Jonathan Ling
@jonling.bsky.social
Reposted by Jonathan Ling
Thrilled to share our new paper @cp-cell.bsky.social:
“Microglia–astrocyte crosstalk regulates synapse remodeling via Wnt signaling.”
This work demonstrates the necessity of glia–glia communication and coordination during synapse remodeling.
🔗 www.cell.com/cell/fulltex...
Faust et al., Cell 2025
“Microglia–astrocyte crosstalk regulates synapse remodeling via Wnt signaling.”
This work demonstrates the necessity of glia–glia communication and coordination during synapse remodeling.
🔗 www.cell.com/cell/fulltex...
Faust et al., Cell 2025
September 12, 2025 at 1:21 PM
Thrilled to share our new paper @cp-cell.bsky.social:
“Microglia–astrocyte crosstalk regulates synapse remodeling via Wnt signaling.”
This work demonstrates the necessity of glia–glia communication and coordination during synapse remodeling.
🔗 www.cell.com/cell/fulltex...
Faust et al., Cell 2025
“Microglia–astrocyte crosstalk regulates synapse remodeling via Wnt signaling.”
This work demonstrates the necessity of glia–glia communication and coordination during synapse remodeling.
🔗 www.cell.com/cell/fulltex...
Faust et al., Cell 2025
Reposted by Jonathan Ling
Happy to share our new study that was just published in Neuron! www.cell.com/neuron/fullt...
Seeded aggregation of TDP-43 induces its loss of function and reveals early pathological signatures
TDP-43 pathology characterizes neurodegenerative diseases. Scialò et al. use in vitro-generated
and patient-derived TDP-43 aggregates as seeds to show that seed-induced TDP-43 cytoplasmic
aggregation ...
www.cell.com
March 28, 2025 at 3:15 PM
Happy to share our new study that was just published in Neuron! www.cell.com/neuron/fullt...
Reposted by Jonathan Ling
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species https://www.biorxiv.org/content/10.1101/2025.03.20.644351v1
March 24, 2025 at 1:51 PM
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Reposted by Jonathan Ling
Bluetorial:
The announcement to move scientific review out of the institutes and centers into the Center for Scientific Review (CSR) and its potential consequences
The announcement to move scientific review out of the institutes and centers into the Center for Scientific Review (CSR) and its potential consequences
a cartoon of homer simpson holding a card
ALT: a cartoon of homer simpson holding a card
media.tenor.com
March 7, 2025 at 3:32 AM
Bluetorial:
The announcement to move scientific review out of the institutes and centers into the Center for Scientific Review (CSR) and its potential consequences
The announcement to move scientific review out of the institutes and centers into the Center for Scientific Review (CSR) and its potential consequences
Reposted by Jonathan Ling
Ecstatic to see our paper "Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing" now published in @naturegenet.bsky.social with @trajnp.bsky.social and @panosroussos.bsky.social @sinaibrain.bsky.social www.nature.com/articles/s41...
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing - Nature Genetics
This isoform-centric microglia genomic atlas includes 35,879 novel human microglia isoforms identified by long-read RNA sequencing. A multi-ancestry quantitative trait locus meta-analysis of known and...
www.nature.com
March 4, 2025 at 5:47 PM
Ecstatic to see our paper "Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing" now published in @naturegenet.bsky.social with @trajnp.bsky.social and @panosroussos.bsky.social @sinaibrain.bsky.social www.nature.com/articles/s41...
Reposted by Jonathan Ling
Roche's SBX sequencing by expansion - preprint out!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 24, 2025 at 11:00 PM
Roche's SBX sequencing by expansion - preprint out!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jonathan Ling
New essay on NIH and indirect costs:
goodscience.substack.com/p/indirect-c...
goodscience.substack.com/p/indirect-c...
Indirect Costs at NIH . . .
I wasn’t planning on spending part of a Saturday writing about cost accounting principles and the like, but NIH-world was hit with a doozy of a policy announcement on Friday night:
goodscience.substack.com
February 8, 2025 at 11:53 PM
New essay on NIH and indirect costs:
goodscience.substack.com/p/indirect-c...
goodscience.substack.com/p/indirect-c...
Reposted by Jonathan Ling
On changes to #NIH indirect rates, there is a law in place that prohibits NIH from making such changes without the approval of Congress. See Division D, Title II Section 224 of The Further Consolidated Appropriations Act, 2024 (Public Law No: 118-47) grants.nih.gov/grants/guide...
NOT-OD-24-110: Notice of Legislative Mandates in Effect for FY 2024
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Notice of Legislative Mandates in Effect for FY 2024 NOT-OD-24-110. NIH
grants.nih.gov
February 8, 2025 at 12:56 AM
On changes to #NIH indirect rates, there is a law in place that prohibits NIH from making such changes without the approval of Congress. See Division D, Title II Section 224 of The Further Consolidated Appropriations Act, 2024 (Public Law No: 118-47) grants.nih.gov/grants/guide...
