Podcast appearances and mentions of Sage Bionetworks

Christopher Gaiteri, Ph.D., is Associate Professor of Psychiatry & Behavioral Sciences and Empire Innovation Scholar at SUNY Upstate Medical University. Dr. Gaiteri earned his undergraduate degree from Washington & Lee University and his doctorate from the University of Pittsburgh. He joined Rush University as assistant professor of neurological sciences and computational neuroscientist after serving as Research Scientist at the Allen Institute for Brain Science and Senior Scientist at Sage Bionetworks. In today's podcast, Dr. Gaiteri responds to the following questions: 1. What were the origins to your approach and how does it differ from the more traditional way of framing research about the onset and development of Alzheimer's disease? 2.  Statistical techniques such as factor analysis and canonical correlation were used in research to take a large number of measures of variables and allow those statistical techniques to sort out which of those variables covaried and which patterns emerged that could suggest relationships to be looked at more closely. In your approach using "big data" do you have a particular notion of which variables you select ought to covary? In other words, do you have a "pre-theory" that guides your selection of variables? 3.  Alzheimer's is nearly always associated with the aging process, perhaps implicitly arguing that the aging process alone is a causal agent for the onset and progression of the disease. More recently and not without some controversy, some researchers have suggested that aging itself should be considered a disease. From your perspective, does the question of age influence your view on how to go about framing analyses of data bearing on the inception and development of Alzheimer's? 4.  In your career to date, how has the leadership of organizations in which you have worked influenced you and your research? Are there characteristics of persons who hold leadership roles that you single out as especially important to your work? INNOVATORS is a podcast production of Harris Search Associates.  *The views and opinions shared by the guests on INNOVATORS do not necessarily reflect the views of the interviewee's institution or organization.*

Today's episode features a conversation with Juliane Schneider, Senior Bioinformatics Analyst and Data Liaison at Sage Bionetworks. The interview was conducted by Matthew Ismail, Editor in chief of the Charleston Briefings and Conference Director at the Charleston Conference.  Juliane obtained a dual degree in Library Science and Information Systems from Drexel University. This training, and her knowledge of databases, has helped her successfully navigate her career path over the years.  She currently works at Sage Bionetworks, a nonprofit that works mostly with NIH and with data collection, curation and making it available to users.  Juliane says, "she has always been interested in making things discoverable in some way." Juliane and Matthew discuss research data management and how time affects the research data cycle, how challenging it is to get in at the very beginning of the cycle, and the problems with grant funding of research data management. She believes research data management should be a line item in the operational budget of the university or institution. She also believes there is a great deal of responsibility when it comes to data and how algorithms are created, and the way data is searched that we need to be aware of. The open access and open data conversation of how to responsibly use data is not occurring often enough.

Jesse Wiley discusses his work on the TREAT-AD project and their attempt to identify new candidates for drug development to protect against Alzheimer's. Jesse explains that he and his team have identified 15 biological domains that are associated with the development of Alzheimer's (not 18 as I say in the podcast).  Intriguingly, Mitochondrial malfunction and chronic immune response rose to the top of the list of domains. Jesse also explains "pseudotime" which is a new tool for tracking the trajectory of disease development. Our discussion of mitochondrial malfunction led us to discussions  of epigenetic factors,  and the role of behavior and lifestyle interventions. 

Jesse Wiley of Sage Bionetworks talks about his involvement with TREAT-AD, which is an exciting open-science, community approach to developing data-drive hypotheses that may lead towards new kinds of treatments for Alzheimer's disease.  These new approaches will go beyond the amyloid hypothesis that has dominated research and drug development approaches over the last two decades, yet failed to produce any effective drug.  

On Episode 10 of the OmicsXchange Podcast, we're speaking with Meg Doerr, a Principal Scientist in Data Governance and Ethics at Sage Bionetworks. Meg is the Programme Committee Chair for the upcoming GA4GH 8th Plenary meeting, which will take place on September 29 and 30. It will be our first fully virtual meeting and we are delighted to have had Meg’s guidance in developing the programme.

