Posts Tagged ‘x78qtcore’

Journal of Medical Internet Research – From Virtual Molecules to Clinical Trials: How AI Is Reshaping Preclinical Drug Discovery

May 31, 2026

https://www.jmir.org/2026/1/e101366
QT:{{”
Mark Gerstein, PhD—professor of biomedical informatics, molecular biophysics, and computer science at Yale University—said that this paradox helps explain why enthusiasm around AI should be tempered with realism. “There is a lot of excitement with AI in drug discovery,” Gerstein said, “but the reality is that we have not been as successful at discovering drugs as we would have hoped.”
…Gerstein also points to equivariant neural networks as a promising advance in AI-driven drug discovery. Since molecules obey physical laws and can rotate, stretch, or change their conformation, predictive models must account for these transformations. Equivariant
architectures are designed to preserve these relationships, making them especially valuable for molecular modeling and binding prediction “}}

Cuffari, B. (2026). From virtual molecules to clinical trials: How AI is reshaping preclinical drug discovery. Journal of Medical Internet Research, 28, e101366. https://doi.org/10.2196/101366

With AlphaGenome, Researchers Are Using A.I. to Decode the Human Blueprint – The New York Times

January 28, 2026

https://www.nytimes.com/2026/01/28/science/alphagenome-ai-deepmind-genetics.html

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But Dr. Koo and other outside experts cautioned that it represented just one step on a long road ahead. “This is not AlphaFold, and it’s not going to win the Nobel Prize,” said Mark Gerstein, a computational biologist at Yale.

AlphaGenome will be useful. Dr. Gerstein said that he would probably add it to his toolbox for exploring DNA, and others expect to follow suit. But not all scientists trust A.I. programs like AlphaGenome to help them understand the genome.

In 2021, Dr. Avsec and his colleagues unveiled a preliminary A.I. called Enformer, which they have since expanded into AlphaGenome. They trained the program on an even greater expanse of biological data. “It’s really an industrial scale,” Dr. Gerstein said
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Media query (Nature Medicine): Quantum computing and health

January 19, 2025

Guenot, M. (2025). Can quantum computing crack the biggest challenges in health? Nature Medicine. https://doi.org/10.1038/s41591-024-03369-w

Great story by @Marianne_Guenot, providing good & *not* good news about QC for biomedicine.

QT:{{

The potential power of quantum computers in cracking problems that classical computers cannot is not all good news, says Mark Gerstein, a professor of biomedical informatics at Yale University who recently co-authored a review about quantum computing and health for Nature Methods3.

Experts predict that quantum computers could become fiendishly good at breaking through current encryption algorithms, says Gerstein, which could pose a problem for the privacy of confidential patient data. “There’s a huge push right now to get post-quantum cryptography to work,” he says.

The idea, then, is not for quantum computers to replace classical computers, says Gerstein. Instead, they should be considered as adding a node to a computing chain, as each can contribute different strengths to solve a problem. “The art here is figuring out which bit of this big calculation you can quantize,” says Gerstein.
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AI tool that predicts gene activity could open path for disease treatments – The Washington Post

January 18, 2025

https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/

Johnson, M. (2025, January 8). Scientists trained AI to predict gene activity, a potentially powerful tool. Washington Post.
https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/

QT:{{”
Mark Gerstein, a professor of biomedical informatics at Yale School of Medicine, who was not involved in the new study, said that for 15 to 20 years experts have been systematically trying to make predictions about gene regulation, building on a trove of carefully made datasets. The data examined all genes in specific types of human cells ― for example, retinal cells or neurons ― measuring, among other things, gene expression and the binding of key proteins called transcription factors.
“This is a field poised to have this type of advancement by AI,” Gerstein said. “}}

NYTimes.com: As 23andMe Struggles, Concerns Surface About Its Genetic Data

October 6, 2024

As 23andMe Struggles, Concerns Surface About Its Genetic Data

A plummet in the company’s valuation and a recent board resignation have raised questions about the future of genetic data collected from millions of customers.

https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html?smid=em-share

QT:{{”
“People don’t, I think, appreciate how large the genetic information for a person is,” Mark Gerstein, a professor of biomedical informatics at Yale University, said on Saturday.
“In theory, if there’s a mess-up with your credit card or Social Security number, you get a new one, it can be fixed,” Professor Gerstein said. “But there’s absolutely no way to get a new genome.” …
Looking at a genome can reveal a complicated structure, akin to ones and zeros of binary code, Professor Gerstein said. That might make it seem like the information is harder to glean than from a personal tech device.
“Superficially, there might be a comforting aspect to that, as opposed to if I peek in your email box,” he said. However complex the genome is, though, it can still hold sensitive private data.
“In the longer term, maybe it actually is more revealing,” he said. “}}

LLMs predict protein phases | Nature Methods

September 10, 2024

https://www.nature.com/articles/s41592-024-02421-4

Singh, A. (2024). LLMs predict protein phases. Nature.
https://doi.org/10.1038/s41592-024-02421-4

Mark bio

October 22, 2023

https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511

2023 ISCB accomplishments by a senior scientist award: Mark Gerstein Christiana N Fogg, Diane E Kovats, Martin Vingron
Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i9–i10, https://doi.org/10.1093/bioinformatics/btad316
Published: 30 June 2023

Yale News on ISMB Award

August 27, 2023

https://news.yale.edu/2023/08/01/mark-gerstein-receives-iscb-accomplishments-senior-scientist-award

Hospital and Drugmaker Move to Build Vast Database of New Yorkers’ DNA – The New York Times

August 13, 2022

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Mark Gerstein, a professor of Biomedical Informatics at Yale University, said there was no question that genomic datasets were driving great medical discoveries. But he said he still would not participate in one himself, and he urged people to consider whether adding their DNA to a database might someday affect their
grandchildren.

“I tend to be a worrier,” he said.

Our collective knowledge of mutations and what illnesses they are associated with — whether Alzheimer’s or schizophrenia — would only increase in the years ahead, he said. “If the datasets leaked some day, the information might be used to discriminate against the children or grandchildren of current participants,” Dr. Gerstein said. They might be teased or denied insurance, he added.

He noted that even if the data was anonymous and secure today, that could change. “Securing the information over long periods of time gets much harder,” he said, noting that Regeneron might not even exist in 50 years. “The risk of the data being hacked over such a long period of time becomes magnified,” he said.
“}}

How ‘Trustless’ Is Bitcoin, Really? – The New York Times

June 18, 2022

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Mark Gerstein, a professor of bioinformatics at Yale University, found in the research implications for data privacy. He recently stored a genome on a private blockchain, which allowed for a secure and tamperproof record. But he noted that in a public setting, as with Bitcoin’s blockchain, a data set’s size and subtle patterns made it susceptible to breaches, even as the data remained immutable. (Ms. Blackburn wasn’t tampering with the Bitcoin blockchain’s records.)

“That’s the amazing thing about big data,” Dr. Gerstein said. “If you have a big enough data set, it starts to leak information in unexpected ways.” Even more so when data from different sources are connected, he said: “When you combine one data set with another to make a bigger data set, nonobvious linkages can arise.”
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https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html

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