Reposted by Jonathan Ling
Reposted by Jonathan Ling
A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it.
www.science.org/content/blog...
www.science.org/content/blog...
What's Happening Inside the NIH and NSF
www.science.org
February 4, 2025 at 4:40 PM
A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it.
www.science.org/content/blog...
www.science.org/content/blog...
Reposted by Jonathan Ling
Insanely good news if this holds up.
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
www.science.org/doi/10.1126/...
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
www.science.org/doi/10.1126/...
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts...
www.science.org
February 5, 2025 at 4:12 AM
Insanely good news if this holds up.
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
www.science.org/doi/10.1126/...
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
www.science.org/doi/10.1126/...
Reposted by Jonathan Ling
SOME GOOD NEWS ABOUT NIH FUNDING
Closed sessions of institute and center Advisory Counsel meetings are now permitted. This is where grant applications are discussed and approved for potential funding.
Open sessions where there are public presentations and discussions are still not allowed.
Closed sessions of institute and center Advisory Counsel meetings are now permitted. This is where grant applications are discussed and approved for potential funding.
Open sessions where there are public presentations and discussions are still not allowed.
a man with glasses and a black shirt says " it 's a small step that really goes a long way "
ALT: a man with glasses and a black shirt says " it 's a small step that really goes a long way "
media.tenor.com
February 3, 2025 at 6:35 PM
SOME GOOD NEWS ABOUT NIH FUNDING
Closed sessions of institute and center Advisory Counsel meetings are now permitted. This is where grant applications are discussed and approved for potential funding.
Open sessions where there are public presentations and discussions are still not allowed.
Closed sessions of institute and center Advisory Counsel meetings are now permitted. This is where grant applications are discussed and approved for potential funding.
Open sessions where there are public presentations and discussions are still not allowed.
Reposted by Jonathan Ling
Just coincidentally found GenBank Release 84.0 from 1994 in the neighboring lab. Anyone out there with an even older version?
January 26, 2025 at 2:28 AM
Just coincidentally found GenBank Release 84.0 from 1994 in the neighboring lab. Anyone out there with an even older version?
Reposted by Jonathan Ling
Can AI really help with literature reviews? 🧐
Meet Ai2 ScholarQA, an experimental solution that allows you to ask questions that require multiple scientific papers to answer. It gives more in-depth and contextual answers with table comparisons and expandable sections 💡
Try it now: scholarqa.allen.ai
Meet Ai2 ScholarQA, an experimental solution that allows you to ask questions that require multiple scientific papers to answer. It gives more in-depth and contextual answers with table comparisons and expandable sections 💡
Try it now: scholarqa.allen.ai
January 21, 2025 at 7:31 PM
Can AI really help with literature reviews? 🧐
Meet Ai2 ScholarQA, an experimental solution that allows you to ask questions that require multiple scientific papers to answer. It gives more in-depth and contextual answers with table comparisons and expandable sections 💡
Try it now: scholarqa.allen.ai
Meet Ai2 ScholarQA, an experimental solution that allows you to ask questions that require multiple scientific papers to answer. It gives more in-depth and contextual answers with table comparisons and expandable sections 💡
Try it now: scholarqa.allen.ai
Reposted by Jonathan Ling
1/5
So, how did DeepSeek develop DeepSeek R1?
They used both DeepSeek-V3-Base and a simple prompt:
1. They asked the same question multiple times to DeepSeek-V3-Base as a group.
2. They then graded the answers, assigning an accuracy score and a format score (e.g., <think></think>).
So, how did DeepSeek develop DeepSeek R1?
They used both DeepSeek-V3-Base and a simple prompt:
1. They asked the same question multiple times to DeepSeek-V3-Base as a group.
2. They then graded the answers, assigning an accuracy score and a format score (e.g., <think></think>).
January 21, 2025 at 7:49 AM
1/5
So, how did DeepSeek develop DeepSeek R1?
They used both DeepSeek-V3-Base and a simple prompt:
1. They asked the same question multiple times to DeepSeek-V3-Base as a group.
2. They then graded the answers, assigning an accuracy score and a format score (e.g., <think></think>).
So, how did DeepSeek develop DeepSeek R1?
They used both DeepSeek-V3-Base and a simple prompt:
1. They asked the same question multiple times to DeepSeek-V3-Base as a group.
2. They then graded the answers, assigning an accuracy score and a format score (e.g., <think></think>).
Reposted by Jonathan Ling
Researchers at tech giant Meta have created a machine-learning system that almost instantaneously translates speech in 101 languages into words spoken by a voice synthesizer in any of 36 target languages.
https://go.nature.com/3WiibUA
https://go.nature.com/3WiibUA
Meta AI creates speech-to-speech translator that works in dozens of languages
Machine-learning system can process words spoken in 101 languages, spitting out voice-synthesized translations in 36 target languages.
go.nature.com
January 16, 2025 at 12:16 PM
Researchers at tech giant Meta have created a machine-learning system that almost instantaneously translates speech in 101 languages into words spoken by a voice synthesizer in any of 36 target languages.
https://go.nature.com/3WiibUA
https://go.nature.com/3WiibUA
Reposted by Jonathan Ling
www.prnewswire.com/news-release...
