Diabetes App Forecasts Blood Sugar Levels

First-of-its-kind, personalized glucose forecasting tool may make meal planning simpler for type 2 diabetes patients

Columbia University researchers have developed a personalized algorithm that predicts the impact of particular foods on an individual’s blood sugar levels. The algorithm has been integrated into an app, Glucoracle, that will allow individuals with type 2 diabetes to keep a tighter rein on their glucose levels—the key to preventing or controlling the major complications of a disease that affects 8 percent of Americans.

The findings were published online today in PLoS Computational Biology.

Medications are often prescribed to help patients with type 2 diabetes manage their blood sugar levels, but exercise and diet also play an important role.

“While we know the general effect of different types of food on blood glucose, the detailed effects can vary widely from one person to another and for the same person over time,” said lead author David Albers, PhD, associate research scientist in biomedical informatics at Columbia University Medical Center (CUMC). “Even with expert guidance, it’s difficult for people to understand the true impact of their dietary choices, particularly on a meal-to-meal basis. Our algorithm, integrated into an easy-to-use app, predicts the consequences of eating a specific meal before the food is eaten, allowing individuals to make better nutritional choices during mealtime.”

The algorithm uses a technique called data assimilation, in which a mathematical model of a person’s response to glucose is regularly updated with observational data—blood sugar measurements and nutritional information—to improve the model’s predictions, explained co-study leader George Hripcsak, MD, MS, the Vivian Beaumont Allen Professor and chair of biomedical informatics at Columbia. Data assimilation is used in a variety of applications, notably weather forecasting.

“The data assimilator is continually updated with the user’s food intake and blood glucose measurements, personalizing the model for that individual,” said co-study leader Lena Mamykina, PhD, assistant professor of biomedical informatics at Columbia, whose team designed and developed the Glucoracle app.

Glucoracle allows the user to upload fingerstick blood measurements and a photo of a particular meal to the app, along with a rough estimate of the nutritional content of the meal. This estimate provides the user with an immediate prediction of post-meal blood sugar levels. The estimate and forecast are then adjusted for accuracy. The app begins generating predictions after it has been used for a week, allowing the data assimilator to learn how the user responds to different foods.

The researchers initially tested the data assimilator on five individuals using the app, including three with type 2 diabetes and two without the disease. The app’s predictions were compared with actual post-meal blood glucose measurements and with the predictions of certified diabetes educators.

For the two nondiabetic individuals, the app’s predictions were comparable to the actual glucose measurements. For the three subjects with diabetes, the app’s forecasts were slightly less accurate, possibly due to fluctuations in the physiology of patients with diabetes or parameter error, but were still comparable to the predictions of the diabetes educators.

“There’s certainly room for improvement,” said Dr. Albers. “This evaluation was designed to prove that it’s possible, using routine self-monitoring data, to generate real-time glucose forecasts that people could use to make better nutritional choices. We have been able to make an aspect of diabetes self-management that has been nearly impossible for people with type 2 diabetes more manageable. Now our task is to make the data assimilation tool powering the app even better.”

Encouraged by these early results, the research team is preparing for a larger clinical trial. The researchers estimate that the app could be ready for widespread use within two years.

Link to app: http://glucoracle.com

Noemie Elhadad gets new grant from the Endometriosis Foundation of America

Noemie Elhadad

Congratulations to Noémie Elhadad for receiving a grant from the Endometriosis Foundation of America for her Citizen Endo project (citizenendo.org) to phenotype endometriosis through citizen science and data science.

In addition, the Health Natural Language Processing (hNLP) Center is a new initiative founded by Noémie Elhadad (Columbia University), Martha Palmer (Colorado Boulder), and Guergana Savova (Boston Children’s Hospital). The Center’s primary activities are to (1) provide a repository and a data curation, distribution and management point for health-related language resources; (2) support sponsored research programs and health-related language-based technology evaluations; (3) engage in collaborations with US and foreign researchers, institutions and data centers; and (4) host and participate in various workshops. More at http://center.healthnlp.org.

