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Big Data in Biomedicine conference kicks off today

Big Data in Biomedicine conference kicks off today

14243103692_67ec6354f0_zThe third annual Big Data in Biomedicine conference kicks off today on the Stanford campus. The three-day event brings together thought leaders from academia, information technology companies, venture capital firms and public health institutions to explore opportunities for extracting knowledge from the rapidly growing reservoirs of health and medical information to transform how we diagnose, treat and prevent disease.

The year’s program will cover the intersection of disciplines as widespread as genomics, population health, neuroimaging and immunology; it will also touch on crowdsourcing, ethical and legal issues and “learning” health systems. Delivering the opening keynote will be Sharon Terry, president and CEO of Genetic Alliance. Other keynote speakers include Kathy Hudson, PhD, deputy director for science, outreach and policy at the National Institutes of Health; France Córdova, PhD, director of the National Science Foundation; Michael Levitt, PhD, professor of structural biology at Stanford and recipient of the 2013 Nobel Prize in Chemistry; and Lloyd Minor, MD, dean of Stanford’s School of Medicine.

Those unable to attend in person can tune in to the live webcast via the conference website. We’ll also be live tweeting the keynote talks and other proceedings from the conference; you can follow the coverage on the @StanfordMed feed or by using the hashtag #bigdatamed.

Previously: Countdown to Big Data in Biomedicine: Leveraging big data technology to advance genomics, Countdown to Big Data in Biomedicine: Mining medical records to identify patterns in public health and Harnessing mobile health technologies to transform human health
Photo from the 2014 Big Data in Biomedicine conference by Saul Bromberger

Big data, Events, Stanford News

Countdown to Big Data in Biomedicine: Technical showcase to spotlight companies’ innovations

Countdown to Big Data in Biomedicine: Technical showcase to spotlight companies' innovations

14222209716_d3072f7737_zLater this week, thought-leaders from academia, information technology corporations, venture capital firms, the U.S. government and foundations will convene for the Big Data in Biomedicine conference to explore opportunities for mining the rich repositories of biomedical information.

In addition to sessions on topics ranging from crowdsourcing to genomics, the conference will include a technical showcase where conference-goers can peruse displays and demos highlighting companies’ innovations related to big data. Part technology expo and part networking opportunity, the technical showcase will include light refreshments and be held under a tent on the lawn of the medical school’s Li Ka Shing Center for Learning and Knowledge.

Participants for this year’s event include advanced patient monitoring firm Flashback Technologies, which will present an innovative index for body-fluid levels in trauma situations and a device to do it on the spot; Zephyr Health, a company that pairs real-world data with predictive analytics to provide insights that are strategic and actionable; Samsung, which will show how the company’s personal devices are moving into human health solutions; and Personalis, a startup providing researchers and clinicians with accurate DNA sequencing and interpretation of human exomes and genomes.

The conference is part of Stanford Medicine’s Biomedical Data Science Initiative, which strives to make powerful transformations in human health and scientific discovery by fostering innovative collaborations among medical researchers, computer scientists, statisticians and physicians. The event runs from Wednesday through Friday.

Previously: Countdown to Big Data in Biomedicine: Leveraging big data technology to advance genomics, Countdown to Big Data in Biomedicine: Mining medical records to identify patterns in public health and Harnessing mobile health technologies to transform human health
Photo from last year’s technical showcase by Saul Bromberger

Cancer, Neuroscience, Pediatrics, Research, Stanford News, Videos

How one family’s generosity helped advance research on the deadliest childhood brain tumor

How one family’s generosity helped advance research on the deadliest childhood brain tumor

Back in February 2014, Libby and Tony Kranz found themselves at the center of every parent’s worst nightmare. Their six-year-old daughter Jennifer died just four months after being diagnosed with diffused intrinsic pontine glioma (DIPG), an incurable and fatal brain tumor. At the time, the Kranzes decided to generously donate their daughter’s brain to research in hopes that scientists could hopefully develop more effective treatments for DIPG, which affects 200-400 school-aged children in the United States annually and has a five-year survival rate of less than 1 percent.

As reported in the above Bay Area Proud segment, Michelle Monje, MD, PhD, an assistant professor of neurology and neurological sciences who sees patients at Lucile Packard Children’s Hospital Stanford, and colleagues harvested Jennifer’s tumor and successfully created a line of DIPG stem cells, one of only 16 in existence in the world. More from the story:

Using Jennifer’s stem cell lines and others, Monje and her team tested dozens of existing chemotherapy drugs to see if any were effective against DIPG. One appears to be working.

