Pioneering the Future

WelcomeAnnual Report 2015

For ISB’s 2015 Annual Report, we begin with “ISB & Tipping Points” from our President Dr. Lee Hood. He describes the six paradigm shifts that mark his career, the most recent of which is bringing P4 medicine to Providence Health & Services and the U.S. healthcare system. Dr. Hood makes a compelling case that ISB’s leadership in the arena of scientific wellness will engender vast opportunities for innovation.

In our commitment to catalyzing a new sustainable future, our Director and Senior Vice President Dr. Nitin Baliga and his colleagues are tackling questions about the environment’s ability to support a global population spike to 10 billion people. Dr. Baliga addresses some of the complex, pressing issues and how his team has begun to make an impact.

The belief that we must transfer our knowledge to the public and champion equitable access to quality science education is so intrinsic to ISB that we have known no other way. In 2015, we began a partnership to grow our impact beyond K-12 school districts into community college-level instruction. Dr. Jen Eklund shares some of the successes in that crucial work.

ISB’s generous supporters have made all the difference in how we diversify our funding sources. Our Director of Development Nick Newcombe offers a report on the Wilke Cohen Lyme Disease Project, which has received $6.3 million in gifts and pledges.

ISB &
Tipping Points

By Lee Hood, MD, PhD
President & Co-founder, Institute for Systems Biology
SVP & CSO, Providence Health & Services

"The tipping point is that magic moment when an idea, trend, or social behavior crosses a threshold, tips, and spreads like wildfire."

– Malcolm Gladwell, The Tipping Point

paradigms

I participated in six major changes in biology - from bringing engineering to biology in the 1970s to, in 2016, bringing medicine that is predictive, preventive, personalized and participatory (P4 Medicine) to the U.S. healthcare system. This change, the most recent ISB tipping point, is the result an affiliation between Institute for Systems Biology and Providence Health & Services.

VISION OF THE INSTITUTE FOR SYSTEMS BIOLOGY

Major advances in science and technology from 1970 through the 1990s led to the creation of ISB in 2000. In the 1970s when I was at Caltech, we began to understand that big science requires not just biologists but also chemists, engineers, and other types of scientists. The Human Genome Project was the first successful application of the concept of big science and, in the 1990s, these concepts were further advanced by the establishment of the cross-disciplinary Department of Molecular Biology at the University of Washington.

In 2000, three well-established senior scientists departed from their conventional and cloistered academic careers. They started a non-profit research organization – ISB – dedicated to pioneering the emerging discipline of systems biology – which entails a global or holistic approach to deciphering the complexities of biology and disease.

ISB was launched with the conviction that leading-edge systems biology would require the development of new technologies and systems-driven strategies to more effectively generate data and explore untapped areas of data space in living organisms (molecules, cells, organs, individuals). This also required developing the analytical tools to capture, standardize, analyze, integrate and model these data to reveal deep insights into biological and disease mechanisms. ISB strongly believes that these technologies, data and analytical tools should be made widely available to the scientific community in a timely manner – a policy of open data and open software.

Tipping Point

ISB defined systems biology and catalyzed a revolution in how biology is done. In 2000, ISB was the first institute devoted to systems biology. Today, there are more than 100 systems biology centers, institutes and departments worldwide. Systems approaches are recognized throughout the life sciences as key to unraveling the complexities of biology and disease.

THE FEATURES OF ISB THAT HAVE CATALYZED A VARIETY OF TIPPING POINTS ARE:

CROSS-DISCIPLINARY ENVIRONMENT

To achieve our vision of systems biology, we created a cross-disciplinary environment, bringing together biologists, chemists, computer scientists, engineers, mathematicians, physicists and academic physicians in close proximity at ISB. They learned one another’s languages and how to effectively work together in teams.

Working collaboratively across disciplines enables leading-edge biology to drive the development of relevant technologies. In turn, the resulting data can catalyze the pioneering of analytical tools. Thus, a fundamental mantra of ISB is “biology drives technologies and technologies drive analytical tools.” When these are seamlessly integrated around a biological challenge, game-changing concepts, technologies and analytical tools emerge and catalyze both scientific discovery and innovation.

trinity
CREATION OF NEW CONCEPTS

ISB has played a major role in conceptualizing and reducing to practice a variety of new concepts in biology and medicine:

  • Systems biology, systems medicine (a systems approach to disease)
  • P4 medicine: a predictive, preventive, personalized and participatory approach to healthcare
  • It focuses on the importance of addressing wellness and disease rather than primarily disease
  • Scientific wellness, which employs and assesses dense, dynamic, personal data clouds for each individual, focusing on the so-revealed interactions of one’s genetics and environment to identify “actionable possibilities” that, if acted upon promote wellness or avoid disease
Big vs. Small Science

The complexity of biology led to the distinction between big vs. small science. Small science is generally a single investigator and a laboratory group working on a very discrete and focused problem (e.g. what does the cancer molecule P53 do?).

On the contrary, complex biological challenges often require an integrative and coordinated “big science” strategy that includes a systems-driven approach to attacking a difficult problem, combined with a cross-disciplinary environment of scientists and engineers that can take on the many different dimensions of the challenge. Big science also requires the integration of technologies, diverse types of data and appropriate analytical tools. Big science must be driven by an integrated vision, milestones and appropriate timelines.

big science

The Human Genome Project (HGP) was biology’s first “big science” project – and the largest single undertaking in the history of biological science. The HGP provided a vision and a roadmap for success, which included generating technologies essential for scaling up the sequencing and related analyses, assembly of a global, cross-disciplinary team of scientists, and a laser-focused execution of that vision. The combined elements enabled the scientific community to bring the human genome sequence to society faster than anyone thought possible. The HGP transformed virtually every aspect of the life sciences.

ISB has successfully employed these approaches for a wide variety of big science problems that has enabled ISB to transform the global understanding of human diseases and to pioneer the emerging sector of scientific wellness.

Some examples:

  • Developing the tools and strategies for P4 medicine in collaboration with the nation of Luxembourg
  • The Cancer Genome Atlas (TCGA) project in collaboration with the National Cancer Institute and the National Human Genome Research Institute
  • United States Army project to study Post-Traumatic Stress Disorder
  • Department of Defense (DTRA) project on sepsis
Transferring Knowledge to Society

Since ISB’s inception, a fundamental principle has been our commitment for all scientists to transfer the useful and relevant knowledge they gain to society. In this regard we have:

  • Fostered K-12 science education throughout the Puget Sound region and beyond through the Logan Center for Education, the Systems Education Experiences program and the Center for Systems Biology
  • Spun out 8 companies – all successful and all running effectively
    • These companies have returned more than $6 million to ISB for research support
    • Several of these companies have the potential to provide an endowment to ISB in the future
Organization

ISB has a very flat organization, little bureaucracy, focused leadership and an excellent administrative staff. Decisions can be made rapidly in order to take on big and small projects.