Marissa Burgermaster receives Sackler Institute Research Award

The Sackler Institute for Nutrition Science Names Winner of Research Award

Columbia University researcher awarded grant for research in behavioral nutrition

 Marissa_Burgermaster

NEW YORK, February 2, 2017The Sackler Institute for Nutrition Science at the New York Academy of Sciences today announced Marissa Burgermaster, PhD, a Postdoctoral Research Fellow of Biomedical Informatics and Behavioral Nutrition at Columbia University Medical Center, is the winner of its fifth annual research award for her proposal, Personalizing Prevention: Developing Methods for Precision Behavioral Nutrition.”

 

Dr. Burgermaster will receive $35,000 to pursue an innovative research project at the intersection of digital health and nutrition science. It is intended to provide support to researchers working on under-explored, and often under-funded, research topics.

 

The Sackler Institute’s 2016 Small Grant program for early career scientists focuses on research that explores the potential of emerging digital technologies in supporting evidence-based nutrition interventions for the benefit of public health. As Dr. Gilles Bergeron, Executive Director of the Sackler Institute of Nutrition Science explains: “This award gives an opportunity for innovative researchers at the start of their career to make an immediate impact. This year our research interest focused on promoting behavior change in nutrition, a difficult but fundamental issue in improving public health and preventing chronic disease.”

 

The winner’s research focuses on personalizing nutritional interventions by identifying psychosocial phenotypes. In her proposal Dr. Burgermaster hypothesized that different people respond to nutritional interventions in different ways. Using the example provided by precision medicine, in the treatment of disease, she sought to develop an individualized approach to improving nutrition. Known as psychosocial phenotyping this represents the first step towards precision behavioral nutrition and personally optimized nutrition interventions. “The Sackler Nutrition Award will support the development of methods for psychosocial phenotyping – characterizing the combination of barriers and resources that determine individuals’ nutrition behaviors,” said Dr. Burgermaster. “Then we will develop an app-based tool that efficiently identifies individuals’ psychosocial phenotypes. Psychosocial phenotyping represents a first step toward precision behavioral nutrition and personally optimized nutrition interventions.” This process represents the first step towards developing more precise behavioral nutrition and personally optimized nutrition intervention approach to remedy malnutrition.

 

Research Award Process
The Sackler Institute disseminated a call for proposals and received abstracts from early career scientists from around the world.  Five reviewers were invited to grade, rank and provide comments on the abstracts related to their areas of expertise. The reviewers are all highly respected experts in their specific research areas related to the submitted proposals.

They include:

Jeannette Beasley, PhD, Assistant Professor in the Department of Epidemiology and Population Health at the Albert Einstein College of Medicine

Rolf Klemm, MPH, DrPH, Vice President of Nutrition at Helen Keller International and Senior Associate at the Johns Hopkins Bloomberg School of Public Health

Tooraj Mirshahi, PhD, Associate Professor at the Weis Center for Research at the Geisinger Clinic

Karandeep Singh, MD, MMSc, Assistant Professor of Learning Health Sciences and of Medicine in the Division of Nephrology at the University of Michigan Medical School.

Claire Wang, MD, ScD, Associate Professor of Health Policy and Management at Columbia University Mailman School of Public Health

The selection committee gave the most consideration to proposals addressing an important gap in nutrition science and instances where results could trigger significant advances in behavioral interventions and support systems in the interface of digital health and nutrition science. These criteria emphasize the New York Academy of Sciences’ mission in promoting the resolution of society’s global challenges through science-based solutions.

 

For more information on the winners and judging panel, as well as The Sackler Institute’s efforts to advance research, please visit www.nyas.org/WhatWeDo/Nutrition and click on the “Research Fund” tab.

 

Calls for abstracts for The Sackler Institute’s sixth research award will begin in the fall of 2017.

2017/01/31 Special Seminar – Dr. David Shaw at Vagelos Education Center, Room 201 (Wu Auditorium)

Department of Biomedical Informatics Special Seminar

Date/Time: Tuesday, January 31, 2017 at 4:00 pm

Location: Vagelos Education Center, Room 201 (Wu Auditorium)
Speaker:
David Shaw
Dr. David Shaw, Chief Scientist, D.E. Shaw Research

Title:
Can Molecular Dynamics Simulations Cure What Ails Ya?