The drug was able to slow the growth of a DIPG tumor in a laboratory setting. Monje’s hope is that this treatment one day could extend the life of children diagnosed with DIPG by as many as six months.

That would have more than doubled Jennifer’s life expectancy.

“It’s a step in the right direction if we can effectively prolong life and prolong quality of life,” Monje said.

Libby Kranz says that for their family, donating their daughter’s tumor to researchers “just felt right.” She and Tony hope that by aiding the research efforts, parents and families will have more, and better quality time with their sick children.

“It’s incredible and it’s humbling,” she said, “to know my daughter is part of it, and that we’re part of it too.”

Previously: Existing drug shows early promise against deadly childhood brain tumor, Stanford brain tumor research featured on “Bay Area Proud,Emmy nod for film about Stanford brain tumor research – and the little boy who made it possible and Finding hope for rare pediatric brain tumor

Medical Education, Research, Videos

Students draw inspiration from Jimmy Kimmel Live! to up the cool factor of research careers

Students draw inspiration from Jimmy Kimmel Live! to up the cool factor of research careers

To better understand how teens feel about scientific research and to make a career in health or medicine a more desirable occupation among adolescents, University of Chicago researchers and a group of high-school students from Chicago Public Schools took a page out of the Jimmy Kimmel Live! playbook.

Using the model of Kimmel’s “Lie Witness News” segment, the predominantly minority teens asked their peers what they think about research. The project was part of the NIH-funded TEACH STRIVES program, which aims to prepare and inspire Chicago public school students to pursue careers in health-related research. Samantha Ngooi, a project manager with TEACH STRIVES, and Vineet Arora, MD, a principal investigator with the program, discuss the students’ project in a recent KevinMD post:

What did these students find when they asked their peers about research? Well, not surprisingly [the] term “research” had a largely negative connotation — “lots of paperwork,” “lab rats.” However, our teens went one step further. They found studies that would be of interest to them — about things they cared about, such as teen health with cell phone use. When presented with research that linked cell phone use at night with depression, teens on the street were inspired to learn more. Unfortunately, this idea that research is esoteric and irrelevant is common amongst teenagers. Ask your average teenager what they aspire to be and more often than not a “researcher” will not be a contender. In fact, data suggests that few high-achieving high school students are considering a career in research, let alone healthcare research.

Why is this important? To make breakthroughs in science and medicine for the future, we need a healthy pipeline of diverse, talented teens to consider entering research careers in STEM fields…

Watch above to see the full video.

Previously: High schoolers share thoughts from Stanford’s Med School 101, At Med School 101, teens learn that it’s “so cool to be a doctor” and Stanford’s RISE program gives high-schoolers a scientific boost

NIH, Obesity, Public Health, Research

Capturing the metabolic signature of obesity

Capturing the metabolic signature of obesity

scale_weightWorldwide obesity rates have more than doubled since 1980, and today the majority of the global population live in areas where being overweight kills more people than being underweight, according to data from the World Health Organization. But new research that provides a comprehensive view of the metabolic signature that may correlate with obesity could help scientists develop more effective ways to manage and prevent obesity, and it offer insights into how variability in genes, environment, metabolism and lifestyle affect our health individually.

As reported today on the NIH Director’s Blog:

The new analysis uncovered changes to 29 molecular metabolites, or biomarkers, that correlated with obesity in 1,880 people from the United States. Most of those biomarkers—25 to be exact—also turned up in the urine of obese people from the other side of the Atlantic, offering confirmation that the findings represent a shared metabolic signature of obesity.

Several of the biomarkers are byproducts of what a person eats, which may reflect differences in the diets of obese and non-obese people. For example, urine from obese people was more likely to contain a metabolite that comes from eating red meat, while thinner folks were more likely to have a metabolite indicative of citrus fruit consumption.

However, not all of the biomarkers were directly related to food. Some appeared to stem from widespread changes in kidney function, skeletal muscle, and metabolism that may occur as a person packs on extra pounds. And, intriguingly, nine of the biomarkers significantly associated with obesity weren’t even produced by the human body, but rather by the trillions of microbes that live inside our guts. Those microbial partners play important roles in the breakdown of essential vitamins, amino acids, and protein. In fact, recent research findings suggest that a significant portion of obesity risk may be explained by the activity of gut microbes. This discovery adds to mounting evidence, spurred in recent years by the NIH-funded Human Microbiome Project, for the intricate and essential role of microbes—collectively known as the microbiome—in many aspects of our health.