“Sometimes the person making the biggest impact is the one who says nothing.”My conversation with Erin was another excellent example of how we all have stories to share and how oftentimes our paths can lead in different directions that ultimately end up bringing something wonderful to our lives.Join me as we hear Erin share her journey starting out on a pre-Nursing path to her current work supporting the President of Sage Bionetworks. Our conversation went from how to navigate a pivot in your career plan to how to overcome imposter syndrome and feel valuable and confident in your role; I appreciated Erin's honesty and for allowing us the opportunity to get to know her better.You’ll especially not want to miss the part of the conversation that caused both of us to roll our eyes at the phrase “not bubbly enough to be an admin.” Yikes!Connect with Erin on LinkedIn: https://www.linkedin.com/in/erinjscanlan/If you enjoyed this or any of the other conversations, don't forget to rate and subscribe!www.haveaseatconversations.comThanks for listening!

Sponsored by Linode Panelists Eric Berry | Justin Dorfman | Pia Mancini | Richard Littauer Guest Kaitlin Thaney Invest in Open Infrastructure (IOI) Show Notes Hello and welcome to Sustain! Today, we have Kaitlin Thaney, who is the Executive Director for Invest in Open Infrastructure (IOI). Kaitlin will tell us all about IOI and what she’s doing there. She also explains the history of the Mozilla Science Lab and how her team came up with it. How has COVID impacted the organization, especially since her first day of the job was when New York City went into lockdown! Download this episode now to find out! [00:01:17] Kaitlin tells us what Invest in Open Infrastructure is and what she’s doing there. [00:04:17] Eric wants to know is this organization built to create essentially just the technology behind these infrastructures or is it primarily ways of sharing data? Kaitlin explains the end goal in simplistic terms. [00:09:50] With Kaitlin’s background and previous organization’s that she’s worked for (Wikimedia, Mozilla, and Creative Commons), Justin wants to know how those former employers shaped her for what she’s doing now as an Executive Director. [00:16:41] Kaitlin explains Mozilla Science Lab. She also has a call to action called “Get credit for your code!” She talks about this and how she and her team came up with it. [00:21:35] Richard asks Kaitlin to tell us what Elsevier is and how they represent what’s happening in academia now. Also, since she started this initiative before COVID happened, she tells us how she’s adapted, how she’s changed, and what’s happening moving forward. [00:28:21] Pia wants to know from Kaitlin what the broad impact COVID has had and what are her plans going forward, and how are folks thinking about this? [00:33:12] Richard gives a s/o to the Schmidt Foundation for funding Invest in Open Infrastructure (IOI). [00:33:42] Kaitlin lets us know how you can get involved with her project if you are a software developer, work at a university, or a researcher. Also, how you can find her and where can you sign up. Spotlight [00:34:35] Richard’s spotlight is BibTeX. [00:35:02] Justin’s spotlight is Undraw.co. [00:35:28] Eric’s spotlight is Betterhelp.com and Therapistaid.com (both worth checking out) [00:37:55] Pia’s spotlight is Excalidraw. [00:38:43] Kaitlin’s spotlight is a portable Informed Consent Toolkit from Sage Bionetworks. Quotes [00:13:55] “You all know the deep roots that Open Source has, and software and the internet have in science. But beyond those initial stories, I think there’s an interesting kind of proof space that this sort of work allows for, because in terms of moving decisions forward, it’s not just talking about researchers. It also touches those in the education sector, universities, policy makers, for profit tech, and non-profit tech. All of these various elements that by their very nature, help bring and incubate different solutions that you can then apply to broader society.” Links Invest in Open Infrastructure (https://investinopen.org/) Open Infrastructure in times of crisis: How IOI can help (https://investinopen.org/2020/04/08/open-infrastructure-in-times-of-crisis.html) Kaitlin Thaney Twitter (https://twitter.com/kaythaney) Kaitlin Thaney (IOI) (https://investinopen.org/participants/) Mozilla Science Lab-Get credit for your code! (http://mozillascience.github.io/code-research-object/#extensions) BibTeX (https://en.wikipedia.org/wiki/BibTeX) unDraw.co (https://undraw.co) Betterhelp.com (https://www.betterhelp.com/) TherapistAid.com (https://www.therapistaid.com/) Excalidraw.com (https://excalidraw.com/) Schmidt Family Foundation (https://en.wikipedia.org/wiki/Schmidt_Family_Foundation) Credits Produced by Justin Dorfman (https://www.justindorfman.com/) Edited by Paul M. Bahr at Peachtree Sound (https://www.peachtreesound.com/) Show notes by DeAnn Bahr at Peachtree Sound (https://www.peachtreesound.com/) Ad Sales by Eric Berry Special Guest: Kaitlin Thaney.

