Cultivating Networks
Annual Report 2012
Leading the way
Sharing our knowledge
Connecting globally

Annual Report 2012 From Our President


Inventing the Future

Institute for Systems Biology was founded in 2000 to invent the future as the first institute to pioneer systems science and its applications to biology and disease. ISB has made remarkable progress in its first 13 years.

We have pioneered the emergence of systems biology as a field, developing new strategies and applying them to fundamental problems in biology and medicine.

We have developed powerful new technologies (e.g. proteomics and genomics) and have pioneered a vast array of analytical tools for the life sciences.

We have applied systems thinking to the study of disease and catalyzed the development of a systems medicine that has already reached a tipping point and is changing the practice of healthcare, improving it, beginning to reduce its costs, and promoting innovation and the creation of new companies. The convergence of three major thrusts in healthcare—systems medicine, big data analysis and patient-activated social networks—has led to the emergence of a medicine that is predictive, preventive, personalized and participatory (P4 medicine) with the two major objectives of quantifying wellness and demystifying disease. P4 medicine will thus catalyze an ability to predict and prevent disease before it happens, empowering individuals with self-knowledge and catalyzing new dimensions of wellness. My own belief is that in the next 10 to 15 years, the wellness industry will grow to far exceed the healthcare industry.

The metrics for our success are many and are exemplified by two recent reports: The National Academy of Science published a report in 2009 on the “New Biology” that described systems biology perfectly and asserted it was the future for solving the fundamental problems of the life sciences—biology, healthcare, environment, agriculture, etc. The Spanish SCImago Institute has ranked almost 3,300 research institutions for the impact of their papers in all areas of science and ISB ranked fourth in the world in excellence of its papers. ISB’s papers cover biology, medicine, technology and computation/mathematics, reflecting the cross-disciplinary culture that lies at the heart of our success.

ISB invented the field of systems biology over the past decade. But how can we foster a new vision that will let us invent a transformational future? Although we are still debating this question, I want to discuss with you one proposal that fascinates me: pioneering the field of wellness.

I would like to propose that ISB catalyze a longitudinal study of 100,000 “well” individuals over 25 years, creating for each a virtual cloud of billions of data points that include (1) their genome sequences to identify actionable gene variants for which suggestions can be made for improving health; (2) longitudinal blood measurements two to three times a year for analysis with traditional clinical chemistries and assays that employ systems strategies (see below); and (3) high-frequency digital measurements coming from “quantified self” assessments that track exercise, sleep, stress, weight and nutrition.

The systems-driven assays that would enable us to track transitions from wellness to disease would include: (1) analyses of 10 or more organ-specific blood fingerprints that will allow us to track wellness in major organs including the brain, heart, liver, lung, etc.; (2) omics-characterizations of white blood cells to track inflammation and immune responses in each individual; (3) protein chips with 10,000 human proteins to identify autoantibodies (characteristic of autoimmune diseases such as rheumatoid arthritis and perhaps other diseases such as cancers and neurodegenerative diseases); and (4) track the human gut microbiome through stool analyses (which correlates in many different ways with wellness and susceptibility to diseases such as diabetes and heart disease).

These 100,000 virtual data clouds for individuals will provide invaluable data for optimizing wellness for each individual and they will permit us to identify effective metrics for assessing wellness of each individual, as well as markedly cut his or her costs for healthcare. In addition, we will see among these 100,000 patients transitions from wellness into major diseases. This will provide an early molecular warning for each of these diseases that will permit many to be managed more effectively. In the long run, we will accumulate massive amounts of information from these virtual data clouds that can be mined for the predictive medicine of the future. This effort would require the recruitment of patients from medical centers and community hospitals in the Seattle area, as well as research and academic centers to help develop the strategies, technologies and analytical tools necessary to generate and analyze these data. In the longer run, this database could provide information for spinning off diverse wellness and healthcare companies. This is a vision that could transform two massive industries and, indeed, make Seattle the Silicon Valley of the wellness market.

ISB is in a unique position to initiate such an effort, because it has been pioneering P4 medicine, with a focus on wellness; it has developed a variety of technologies that will contribute to diagnostic assays that will reveal new dimensions of patient data space; and it has strong computation and mathematical skills for acquiring, storing, mining, integrating and creating predictive and actionable models from each of the 100,000 virtual data clouds. It would be an exciting challenge for the scientists in all our labs to invent this future, utilizing powerful systems biology and systems medicine approaches to explore new dimensions of patient data space and develop new analytical tools to integrate and model the data.

In addition to the technical challenges, there would be striking societal challenges that could be the domain of the P4 Medicine Institute, a nonprofit institute dedicated to the fourth P—participatory—in P4 medicine. A key challenge is to develop a value proposition for healthcare consumers that would (1) engage them in using the actionable personalized health information which systems medicine can provide and (2) incentivize them to collect data that can be made available to mine for the predictive medicine of the future that will revolutionize healthcare for our children and grandchildren. Major questions would include how we can capture data in a way that is seamlessly incorporated in people’s daily lives; how to properly de-identify the data and protect people from abuses—which will involve additional legislation and regulatory action.