The piece goes on to say that the findings also “raise the intriguing possibility that people might one day be able to visit their health-care providers, receive a blood or urine test, and leave with precise, individualized information regarding their risk” for obesity and other health issues.

Previously: Childx speaker Matthew Gillman discusses obesity prevention, Discussing how obesity and addiction share common neurochemistry, Stanford team awarded NIH Human Microbiome Project grant and Obesity is a disease – so now what?
Photo by Matthew

Big data, In the News, Technology

Vinod Khosla shares thoughts on disrupting health care with data science

Vinod Khosla shares thoughts on disrupting health care with data science

14252833785_63316bba75_zProminent Silicon Valley venture capitalist Vinod Khosla is a strong believer that data science will reinvent health care as we know it – and it’s position he has reiterated on a number of occasions, including at the 2014 Big Data in Biomedicine conference at Stanford. In a recently published Washington Post Q&A, Khosla expands on his comment that over the next ten years “data science and software will do more for medicine than all of the biological sciences together.”

On the topic of books and papers that have influenced his views, Khosla said:

A lot of what I’ve been thinking about started with articles by Dr. John Ioannidis at Stanford School of Medicine. What he found through decades of meta-research is that half of what’s in medical studies is just plain wrong… His research is focused on why they are wrong and why all sorts of biases are introduced in medical studies and medical practice.

He also explains one of the reasons he believes innovation in data science and software is outpacing the biological sciences:

The pace of innovation in software, across all industries, has consistently been much faster than anything else. Within traditional health-care innovation (which intersects with “biological sciences”) such as the pharma industry, there are a lot of good reasons those cycles of innovation are slow.

It takes 10 to 15 years to develop a drug and actually be in the marketplace, with an incredibly high failure rate. Safety is one big issue, so I don’t blame the process. I think it’s warranted and the [Food and Drug Administration] is appropriately cautious. But because digital health often has fewer safety effects, and iterations can happen in 2- to 3-year cycles, the rate of innovation goes up substantially.

Previously: Countdown to Big Data in Biomedicine: Leveraging big data technology to advance genomicsCountdown to Big Data in Biomedicine: Mining medical records to identify patterns in public health, Collecting buried biomedical treasure – using big data, Big data used to help identify patients at risk of deadly high-cholesterol disorder and Examining the potential of big data to transform health care
Photo of Khosla at the 2014 Big Data in Biomedicine conference by Saul Bromberger

Big data, Events, Videos

Countdown to Big Data in Biomedicine: Leveraging big data technology to advance genomics

Countdown to Big Data in Biomedicine: Leveraging big data technology to advance genomics

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During last year’s Big Data in Biomedicine conference, David Glazer, director of engineering at Google, described how the search giant is developing technological tools to help those working in life sciences to store, process, explore, and share genomic data.

In this 2014 Big Data in Biomedicine video, Glazer explains how he and colleagues fed a computer network 10 million random YouTube videos and asked the system to look for patterns. The computer determined that most frequently occurring sequence of 1s and 0s in the sample was that of a human face. Not surprisingly, the face of a cat was the second most-frequent pattern the computer found.

While these examples of machine pattern-recognition capabilities may not be earth-shattering to those who spent an inordinate amount of time watching YouTube videos, the findings demonstrate the potential of computers to rapidly identify significant patterns in large volumes of biomedical information. Imagine researchers performing the same experiment, but instead of YouTube videos they used genomic data. “We don’t have 10 million genomes available for this type of analysis, yet,” he said. “But as we move in that direction the tools are ready.”

Watch the full presentation to learn how Google is working to remove computing restraints to advance genomic research. And check out Glazer at the 2015 Big Data in Biomedicine conference, which will be held May 20-22 at the Li Ka Shing Center for Learning and Knowledge at Stanford.