Science and Technology

ISB has made important advances in technology. ISB has pioneered:

  • Targeted and global (SWATH) mass spectrometry
  • Single molecule measurements of nucleic acids through the company Nanostring
  • Inkjet printer technology - which Agilent commercialized - that allows large amounts of DNA to be rapidly synthesized and DNA arrays to be readily manufactured
  • Use of single-cell analysis to interrogate the complexities of human development and cancer
  • Developing peptide protein-capture agents by co-founding a company (Indi Molecular) that is developing agents that will in 10 years replace monoclonal antibodies because they are stable, digital, high affinity and can be designed to lack cross reactivity – and they can be employed as in vitro or in vivo diagnostic reagents or as drugs
Systems-Driven Strategies

ISB has also pioneered a series of systems-driven strategies:

  • Targeted and global (SWATH) mass spectrometry
  • The complete genome sequence analyses of families allows us to readily identify disease genes
  • We have made blood a window into health and disease by employing targeted mass spectrometry to identify protein biomarkers for diseases (e.g., lung cancer and preterm birth)
  • We pioneered the use of dense, dynamic, personal data clouds to investigate scientific wellness, wellness-to-disease transitions and the progression and treatment of disease itself
  • We employ computational methods with disease-perturbed biological networks to identify possible disease drug targets

LUXEMBOURG PARTNERSHIP & SCIENTIFIC WELLNESS

ISB enters into strategic partnerships with government, industry and philanthropy that:

  • Provide scientific and technical talent and expertise to address a big science problem
  • Bring new technologies, strategies and analytical tools to ISB
  • Bring additional funding sources
  • Enable the very best scientists in the world to combine with those at ISB in attacking challenging big problems

In 2008, ISB began a five-year strategic partnership with the nation of Luxembourg – to bring biotechnology and healthcare to the newly founded University of Luxembourg in the form of a new Center for Systems Biomedicine, which today is one of the leading such institutes in Europe. In return, Luxembourg provided ISB $100 million over five years to invent the technologies and strategies of systems (P4) medicine. This funding generated 10 new technologies and systems-driven strategies, and allowed ISB to explore the patient data space in powerful and innovative new ways.

Tipping Point

The ten new technologies and strategies developed by the Luxembourg partnership placed ISB at a tipping point in systems medicine and allowed us to explore patient data space in powerful and innovative new ways.

LAUNCHING A NEW INDUSTRY – SCIENTIFIC WELLNESS

In 2014, ISB partnered with Maveron, a consumer-only venture firm to conduct the Hundred Person Wellness Project, a 10-month scientific study on 108 individuals. Dense, dynamic, personal data clouds were generated for each individual from whole genome sequences, clinical chemistries, metabolites and proteins from blood obtained every three months, gut microbiome bacterial quantification from stool samples every three months and quantified-self measurements for activity and sleep quality from a Fitbit.

These data were analyzed and integrated for each individual, and through behavioral coaching, actionable recommendations were made to the participants to optimize their wellness or avoid disease. Seventy percent of the participants were compliant with the coaching recommendations. The data, on a de-identified basis, have been transformational in providing insights both into human biology and disease. We termed this transformational approach “scientific wellness.”

In July, 2015, in partnership with venture firms ARCH Venture Partners, Polaris Partners and Maveron, ISB co-founded Arivale, a consumer-focused, scientific wellness company.

Tipping Point

We believe Arivale will create an entirely new thrust in healthcare – scientific wellness. It is our view that in a 10- to 15-year period, the market cap of the scientific wellness sector will far exceed that of the current healthcare (or disease care) industry.

ISB AFFILIATION WITH PROVIDENCE HEALTH & SERVICES

With the goal of bringing P4 medicine to every patient, Providence Health & Services and ISB affiliated in April 2016. Together ISB and Providence will transform healthcare to a proactive mode that is focused on keeping patients well and identifying the earliest opportunities to reverse or even prevent disease.

This exciting new relationship will enable ISB to expand its research capacity during the next few years and recruit outstanding new faculty in the areas of systems biology, technology development, data and analytics, and translational medicine. Further, it will enable us for the first time ever to apply ISB-driven systems approaches for optimizing wellness and minimizing disease to patient care.

translational

We will combine our basic research with the clinical expertise at Providence, bringing P4 medicine directly to the patient’s bedside through an initial four translational pillars, each employing the platform of dense, dynamic, de-identified personal data clouds:

  • Scientific wellness
  • Cancer survivorship
  • Alzheimer’s disease
  • Brain cancer (glioblastoma)

With each of these translational pillars, we will employ innovative approaches made possible by ISB’s new technologies, systems-driven strategies and new conceptual approaches.

Tipping Point

The affiliation between ISB and Providence will bring systems medicine that is predictive, preventive, personalized and participatory (P4) to a major health system and ultimately to U.S. healthcare more broadly.

THE FUTURE OF HEALTHCARE

ISB has opened the possibility of transforming some of society’s most challenging problems by:

  • Employing P4 medicine to greatly reduce the cost of healthcare and thus begin to change one of the biggest challenges to all nations – the runaway costs of healthcare
  • Using scientific wellness to greatly diminish the challenges of aging and ensure each individual life-long wellness

Scientific wellness will create a new healthcare industry and – if Washington State or the U.S. is the center of this industry, as it is now, it will provide enormous economic benefits and possibilities for innovation.

Tipping Point of the Future

As the cost of scientific wellness diminishes significantly (just as the cost of DNA sequencing has diminished by a million-fold over the course of about 12 years), then we can bring this opportunity to the poor as well as the rich nations of the world, leading to a democratization of healthcare unimaginable even a few years ago.

CODA

Recall once again Gladwell’s opening quote: “The tipping point is that magic moment when an idea, trend, or social behavior crosses a threshold, tips, and spreads like wildfire.”

From my vantage point, it is fair to say that ISB has catalyzed many tipping points – some of which have spread like wildfire. So the future will continue to see the evolution of ISB-catalyzed tipping points, and it will be fascinating to determine just how long some of the most interesting take to spread like wildfire.

Headlines 2015Click on any of the images to learn more

FinancialsFor the Year Ending December 31, 2015

5-Year Overview
Research Operating Expenses vs. Total Revenue

Statement of Activities
Dollars in Thousands

Revenues
$
%
Grants & Contract Revenue
25,081
70.2
Contributions
4,465
12.5
Investment & Other Income
6,188
17.3
Total Revenues
35,734
100.0
Expenditures
$
Research & Other Direct Costs
24,894
Management & General
11,862
Fundraising & Other
153
Total Expenditures
36,909
Decrease in Net Assets
(1,175)

Balance Sheet
Dollars in Thousands

Assets
$
Cash & Investments
16,816
Other Assets
13,462
Property & Equipment (Net)
8,662
Total Assets
38,940
Liabilities
$
Accounts Payable & Accrued Expenses
13,624
Deferred Revenues
3,024
Notes Payable
7,782
Total Liabilities
24,430
Net Assets
$
Unrestricted Net Assets
(1,373)
Temporarily Restricted Net Assets
7,211
Permanently Restricted Net Assets
8,672
Total Net Assets
14,510

A New Sustainable Future
Nitin Baliga, PhD, SVP & Director, ISB


A human crisis of unprecedented proportions is in the making. Diminishing arable land, water shortage and expected population growth to 10 billion portend a catastrophic food security crisis by 2030. This threat requires a dramatic reduction of the environmental footprint of agricultural practices. A paradigm shift to the food supply chain is necessary to meet an expected 70 percent or more increase in food demand.

