Diego Calderon
@diegoisworking.bsky.social
Assistant Professor at UCSF | CZ Biohub – SF Investigator
https://diego-calderon-lab.github.io
https://pharmacy.ucsf.edu/diego-calderon
https://diego-calderon-lab.github.io
https://pharmacy.ucsf.edu/diego-calderon
Reposted by Diego Calderon
My lab at UCSF is recruiting postdoc candidates interested in CRISPR synthetic biology and functional genomics approaches to study and engineer tissue injury responses! hsiunglab.org
November 19, 2025 at 6:06 AM
My lab at UCSF is recruiting postdoc candidates interested in CRISPR synthetic biology and functional genomics approaches to study and engineer tissue injury responses! hsiunglab.org
Reposted by Diego Calderon
Super cool paper from Sheel Chandra + Ziyue Gao. kmer context matters a lot for mutability of both methylated and unmethylated CpGs.
But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs!
www.biorxiv.org/content/10.1...
But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs!
www.biorxiv.org/content/10.1...
Sequence context and methylation interact to shape germline mutation rate variation at CpG sites
A prominent example of sequence context-dependent mutation rate variation is the elevated transition rate at CpG sites, which is largely attributed to cytosine methylation. CpGs with different flankin...
www.biorxiv.org
November 18, 2025 at 8:13 PM
Super cool paper from Sheel Chandra + Ziyue Gao. kmer context matters a lot for mutability of both methylated and unmethylated CpGs.
But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs!
www.biorxiv.org/content/10.1...
But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs!
www.biorxiv.org/content/10.1...
Reposted by Diego Calderon
My center at NYU SoM is hiring an Assistant/Associate Professor in human genetics and genomics. It's a wonderful place to do science. Please apply or pass along. apply.interfolio.com/177375
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 14, 2025 at 3:51 PM
My center at NYU SoM is hiring an Assistant/Associate Professor in human genetics and genomics. It's a wonderful place to do science. Please apply or pass along. apply.interfolio.com/177375
Reposted by Diego Calderon
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology
Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.
go.nature.com
November 12, 2025 at 6:06 PM
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
Reposted by Diego Calderon
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:57 PM
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
Reposted by Diego Calderon
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Diego Calderon
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
November 5, 2025 at 3:09 PM
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Reposted by Diego Calderon
Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/
November 4, 2025 at 3:10 PM
Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/
Reposted by Diego Calderon
🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
October 24, 2025 at 6:26 PM
🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
Reposted by Diego Calderon
Building community! Finishing undergrad (or just finished) and interested in gaining research experience before applying to PhD programs and also want to be part of a group that cares about you? Join our next matchmaking event!! Jan 30th 9am - 1pm PT propelscholars.org/matchmaking-...
October 22, 2025 at 1:04 AM
Building community! Finishing undergrad (or just finished) and interested in gaining research experience before applying to PhD programs and also want to be part of a group that cares about you? Join our next matchmaking event!! Jan 30th 9am - 1pm PT propelscholars.org/matchmaking-...
Reposted by Diego Calderon
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 29, 2025 at 4:47 PM
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
Reposted by Diego Calderon
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
September 26, 2025 at 6:06 PM
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
Reposted by Diego Calderon
I am thrilled to share a joint work with Melissa Gymrek that spans several years to study what is the impact of promoter proximal short tandem repeats (STRs) on expression by using MPRAs. I am sure you'd enjoy!
Awesome effort by @xzhangbsky.bsky.social and the team!
www.biorxiv.org/content/10.1...
Awesome effort by @xzhangbsky.bsky.social and the team!
www.biorxiv.org/content/10.1...
xzhangbsky.bsky.social
xzhangbsky.bsky.social
September 21, 2025 at 4:00 AM
I am thrilled to share a joint work with Melissa Gymrek that spans several years to study what is the impact of promoter proximal short tandem repeats (STRs) on expression by using MPRAs. I am sure you'd enjoy!
Awesome effort by @xzhangbsky.bsky.social and the team!
www.biorxiv.org/content/10.1...
Awesome effort by @xzhangbsky.bsky.social and the team!
www.biorxiv.org/content/10.1...
Reposted by Diego Calderon
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
September 20, 2025 at 4:10 PM
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
Reposted by Diego Calderon
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
September 12, 2025 at 7:00 PM
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
Reposted by Diego Calderon
Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
September 8, 2025 at 5:13 PM
Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
Reposted by Diego Calderon
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
August 22, 2025 at 7:50 PM
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
Reposted by Diego Calderon
happy to say my new department is hiring an associate/full professor: academicjobsonline.org/ajo/jobs/30328
please apply!
please apply!
August 18, 2025 at 10:22 PM
happy to say my new department is hiring an associate/full professor: academicjobsonline.org/ajo/jobs/30328
please apply!
please apply!
Reposted by Diego Calderon
New preprint with @gfudenberg.bsky.social
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion
Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...
www.biorxiv.org
August 16, 2025 at 3:03 AM
New preprint with @gfudenberg.bsky.social
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
Reposted by Diego Calderon
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
August 6, 2025 at 5:18 PM
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
Reposted by Diego Calderon
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader - Genome Biology Unit
Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...
embl.wd103.myworkdayjobs.com
July 30, 2025 at 1:41 PM
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Diego Calderon
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Dissecting functional regulatory convergence over 160 million years of therian evolution https://www.biorxiv.org/content/10.1101/2025.07.10.662670v1
July 11, 2025 at 9:46 PM
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Reposted by Diego Calderon
I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
June 2, 2025 at 5:45 PM
I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
We'll work at the intersection of statistical genetics, population genetics, and machine learning.
Reposted by Diego Calderon
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...
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 ...
www.philanthropy.cam.ac.uk
June 3, 2025 at 6:23 PM
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...
Reposted by Diego Calderon
Excited to share our first anti-aging intervention analysis, led by brilliant Zehao @tommyz626.bsky.social, Alex, and Chloe from our lab at @rockefelleruniv.bsky.social! We identified the aging-associated cell populations that can be rescued by caloric restriction in the mammalian brain!
May 12, 2025 at 6:12 PM
Excited to share our first anti-aging intervention analysis, led by brilliant Zehao @tommyz626.bsky.social, Alex, and Chloe from our lab at @rockefelleruniv.bsky.social! We identified the aging-associated cell populations that can be rescued by caloric restriction in the mammalian brain!