Frkic, Alex Giang, Colin Jackson and the team.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 9, 2025 at 1:13 AM
This paper started probably 20 years ago when I was working with John Oakeshott, a long time in the making and I think a nice summary of a complex real world evolutionary process
Reposted by Colin Jackson
Seriously.
Pay for review, not publication
Publish public reviews
Editorial assessment changes until version of record
Flexible article types elife-rp.msubmit.net/html/elife-r...
Some work todo on reviewer credit (add @prereview.bsky.social to you cv!)
Pay for review, not publication
Publish public reviews
Editorial assessment changes until version of record
Flexible article types elife-rp.msubmit.net/html/elife-r...
Some work todo on reviewer credit (add @prereview.bsky.social to you cv!)
Please note: authors do not need to have already posted their research as a preprint for an initial evaluation by eLife. During submission authors can indicate if they have already posted a preprint, and if not, can ask us to deposit the work as a preprint to bioRxiv or medRxiv, as appropriate.
elife-rp.msubmit.net
June 30, 2025 at 1:13 PM
Seriously.
Pay for review, not publication
Publish public reviews
Editorial assessment changes until version of record
Flexible article types elife-rp.msubmit.net/html/elife-r...
Some work todo on reviewer credit (add @prereview.bsky.social to you cv!)
Pay for review, not publication
Publish public reviews
Editorial assessment changes until version of record
Flexible article types elife-rp.msubmit.net/html/elife-r...
Some work todo on reviewer credit (add @prereview.bsky.social to you cv!)
Reposted by Colin Jackson
New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...
High-performance genetically-encoded green and red fluorescent biosensors for pyruvate
Pyruvate is the end-product of glycolysis and a central metabolite involved in many biochemical pathways. However, a lack of high-performance (i.e., Δ F / F > 10) single fluorescent protein (FP)-base...
www.biorxiv.org
April 19, 2025 at 6:42 AM
New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...
Reposted by Colin Jackson
Average zero-shot mutation effect predictions across related sequences to reduce noise and improve accuracy.
@cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias
www.biorxiv.org/content/10.1...
@cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias
www.biorxiv.org/content/10.1...
June 9, 2025 at 2:49 PM
Average zero-shot mutation effect predictions across related sequences to reduce noise and improve accuracy.
@cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias
www.biorxiv.org/content/10.1...
@cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias
www.biorxiv.org/content/10.1...
Canberra has excellent sky
May 31, 2025 at 2:25 AM
Canberra has excellent sky
Reposted by Colin Jackson
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org.
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
Junior/Assistant/Associate/Full Specialist Positions Available
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
May 20, 2025 at 5:26 PM
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org.
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
Reposted by Colin Jackson
🚨 preprint 2️⃣ this month: our (purely experimental🧪) venture into #ChemBio
We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins.
Led by superstar @wahyuwidodo.bsky.social
www.biorxiv.org/content/10.1...
A 🧵👇🏽
We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins.
Led by superstar @wahyuwidodo.bsky.social
www.biorxiv.org/content/10.1...
A 🧵👇🏽
May 20, 2025 at 12:30 PM
🚨 preprint 2️⃣ this month: our (purely experimental🧪) venture into #ChemBio
We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins.
Led by superstar @wahyuwidodo.bsky.social
www.biorxiv.org/content/10.1...
A 🧵👇🏽
We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins.
Led by superstar @wahyuwidodo.bsky.social
www.biorxiv.org/content/10.1...
A 🧵👇🏽
Reposted by Colin Jackson
Are you (or a recent grad or tech/lab manager) looking for an awesome, mission-driven job? Come join us @addgene.bsky.social! Put your lab skills to work making impact for thousands of scientists around the world 💪🧬🧪
Love Addgene? Come work with us! We are hiring a Plasmid Production Manager - come find out why Addgene is recognized as a Top Place to Work by the Boston Globe (8 years running), BuiltIn, and NABR!
addgene.applytojob.c...
addgene.applytojob.c...
Plasmid Production Manager - Addgene - Career Page
Come find out why Addgene is recognized as a Top Place to Work by the Boston Globe (8 years running), BuiltIn, and NABR!
addgene.applytojob.com
May 20, 2025 at 1:58 PM
Are you (or a recent grad or tech/lab manager) looking for an awesome, mission-driven job? Come join us @addgene.bsky.social! Put your lab skills to work making impact for thousands of scientists around the world 💪🧬🧪
Reposted by Colin Jackson
Protein Engineering, Design & Selection (PEDS) invites contributions to a Special Collection titled, “Non-Canonical Amino Acids", with guest editors Prof. Huiwang Ai (Virginia) and Prof. Peng Chen (Peking). Send us your best work!
academic.oup.com/peds/pages/c...
academic.oup.com/peds/pages/c...
May 15, 2025 at 12:25 AM
Protein Engineering, Design & Selection (PEDS) invites contributions to a Special Collection titled, “Non-Canonical Amino Acids", with guest editors Prof. Huiwang Ai (Virginia) and Prof. Peng Chen (Peking). Send us your best work!
academic.oup.com/peds/pages/c...
academic.oup.com/peds/pages/c...
Reposted by Colin Jackson
Some interesting links I'm collecting for folks who want to do advocacy in their local districts.
www.ucsf.edu/cgr/advocacy... - easy way to write to your reps!
sciencehomecoming.com - write a letter to a hometown newspaper (great for where you grew up or went to undergrad/grad school)
www.ucsf.edu/cgr/advocacy... - easy way to write to your reps!
sciencehomecoming.com - write a letter to a hometown newspaper (great for where you grew up or went to undergrad/grad school)
Current Advocacy Issues
Details about the current priorities for UCSF Advocates.
www.ucsf.edu
May 5, 2025 at 7:01 PM
Some interesting links I'm collecting for folks who want to do advocacy in their local districts.
www.ucsf.edu/cgr/advocacy... - easy way to write to your reps!
sciencehomecoming.com - write a letter to a hometown newspaper (great for where you grew up or went to undergrad/grad school)
www.ucsf.edu/cgr/advocacy... - easy way to write to your reps!
sciencehomecoming.com - write a letter to a hometown newspaper (great for where you grew up or went to undergrad/grad school)
Good autumn in Canberra
April 26, 2025 at 11:38 AM
Good autumn in Canberra
Choosing ML architectures for protein engineering is often challenging. Our “new” updated preprint provides a rational framework to match ML models to protein fitness tasks, showing landscape ruggedness influences prediction accuracy. Mahakaran dana Adam et al www.biorxiv.org/content/10.1...
Investigating the determinants of performance in machine learning for protein fitness prediction
Machine learning (ML) has revolutionized protein biology, solving long-standing problems in protein folding, scaffold generation and function design tasks. A range of architectures have shown success ...
www.biorxiv.org
April 22, 2025 at 12:41 PM
Choosing ML architectures for protein engineering is often challenging. Our “new” updated preprint provides a rational framework to match ML models to protein fitness tasks, showing landscape ruggedness influences prediction accuracy. Mahakaran dana Adam et al www.biorxiv.org/content/10.1...