Advances in precision agriculture and the development of higher-yielding, disease-resistant crops are addressing a number of these issues. For example, there are technologies to minimize the application of pesticides and fertilizers and optimize water usage. But these advances alone will not cut it. Even with improvements in the efficiency of water usage, it is estimated that there will be about a 30 percent shortage in water supply by 2030. Agriculture alone will require approximately 4.5 trillion cubic meters of water, but the total supply of fresh water is just 4.2 trillion cubic meters – and this does not take into account home and industrial water needs. Shrinking arable land due to desertification and salination, and projected water shortages, both exacerbated by climate change, are threatening food security. This is a multi-scale systems problem that will require concerted advances in technologies for sustainable production of food, as well as responsible consumption of natural resources and food.

ISB launched Project Feed 1010 (1010=10 billion) to catalyze this paradigm shift and create a new sustainable agriculture economy. PF1010 is pioneering a crowd-sourced network of scientists, teachers, students and farmers to optimize aquaponics – a sustainable food production solution that combines aquaculture (fish farming) and hydroponics (growing plants in water) to support year-round crop production with up to 90 percent less water usage than conventional agriculture. This project aims to make scientific breakthroughs for scaling up sustainable agriculture while transforming STEM education to generate a massive workforce and entrepreneurs for a new economy. We dream of a future where every unused urban space is repurposed for sustainable food production, where everyone is a citizen scientist, and we are all prosumers (producers + consumers) in a smart food supply chain.

This is an audacious and bold vision that requires an approach that is rapidly scalable and one that integrates education, research and farming – nationally and internationally. PF1010 is developing a network of educators, farmers and scientists to coordinate and leverage simultaneous advancements in teaching and curriculum development, research and innovation, and agricultural practices.

We recognized the importance of targeting high school students, because nearly 47 percent of mid-scale jobs, most of which require a high-school diploma, are predicted to be at high risk of being replaced by technology and automation. By targeting this segment of the population, we could create awareness of the food security crisis, its underlying causes and potential solutions, and simultaneously address the massive unemployment crisis by preparing these students to enter the workforce in the sustainable agricultural economy of the future. In just one year of existence, PF1010 has created an international network that has made tremendous, impactful contributions toward training hundreds of teachers and students across the United States and beyond, while engaging students across high schools, skill centers, colleges and universities in the development of key components of the education and research infrastructure.

PF1010 is laying the foundation for a sustainable future. A new paradigm is emerging. By engaging students in the development of solutions for real-world problems we are transforming them into producers, and not just consumers of knowledge. More importantly, the students are directly involved in innovating new solutions to a complex problem that threatens us all: creating proficient and creative problem solvers who are prepared to immediately participate in the workforce of a new sustainable economy they are helping create.

Key PF1010 Milestones Include:

  • Partnering with Northeastern University to develop a modularized post-graduate course in advanced software development focused on creating cloud infrastructure of databases, web/iOS/Android apps, data analytics, visualization, and social networking for monitoring and coordinating sustainable agricultural systems across a network.
  • Establishing a network of high school science educators to implement ISB-developed curriculum on sustainable agriculture and providing personalized support to integrate systems education principles.
  • Partnering with Washington Network for Innovative Careers to offer a year-long high school course for students in which they participated as citizen scientists to innovate designs for aquaponics systems. Through this program, the students were invited to participate in the Bill and Melinda Gates Teen Action Fair, the E Environmental and Adventure School’s Healthy Choices Fair, and the University of Washington’s 2016 Earth Day celebration.
  • Partnering with the National Science Foundation to create an Ambassadors of Change training program for high school and undergraduate students to learn about sustainable agriculture through Project Feed 1010 and how to transfer that knowledge to their respective schools and communities.
  • Inspiring and supporting the Florida high school team that incorporated PF1010 curriculum into their science classes and took first place in the Global Change Challenge with their aquaponics project.

Inspiring Change in Education
Jen Eklund, Interim Director & Education Liaison, Logan Center for Education, ISB


The paradigm shifts in science, technology, engineering and mathematics (STEM) fields are leading to abounding opportunities for STEM careers and a need for all people to have STEM literacy to participate in decisions that affect their own health, the health of their communities and the health of our environment.

Shifting paradigms in classrooms is challenging and STEM educators need support to integrate adjustments that reflect the profound changes in STEM fields.

In 2015, ISB’s Logan Center for Education continued to play an important role in leading our region to provide educators with the knowledge and resources to inspire paradigm shifts in science classrooms. Those shifts include implementing new standards in math and science, integrating engineering into science learning, and developing quantitative reasoning skills that students will need in all STEM careers of the future.

Sixth grade science teachers in the Renton school district worked with a biologist from the University of Washington to explore local phenomena that would support students to engage their curiosity and explore the characteristics of living things. Middle school science teachers in the Renton School district partnered with the Logan Center for Education to continue the implementation of Washington State’s new science standards.

The new standards push students beyond memorizing facts and “cookbook” experiments; they ask students to think, behave and interact as scientists and engineers do. This new perspective in the classroom allows students in the Renton School District to be the STEM professionals and STEM literate citizens of the future.

This year, elementary, middle and high school teachers from the Marysville school district worked with the Logan Center team and engineers from the University of Washington and Edmonds College to develop a suite of experiences and lessons like this. Students in Marysville are learning that engineering is more than tinkering; engineering requires an understanding of science to address real-world problems.

At Lower Columbia College, non-major biology students wrestled with data from The Cancer Genome Atlas project to develop a deeper understanding of the role of gene regulation in cancer. The assignment gave students a sense of the landscape of contemporary biological research exemplified by ISB and asked students to begin the practice of using quantitative reasoning (QR) and systems thinking skills that have not traditionally been part of undergraduate biology courses.

Through its partnership with Washington’s State Board of Community and Technical Colleges, the Logan Center has strategically expanded its education work to the postsecondary level in 2015. This partnership uniquely applies the Logan Center’s knowledge and experience of educator professional development with ISB scientists expertise in contemporary biology. The work supports community and technical college faculty to make instructional shifts to include QR skills comprised of accessing data (big data and multi-scale data), analyzing and interpreting data (mathematics and statistics, computational modeling, and simulation), and organizing and communicating data (for visualization, presentation, and publication) in their courses. Students in these courses will be better prepared for STEM careers that rely increasingly on QR skills.