UK Biobank to run 5.4K protein Olink assay on 600K samples using Ultima UG100
UK Biobank to run 5.4K protein Olink assay on 600K samples using Ultima UG100
Ultima Genomics Announces UG 100™ Sequencing Platform Selected for UK Biobank's Groundbreaking Human Proteome Study
/PRNewswire/ -- Ultima Genomics, Inc., a developer of an ultra-high throughput next-generation sequencing (NGS) platform, today announced that its UG 100™ was...
www.prnewswire.com
January 10, 2025 at 3:10 AM
www.prnewswire.com/news-release...
UK Biobank to run 5.4K protein Olink assay on 600K samples using Ultima UG100
UK Biobank to run 5.4K protein Olink assay on 600K samples using Ultima UG100
Reposted by Jonathan Ling
Reposted by Jonathan Ling
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
A foundation model of transcription across human cell types - Nature
A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...
www.nature.com
January 8, 2025 at 4:27 PM
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
Reposted by Jonathan Ling
So here's an interesting development...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
The recombinant shingles vaccine is associated with lower risk of dementia - Nature Medicine
A natural experiment including more than 200,000 people who received a shingles vaccine reveals that, within 6 years of vaccination, the recombinant vaccine is associated with lower risk of dementia t...
www.nature.com
January 7, 2025 at 9:54 PM
So here's an interesting development...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
Reposted by Jonathan Ling
You may have heard that it took a long time for penicillin to be scaled up.
What about other antibiotics? How long did it take for them to be mass produced and introduced clinically, after they were discovered?
I created a visualization of this here:
What about other antibiotics? How long did it take for them to be mass produced and introduced clinically, after they were discovered?
I created a visualization of this here:
December 23, 2024 at 10:44 AM
You may have heard that it took a long time for penicillin to be scaled up.
What about other antibiotics? How long did it take for them to be mass produced and introduced clinically, after they were discovered?
I created a visualization of this here:
What about other antibiotics? How long did it take for them to be mass produced and introduced clinically, after they were discovered?
I created a visualization of this here:
Reposted by Jonathan Ling
Google research scholar programme applications open until 27th Jan. support early-career professors (received PhD within seven years of submission).
research.google/programs-and...
research.google/programs-and...
Research scholar program
Overview
research.google
December 21, 2024 at 9:47 AM
Google research scholar programme applications open until 27th Jan. support early-career professors (received PhD within seven years of submission).
research.google/programs-and...
research.google/programs-and...
Reposted by Jonathan Ling
Delighted to highlight our new paper in
@natureportfolio.bsky.social entitled 'Synaptic basis of feature selectivity in hippocampal neurons' (thread below 👇): www.nature.com/articles/s41...
@natureportfolio.bsky.social entitled 'Synaptic basis of feature selectivity in hippocampal neurons' (thread below 👇): www.nature.com/articles/s41...
Synaptic basis of feature selectivity in hippocampal neurons - Nature
A temporally asymmetric synaptic plasticity kernel results from bidirectional modifications of synaptic weights around the induction of a place field.
www.nature.com
December 18, 2024 at 10:00 PM
Delighted to highlight our new paper in
@natureportfolio.bsky.social entitled 'Synaptic basis of feature selectivity in hippocampal neurons' (thread below 👇): www.nature.com/articles/s41...
@natureportfolio.bsky.social entitled 'Synaptic basis of feature selectivity in hippocampal neurons' (thread below 👇): www.nature.com/articles/s41...
Reposted by Jonathan Ling
@markhisted.org lays down some knowledge.
What are recurrent networks doing in the brain?
www.thetransmitter.org/neural-netwo...
#neuroscience
What are recurrent networks doing in the brain?
www.thetransmitter.org/neural-netwo...
#neuroscience
What are recurrent networks doing in the brain?
The cortex is filled with excitatory local synapses, but we know little about their role in brain function. New experimental tools, along with ideas from artificial intelligence, are poised to change…
www.thetransmitter.org
December 16, 2024 at 6:00 PM
@markhisted.org lays down some knowledge.
What are recurrent networks doing in the brain?
www.thetransmitter.org/neural-netwo...
#neuroscience
What are recurrent networks doing in the brain?
www.thetransmitter.org/neural-netwo...
#neuroscience
Reposted by Jonathan Ling
Last update of our databases for the year.
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
December 14, 2024 at 6:28 PM
Last update of our databases for the year.
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...