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Biomed Bites, Cancer, Genetics, Microbiology, Research, Videos

Packed and ready to go: The link between DNA folding and disease

Packed and ready to go: The link between DNA folding and disease

Welcome to Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers.

In cells, DNA doesn’t make a lovely, languid helix as popularly depicted. It’s scrunched up, bound with proteins that smoosh one meter of DNA into just one micrometer, a millionth of its size. DNA wound around proteins form a particle called a nucleosome.

Yahli Lorch, PhD, associate professor of structural biology, has studied nucleosomes since they were first discovered more than 20 years ago, as she mentions in the video above:

When I began working on the nucleosome, it was a largely neglected area since most people considered it just a packaging and nothing beyond that.

Since I discovered that it has a role and a very important role in the regulation of gene expression, the field has grown many fold and it’s one of the largest areas in biology now.

Many diseases have been linked to the packaging of DNA, including neurodegenerative diseases, autoimmune diseases and several types of cancer such as some pancreatic cancers. Enhancing the understanding of the basic biology of DNA folding is leading to new and improved treatments for these conditions, Lorch says.

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: DNA origami: How our genomes fold, DNA architecture fascinates Stanford researcher — and dictates biological outcomes and More than shiny: Stanford’s new sculpture by Alyson Shotz

Big data, Genetics, Research, Technology, Videos

“An extremely interesting time to be a geneticist”: Using big data to identify rare diseases

"An extremely interesting time to be a geneticist": Using big data to identify rare diseases

With cheaper, faster genetic sequencing, researchers are able to pinpoint rare gene variants that may be contributing to disease.

But to find “the actual, causal rare variant contributing to the trait is like looking for a needle in a haystack,” says Stephen Montgomery, PhD, in the video above.

Montgomery and his team have plans to boost the efficacy of using genome sequencing to identify rare diseases by incorporating all of the information from genes that are actually turned on — using RNA in addition to its parent DNA to make that needle really stand out.

Eventually, Montgomery hopes to mix in even more information including details about individual lifestyles, environmental exposures and family histories to glean further insights into the origins of rare disease. His team received a 2014 Big Data for Human Health Seed Grant to support the work.

“We’re going to be able to answer very quickly questions about how the genome is influencing our lives and then we’re also going to be able to treat (these conditions),” Montgomery says. “This is an extremely interesting time to be a geneticist and these large data sets are just empowering a large number of discoveries.”

This effort is part of Stanford Medicine’s Biomedical Data Science Initiative (BDSI), which strives to make powerful transformations in human health and scientific discovery by fostering innovative collaborations among medical researchers, computer scientists, statisticians and physicians. Work being done in this area is the focus of Stanford’s Big Data in Biomedicine conference, which kicks off tomorrow morning.

Previously: Collecting buried biomedical treasure – using big data, All data – big and small – informs large-scale neuroscience project, Registration for Big Data in Biomedicine conference now open, Parent details practical ways to get care and support for your child’s rare disease, New search engine designed to help physicians and the public in diagnosing rare diseases and Big data used to help identify patients at risk of deadly high-cholesterol disorder

Neuroscience, Sleep, Stanford News, Videos

Exploring the history and study of sleep with Stanford’s William Dement

Exploring the history and study of sleep with Stanford's William Dement

The Good Stuff, a playlist-based online show, kicked off a week-long series about sleep with an interview with well-known sleep researcher William Dement, MD, PhD, who many refer to as the “father of sleep medicine.”

It’s surprising how new the field of sleep research is. As host Matt says about the discovery of rapid eye movement during sleep in the 1950s, “We developed the atom bomb before we noticed people’s eyes were moving while they slept?” Dement was the first to find that we sleep during REM sleep as a medical student at the University of Chicago. He later went on to describe the five stages of sleep as well as to study sleep disorders and the effects of sleep deprivation.

Dement is amusing and charming in the interview, and I feel like I got a glimpse into why Dement’s Sleep and Dreams class at Stanford is so popular.

Part two of the series – which addresses the question “Why do we sleep?” and features Dement and Clete Kushida, MD, PhD, medical director of the Stanford Sleep Medicine Center – was posted today, and parts three and four will be posted later this week.

Previously: “Father of Sleep Medicine” talks with CNN about what happens when we don’t sleep well, Stanford doc gives teens a crash course on the dangers of sleep deprivation, William Dement: Stanford Medicine’s “Sandman”, Stanford docs discuss all things sleepThanks, Jerry: Honoring pioneering Stanford sleep research and An afternoon with bedheads and Deadheads

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

Biomed Bites, Clinical Trials, Health Policy, Videos

The mathematics of clinical trials: A career

The mathematics of clinical trials: A career

Welcome to Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers.