Battling Lyme
Nick Newcombe, Director of Development, ISB


"There’s a great void of knowledge in the world of Lyme. I believe that only the biggest, most elegant computational science can fill it, and ISB is uniquely positioned to do just that."

– Liesl Wilke


 In 2015, ISB embarked on a comprehensive study of Lyme disease, which is a highly complex and often misdiagnosed disease that can be debilitating for those who do not respond to a standard course of antibiotics. This important research was spearheaded by Liesl and Jeff Wilke and their magnanimous gifts. Since then, thanks to their generosity and that of the Steven & Alexandra Cohen Foundation, Jeff and MacKenzie Bezos, and the Bay Area Lyme Foundation, the project has received a total of $6.3 million.

The Wilke Cohen Lyme Disease Project is a three-year study that is leveraging the tools and technologies of systems biology to understand the fundamentals of Lyme, identify biomarkers, and gain insights about the genomics and proteomics of the infecting Borrelia organism. Of the research on Lyme disease currently under way in the U.S., ISB’s Wilke Cohen Lyme Disease Project is one of the most prolifically funded by private philanthropy.
 

"We believe in ISB’s holistic, systems approach and share their commitment to finding more effective diagnostics and treatments."

– Alexandra Cohen

2015 ContributorsSpecial thanks to the following believers in the promise of systems biology

$100,000+
Jeff and MacKenzie Bezos
William K. Bowes, Jr. Foundation
Lee Hood and Valerie Logan
Douglas Howe and Robin DuBrin
Roger M. Perlmutter
Dave and Sandra Sabey
Liesl and Jeff Wilke
$25,000 - $99,999
Dalio Foundation, Inc.
Franklin and Catherine Johnson
Drew and Noni Senyei
$10,000 - $24,999
Janet Levinger and William Poole
$2,500 - $9,999
Amgen, Inc.
The Boeing Company
Bill and Paula Clapp Fund
Fenwick & West LLP
HomeStreet Bank
Intellectual Ventures, Inc.
KeyBank
Kilroy Realty Corporation
Dan Ling and Lee Obrzut
Peter McCormick and Kathleen Albrecht
Muckleshoot Charity Fund
Robert T. Nelsen
Novo Nordisk, Inc.
Gil Omenn and Martha Darling
Omeros Corporation
Ron and Sara Seubert
Silicon Valley Community Foundation
TD's of Clemson, Inc.
Janine Terrano
Thermo Fisher Scientific, Inc.
Aron and Sara Thompson
Tulalip Tribes Charitable Contributions
Brian Turner and Susan Hoffman
Washington Research Foundation
Adam J. Weissman
Mary Woolley
Timothy Zenk and Perrin Kaplan
Anonymous
$1,000 - $2,499
John and Leslie Aitchison
Marne Anderson
Nitin Baliga and Janet Ceballos
Carolynne Bryant-Dowdy
Suzie Burke
Jane and Terry Chadsey
Cockrum Family Charitable Fund
Lisa B. Cohen
Christopher and Stephanie Daley-Watson
Dee Dickinson
Carole Ellison
Myron and Sue Hood
Jim and Sherry Ladd
Marie Mentor
Craig and Marie Mundie
Nick Newcombe
Dana Riley Black and Ben Black
John and Mary Ann Romeril
Gene and Carol Sharratt
Erich C. Strauss
Sheryl and Pack Suchoknand
Thomas Weingarten and Wendy Thon
Ger van den Engh
$500 - $999
Arne and Mary Anderson
Stephen D. Arnold
Katherine Barnett and David Badders
Arvind Baliga
Terry Bergeson
David J. Burman
Marjorie B. Chadsey
Mary Alice Heuschel
Allen and Nancy Jones
Inyoul Lee and Myungkee Min
B Lippit and Liz Van Volkenburgh
Claudia and Adam Ludwig
Tony Marshall
Douglas M. McCracken
John R. O’Halloran
Nathan and Brenda Price
Carmie Puckett-Robinson
Ann M. Stephens
Ann Stevens
Tayloe Washburn and Deborah Winter
Fred and Ann Whitney Family
$250 - $499
David Abbott
Bob Alexander and Kathleen Devon
Anthony J. Cavalieri, II
JoAnn Chrisman
Roy and Mary Currence
Maud Daudon
Phillip Day
Jennifer and Matt Donelan
Caitlin Echelbarger
Patricia W. Gaillard
Corinne and Russell Hagen
Geof Hamlin
Rebecca E. Jansson
Kim and Ralph Klinke
Hilde Cheroutre and Mitchell Kronenberg
Sarah Li
Cammi Libby
Marcie and Steve Maxwell
Cindy McCall
Chun M. Ng
Victor Ng
Lourdes Orive
Ronald G. Payne
Judith Peacock
Maurice J. Pirio
Harmon H. Rulifson
Kathy Scanlan
Cynthia Shumate
Judith L. Siders
Todd Smith and Sandra Porter
Gretchen Sorensen
Bob Sotak
James and Fawn Spady
Paula Stokes
Susan M. Talton
Qiang Tian and Danbin Xu
K. Allyn Tolmie
Washington STEM
$150 - $249
Arthur D. Becker
Becky Beers
Becky Birch
Jim Black
Sissy and Tom Bouchard
Tom and Barbara Cable
Jan Chalupny
Patti J. Dill
Leonard T. Garfield
Richard Gelinas
Michael Golden
Roger B. Gulrajani
Linda Haugen
Barb Jagels
Robert C. Jernigan
Jeremy Johnson
John Kapernick
Sid and Heather Logan
Caroline Maillard
Erin M. McCallum
Gloria and George Northcroft
Carl and Carole Scandella
David Schaefer and Pat Moriarty
Ellen Shockro
Sally Goetz Shuler
Donald M. Tolmie
Washington Alliance for Better Schools
Elaine and Larry Woo
Anonymous
$50 to $149
Patricia H. Aitken
AmazonSmile Foundation
Seth A. Ament
Mary M. Aronen
D. Robert Ayers
Lisa M. Barbee
Armandino Batali
Julie Bletz
Mary Brunkow
Anthony A. Byrd
Marni A. Campbell
Richard J. Cavallaro
Michael C. Cavallaro
George Chadick
Monica A. Chandler
Hsiao-Ching Chou
Kevin Q. Costanza
Brenda Crumpler
Diane K. Del Chiaro
Svetlana Dimovski
Robert A. Dinning
William A. Dow
Mary Kay Dugan
Campbell E. Enarson
Stephen A. Eraker
Marion S. Fall
Rose Ann and Charles Finkel
Mary Fox
L. Bryan Gibson
Lena Glennon
Richard C. Grove
Kevin J. Hamilton
Lori J. Hansen
Carl L. Higginbotham
Jane B. Homesley
Yingzhi Z. Huang
Matthew W. Hubbard
A. Sherrill Hudspeth
Kathlyn Huson
Francis M. James, IV
Judith B. Jennison
L. Andrew Koman
Roseann M. London
MaryBee and Bob Longabaugh
Karen J. Manuel
Daniel W. Mathis
John McLaughlin
Bernard W. Miner, Jr.
Bev and Dan Morrow
Antoine Nahra
Lewis H. Nelson, III
Operation Stand Down Tennessee
Steven J. Oscherwitz
Sandra M. Ouellette
$50 to $149 (continued)
Erlinda Partridge
J. Greg Perkins
Deborah L. Person
Betty C. Petree
Shizhen Qin
Paula Rees
Roger H. Ressmeyer
Anne W. Richards
Kristin E. Ritter
Abbie McLean Roberts
Gregory Rosenthal
Raymond C. Roy
John C. Schaefer
Norm Fox and Tracy Schmitz
John A. Schukar
Myrle G. Scripps
The Seattle Foundation
Darrel L. Seibert
Taunya R. Sell
Devon Sharp
Martin Shelton
Fern Shierson
Christine Silva
Herbert Spaugh, Jr.
Mark A. Stensager
Kathleen M. Stilwell
Bingyun Sun
Michael H. Tibbits
Julie and Joe Tilton
Alexander Y. Tokman
Suzie Tolmie
Brandon Treen
Kelly Tremblay
Mia Tuan
Josefina M. Vallarta
Valerie Voss
Maureen Wall
Mark E. Wilkins
Anonymous (2)
Up to $49
John W. Arzonico
Debbie Baird
J. Christopher Bare
Shawn Behling
Amy L. Bergin
John C.P. Boylan
Aaron Brooks
Bryan Carnes
Cora H. Chadick
Kay Chinn
Sandra Crabtree
Anita V. Crofts
Jessica Day
Sam H. Dorsett, Jr.
Mary and Martin Ensley
James R. Evans
Shelley A. Fugitt
Michal Galdzicki
Anita P. Griffin
Amber N. Hageman
James A. Hallock, Sr.
Jesse Hunter
Russel H. Ingram
Rebecca A. Johnson
Alisa Johnson
Steve Koh
Jesse Kruchoski
Allison Kudla
Bria Lange
Joan Leonard
Mending Hearts, Inc.
Up to $49 (continued)
Victoria Neer
Deborah Nelson
Conor O'Neil
Arvind S. Patil
Joey Petosa
Kathy Petosa
Robert G. Piper
David Reeves
Andrew Riddle
Michaela C. Ritter
Keri Salemme
Diego Martinez Salvanha
Carlos Orellana Sanchez
Kelly Shepardson
Zachary J. Simon
Rita A. Simpson
Rebecca A. Staffel
Brenda Sullivan
Rhonda N. Sweat
Anne Thompson
Pamela Troisch
Serdar Turkarslan
Victoria VanBruinisse
Jake Valenzuela
Phu T. Van
Welcome Home Ministries
Katherine Weybright
Jason M. Winget
Amanda Wood
Wei-Ju Wu
Pavel Zrazhevskiy
Anonymous (2)

