David Angeles
@davidangeles.bsky.social
Focused on developing molecular technologies to control cell fate with precise spatiotemporal resolution. Recovering computational geneticist, ex-Altos, ex-eGenesis. Caltech PhD.
Currently at #TERMIS2025, sitting at an award plenary, and though the speaker has done amazing science and is a great speaker, 100% of the data she presented is 2008-2018. Why? I can read all of these papers. The point of conferences used to be to show cutting edge work.
November 10, 2025 at 3:57 PM
Currently at #TERMIS2025, sitting at an award plenary, and though the speaker has done amazing science and is a great speaker, 100% of the data she presented is 2008-2018. Why? I can read all of these papers. The point of conferences used to be to show cutting edge work.
Reposted by David Angeles
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 David Angeles
27 years ago, two years after the introduction of effective HIV treatment, the Bay Area Reporter, San Francisco’s lesbian and gay community newspaper, ran ‘No Obits’ as its headline.
It was the first edition not to report an AIDS death in almost 15 years.
It was the first edition not to report an AIDS death in almost 15 years.
August 13, 2025 at 6:56 AM
27 years ago, two years after the introduction of effective HIV treatment, the Bay Area Reporter, San Francisco’s lesbian and gay community newspaper, ran ‘No Obits’ as its headline.
It was the first edition not to report an AIDS death in almost 15 years.
It was the first edition not to report an AIDS death in almost 15 years.
Reposted by David Angeles
🗃️
A history mystery solved: where do potatoes come from?
Nine million years ago, as the Andes were rising, a tomato cross pollinated a plant from the S. etuberosum lineage. Each plant contributed a gene, that together enabled underground stems to form tubers.
www.sciencenews.org/article/pota...
A history mystery solved: where do potatoes come from?
Nine million years ago, as the Andes were rising, a tomato cross pollinated a plant from the S. etuberosum lineage. Each plant contributed a gene, that together enabled underground stems to form tubers.
www.sciencenews.org/article/pota...
Potatoes have their roots in ancient tomatoes
Knowing potatoes’ origin story could help future-proof the crucial crop against climate threats.
www.sciencenews.org
August 1, 2025 at 1:38 PM
🗃️
A history mystery solved: where do potatoes come from?
Nine million years ago, as the Andes were rising, a tomato cross pollinated a plant from the S. etuberosum lineage. Each plant contributed a gene, that together enabled underground stems to form tubers.
www.sciencenews.org/article/pota...
A history mystery solved: where do potatoes come from?
Nine million years ago, as the Andes were rising, a tomato cross pollinated a plant from the S. etuberosum lineage. Each plant contributed a gene, that together enabled underground stems to form tubers.
www.sciencenews.org/article/pota...
huh.
[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...
Gastruloid patterning reflects division of labor among biased stem cell clones
Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against....
www.biorxiv.org
July 15, 2025 at 6:03 PM
huh.
What does it say if you see circles at the bottom and rectangles at the top? Asking for a friend...
What you see when you look at this image depends on the culture you grew up in. The question is: Are you shocked to hear that some people see rectangles or circles? That and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti...
June 23, 2025 at 3:24 PM
What does it say if you see circles at the bottom and rectangles at the top? Asking for a friend...
Reposted by David Angeles
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 8:55 PM
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 13, 2025 at 1:31 AM
up next @tatianasg.bsky.social
shared and distinct mechanisms in salamander limb and human fingertip regeneration.
shared and distinct mechanisms in salamander limb and human fingertip regeneration.
June 13, 2025 at 1:24 AM
up next @tatianasg.bsky.social
shared and distinct mechanisms in salamander limb and human fingertip regeneration.
shared and distinct mechanisms in salamander limb and human fingertip regeneration.
ALBERT ERNESTO ALMADA Quiescent preexisting cells in skeletal muscle heal tail injuries in anole lizards 🦎
after tail amputation you see a thing called a blastema forming, muscle only starts to reappear after ~28 days of growth though.
#isscr2025
after tail amputation you see a thing called a blastema forming, muscle only starts to reappear after ~28 days of growth though.