Under the DataScope is a six-episode podcast series from the Kraft Precision Medicine Accelerator at Harvard Business School, showcasing the most important companies that bring data & analytics technologies to precision medicine today. You’ll hear from Professors Richard Hamermesh and Kathy Guisti, plus leaders in the field, including John Wilbanks of Sage Bionetworks, David Shaywitz of Takeda Ventures, Jeff Elton from Concerto Health AI, Wout Brusselaers, Founder & CEO of Deep6, Richard Williams of Wuxi NextCode, and Eyal Gura, Founder & CEO, Zebra Medical Vision. Hosted by Gabriel Eichler.

This week, you’ll hear from John Wilbanks, Chief Commons Officer at Sage Bionetworks. Yeah, that’s most definitely a Nerdus Maximus title, but John does very cool stuff around making data more accessible and usable by the research community AND he’s down with the idea of data as an economic resource for not just the big-money players, but also the humans who create that data. Full show notes and links here: https://www.patreon.com/posts/john-wilbanks-on-23314230

DREAM Challenges pose fundamental questions about systems biology and translational medicine. Designed and run by a community of researchers from a variety of organizations, the challenges invite participants to propose solutions, fostering collaboration and building communities in the process. The Sage Bionetworks Synapse platform, which powers many research consortiums including the DREAM Challenges, are starting to put into practice model cloud-initiatives that not only provide impactful discoveries in the areas of neuroscience, infectious disease, and cancer, but are also revolutionizing scientific research by enabling an interactive consortium science platform. In this session, you learn how to build a "consortium model" of research in order to connect research organizations with non-profit organizations, technology companies, biotechnology, and pharmaceutical companies. You can also learn about how to leverage machine learning, Amazon ECS, and R for consortium-based science initiatives.

In Episode 15 of Hidden Forces, host Demetri Kofinas speaks with Dr. Eric Schadt. Eric Schadt is founder and CEO of Sema4, as well as Dean of Precision Medicine at the Icahn School of Medicine at Mount Sinai. During the course of his 20-year career, Dr. Eric Schadt has built genetics and systems biology groups at Merck. He built the computational biology group at Rosetta. He has served as co-founder of Sage Bionetworks and as Chief Science Officer of Pacific Biosciences. He now serves as the founder and CEO of Sema4. He has published more than 300 peer-reviewed papers in leading scientific journals, and he has contributed to a number of discoveries relating to the genetic basis of common human diseases such as diabetes, obesity and Alzheimer’s. In today’s conversation, we explore the information technology of biology – DNA – the world of genomics, where big data looms large. We begin by mapping the territory of the human genome and exploring the pathways of disease. We look to understand the ways in which complex genetic combinations express themselves as phenotypes such as height, bone structure, intelligence, and personality. How are these traits coded for? What are the instructions our body uses to repair a damaged cell? What blueprint does it consult before trying to grow new arteries? How does it know to regulate our appetite or when start us down the path of puberty? What happens when these instructions are damaged? How can the smallest difference in the order of life’s code make all the difference for our success, our happiness, and even our survival? 50 years have passed, between the discovery of the double-helix and the mapping of the first human genome. What progress have we made in the 15 years since? How has our ability to sequence new genomes created a paradigm shift in medicine? What is the role of big data and artificial intelligence in finding the correlations needed in order to treat malignancies and prevent diseases? What is the promise of genomics? What are the perils of big data in medicine? What stands between us and some superhuman future? Producer & Host: Demetri Kofinas Editor & Engineer: Stylianos Nicolaou Join the conversation on Facebook, Instagram, and Twitter at @hiddenforcespod