Demonstrate your belief in the promise of systems biology:

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

Board of Directors

David A. Sabey

Chairman of the board

President
Sabey Corporation & Sabey Construction
Bill Bowes
Co-Founder
U.S. Venture Partners
Thomas J. Cable
Board Member
Omeros Corporation
Stephen M. Graham
Managing Partner, Seattle Office
Fenwick & West LLP
Leroy Hood, MD, PHD
President and Co-Founder
Institute for Systems Biology
Douglas Howe
President
Touchstone Corporation
Daniel T. Ling
Retired
Corporate Vice President
Microsoft Research
Craig Mundie
Senior Advisor to the CEO
Microsoft
Roger Perlmutter, MD, PhD
Executive Vice President and President
Merck Research Laboratories
Drew Senyei, MD
Managing Director
Enterprise Partners Venture Capital
Brian Turner
Retired CFO
Coinstar, Inc.
Douglas Walker
Retired Software CEO
Civic Volunteer
Mary Woolley
President Research!America

Senior Leadership

hood
Leroy Hood, MD PHD
President and Co-founder
baliga
Nitin Baliga, PHD
Senior Vice President and Director
price
Nathan D. Price, Phd
Associate Director
scanlan
Kathy Scanlan
Chief Operating Officer & Treasurer
shumate
Cynthia Shumate, JD
Chief Legal Officer, Chief Compliance Officer & Secretary

Faculty

John Aitchison, PhD
Nitin Baliga, PhD
Leroy Hood, MD, PhD
Sui Huang, MD, PhD
Robert Moritz, PhD
Nathan Price, PhD
Jeff Ranish, PhD
Ilya Shmulevich, PhD
Naeha Subramanian, PhD

Principal Scientists

Gustavo Glusman, PhD
Monica Orellana, PhD
Kai Wang, PhD

Senior Research Scientists

Brady Bernard, PhD
Eric Deutsch, PhD
Richard Gelinas, PhD
Nathan Goodman, PhD
Andrew Keller, PhD
Theo Knijnenburg, PhD
Ulrike Kusebauch, PhD
Inyoul Lee, PhD
Chris Plaisier, PhD
Shizhen Qin, PhD
David Reiss, PhD
Sheila Reynolds, PhD
Jared Roach, MD, PhD
Lee Rowen, PhD
Arian Smit, PhD

Senior Research Scientists (continued)

Sergey Stolyar, PhD
Vesteinn Thorsson, PhD
Qiang Tian, MD, PhD
Serdar Turkarslan, PhD
Kathie Walters, PhD