#isscr2025
June 13, 2025 at 1:23 AM
ALBERT ERNESTO ALMADA Quiescent preexisting cells in skeletal muscle heal tail injuries in anole lizards 🦎
after tail amputation you see a thing called a blastema forming, muscle only starts to reappear after ~28 days of growth though.
#isscr2025
after tail amputation you see a thing called a blastema forming, muscle only starts to reappear after ~28 days of growth though.
#isscr2025
Yesterday i didn't post my conference notes. Let's catch up.
animal models in regeneration.
MAYSSA MOKALLED washington u in st louis - approaches to spinal cord regeneration. a critical challenge in spinal cord therapies is in providing physical support for implanted neurons.
#isscr2025
animal models in regeneration.
MAYSSA MOKALLED washington u in st louis - approaches to spinal cord regeneration. a critical challenge in spinal cord therapies is in providing physical support for implanted neurons.
#isscr2025
June 13, 2025 at 1:22 AM
Yesterday i didn't post my conference notes. Let's catch up.
animal models in regeneration.
MAYSSA MOKALLED washington u in st louis - approaches to spinal cord regeneration. a critical challenge in spinal cord therapies is in providing physical support for implanted neurons.
#isscr2025
animal models in regeneration.
MAYSSA MOKALLED washington u in st louis - approaches to spinal cord regeneration. a critical challenge in spinal cord therapies is in providing physical support for implanted neurons.
#isscr2025
speechless. wow!
1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs.
Full story here:
www.biorxiv.org/content/10.1...
Full story here:
www.biorxiv.org/content/10.1...
June 11, 2025 at 5:38 PM
speechless. wow!
Reposted by David Angeles
This is a cumulative maximum intensity projection movie of the endoplasmic reticulum labeled with the membrane marker mEmerald-Sec61B.
June 11, 2025 at 12:55 AM
This is a cumulative maximum intensity projection movie of the endoplasmic reticulum labeled with the membrane marker mEmerald-Sec61B.
next up masayo takahashi talking about ipsc based replacement of RPEs to cure vision loss from AMD and how to bring an experimental therapy to a trial. makes a big point that there is more to a product than just treatment.
#isscr25
#isscr25
June 11, 2025 at 4:53 AM
next up masayo takahashi talking about ipsc based replacement of RPEs to cure vision loss from AMD and how to bring an experimental therapy to a trial. makes a big point that there is more to a product than just treatment.
#isscr25
#isscr25
Michael S Pepper just gave a powerful talk about inequality in gene and cell therapy access.
Africa accounts for 1/5 people on the planet. Of 2850 clinical trials worldwide, there are 5 clinical trials in the entire African continent.
Entire room was silent for a couple of minutes afterwards.
Africa accounts for 1/5 people on the planet. Of 2850 clinical trials worldwide, there are 5 clinical trials in the entire African continent.
Entire room was silent for a couple of minutes afterwards.
June 11, 2025 at 4:09 AM
Michael S Pepper just gave a powerful talk about inequality in gene and cell therapy access.
Africa accounts for 1/5 people on the planet. Of 2850 clinical trials worldwide, there are 5 clinical trials in the entire African continent.
Entire room was silent for a couple of minutes afterwards.
Africa accounts for 1/5 people on the planet. Of 2850 clinical trials worldwide, there are 5 clinical trials in the entire African continent.
Entire room was silent for a couple of minutes afterwards.
Claire Booth talked at #isscr25 about gene editing therapeutics in SCID patients. Basically, we can cure many monogenic types of SCID… but we cant get them to the clinic.
heartbreaking to see that the science is solid, yet the reasons for lack of advancement are regulatory.
heartbreaking to see that the science is solid, yet the reasons for lack of advancement are regulatory.
June 11, 2025 at 3:48 AM
Claire Booth talked at #isscr25 about gene editing therapeutics in SCID patients. Basically, we can cure many monogenic types of SCID… but we cant get them to the clinic.
heartbreaking to see that the science is solid, yet the reasons for lack of advancement are regulatory.
heartbreaking to see that the science is solid, yet the reasons for lack of advancement are regulatory.