Data has the potential to help fuel social change across the world, yet many relevant datasets remain locked away and siloed across government agencies, nonprofits, and corporations. What kind of collaboration does it take to make this data available to different actors working to create change? In a series of TED-style talks, Melinda Rolfs of the MasterCard Center for Inclusive Growth, John Wilbanks of Sage Bionetworks, Greg Bloom of Civic Hall Labs and Open Referral, and ST Mayer of Code for America talk about how to develop not only the right tools, but also the right relationships to make data collaboration happen. Jake Porway of DataKind then leads a discussion on how we can collectively harness data for the greater good. View the slides from this session here. https://ssir.org/podcasts/entry/unlocking_data_and_unleashing_its_potential

Jeff Hammerbacher gives an overview of his work at Hammer Lab where he and his colleagues use data science to understand and improve the immune response to cancer. He also discusses the design of Hammer Lab, particularly focusing on ways that the lab is directly informed and motivated by his prior work experience at Bear Stearns, Facebook, and Cloudera. Jeff is an Assistant Professor at the Medical University of South Carolina and the Icahn School of Medicine at Mount Sinai, a founder and the Chief Scientist of Cloudera, an angel investor with his wife Halle Tecco at Techammer, and a board member of CIOX Health and Sage Bionetworks. Jeff was an Entrepreneur in Residence at Accel Partners immediately prior to founding Cloudera. Before Accel, he conceived, built, and led the Data team at Facebook. Before joining Facebook, Jeff was a quantitative analyst on Wall Street. Jeff earned his Bachelor's Degree in Mathematics from Harvard University.

John Wilbanks, Chief Commons Officer of Sage Bionetworks, says “the very containers” that we used to put data in, “that kept it human-scale,” have been “blown to bits.” The question is: How do we pick up the pieces and reassemble them in the aftermath? In this "Resonance Test" podcast, Wilbanks and Continuum SVP Mike Dunkley dive down into the many issues surrounding healthcare data. “We basically throw darts at the dartboard with a blindfold on right now," says Wilbanks. “Using data, statistical modeling, and machine learning *has* to be better than that.” Together, Wilbanks and Dunkley talk about smartphones and increasing sample size in health research, the idea of a “credit union” for data, and the challenge of measuring the success of precision medicine. The work is, for the passionate Wilbanks, a very human-centric activity. “Health is personal," he says. "Experience of disease is personal. Lived experience is personal, and you can start to capture these lived experiences and aggregate them in ways that tell us a lot about disease that we didn't used to know.”

When researchers explore the human genome, they usually look for genetic causes of disease, but a global study being led by scientists at the Icahn School of Medicine at Mount Sinai and Sage Bionetworks is looking for genes that might keep people healthy. Their study, the largest genome study to date, seeks to find people with genetic mutations that should have caused rare childhood diseases, but didn’t. Dubbed the Resilience Project, they are looking for clues in these genomes for why these people never became stricken. We spoke to Jason Bobe, associate professor and director of the Sharing Lab at the Icahn Institute and Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai, about the study, what’s been learned so far, and how this may lead to new treatments for rare and deadly diseases.

Today we’re learning from John Wilbanks, chief commons officer at Sage Bionetworks, who has authored numerous publications about data sharing. On this panel, The Evolving Nature of Privacy and Confidentiality from the 2014 AER Conference, he discusses the evolving nature of privacy, confidentiality and anonymity when it comes to collecting and analyzing “big data.”

