Archive for the 'x78qt' Category

University Science Strategy Committee Report

June 20, 2018

Long-awaited @Yale STEM report calls for new research institutes Top recommendation is a new #DataScience institute! Followed by one for #Neuroscience. Cross-cutting recommendations on grad. student support & sci. cores (

Blog post itself has some interesting “text evolution”:

Points from the new University Science Strategy Committee Report :

Under Five Ideas for Top-Priority Investment: (University-wide Institute for) Integrative Data Science and its Mathematical Foundations and Neuroscience, from Molecules to Mind

Under Five Additional Priority Ideas: Computer Science, Conquering Cancer, Precision Medicine, Regenerative Medicine

Mark Gerstein — a professor of biomedical informatics— similarly emphasized the value of a new data science institute that would integrate Yale’s science campuses and discourage research “silos.” …
Another concern is establishing the specific role of the institute amid the various departments and programs at Yale that perform data science research, Gerstein said. For example, he said, Yale’s new Center for Biomedical Data Science, which Gerstein co-directs, might eventually be folded into the proposed institute.

Carl Zimmer To Speak At Bio-IT World, Tackle Heredity, Genes, And How Our Understanding Of The Two Is Changing – Bio-IT World

May 11, 2018

“It was a huge amount of fun watching them take that raw data and put it through their own pipelines,” Zimmer told me, but he also felt uncomfortable pointing out discrepancies to the scientists he worked with. “I still remember, I was sitting down with Chris Mason at Weill Cornell. He and his students were so enthusiastically going through their findings with me… and they showed me, among other things, how many SNPs I had. Not too long beforehand I’d gone through the same experience with Mark Gerstein and his team at Yale, and their numbers for my SNPs were off by hundreds of thousands. … It was a little awkward with Chris, but I just said, ‘Hey, I got a very different number from Mark Gerstein,’ and Chris just shrugged and said, ‘Oh yeah, that happens.’”

It turns out, there’s a lot about our current understanding of our genes and how we pass them on that isn’t perfectly clear cut. “}}

UP CLOSE: Ahead of STEM report, Yale takes stock | Yale Daily News

April 29, 2018

Mark Gerstein, a professor of biomedical informatics, molecular biophysics and biochemistry and computer science, lauded the committee’s creation. It is crucial, he said, to determine a strategy for science at Yale, as opposed to just narrow “tactics,” like specific programs or buildings.

“If we want to maintain our strength as a university — not just in the sciences — we really need to field a full team,” Gerstein said. “It’s like a football team — you can’t win the Super Bowl if you don’t have all the different positions.”

Gerstein suggested that Yale’s location in New Haven also serves as a “major factor,” potentially hindering success in faculty recruitment. Especially when compared to California, Boston or New York, living in New Haven may be less appealing to potential professors, he added. “}}

Written by Amy Xiong
Photos by Daniel Zhao
Graphics by Rebecca Goldberg
Published on April 27, 2018

Put your email inbox on a low-spam diet : Naturejobs Blog

April 15, 2018

Put your email inbox on a low-spam diet by @j_perkel #Email hygiene for the researcher – ie how to escape fake conference & journal invites + #spam calendar invites

The practice of publishing their email addresses on journal articles and university web sites makes research academics ready targets for email spammers. Spam, Clemons insists, is not merely a nuisance but a time-sink. Mark Gerstein, a professor of biomedical informatics at Yale University in New Haven, Connecticut, estimates that maybe a quarter of the 200-or-so messages he receives in a day are important. “I spend many, many, many hours a week, days a week probably, going through my correspondence,” he says.

Gerstein, for instance, uses a multi-tiered approach to triage his correspondence, relying on Gmail filters, labels, and artificial intelligence. Gerstein has a whitelist — a list of ‘approved’ email addresses. Messages from those addresses are automatically routed to his inbox, where they receive the highest priority. New senders can get on that list by placing a special keyword (available on his web site) in the subject line of their message — which is how I was able to contact him.

Below that top tier are departmental messages, messages from mailing lists, and the like. At the very bottom is the obvious spam, the stuff that gets picked up by Google’s spam-detection algorithms. And in the middle is what Gerstein calls ‘almost-spam’ — messages from predatory journals and conferences, spam invitations to join editorial boards, and even spam calendar invites, which automatically add themselves to his calendar and clog up his schedule.

