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
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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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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
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.”
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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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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.
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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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“Ironically, a lot of these tools are about not having people sit in front of a screen all the time,” says computational biologist Mark Gerstein at Yale University in New Haven, Connecticut. “I don’t think that helps people think.” Instead, he says, researchers spawn creativity when talking and scribbling down ideas together, be that on a phone, tablet, laptop or in person.
…
Like Brown, Gerstein prizes face-to-face conversation and
collaboration in his group, which works on large-scale analyses of biosensor and wearable data. As such, it attracts “hard-core computer geeks”, he says, so he’s thought deeply about how to entice them out from behind their screens.
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“Computers now let us dictate, write and draw with our hands in much more relaxing and natural ways,” he says. Gerstein sets his phone on a nearby table, then uses Google Recorder to capture discussions, and the app (which is available only on Pixel phones) transcribes it in real time. The transcript is coupled to the audio and can be searched by keyword. Another dictation app, known as Rev, offers
quick-turnaround manual transcriptions for $1.25 per minute of recording. Gerstein also uses the app Grammarly to “take the yucky voice-to-text transcript and fix the language up quickly”.
Gerstein describes his group’s use of these tools together as a “stack” to go from conversation to a rough draft of a manuscript in just a few clicks, he says. He estimates that the tools cut the time they spent on that task in half.
Gerstein has also investigated tools that digitally recreate the experience of scientists gathered around a whiteboard. Zoom’s Annotate feature is one option, which he has deployed during remote meetings both before and during the pandemic. Another is Rocketbook, a reusable physical notebook ($16–45) that has whiteboard-like paper paired with a mobile-phone app that converts photos of notebook scribbles, cartoons and diagrams into digital files. Both Rocketbook and Google Lens use optical character recognition to interpret handwriting and translate it into searchable text. “I’ve saved thousands of sheets of paper this way,” says Gerstein.
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The Naked Scientists
Data sanitisation tool plugs privacy gap
Functional genomics data is vulnerable to de-anonymising attacks… 17 December 2020
Interview with
Mark Gerstein, Yale University
Part of the show RNA Vaccines, Privacy, and Penguins
part of the Naked Genetics podcast, on all podcast platforms and o
site here: https://www.thenakedscientists.com/podcasts/naked-genetics/rna-vaccines-privacy-and-penguins
direct link: https://www.thenakedscientists.com/articles/interviews/data-sanitisation-tool-plugs-privacy-gap
Reunion coverage + Useful suggestion for ORCID that can be done with a secondary email
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Mark Gerstein, the Albert Williams Professor of Biomedical Informatics at Yale University in New Haven, Connecticut, lists over 200 members on his lab’s alumni page, about half of whom were PhD students and postdocs. Recently, he invited many of them to a lab reunion. But first, he had to find them.
“It’s a nontrivial thing keeping track of peoples’ emails,” he says. The lab maintains a database of past members, but he’s now established a LinkedIn group, which has been particularly useful, he says. Former lab members who are on the social network can associate themselves with the lab, thus providing a mechanism for staying in touch. If nothing else, Gerstein notes, he likes to be able to contact lab expats in case there’s ever a question about an old project – for instance, to clarify a protocol or locate a file.
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A third solution would be for a third-party ‘scientific directory’ service such as ORCID to add a mechanism for contacting authors, such as a button or form to send a message.
Laure Haak, Executive Director of ORCID, says, “At the current time, ORCID does not have these features on our roadmap.”
In the meantime, it is possible to make the email addresses in an ORCID profile public; go to Account Settings > Email and Notification Preferences, and change “who can see this” from “only me” to “everyone”.
Of course, even were the organization to add a messaging feature, overtaxed researchers may not read them.
“People get so much email,” Gerstein says. “I suspect people would ignore the messages.”
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