Abstract:
Molecular dynamics simulations have in recent years been playing an increasingly important role in advancing our understanding of biological processes at an atomic level of detail. Such simulations are often capable of providing new insights into the interactions of biological macromolecules with each other and with endogenous and pharmaceutical ligands, suggesting that they may ultimately make important contributions to the process of drug discovery. This talk will examine several ways in which MD simulations might seem to be of potential use in designing new drugs. Examples will be given of both current capabilities and current limitations, with a focus on their potential implications for the use of MD as a tool for drug discovery.

Biography:
David E. Shaw serves as Chief Scientist of D. E. Shaw Research and as a Senior Research Fellow at the Center for Computational Biology and Bioinformatics at Columbia University. He received his Ph.D. from Stanford University in 1980, served on the faculty of the Computer Science Department at Columbia until 1986, and founded the D. E. Shaw group in 1988. Since 2001, Dr. Shaw has devoted his time to hands-on research in the field of computational biochemistry.

Dr. Shaw was appointed to the President’s Council of Advisors on Science and Technology by President Clinton in 1994, and again by President Obama in 2009. He is a two-time co-recipient of the ACM Gordon Bell Prize, and was elected to the American Academy of Arts and Sciences in 2007, to the National Academy of Engineering in 2012, and to the National Academy of Sciences in 2014.

AMIA 2016 Annual Symposium in Chicago, IL

2016AMIA_Chicago

We once again had a great symposium this year. Here are some highlights and awards.
The Columbia DBMI reception was very fun and great to catch up with our huge network of successful alumni, who are running much of informatics in the US. Scroll down to see photos from the event.

 

Running the symposium:

Noemie Elhadad – Symposium Vice Chair
Scientific Program Committee members – Jessica Ancker, David Kaufman, Casey Overby, Adler Perotte, Colin Walsh, Chunhua Weng, Adam Wilcox, Lauren Wilcox

 

Symposium awards:

Nick Tatonetti – AMIA New Investigator Award
William Brown – 2nd place Student Paper Competition
Shaodian Zhang – AMIA Best Student Paper for Consumer & Pervasive Health Informatics, and Student Paper Finalist in the regular competition
Genevieve Melton-Meaux, Liz Chen – advisors for the 1st place Student Paper Competition winner
Trevor Cohen, Sunny Shang – advisors for Student Paper Competition finalists
Jessica Ancker – Homer R. Warner Award
Sarah Collins – Harriet H. Werley Award
Distinguished Paper Award – Rimma Pivovarov, Yael Coppleson, Sharon Lipsky Gorman, David Vawdrey, Noemie Elhadad (Can Patient Record Summarization Support Quality Metric Abstraction?)
Distinguished Paper Award – Qing Zeng-Treitler (Identification and Use of Frailty Indicators from Text to Examine Associations with Clinical Outcomes Among Patients with Heart Failure)
Maya Ramachandran – Columbia undergrad invited to present “Undergraduate informatics at Columbia” (Ignite) and to join a regular panel

 

ACMI fellowship inductees:

Noemie Elhadad
Liz Chen
Jessica Ancker
Hongfang Liu

 

A Oscar Beitia Katie Zhu Adler Perotte

MA alumnus A. Oscar Beitia, PhD Alumna Xinxin “Katie” Zhu, and MA and postdoctoral research fellow alumnus, P&S alumnus and Columbia University DBMI faculty Dr. Adler Perotte

Albert Lai Silis Jiang Jamie Hirsch William Brown III

PhD alumnus and Washington University-St Louis faculty Albert Lai, current PhD student representative Silis Jiang, MA postdoctoral fellow alumnus and Hofstra Northwell School of Medicine faculty Jamie Hirsch, and PhD alumnus and UCSF faculty William Brown III

Amelia Averitt Marina Fernanda Ben

PhD student Amelia Averitt, Marina Bonanno, PhD student Fernanda Polubriaginof, and MA student and postdoctoral research fellow Dr Benjamin Slovis

 

Amelia Averitt Shruti Jung Hoon Anando Barnett

MA & postdoctoral research fellow alumna and Columbia University DBMI faculty Lena Mamykina (background), PhD student Amelia Averitt, Postdoctoral Research Scientist Shreya Chakrabarti, MA student and NLM postdoctoral research fellow Dr Jung Hoon Son, Postdoctoral Research Scientist Anando Sen, Postdoctoral Research Scientist Po-Hsiang “Barnett” Chiu

 

Congrats Adler Perotte

Congratulations to MA postdoctoral research fellow alumnus and Columbia University DBMI faculty Dr Adler Perotte (center) on his recently awarded Department of Defense grant!