Math was Philip Lavori‘s first intellectual love. After earning his PhD in mathematics at Cornell University, Lavori spent his time solving tricky calculations. But the disconnect between the world of pure mathematics, and the messy outside world where people were living and dying started to bug him.

“It soon became obvious to me that I would have enormous interest in doing research that would have direct benefits to human beings,” Lavori says in the video above.

He began offering his skills as a consultant to physicians, where he discovered a new intellectual love.

“I’ve found the problems that arose in the design of clinical trials were problems that I could attack with my mathematical skills…. That quickly led to an entire career.”

Now Lavori is chair of the Department of Health Research and Policy, and he co-directs the Stanford Center for Clinical and Translational Research and Education (Spectrum).

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: Survey confirms that small number of U.S. adults, children participate in research studies, A faster, better, cheaper clinical trial (electronic record system not included) and Re-analyses of clinical trial results rare, but necessary, say Stanford researchers

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

Biomed Bites, Genetics, Medicine and Society, Microbiology, Research, Science, Videos

From yeast to coral reefs: Research that extends beyond the lab

From yeast to coral reefs: Research that extends beyond the lab

Welcome to Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers. 

John Pringle, PhD, focused most of his career on yeast. Easy to culture in the lab, yeast offer scientists a malleable model to learn about all types of cells, including human cells.

As a professor of genetics, he still does a bit of that. But now, his heart is focused on saving the world’s coral reefs – no small task given that these living ecosystems are vulnerable to temperature changes, carbon dioxide concentrations and overfishing.

Pringle’s research concentrates on a small sea anemone known as Aiptasia pallida, as he explains in the video above:

We picked an experimental system that has huge advantages over the corals themselves and we try to learn basic things about their molecular and cellular biology that will help us with the more complex and less experimentally tractable system of the reefs.

Just as with his yeast work, the lessons learned from the anemones are directly applicable to human well-being. “Corals are important to hundreds of millions of people around the world for livelihood and for the beauty they bring and the food they provide,” he says. “We have the hopes that by doing basic research, we’ll contribute to an understanding of how coral reefs might be preserved.”

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: Bubble, bubble, toil and trouble — yeast dynasties give up their secrets, Yeast advance understanding of Parkinson’s disease, says Stanford study and My funny Valentine — or, how a tiny fish will change the world of aging research

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

Big data, Cancer, Medicine and Society, Research, Stanford News, Videos

Collecting buried biomedical treasure – using big data

Collecting buried biomedical treasure - using big data

The answers to some of today’s most pressing biomedical questions may be hiding in medical centers – and physicians’ offices – across the country. Buried in medical files are the experiences of thousands of patients, far more than have participated in any clinical trial. These files chronicle their conditions, treatments and outcomes – valuable information that could improve care for millions of current and future patients.

But, and a big but here, accessing the data securely and transforming it into a format available for inquiry can be a logistical nightmare. And that’s where Stanford’s Daniel Rubin, MD, and his team, step in.

“We’re developing methods that will permit us to leverage national data without requiring centers to actually send the data to a central site, which overcomes a big barrier to these kinds of efforts because of privacy and other regulatory concerns,” Rubin said in the video above.

His group is concentrating on cancer and received a 2014 Big Data for Human Health Seed Grant to support the work.

“We’ve developed software that we’ve deployed at these local sites… They run it on their local data and we aggregate the results,” Rubin said. He said the primary challenge is creating a system that is open and invites broad participation, but also keeps the data secure. His project exemplifies the uses of big data. From the video:

You couldn’t do this without big data because there are so many variables that affect a patients’ disease… and you need big data to find enoguht patietns that match those charactoristics to be able to look for similar cohorts to guide decision making.

This effort is part of Stanford Medicine’s Biomedical Data Science Initiative (BDSI), which strives to make powerful transformations in human health and scientific discovery by fostering innovative collaborations among medical researchers, computer scientists, statisticians and physicians. For more on important work being done in this area, mark your calendars for Stanford’s Big Data in Biomedicine conference on May 20-22. More information is available here.

Previously: All data – big and small – informs large-scale neuroscience projectExamining the potential of big data to transform health care, Registration for Big Data in Biomedicine conference now open and Stanford researchers develop web-based tool to streamline interpretation of medical images,

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