Senior Research Engineer

Chris Lausted

Senior Software Engineers

David Campbell
Robert Hubley
Bill Longabaugh
Denise Mauldin
Natalie Tasman

Senior Bioinformatics Scientist

Lisa Iype, PhD

Publications2015 Aggregate

  • Aitchison, J. D., and M. P. Rout. 2015. “The Interactome Challenge.” The Journal of Cell Biology 211 (November): 729–32. http://doi.org/10.1083/jcb.201510108.
  • Ament, Seth A., Szabolcs Szelinger, Gustavo Glusman, Justin Ashworth, Liping Hou, Nirmala Akula, Tatyana Shekhtman, et al. 2015. “Rare Variants in Neuronal Excitability Genes Influence Risk for Bipolar Disorder.” Proceedings of the National Academy of Sciences of the United States of America 112 (11): 3576–81. http://doi.org/10.1073/pnas.1424958112.
  • Ameziane, N., P. May, A. Haitjema, H. J. van de Vrugt, S. E. van Rossum-Fikkert, D. Ristic, G. J. Williams, et al. 2015. “A Novel Fanconi Anaemia Subtype Associated with a Dominant-Negative Mutation in RAD51.” Nature Communications 6: 8829. http://doi.org/10.1038/ncomms9829.
  • Argyropoulos, C., K. Wang, J. Bernardo, D. Ellis, T. Orchard, D. Galas, and J. P. Johnson. 2015. “Urinary MicroRNA Profiling Predicts the Development of Microalbuminuria in Patients with Type 1 Diabetes.” Journal of Clinical Medicine 4: 1498–1517. http://doi.org/10.3390/jcm4071498.
  • Ashworth, J., S. Turkarslan, M. Harris, M. V. Orellana, and N. S. Baliga. 2015. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics, November. http://doi.org/10.1016/j.margen.2015.10.011.
  • Basler, Georg, and Evangelos Simeonidis. 2015. “Integrating Food Webs with Metabolic Networks: Modeling Contaminant Degradation in Marine Ecosystems.” Frontiers in Genetics 6. http://doi.org/10.3389/fgene.2015.00020.
  • Bennett, K. L., X. Wang, C. E. Bystrom, M. C. Chambers, T. M. Andacht, L. J. Dangott, F. Elortza, et al. 2015. “The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.” Molecular & Cellular Proteomics : MCP 14 (December): 3299–3309. http://doi.org/10.1074/mcp.O115.051888.
  • Boissel, J. P., C. Auffray, D. Noble, L. Hood, and F. H. Boissel. 2015. “Bridging Systems Medicine and Patient Needs.” CPT: Pharmacometrics & Systems Pharmacology 4 (March): e00026. http://doi.org/10.1002/psp4.26.
  • Bressler, R., R. B. Kreisberg, B. Bernard, J. E. Niederhuber, J. G. Vockley, I. Shmulevich, and T. A. Knijnenburg. 2015. “CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.” PloS One 10: e0144820. http://doi.org/10.1371/journal.pone.0144820.
  • Cancer Genome Atlas Network. 2015. “Genomic Classification of Cutaneous Melanoma.” Cell 161 (7): 1681–96. http://doi.org/10.1016/j.cell.2015.05.044. .
  • Cancer Genome Atlas Research Network, Daniel J. Brat, Roel G. W. Verhaak, Kenneth D. Aldape, W. K. Alfred Yung, Sofie R. Salama, Lee A. D. Cooper, et al. 2015. “Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.” The New England Journal of Medicine 372 (26): 2481–98. http://doi.org/10.1056/NEJMoa1402121.
  • Cancer Genome Atlas Research Network. Electronic address: schultz@cbio.mskcc.org, and Cancer Genome Atlas Research Network. 2015. “The Molecular Taxonomy of Primary Prostate Cancer.” Cell 163 (4): 1011–25. http://doi.org/10.1016/j.cell.2015.10.025.
  • Caron, E., L. Espona, D. J. Kowalewski, H. Schuster, N. Ternette, A. Alpizar, R. B. Schittenhelm, et al. 2015. “An Open-Source Computational and Data Resource to Analyze Digital Maps of Immunopeptidomes.” eLife 4. http://doi.org/10.7554/eLife.07661.
  • Cary, G. A., D. B. Vinh, P. May, R. Kuestner, and A. M. Dudley. 2015. “Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly.” G3 5 (November): 2497–2511. http://doi.org/10.1534/g3.115.021444.
  • Chakrabarty, Paramita, Andrew Li, Carolina Ceballos-Diaz, James A. Eddy, Cory C. Funk, Brenda Moore, Nadia DiNunno, et al. 2015. “IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior.” Neuron 85 (3): 519–33. http://doi.org/10.1016/j.neuron.2014.11.020.
  • Chandrasekaran, S., C. C. Rittschof, D. Djukovic, H. Gu, D. Raftery, N. D. Price, and G. E. Robinson. 2015. “Aggression Is Associated with Aerobic Glycolysis in the Honey Bee Brain.” Genes, Brain, and Behavior 14 (2): 158–66.http://doi.org/10.1111/gbb.12201.
  • Cheng, Zhiqiang, Zhiyou Wang, Doreen E. Gillespie, Christopher Lausted, Zheng Zheng, Mo Yang, and Jinsong Zhu. 2015. “Plain Silver Surface Plasmon Resonance for Microarray Application.” Analytical Chemistry 87 (3): 1466–69. http://doi.org/10.1021/ac504110t.
  • Corpas, M., W. Valdivia-Granda, N. Torres, B. Greshake, A. Coletta, A. Knaus, A. P. Harrison, et al. 2015. “Crowdsourced Direct-to-Consumer Genomic Analysis of a Family Quartet.” BMC Genomics 16: 910. http://doi.org/10.1186/s12864-015-1973-7.
  • Craciun, F. L., V. Bijol, A. K. Ajay, P. Rao, R. K. Kumar, J. Hutchinson, O. Hofmann, et al. 2015. “RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis.” Journal of the American Society of Nephrology : JASN, October. http://doi.org/10.1681/ASN.2015020225.
  • Depke, M., S. Michalik, A. Rabe, K. Surmann, L. Brinkmann, N. Jehmlich, J. Bernhardt, et al. 2015. “A Peptide Resource for the Analysis of Staphylococcus Aureus in Host-Pathogen Interaction Studies.” Proteomics 15 (November): 3648–61. http://doi.org/10.1002/pmic.201500091.
  • Deutsch, E. W., Z. Sun, D. Campbell, U. Kusebauch, C. S. Chu, L. Mendoza, D. Shteynberg, G. S. Omenn, and R. L. Moritz. 2015. “State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.” Journal of Proteome Research 14 (September): 3461–73. http://doi.org/10.1021/acs.jproteome.5b00500.
  • Deutsch, E. W., J. P. Albar, P. A. Binz, M. Eisenacher, A. R. Jones, G. Mayer, G. S. Omenn, S. Orchard, J. A. Vizcaino, and H. Hermjakob. 2015. “Development of Data Representation Standards by the Human Proteome Organization Proteomics Standards Initiative.” Journal of the American Medical Informatics Association : JAMIA, February.