Congrats Carol Friedman

Congratulations to Columbia University DBMI faculty Prof Carol Friedman on her induction into the National Academy of Medicine!

 

Daniel Fort Drashko Nakikj William Ogallo

PhD alumnus Daniel Fort, PhD candidate Drashko Nakikj, PhD student William Ogallo

David Albers Noemie Elhadad Rimma Pivovarov Dan Fort Nicole Weiskopf Adam Samantha Kleinberg

Prof David Albers, Prof Noemie Elhadad, PhD alumna Rimma Pivovarov, PhD alumnus Daniel Fort, PhD alumna and OHSU faculty Nicole Weiskopf, PhD alumnus Adam Wilcox, Postdoctoral Research Scientist alumna and Stevens Institute of Technology faculty Samantha Kleinberg

Chips

Victuals

Dessert

Dessert

Dessert2
Dessert

Elliot Mitchell Lisa Grossman

PhD student Elliot Mitchell and MD-PhD student Lisa Grossman

Fernanda Polubriaginof Amelia Averitt Ben Slovis

PhD student Fernanda Polubriaginof, PhD student Amelia Averitt, and MA  Postdoctoral Research Fellow Dr Benjamin Slovis

Fernanda Polubriaginof Ben Slovis

PhD student Fernanda Polubriaginof and MA Postdoctoral Research Fellow Benjamin Slovis

Haoquan Zhao Sylvia Cho

PhD students Haoquan Zhao and Silvia Cho

Herbert Chase Colin Walsh

MA postdoctoral research fellow alumnus and current faculty member Dr Herbert Chase and MA postdoctoral research fellow alumnus and Vanderbilt University faculty Dr Colin Walsh

 

Hua Xu Trevor Cohen

PhD alumni and University of Texas Health Science Center at Houston faculty Hua Xu and Trevor Cohen

Jessica Ancker Neil Sarkar Michael Cantor Jan Horsky

PhD alumna and Weill Cornell Medical College faculty Jessica Ancker, PhD alumnus and Brown University faculty Neil Sarkar, MA postdoctoral research fellow alumnus and NYU faculty Dr Michael Cantor, PhD alumnus Jan Horsky

Jung Wei Fan

PhD alumnus and University of Arizona faculty Jung-Wei Fan (right)

Justin Starren

PhD alumnus and Northwestern University faculty Justin Starren (left)

Fish

Grouper tacos

Pad Thai

Pasta

Pasta

Pad thai

Matt Levine David Albers Rimma Pivovarov Marina Bonanno

Matthew Levine, Columbia University DBMI faculty David Albers, PhD alumna Rimma Pivovarov, Marina Bonanno

Matt Levine David Albers Rimma Pivovarov

Matthew Levine, Columbia University DBMI faculty David Albers, PhD alumna Rimma Pivovarov

Matt Levine Lena Mamykina Marissa Burgermaster Jessica Ancker

Matthew Levine, MA Postdoctoral Research Fellow alumna and Columbia University DBMI faculty Lena Mamykina, PhD alumna and Weill Cornell Medical College faculty Jessica Ancker

Matt Levine Lena Mamykina Marissa Burgermaster

Matthew Levine, MA Postdoctoral Research Fellow alumna and current faculty member Lena Mamykina, MA Postdoctoral Research Fellow Marissa Burgermaster

Michael Cantor

MA postdoctoral research fellow alumnus and NYU faculty Dr Michael Cantor (left)

Michelle Chau William Ogallo Victor Rodriguez Marissa Burgermaster Drashko Nakikj Mollie McKillop

PhD students Michelle Chau and William Ogallo, MD-PhD student Victor Rodriguez, MA Postdoctoral Research Fellow Marissa Burgermaster, PhD Candidate Drashko Nakikj, PhD student Mollie McKillop