Gerstein advises researchers to use multiple email addresses in dealing with journals, vendors, and the like. Then, by funneling those messages to a single inbox, one can sort the messages by account and prioritize them accordingly.

Gmail is particularly useful for this purpose, Gerstein notes. Suppose you have the address ‘’. Google allows users to modify their addresses by placing a plus sign and additional text between the username and the at-symbol — for instance,
‘’ and ‘’. These messages all go to the original address, but users can sort their messages based on the specific address used.

“You can use that quite powerfully to create unique addresses for all sorts of things, and to filter your email on the basis of that,” Gerstein says.

Still, Gerstein admits, spam inevitably falls through the cracks. How to spot it?

Yale Daily News article about the new Yale Center for Biomedical Data Science (CBDS)

February 10, 2018

Yale establishes biomedical data science center

“The field of data science has become particularly relevant in the biomedical realm — in genomic sequencing, imaging data, patient record data, data on molecules like nucleotides, proteins and metabolites and wearable personal health devices,” Gerstein said. “All of these create data streams that are growing particularly large, and there’s a lot of value in mining and integrating these different data streams.” …

“Although this initiative was started by the medical school, it is meant for the whole campus,” Gerstein said. “We want undergraduates to do research and take courses in biomedical data science — and to be engaged in this center.”

Putting the precise in precision medicine > Features > Autumn 2017 | Yale Medicine

November 22, 2017

Center co-director Mark B. Gerstein, Ph.D., the Albert L. Williams Professor of Biomedical Informatics, explains that succeeding with what researchers term “Big Data” requires “real thought about standards, the uniform collection of data, the distribution of samples, and the presentation and packaging of results.” After three years of planning, Gerstein and co-director Hongyu Zhao, Ph.D., a geneticist and the Ira V. Hiscock Professor of Biostatistics, have assembled a kind of central clearinghouse for research and development of these issues, particularly cloud computing and privacy, as well as for education and bridge-building collaboration on university, national, and international levels. “Our mission is really about connecting and coordinating the people and resources already here, and becoming a way to recruit the scientists we want to attract in the future for the Big Data initiatives we want to participate in,” says Gerstein. “We expect the center to have a very broad impact.” “}}

cybersecurity story

August 5, 2017

The absent-minded prof in the news…!

Cybersecurity for the travelling scientist

Virtual private networks, tracking apps and ‘burner’ laptops: how to protect sensitive data when you take your research on the road.

Brian Owens

02 August 2017

Mark Gerstein has had his fair share of scares when it comes to losing track of his electronic devices — and, along with them, access to his private information and research data.

“I’m very security conscious, but also a bit of an absent-minded professor,” says Gerstein, a bioinformatician at Yale University in New Haven, Connecticut.

He recalls one trip to Boston, Massachusetts, when he left his phone in a taxi, and watched it get farther and farther away on the tracking app on his iPad while he ran after the car in vain. Luckily, Gerstein was able to contact the taxi company, and eventually watched his phone make the return journey to his pocket.

Gerstein’s story had a happy ending, but all too often, hardware lost on the road is lost for good.

Quick comment on AI for pharma?

July 18, 2017

Please find the article at link:

Is big pharma really on cusp of AI shake-out?

By: Pharma IQ
Posted: 07/14/2017


The promises of “disruptive technologies” have failed to live up to expectations in the past. For example, the development of ‘high throughput screening’ – a process that employs robotics to conduct millions of chemical, genetic and pharmacological tests in rapid time – in the 1990s failed to significantly reduce R&D inefficiencies and offered sporadic success rates.

“The major cost in drug R&D is last-phase clinical trials,” said Dr Mark Gerstein, professor of biomedical informatics at Yale University. “It is not clear whether AI can be as useful for these as it has been in target selection for the initial phases.”

“One of the first principles of data mining is that history is a good predictor of the future. AI has a track record of not living up to its expectations and therefore caution about how great its impact will be in the healthcare industry is now warranted.”

Archives | HCR Clarivate Analytics

November 21, 2016



2016 HCR List as of November 16 2016
2015 HCR List as of December 1 2015
2014 HCR List as of December 31 2014
2014 HCR as of September 8 2015


2001 HCR List as of December 31 2001
2001 HCR as of September 8 2015

Steven Girvin, Robert Schoelkopf, and Nikhil Padmanabhan among the most influential scientific minds of 2015 | Department of Physics

February 21, 2016

MG mentioned on Thomson Reuter’s
in 2 categories: Biochem & Genetics