1) Mid-life milk consumption and substantia nigra neuron density at death2) What's Trending: Interview with Dr. Ray Dorsey about new Neurology site, which will be called Innovations in Care Delivery3) Topic of the month: Neurology Today story about should there be a moratorium on human germline editingThis podcast for the Neurology Journal begins and closes with Dr. Robert Gross, Editor-in-Chief, briefly discussing highlighted articles from the print issue of Neurology. In the second segment Dr. Binit Shah interviews Dr. Robert Abbott about his paper on mid-life milk consumption and substantia nigra neuro density at death. Dr. Robert Gross is interviewing Dr. Ray Dorsey for our “What's Trending” feature of the week about being the section editor and curator of our new Neurology site, which will be called Innovations in Care Delivery. In the next part of the podcast Dr. Ted Burns interviews Dr. Thomas Bird about a Neurology Today story on the topic of should there be a moratorium on human germline editing. DISCLOSURES: Dr. Abbott serves as an editorial board member of Keio Journal of Medicine Journal of Epidemiology, and receives non-profit research support from Pacific Health Research and Education Institute.Dr. Gross is supported for educational endeavors from the University of Rochester Medical Center's Clinical and Translational Science Award from the NIH; since his appointment as Editor-in-Chief in 2009, he has ceased participation in industry-sponsored clinical trials and speakers' bureaus and receives an honorarium from AAN as Editor-in-Chief of Neurology.Dr. Dorsey serves on the scientific advisory board of Shire Pharmaceuticals, Huntington's Disease Society of America and NINDS; serves as Editor for HD Insights; serves as an editorial board member of the Journal of Huntington's Disease; serves as Section Editor and Curator for Innovations in Care Delivery mini-site Neurology; received travel funding and honoraria from the American Academy of Neurology; has a patent application related to telemedicine; includes telemedicine in his clinical practice as a movement disorder neurologist (20% effort); has received compensation for expert testimony; is a consultant for 23andME, Amgen, Avid radiopharmaceuticals, Clintrex, Lundbeck Inc, MC10, Inc., Shire Pharmaceuticals, MedAvante, Transpanency Life Sciences and NINDS; receives research support from AMC Health, Avid Radiopharmaceuticals, Biogen Idec, Great Lakes Neurotechnologies, Lundbeck Inc, Medtronic, Inc., Prana Biotechnology, Agency for Health Care Research and Quality; NINDS, National Science Foundation, Patient-Centered Outcomes Research Institute; Davis Phinney Foundation, Michael J. Fox Foundation, Sage Bionetworks.Dr. Ted Burns serves as Podcast Editor for Neurology; and has received research support for consulting activities with UCB, CSL Behring, Walgreens and Alexion Pharmaceuticals, Inc.Dr. Bird serves as an editorial board member of GeneReviews.org; has a patent for Genetic testing technology for CMT1C and SCA14 and receives research support from the Department of Veterans' Affairs, Merit Research Grant.

The American Association for Cancer Research (AACR) announced the launch of an international initiative known as AACR Project Genomics, Evidence, Neoplasia, Information, Exchange (GENIE). The initial phase of the project, which is being conducted in partnership with seven global leaders in genomic sequencing for clinical utility, as well as two informatics partners, will aggregate project members’ clinical-grade sequencing data to improve patient treatment decisions and catalyze clinical and translational research. The seven founding members of the consortium and phase 1 participants are: The Center for Personalized Cancer Treatment, Utrecht, Netherlands; Dana-Farber Cancer Institute, Boston; Institut Gustave Roussy, Villejuif, France; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore; Memorial Sloan Kettering Cancer Center, New York; Princess Margaret Cancer Centre, Toronto; and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. The two informatics partners are: Sage Bionetworks, Seattle; and cBioPortal, New York.