  • Deutsch, Eric W., Luis Mendoza, David Shteynberg, Joseph Slagel, Zhi Sun, and Robert L. Moritz. 2015. “Trans-Proteomic Pipeline, a Standardized Data Processing Pipeline for Large-Scale Reproducible Proteomics Informatics.” Proteomics. Clinical Applications 9 (7-8): 745–54. http://doi.org/10.1002/prca.201400164.
  • Ebrahim, Ali, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Drager, et al. 2015. “Do Genome-Scale Models Need Exact Solvers or Clearer Standards?” Molecular Systems Biology 11 (10): 831.
  • Eddy, James A., Cory C. Funk, and Nathan D. Price. 2015. “Fostering Synergy between Cell Biology and Systems Biology.” Trends in Cell Biology, May. http://doi.org/10.1016/j.tcb.2015.04.005.
  • Elbelt, U., A. Trovato, M. Kloth, E. Gentz, R. Finke, J. Spranger, D. Galas, et al. 2015. “Molecular and Clinical Evidence for an ARMC5 Tumor Syndrome: Concurrent Inactivating Germline and Somatic Mutations Are Associated with Both Primary Macronodular Adrenal Hyperplasia and Meningioma.” The Journal of Clinical Endocrinology and Metabolism 100 (1): E119–28.
  • Eng, J. K., M. R. Hoopmann, T. A. Jahan, J. D. Egertson, W. S. Noble, and M. J. MacCoss. 2015. “A Deeper Look into Comet--Implementation and Features.” Journal of the American Society for Mass Spectrometry 26 (November): 1865–74. http://doi.org/10.1007/s13361-015-1179-x.
  • Gabora, L., and S. Kauffman. 2015. “Toward an Evolutionary-Predictive Foundation for Creativity : Commentary on ‘Human Creativity, Evolutionary Algorithms, and Predictive Representations: The Mechanics of Thought Trials’ by Arne Dietrich and Hilde Haider, 2014 (Accepted Pending Minor Revisions for Publication in Psychonomic Bulletin & Review).” Psychonomic Bulletin & Review, November. http://doi.org/10.3758/s13423-015-0925-1.
  • Gatto, L., K. D. Hansen, M. R. Hoopmann, H. Hermjakob, O. Kohlbacher, and A. Beyer. 2015. “Testing and Validation of Computational Methods for Mass Spectrometry.” Journal of Proteome Research, November. http://doi.org/10.1021/acs.jproteome.5b00852.
  • Geman, Donald, Michael Ochs, Nathan D. Price, Cristian Tomasetti, and Laurent Younes. 2015. “An Argument for Mechanism-Based Statistical Inference in Cancer.” Human Genetics 134 (5): 479–95. http://doi.org/10.1007/s00439-014-1501-x.
  • Gillespie, Mark A., Elizabeth S. Gold, Stephen A. Ramsey, Irina Podolsky, Alan Aderem, and Jeffrey A. Ranish. 2015. “An LXR-NCOA5 Gene Regulatory Complex Directs Inflammatory Crosstalk-Dependent Repression of Macrophage Cholesterol Efflux.” The EMBO Journal 34 (9): 1244–58. http://doi.org/10.15252/embj.201489819.
  • Glusman, G., A. Severson, V. Dhankani, M. Robinson, T. Farrah, D. E. Mauldin, A. B. Stittrich, et al. 2015. “Identification of Copy Number Variants in Whole-Genome Data Using Reference Coverage Profiles.” Frontiers in Genetics 6: 45.
  • Gomes-Filho, José Vicente, Livia Soares Zaramela, Valéria Cristina da Silva Italiani, Nitin S. Baliga, Ricardo Z. N. Vêncio, and Tie Koide. 2015. “Sense Overlapping Transcripts in IS1341-Type Transposase Genes Are Functional Non-Coding RNAs in Archaea.” RNA Biology 12 (5): 490–500. http://doi.org/10.1080/15476286.2015.1019998.
  • Grosse-Wilde, Anne, Aymeric Fouquier d’Hérouël, Ellie McIntosh, Gökhan Ertaylan, Alexander Skupin, Rolf E. Kuestner, Antonio Del Sol, K. A. Walters, and S. Huang. 2015. “Stemness of the Hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.” PLoS One 10: e0126522. http://doi.org/10.1371/journal.pone.0126522.
  • Hakhverdyan, Zhanna, Michal Domanski, Loren E. Hough, Asha A. Oroskar, Anil R. Oroskar, Sarah Keegan, David J. Dilworth, et al. 2015. “Rapid, Optimized Interactomic Screening.” Nat Methods 12 (June): 553–60. http://doi.org/10.1038/nmeth.3395.
  • Han, Bingshe, Dongkyoo Park, Rui Li, Maohua Xie, Taofeek K. Owonikoko, Guojing Zhang, Gabriel L. Sica, et al. 2015. “Small-Molecule Bcl2 BH4 Antagonist for Lung Cancer Therapy.” Cancer Cell 27 (June): 852–63. http://doi.org/10.1016/j.ccell.2015.04.010.
  • Hardies, K., C. G. de Kovel, S. Weckhuysen, B. Asselbergh, T. Geuens, T. Deconinck, A. Azmi, et al. 2015. “Recessive Mutations in SLC13A5 Result in a Loss of Citrate Transport and Cause Neonatal Epilepsy, Developmental Delay and Teeth Hypoplasia.” Brain : A Journal of Neurology 138 (November): 3238–50. http://doi.org/10.1093/brain/awv263.
  • Hardies, Katia, Patrick May, Tania Djémié, Oana Tarta-Arsene, Tine Deconinck, Dana Craiu, Ingo Helbig, et al. 2015. “Recessive Loss-of-Function Mutations in AP4S1 Cause Mild Fever-Sensitive Seizures, Developmental Delay and Spastic Paraplegia through Loss of AP-4 Complex Assembly.” Hum Mol Genet 24 (April): 2218–27. http://doi.org/10.1093/hmg/ddu740.
  • He, Y., J. Lin, D. Kong, M. Huang, C. Xu, T. K. Kim, A. Etheridge, Y. Luo, Y. Ding, and K. Wang. 2015. “Current State of Circulating MicroRNAs as Cancer Biomarkers.” Clinical Chemistry 61 (September): 1138–55. http://doi.org/10.1373/clinchem.2015.241190.
  • He, Yuqing, Juanjuan Lin, Yuanlin Ding, Guodong Liu, Yanhong Luo, Mingyuan Huang, Chengkai Xu, et al. 2015. “A Systematic Study on Dysregulated microRNAs in Cervical Cancer Development.” Int J Cancer, May. http://doi.org/10.1002/ijc.29618.
  • He, Y., J. R. Chevillet, G. Liu, T. K. Kim, and K. Wang. 2015. “The Effects of microRNA on the Absorption, Distribution, Metabolism and Excretion of Drugs.” Br J Pharmacol 172 (June): 2733–47. http://doi.org/10.1111/bph.12968.
  • He, Yuqing, Jie Yang, Danli Kong, Juanjuan Lin, Chengkai Xu, Han Ren, Ping Ouyang, Yuanlin Ding, and Kai Wang. 2015. “Association of miR-146a rs2910164 Polymorphism with Cardio-Cerebrovascular Diseases: A Systematic Review and Meta-Analysis.” Gene 565 (July): 171–79. http://doi.org/10.1016/j.gene.2015.04.020.