There are also striking challenges as to how we will educate patients, physicians, the healthcare community, payers and providers, and federal and state policy makers about the nature of this medicine. The solution will undoubtedly require the use of large-scale information technology. We will have to create a new profession of coaches who can bring insights gained from mining individual data clouds to individual patients. Finally, there is the challenge of funding this effort and identifying the types of organizations that should participate in this incredibly ambitious—and transformative—future.

There is no doubt in my mind this vision would further catalyze the profound paradigm change in healthcare that P4 medicine entails. This is a most ambitious new vision that would enable ISB to continue to invent the future through systems thinking around the strategies, technologies and analytics tools of P4 medicine and wellness.

Dr. Lee Hood, President and Co-Founder of ISB

Cultivating NetworksLeading, Transferring, Connecting

Institute for Systems Biology’s mission is to revolutionize science and healthcare by using the power of systems biology to interrogate the complex molecular networks that govern wellness and disease. We are cultivating a global understanding and practice of the systems approach, which we pioneered and for which we serve as its most committed advocate. Here, we highlight nine headlines from 2012. Click on any of the images below to learn more.

LeadershipBoard of Directors, Senior Leadership, Faculty, Principal and Senior Research Scientists & Engineers

Board of Directors

Louis G. Lange,

Chairman of the board

Senior Advisor
Mark Ashida
Bill Bowes
U.S. Venture Partners
Thomas J. Cable
Board Member
Omeros Corporation
Stephen M. Graham
Managing Partner, Seattle Office
Fenwick & West LLP
Chuck Hirsch
Founding Partner
Leroy Hood, MD, PHD
President and Co-Founder
Institute for Systems Biology
Daniel T. Ling
Corporate Vice President
Microsoft Research
Robert T. Nelsen
Co-Founder and Managing Director
ARCH Venture Partners
Roger Perlmutter, MD, PhD
Executive Vice President and President
Merck Research Laboratories
J. Leighton Read, MD
General Partner
Alloy Ventures
David A. Sabey
Sabey Corporation and Sabey Construction

Senior Leadership

President and Co-Founder
Senior Vice President and Executive Director for Integrative Biology
Director for Integrative Biology
Senior Vice President for Finance and Operations
Vice President for Development
Senior Vice President for Strategic Partnerships and Chief Business Officer


John Aitchison, PhD
Nitin Baliga, PhD
Aimée Dudley, PhD
David Galas, PhD
Leroy Hood, MD, PhD
Sui Huang, MD, PhD
Robert Moritz, PhD
Joseph Nadeau, PhD
Adrian Ozinsky, PhD
Nathan Price, PhD
Jeff Ranish, PhD
Ilya Shmulevich, PhD

Principal Scientist

Kai Wang, PhD

Senior Research Scientists

John Boyle, PhD
Nicholas Chia, PhD
Eric Deutsch, PhD
Richard Gelinas, PhD
Gustavo Glusman, PhD
Nathan Goodman, PhD
Andrew Keller, PhD
Inyoul Lee, PhD
Monica Orellana, PhD
Shizhen Qin, PhD
David Reiss, PhD
Jared Roach, MD, PhD
Lee Rowen, PhD
Arian Smit, PhD
Jennifer Smith, PhD
Sabrina Spiezio, PhD
James Spotts, PhD

Senior Research Scientists (continued)

Sergey Stolyar, PhD
Vesteinn Thorsson, PhD
Qiang Tian, PhD
Kathie Walters, PhD
Julian Watts, PhD
Robert West, PhD
Wei Yan, PhD

Senior Research Engineer

Chris Lausted, MS

Senior Software Engineers

Mi-Youn Brusniak, PhD
Sarah Killcoyne
Bill Longabaugh, MS
Hector Rovira
Paul Shannon

Senior IT Analyst

Kerry Deutsch, PhD

FinancialsFor the Year Ending December 31, 2012

While the full impact of sequestration has yet to be seen, there’s no doubt that all nonprofit organizations are experiencing the challenges of facing reduced funding. ISB was able to increase total revenue in 2012, which is bright news in this difficult financial time. We have been diligent about cultivating our funding and contributor networks to ensure ISB can continue to achieve breakthroughs in deciphering some of the most complex diseases that affect our lives. We also have done the hard work of further streamlining our research operating expenses to help create a sustainable financial future.

