linkstream2 microblog

https://medicine.yale.edu/news-article/21150/

https://www.the-scientist.com/news-opinion/the-push-to-replace-journal-supplements-with-repositories–66296

Reunion coverage + Useful suggestion for ORCID that can be done with a secondary email

https://www.natureindex.com/news-blog/one-in-five-email-addresses-researcher-journal-articles-invalid-problem

QT:{{”
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.
…
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.”
“}}

https://medicine.yale.edu/news/article.aspx?id=20962

https://medicine.yale.edu/news/medicineatyale/new-center-to-harness-burgeoning-data.aspx

QT:[[”

It is a kind of “data fusion,” adds Mark B. Gerstein, PhD, Albert L. Williams Professor of Biomedical Informatics, professor of molecular biophysics and biochemistry, of computer science, and of statistics and data science, and CBDS co-director. “We’re integrating all the different types of data together, and that’s just something that is hard to do in a completely generic, automated way. You need to think about what you’re putting together.”
”]]

February 13, 2019
Q&A With Mark B. Gerstein, PhD, on Diagnostic Genomic vs Exomic Sequencing Bryant Furlow
https://www.cancertherapyadvisor.com/home/cancer-topics/general-oncology/qa-with-mark-b-gerstein-phd-on-diagnostic-genomic-vs-exomic-sequencing/

WORKS IN PROGRESS – SPRING 2019
Decoding DNA
On the hunt for the genetic roots of mental illnesses

By Marcus Banks | March 4, 2019

QT:[[”
The model, a form of artificial intelligence, aims to use abstract knowledge gained in the research lab to improve clinical treatments for real patients. The ultimate goal, says Gerstein, is to use the model to develop pharmaceutical treatments that reduce the impact of schizophrenia. Part of the challenge in developing drugs to treat the disease is the fact that it is not a one-size-fits-all condition. “]]

https://theamericanscholar.org/decoding-dna/#.XH7RRlNKiqA

https://www.nature.com/news/2010/100715/full/news.2010.356.html

QT:[[”

It should be possible to scan the genome for sequences encoding peptides shorter than 100 amino acids, says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut, but sorting through the many ‘hits’ to determine which are functional is likely to be much more difficult.

Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. “Maybe this would provide a new way for pseudogenes to have some sort of function,” he says.
“]]

https://www.cancertherapyadvisor.com/general-oncology/mark-gerstein-cancer-diagnostic-genome-exome-sequence/article/833786/

https://omny.fm/shows/kcbsam-on-demand/dna-kits-give-different-results-for-identical-twin

KCBS Radio San Francisco

DNA Kits Give Different Results For Identical Twins

live radio interview

local copy
http://meetings.gersteinlab.org/2019/01.24/DNA%20Kits%20Give%20Different%20Results%20For%20Identical%20Twins.csquare.x57k.mp3