Bing Guo just gave the coolest talk showing spleen and liver HSCs are established embryonically using a parabiosis experiment, spleen cells “remember” the spleen and can target it when transplanted into the marrow more than bone marrow derived HSCs and they respond to different stimuli. super cool
June 11, 2025 at 2:03 AM
Bing Guo just gave the coolest talk showing spleen and liver HSCs are established embryonically using a parabiosis experiment, spleen cells “remember” the spleen and can target it when transplanted into the marrow more than bone marrow derived HSCs and they respond to different stimuli. super cool
#ISSCR25 kicks off and i am listening to the cellular agriculture session. multis ceo talking now. they use ai and robotics to automate media prep and test many conditions.
June 11, 2025 at 12:57 AM
#ISSCR25 kicks off and i am listening to the cellular agriculture session. multis ceo talking now. they use ai and robotics to automate media prep and test many conditions.
Reposted by David Angeles
Hey optical tech dev folks: how do you do alignment? Can you outline your alignment procedures for positioning optics and verifying their correct positioning?
June 3, 2025 at 12:45 AM
Hey optical tech dev folks: how do you do alignment? Can you outline your alignment procedures for positioning optics and verifying their correct positioning?
first time I ever hear of freeze-thaw cycles being a good thing for RNA! Very cool!
New paper from my group rdcu.be/eoaRr "Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme" in Nature Chemistry — great collaboration with attwaterlab.uk.
Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme
Nature Chemistry - Models of abiotic RNA replication suffer from inherent product inhibition arising from the high stability of RNA duplexes. Now, it has been shown that RNA trinucleotide...
rdcu.be
May 30, 2025 at 2:16 AM
first time I ever hear of freeze-thaw cycles being a good thing for RNA! Very cool!
Reposted by David Angeles
The cellular dance that splits vessels
Really appreciate this insightful commentary by Dr. Lance Munn on our recent paper @pnas.org using Microvessel-On-A-Chip to model the pillariogenesis during early #IntussusceptiveAngiogenesis 😎
pnas.org/doi/abs/10.1073/pnas.2508260122
Really appreciate this insightful commentary by Dr. Lance Munn on our recent paper @pnas.org using Microvessel-On-A-Chip to model the pillariogenesis during early #IntussusceptiveAngiogenesis 😎
pnas.org/doi/abs/10.1073/pnas.2508260122
May 29, 2025 at 7:19 PM
The cellular dance that splits vessels
Really appreciate this insightful commentary by Dr. Lance Munn on our recent paper @pnas.org using Microvessel-On-A-Chip to model the pillariogenesis during early #IntussusceptiveAngiogenesis 😎
pnas.org/doi/abs/10.1073/pnas.2508260122
Really appreciate this insightful commentary by Dr. Lance Munn on our recent paper @pnas.org using Microvessel-On-A-Chip to model the pillariogenesis during early #IntussusceptiveAngiogenesis 😎
pnas.org/doi/abs/10.1073/pnas.2508260122
gotta read this carefully, but at a quick glance, looks awesome
Reconstitution of adrenocortical functional zonation from human pluripotent stem cells https://www.biorxiv.org/content/10.1101/2025.05.24.655925v1
May 29, 2025 at 2:01 AM
gotta read this carefully, but at a quick glance, looks awesome
Reposted by David Angeles
Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...
Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...
www.biorxiv.org
May 25, 2025 at 11:00 AM
Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...
Reposted by David Angeles
A new #ScienceSignaling study interrogates crosstalk between mechanical and biochemical signals in epithelial cells, illustrating how mechanical stretching activates a kinase that regulates cell growth, migration, and differentiation.
E-cadherin mechanotransduction activates EGFR-ERK signaling in epithelial monolayers by inducing ADAM-mediated ligand shedding
Epithelial stretching promotes the release of EGF receptor ligands that stimulate ERK activation.
scim.ag
May 26, 2025 at 5:04 PM
A new #ScienceSignaling study interrogates crosstalk between mechanical and biochemical signals in epithelial cells, illustrating how mechanical stretching activates a kinase that regulates cell growth, migration, and differentiation.