Previously: Countdown to Big Data in Biomedicine: Mining medical records to identify patterns in public healthStanford bioengineer discusses mining social media and smartphone data for biomedical research, Using genetics to answer fundamental questions in biology, medicine and anthropologyExamining the potential of big data to transform health care and Registration for Big Data in Biomedicine conference now open

Big data, Neuroscience, Videos

Countdown to Big Data in Biomedicine: Mining medical records to identify patterns in public health

Countdown to Big Data in Biomedicine: Mining medical records to identify patterns in public health

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The routine information contained in medical records holds the potential to unlock important public-health discoveries. That was the message conveyed at the 2014 Big Data in Biomedicine conference at Stanford by Martin Landray, PhD, a professor of medicine and epidemiology at Oxford University and deputy director of the Big Data Institute within the Li Ka Shing Centre for Health Information and Discovery. In the above video from last year’s event, Landray explains how he and colleagues are working to better understand the determinants of common life-threatening and disabling diseases through the design, conduct and analysis of large-scale epidemiological studies and the widespread dissemination of both the findings and methods used to generate them.

This month, Landray will return to the Big Data in Biomedicine conference and moderate a discussion on neuroimaging. Among the panelists are Michael Greicius, MD, associate professor in the Department of Neurology and Neurological Sciences at Stanford, and Brian Wandell, PhD, founding director of Stanford’s Center for Cognitive and Neurobiological Imaging and deputy director of the Stanford Neurosciences Institute.

Registration for the conference, which will be held May 20-22 at Stanford, is currently open. More details about the program can be found on its website.

Previously: Stanford bioengineer discusses mining social media and smartphone data for biomedical research, Using genetics to answer fundamental questions in biology, medicine and anthropologyBig data used to help identify patients at risk of deadly high-cholesterol disorder, Examining the potential of big data to transform health care and Registration for Big Data in Biomedicine conference now open

Events, Global Health, Health Policy, Pediatrics, Stanford News, Videos

Rajiv Shah discusses efforts to end preventable child deaths worldwide at Childx

Rajiv Shah discusses efforts to end preventable child deaths worldwide at Childx

The inaugural Childx conference was held here this month, and video interviews featuring keynote speakers, panelists and moderators are now on the Stanford YouTube channel. To continue the discussion of driving innovation in maternal and child health, we’ll be featuring a selection of the videos this month on Scope.

More than six million children under the age of five die from preventable diseases each year. During this year’s Childx conference, Rajiv Shah, MD, the former administrator of USAID, told the crowd, “I do think it’s possible to end preventable child death.”

In the video above, he explains how innovations in drug development, diagnostics and vaccines are among the solutions that are effectively reducing child mortality rates around the world. But there is still more that can be done. Using global health data to see in real-time where children are dying because of a lack of vaccines and places children are suffering as a result of poor health care, Shah said, could assist in more efficiently directing resources to these areas and other pockets of need. Watch the full interview with Shah to hear more about why he thinks ending preventable child death is achievable in the next 20 years.

Previously: Childx speaker Matthew Gillman discusses obesity prevention, Pediatric health expert Alan Guttmacher outlines key issues facing children’s health today, “It’s not just science fiction anymore”: Childx speakers talk stem cell and gene therapy and Global health and precision medicine: Highlights from day two of Stanford’s Childx conference

Cancer, Events, Pediatrics, Stanford News, Videos

Pediatric nephrologist Mary Leonard discusses bone health in children with chronic diseases at Childx

Pediatric nephrologist Mary Leonard discusses bone health in children with chronic diseases at Childx

The inaugural Childx conference was held here last month video interviews featuring keynote speakers, panelists and moderators are now on the Stanford YouTube channel. To continue the discussion of driving innovation in maternal and child health, we’ll be featuring a selection of the videos this month on Scope.

Stanford pediatric nephrologist Mary Leonard, MD, initially began her career as a physician-scientist by investigating the bone complications of pediatric kidney disease. One of her earlier findings was that a number of the risk factors for poor bone development were also associated with many other childhood diseases, such as inflammatory bowel disease and cancer.

In the above video, Leonard explains how advances in treating pediatric kidney failure, cancer and other diseases is creating a growing population of survivors who are entering adulthood facing other health risks, including poor bone health, insulin resistance and cardiovascular disease. Watch the full interview to understand the magnitude of the problem and learn about efforts to develop prevention methods.

Previously: Childx speaker Matthew Gillman discusses obesity prevention, Pediatric health expert Alan Guttmacher outlines key issues facing children’s health today, “It’s not just science fiction anymore”: Childx speakers talk stem cell and gene therapy and Global health and precision medicine: Highlights from day two of Stanford’s Childx conference

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