5-Year Growth Comparison
Research Operating Expenses vs. Total Revenue

Statement of Activities
Dollars in Thousands

Grants & Contract Revenue
Investment & Other Income
Total Revenues
Research & Other Direct Costs
Management & General
Fundraising & Other
Total Expenditures
Increase in Net Assets

Balance Sheet
Dollars in Thousands

Cash & Investments
Other Assets
Property & Equipment (Net)
Total Assets
Accounts Payable & Accrued Expenses
Deferred Revenues
Notes Payable
Total Liabilities
Net Assets
Unrestricted Net Assets
Temporarily Restricted Net Assets
Permanently Restricted Net Assets
Total Net Assets

ContributorsSpecial thanks to the following believers in the promise of systems biology

Recognition Listing

Arthur Vining Davis Foundations
The Boeing Company
William K. Bowes, Jr. Foundation
Lee Hood and Valerie Logan
Roger M. Perlmutter
$25,000 - $99,999
Complete Genomics, Inc.
Franklin and Catherine Johnson
Nesholm Family Foundation
Sabey Corporation
   Dave and Sandra Sabey
$10,000 - $24,999
Amgen Foundation
Integrated Diagnostics, Inc.
Iverson Genetic Diagnostics, Inc.
The Seattle Foundation
Vulcan Real Estate
The Adam J. Weissman Foundation
$2,500 - $9,999
Amgen, Inc.
Mark Ashida and Lisbet Nilson
Sissy and Tom Bouchard
Carole Ellison
Fenwick & West LLP
Michael R. Flory
Douglas Howe and Robin DuBrin
Intellectual Ventures, Inc.
Louis G. Lange
LI-COR, Inc.
Life Technologies Corporation
Dan Ling and Lee Obrzut
J. Leighton and Carol Read
Ronald C. Seubert
Georges C. St. Laurent, Jr.
Cynthia Stroum
Thermo Fisher Scientific, Inc.
Touchstone Corporation
Elaine and Larry Woo
$1,000 - $2,499
AB Sciex LLC
Agilent Technologies, Inc.
John and Leslie Aitchison
Nitin Baliga and Janet Ceballos
Bristol-Myers Squibb Company
Thomas J. Cable
Jim and Sherry Ladd
Rob Lipshutz and Nancy Wong
Nick Newcombe
Gil Omenn and Martha Darling
Patti Payne
Simon Ramo
Dana and Ben Riley Black
Washington STEM
$500 - $999
Kasra R. Badiozamani
Bruker Daltonics, Inc.
Victoria Buker
Sean and Lauren Clisham
Evergreen Associates, Ltd.
Myron and Sue Hood
Chris Moe
Victor Ng
Nathan D. Price
Proteome Software, Inc.
The Satya & Rao Remala Foundation
The Greer/Solien Fund
Shawn and Jeff Swift
Aron and Sara Thompson
University of Victoria
$250 - $499
Katherine Barnett
Ron and Gail Behar
Suzanne M. Burke
Roy and Mary Currence
Renee Duprel
Lynn and Michael Garvey
Genalyte, Inc.
Kevin Higman
Bob and Rhoda Jensen
Paul and Lucy Lange
Sid and Heather Logan
Mike and Lisa Losh
Lisa Mayfield
Lyle and Nancy Middendorf
Kirsten Nesholm
Amy and Matt Rudolf
Ned and Allison Sander
Carl and Carole Scandella
Haeryung Shin and Andrew von Nordenflycht
William A. Sperling
Erich C. Strauss
Thomas Weingarten and Wendy Thon
Griffith Way
$150 - $249
Trudy Adkins
Susan Adler
Daniel V. Byrne
Jan Chalupny
JoAnn Chrisman
Linette Demers
Jennifer G. Dougherty
Sandra L. Everlove
Richard Gelinas
Eran Hood and Sonia Nagorski
Marqui Hood
Dana Hurley
Kathlyn Huson
Inyoul Lee
Sarah Li
B Lippit
Claudia and Adam Ludwig
Bill and Anita Neil
Marel Norwood
Gary Owen
Shizhen Qin
Salal Credit Union
Natasha Simkovich and Tim Hunt
Social 27
Sergey Stolyar
Peter and Shannon Van Oppen
Janis Wignall
Up to $149
Eric and Audra Adelberger
Ryan Austin
Martha W. Bond
Lisa and Peter Boveng
Mary Brunkow
Hsiao-Ching Chou
Jeanne Ting Chowning
Michele Costa
Ana Crossman
Kori Dunaway
Mary and Martin Ensley
Jo Fiorito
Elizabeth Fulwiler
The Gill Family
Gregory Hart
Mary Alice Heuschel
Charles L. Hirsch
Ron and Mary Hjorth
Bruce and Betty Ann Jansson
Kim Klinke
Kerstin Kramer
Up to $149 (cont'd)
Mitchell and Hilde Kronenberg
Gillia A. Lambert
Mike Lemonde
Laura Lockard
Caroline Maillard
Don McConkey
Fidelma McGinn
Bruce and Joanne Montgomery
Lucy Olson
Stephen Parris
Kim Roeber
Sherri Rogalski
Lee Rowen
Tracy L. Schmitz
Bingyun Sun
Qiang Tian
Top Pot Doughnuts
Cheryl Tuller
Christine Tuller
Victoria VanBruinisse
Doral and David Vial
Tayloe Washburn
Kevin Washington

To demonstrate your belief in the promise of systems biology in 2013:

Publications2012 Aggregate

Journal publications serve as an important metric of success for our scientists. In 2012, we had many high-impact papers, including research published in top journals Nature, Cell and Science.