Neil Sarkar Casey Overby William Ogallo Mary Boland Jessica Ancker Albert Lai

PhD alumnus and Brown University faculty Neil Sarkar, PhD student William Ogallo, and Postdoctoral Research Fellow alumna and Johns Hopkins University faculty Casey Overby

Sarah Collins Victoria Tiase

Postdoctoral Research Fellow alumna and Harvard Medical School faculty Sarah Collins (center) and Victoria Tiase (right)

Silis Jiang Albert Lai

PhD candidate Silis Jiang and PhD alumnus and Washington University-St Louis faculty Albert Lai

Sue Bakken Dan Fort Nicole Weiskopf

Columbia University DBMI and Nursing faculty Prof Suzanne Bakken (it’s her birthday!), PhD alumnus Daniel Fort, and PhD alumna and OHSU faculty Nicole Weiskopf

Umberto Jim Cimino

Umberto Tachinardi and Columbia University DBMI faculty James Cimino

Victor Rodriguez Mollie McKillop Michelle Chau

MD-PhD student Victor Rodriguez, PhD students Mollie McKillop and Michelle Chau

Yalini Senathirajah Fernanda Polubriaginof
PhD alumna and SUNY downstate faculty Yalini Senathirajah (left), PhD student Fernanda Polubriaginof (center)

Soumitra Sengupta John Chelico

Columbia University DBMI faculty Soumitra Sengupta and MA postdoctoral research fellow alumnus and NYU faculty Dr John Chelico

Lena Mamykina David Kaufman

MA Postdoctoral Research Fellow alumna and Columbia University DBMI faculty Lena Mamykina and former Columbia DBMI faculty David Kaufman (now at ASU)

Gil Kuperman

Columbia University DBMI faculty Dr Gil Kuperman (left)

Congratulations to Noemie Elhadad ACMI Induction

Congratulations to Columbia University DBMI faculty Prof Noemie Elhadad for her ACMI induction!

Congratulations Liz Chen ACMI Induction

Congratulations to PhD alumna and Brown University faculty Liz Chen for her ACMI induction!

George Hripcsak Remarks AMIA 2016 Reception

Columbia University DBMI Chair Prof George Hripcsak gave updates on DBMI achievements

Eneida Mendonca Tara Borlawsky Philip Payne

Columbia University DBMI faculty Noemie Elhadad, PhD alumna and Brown University faculty Liz Chen, PhD alumna and OHSU faculty Nicole Weiskopf, Umberto Tachinardi, PhD alumna and University of Wisconsin faculty Dr Eneida Mendonca, MA and postdoctoral fellow and current Columbia DBMI faculty Adler Perotte, MA alumna Tara Borlawsky and PhD alumnus and Washington University-St Louis faculty Philip Payne, PhD candidate Silis Jiang, PhD student Fernanda Polubriaginof, MA and postdoctoral research fellow alumna and Columbia University DBMI faculty Lena Mamykina, Columbia University DBMI faculty David Albers, Matthew Levine, postdoctoral research scientist alumna and Stevens Institute of Technology faculty Samantha Kleinberg

Umberto Tachinardi Carol Friedman

Umberto Tachinardi and Columbia University DBMI faculty Prof Carol Friedman

 

Jonathan Chen Adler Perotte George Hripcsak

MA postdoctoral research fellow alumnus and Columbia University DBMI faculty Adler Perotte (center), Prof George Hripcsak, Columbia University DBMI Chair (right)

 

Krystl Haerian Hojjat Salmasian Adam Wilcox Li Zhou

MA alumna and University of Maryland-Baltimore County faculty Dr Krystl Haerian, PhD alumnus and Columbia University DBMI faculty Dr Hojjat Salmasian, PhD alumnus Adam Wilcox, PhD alumna and Harvard Medical School faculty Dr Li Zhou

Maurine Tong Gil Kuperman

Maurine Tong and Columbia University DBMI faculty Dr Gil Kuperman

 

William Brown III Adriana Colin Walsh Jamie Hirsch

PhD alumnus and UCSF faculty William Brown III, Columbia University Nursing faculty Adriana Arcia, MA and postdoctoral research fellow alumnus and Vanderbilt University faculty Dr Colin Walsh, MA and postdoctoral research fellow alumnus and Hofstra Northwell School of Medicine faculty Jamie Hirsch