Bin Shao
@binshaophy.bsky.social
Broadie. deep learning; synthetic biology; single cell genomics; non-linear dynamics. opinions are my own.
Latest work: https://www.biorxiv.org/content/10.1101/2024.12.30.630741v2
Latest work: https://www.biorxiv.org/content/10.1101/2024.12.30.630741v2
Reposted by Bin Shao
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
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www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Interesting work on plasmid engineering.
We are thrilled to share our latest work: OriGen--the first AI system to generate functional DNA replication sequences! ⬇️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 11, 2025 at 6:34 AM
Interesting work on plasmid engineering.
Reposted by Bin Shao
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
January 22, 2025 at 8:46 PM
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
Reposted by Bin Shao
This gives me such hope for biodiversity conservation, mammals and future mammalogists! Go young people!! 🧪
What an absolute cutie!! www.sfgate.com/bayarea/arti...
An elusive California mammal has just been photographed alive for the first time
Until last year, only one California mammal species had never been caught on camera. A group of Bay Area researchers just shared the first photo of it.
www.sfgate.com
January 19, 2025 at 6:07 AM
This gives me such hope for biodiversity conservation, mammals and future mammalogists! Go young people!! 🧪
Reposted by Bin Shao
A new paper from Lingchong You's group develops a cool amplification circuit that expands the dynamic range of plasmid transfer #ChemBio #synbio #microsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Population-level amplification of gene regulation by programmable gene transfer - Nature Chemical Biology
Gene regulation in engineered microbial populations is often tuned at individual cell levels. Now, a population-wide amplification system has been devised that expands the dynamic range of plasmid tra...
www.nature.com
January 10, 2025 at 7:42 PM
A new paper from Lingchong You's group develops a cool amplification circuit that expands the dynamic range of plasmid transfer #ChemBio #synbio #microsky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Recruiting PhD students: our research covers language model + genomics + systems biology: scholar.google.com/citations?us...
1. Four-year PhD program in Beijing
2. Master's degree required
3. Start date: Sep 2025
Please DM if you are interested.
1. Four-year PhD program in Beijing
2. Master's degree required
3. Start date: Sep 2025
Please DM if you are interested.
January 9, 2025 at 3:09 AM
Recruiting PhD students: our research covers language model + genomics + systems biology: scholar.google.com/citations?us...
1. Four-year PhD program in Beijing
2. Master's degree required
3. Start date: Sep 2025
Please DM if you are interested.
1. Four-year PhD program in Beijing
2. Master's degree required
3. Start date: Sep 2025
Please DM if you are interested.
Reposted by Bin Shao
After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social
rdcu.be/d5put
A thread…
rdcu.be/d5put
A thread…
Two decades of bacterial ecology and evolution in a freshwater lake
Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...
rdcu.be
January 3, 2025 at 11:44 AM
After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social
rdcu.be/d5put
A thread…
rdcu.be/d5put
A thread…
Reposted by Bin Shao
Is it possible to get the transcriptome of any sequenced microbe without doing the experiments? Happy to introduce TXpredict, a transcriptome prediction tool that generalizes to novel microbial genomes: www.biorxiv.org/content/10.1...
Predicting microbial transcriptome using genome sequence
We present TXpredict, a transformer-based framework for predicting microbial transcriptomes using annotated genome sequences. By leveraging information learned from a large protein language model, TXp...
www.biorxiv.org
January 4, 2025 at 11:47 PM
Is it possible to get the transcriptome of any sequenced microbe without doing the experiments? Happy to introduce TXpredict, a transcriptome prediction tool that generalizes to novel microbial genomes: www.biorxiv.org/content/10.1...
Reposted by Bin Shao
Predicting microbial transcriptome using genome sequence https://www.biorxiv.org/content/10.1101/2024.12.30.630741v1
December 31, 2024 at 6:47 PM
Predicting microbial transcriptome using genome sequence https://www.biorxiv.org/content/10.1101/2024.12.30.630741v1
🌏What happens when generative AI meets ecology? How can we use AI to advance biodiversity exploration and monitoring?
Excited to introduce EcoVAE, a generative approach trained on over 100 million high-quality vouchered records to model global biodiversity
www.biorxiv.org/content/10.1...
1/n🧵
Excited to introduce EcoVAE, a generative approach trained on over 100 million high-quality vouchered records to model global biodiversity
www.biorxiv.org/content/10.1...
1/n🧵
A generative deep learning approach for global species distribution prediction
Anthropogenic pressures on biodiversity necessitate efficient and highly scalable methods to predict global species distributions. Current species distribution models (SDMs) face limitations with larg...
www.biorxiv.org
December 18, 2024 at 1:09 AM
🌏What happens when generative AI meets ecology? How can we use AI to advance biodiversity exploration and monitoring?
Excited to introduce EcoVAE, a generative approach trained on over 100 million high-quality vouchered records to model global biodiversity
www.biorxiv.org/content/10.1...
1/n🧵
Excited to introduce EcoVAE, a generative approach trained on over 100 million high-quality vouchered records to model global biodiversity
www.biorxiv.org/content/10.1...
1/n🧵
Preprint alert! A thread is coming soon.
A generative deep learning approach for global species distribution prediction https://www.biorxiv.org/content/10.1101/2024.12.10.627845v1
December 17, 2024 at 2:00 AM
Preprint alert! A thread is coming soon.
Reposted by Bin Shao
The third edition of my textbook, Nonlinear Dynamics and Chaos, was published today. You can preview the first 68 pages on Google Books, or take a look at the preface below to see what's new. The main new thing is a chapter on the Kuramoto model! Hope you enjoy it.
January 16, 2024 at 3:55 PM
The third edition of my textbook, Nonlinear Dynamics and Chaos, was published today. You can preview the first 68 pages on Google Books, or take a look at the preface below to see what's new. The main new thing is a chapter on the Kuramoto model! Hope you enjoy it.
Reposted by Bin Shao
Two BioML starter packs now:
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Anybody have a bioml starter pack?
November 18, 2024 at 5:09 PM
Two BioML starter packs now:
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)