Posts Tagged ‘x78qtcore’

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.

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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.
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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

2022-06-08-09.34.24.NY-Times-story-on-bitcoin.x78qt.jpg
2022-06-08-09.36.23.NY-Times-story-on-bitcoin.x78qt.jpg

Hybrid labs piece went up on Friday

March 14, 2022

https://twitter.com/KendallSciWrite/status/1503508908085760000

CAREER FEATURE
11 March 2022

How hybrid working took hold in science

Two years since COVID-19 forced labs to shut down, group leaders describe how academic research has changed, perhaps forever. Kendall Powell

https://www.nature.com/articles/d41586-022-00729-9

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Principal investigators (PIs), including those who started research groups during the pandemic, are now incorporating the best parts of pandemic flexibility into the future of research. “It’s hard to see any good when we are heading toward six million deaths,” says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut. “But the pandemic has taught us new ways of thinking about things.”

For example, Gerstein has learnt that some group members work most efficiently at home, whereas others really need to come in to work. “I have been a little surprised that the tails of that spectrum have been so wide.”

Gerstein says that increased flexibility should also help to ease some of the thorniest problems that early-career researchers can face, such as childcare support and the two-body problem — the challenge of two partners needing to find a job in the same geographical location. “I want to be very flexible,” Gerstein says. “That’s what talented people want in their workplace.”
….

Hybrid lab working has also changed the dynamics of groups. Gerstein’s weekly Zoom meeting with his 40-strong team can last for several hours, but he’s fine with a healthy dose of zoning out, turning cameras off and multitasking for those who don’t need to engage in the main conversation. His group uses a Google Doc to draw up the agenda and the members share screens to annotate it in real time. He then saves the final document to the lab’s Dropbox account.

Science-ing from home

“It is efficient and works even better than in-person meetings,” says Gerstein, who plans to retain video meetings to accommodate childcare responsibilities, illness and scheduling conflicts. “Now, everyone is equal, even our collaborators in Europe or China. I don’t think we’ll ever go back to a large in-person lab meeting.”

Gerstein has also been rethinking his computational group’s workspace. “Do we want that same traditional look where people come in every day and sit at desks?” he asks. “I’m sceptical — no one wants to be in open-plan cubes.”

Instead, he sees his lab of the future as being one in which, ideally, researchers have their own office and can close the door when they need to think, code or write. There also needs to be a room big enough for three or four people, to host meetings or conference calls. Hybrid working could mean a lot of unoccupied space on certain days. He’s considering a ‘hotelling’ option, with lab members booking larger office spaces in advance as needed, alongside everyone having a smaller dedicated workstation in the group’s shared space.

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Biology begins to tangle with quantum computing | Nature Methods

July 16, 2021

Technology Feature
Published: 23 June 2021
Biology begins to tangle with quantum computing
Vivien Marx
Nature Methods volume 18, pages715–719 (2021)

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“There’s a lot of buzz about quantum computing,” says Yale University researcher Mark Gerstein, whose projects traverse biology and informatics. Enthusiasm among his colleagues about the prospects of quantum computing is especially high in the physical sciences, and interest is growing in computational biology and biology more generally.


Gerstein co-authored a paper4 that grew from a series of discussions at the National Institute of Mental Health (NIMH), part of the US National Institutes of Health (NIH). It’s part of the NIH’s way of exploring how to support biologists interested and involved in quantum computing, he says. The wider neuroscience community, for example, is interested in how quantum approaches can be applied to deep learning and machine learning.

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https://www.nature.com/articles/s41592-021-01199-z