  • He, Yuqing, Kang Zeng, Xibao Zhang, Qiaolin Chen, Jiang Wu, Hong Li, Yong Zhou, et al. 2015. “A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family.” The Journal of Investigative Dermatology 135 (3): 907–9. http://doi.org/10.1038/jid.2014.429.
  • Heavner, B. D., and N. D. Price. 2015. “Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction.” PLoS Computational Biology 11 (November): e1004530. http://doi.org/10.1371/journal.pcbi.1004530.
  • Heavner, Benjamin D., and Nathan D. Price. 2015. “Transparency in Metabolic Network Reconstruction Enables Scalable Biological Discovery.” Current Opinion in Biotechnology 34C (January). http://doi.org/10.1016/j.copbio.2014.12.010.
  • Hennon, Gwenn M. M., Justin Ashworth, Ryan D. Groussman, Chris Berthiaume, Rhonda L. Morales, Nitin S. Baliga, Mónica V. Orellana, and E. V. Armbrust. 2015. “Diatom Acclimation to Elevated CO2 via cAMP Signalling and Coordinated Gene Expression.” Nature Climate Change 5 (8): 761–65. http://doi.org/10.1038/nclimate2683.
  • Hesselager, M. O., M. C. Codrea, Z. Sun, E. W. Deutsch, T. B. Bennike, A. Stensballe, L. Bundgaard, R. L. Moritz, and E. Bendixen. 2015. “The Pig PeptideAtlas: A Resource for Systems Biology in Animal Production and Biomedicine.” Proteomics, December. http://doi.org/10.1002/pmic.201500195.
  • Hoen, D. R., G. Hickey, G. Bourque, J. Casacuberta, R. Cordaux, C. Feschotte, A. S. Fiston-Lavier, et al. 2015. “A Call for Benchmarking Transposable Element Annotation Methods.” Mobile DNA 6: 13. http://doi.org/10.1186/s13100-015-0044-6.
  • Hood, L., and E. V. Rothenberg. 2015. “Developmental Biologist Eric H. Davidson, 1937-2015.” Proceedings of the National Academy of Sciences of the United States of America 112 (November): 13423–25. http://doi.org/10.1073/pnas.1518876112.
  • Hood, Leroy, Jennifer C. Lovejoy, and Nathan D. Price. 2015. “Integrating Big Data and Actionable Health Coaching to Optimize Wellness.” BMC Medicine 13. http://doi.org/10.1186/s12916-014-0238-7.
  • Hoopmann, Michael R., Alex Zelter, Richard S. Johnson, Michael Riffle, Michael J. MacCoss, Trisha N. Davis, and Robert L. Moritz. 2015. “Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes.” Journal of Proteome Research 14 (5): 2190–98. http://doi.org/10.1021/pr501321h.
  • Horvatovich, P., E. K. Lundberg, Y. J. Chen, T. Y. Sung, F. He, E. C. Nice, R. J. Goode, et al. 2015. “Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.” Journal of Proteome Research 14 (September): 3415–31. http://doi.org/10.1021/pr5013009.
  • Hu, Ting, Xiong Li, Qinghua Zhang, Kecheng Huang, Yao Jia, Ru Yang, Fangxu Tang, Qiang Tian, Ding Ma, and Shuang Li. 2015. “Could the Extent of Lymphadenectomy Be Modified by Neoadjuvant Chemotherapy in Cervical Cancer? A Large-Scale Retrospective Study.” PLoS One 10: e0123539. http://doi.org/10.1371/journal.pone.0123539.
  • Ichiyama, Kenji, Tingting Chen, Xiaohu Wang, Xiaowei Yan, Byung-Seok Kim, Shinya Tanaka, Delphine Ndiaye-Lobry, et al. 2015. “The Methylcytosine Dioxygenase Tet2 Promotes DNA Demethylation and Activation of Cytokine Gene Expression in T Cells.” Immunity 42 (April): 613–26. http://doi.org/10.1016/j.immuni.2015.03.005.
  • Imam, S., S. Schauble, J. Valenzuela, A. Lopez Garcia de Lomana, W. Carter, N. D. Price, and N. S. Baliga. 2015. “A Refined Genome-Scale Reconstruction of Chlamydomonas Metabolism Provides a Platform for Systems-Level Analyses.” The Plant Journal : For Cell and Molecular Biology 84 (December): 1239–56. http://doi.org/10.1111/tpj.13059.
  • Imam, Saheed, Sascha Schauble, Aaron N. Brooks, Nitin S. Baliga, and Nathan D. Price. 2015. “Data-Driven Integration of Genome-Scale Regulatory and Metabolic Network Models.” Frontiers in Microbiology 6. http://doi.org/10.3389/fmicb.2015.00409.
  • Kapoor, Prabodh, Yunhe Bao, Jing Xiao, Jie Luo, Jianfeng Shen, Jim Persinger, Guang Peng, Jeff Ranish, Blaine Bartholomew, and Xuetong Shen. 2015. “Regulation of Mec1 Kinase Activity by the SWI/SNF Chromatin Remodeling Complex.” Genes & Development 29 (6): 591–602. http://doi.org/10.1101/gad.257626.114.
  • Kauffman, S. A., and A. Gare. 2015. “Beyond Descartes and Newton: Recovering Life and Humanity.” Progress in Biophysics and Molecular Biology 119 (December): 219–44. http://doi.org/10.1016/j.pbiomolbio.2015.06.003.
  • Kauffman, Stuart A, Colin Hill, Leroy Hood, and S. Huang. 2015. “Transforming Medicine: A Manifesto.” Scientific American Worldview 2014b. http://www.scientificamerican.com/wv/assets/2014_SAWorldView.pdf.
  • Keller, A., S. L. Bader, U. Kusebauch, D. Shteynberg, L. Hood, and R. L. Moritz. 2015. “Opening a SWATH Window on Post-Translational Modifications: Automated Pursuit of Modified Peptides.” Molecular & Cellular Proteomics : MCP, December. http:/http://doi.org/10.1074/mcp.M115.054478.
  • Keller, A., S. L. Bader, D. Shteynberg, L. Hood, and R. L. Moritz. 2015. “Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS Using SWATHProphet.” Molecular & Cellular Proteomics : MCP, February.
  • Kim, T. K., A. Bheda-Malge, Y. Lin, K. Sreekrishna, R. Adams, M. K. Robinson, C. C. Bascom, J. P. Tiesman, R. J. Isfort, and R. Gelinas. 2015. “A Systems Approach to Understanding Human Rhinovirus and Influenza Virus Infection.” Virology 486 (December): 146–57. http://doi.org/10.1016/j.virol.2015.08.014.
  • Knijnenburg, T. A., T. Bismeijer, L. F. Wessels, and I. Shmulevich. 2015. “A Multilevel Pan-Cancer Map Links Gene Mutations to Cancer Hallmarks.” Chinese Journal of Cancer 34 (March): 48. http://doi.org/10.1186/s40880-015-0050-6.
  • Lalli, M. A., B. M. Bettcher, M. L. Arcila, G. Garcia, C. Guzman, L. Madrigal, L. Ramirez, et al. 2015. “Whole-Genome Sequencing Suggests a Chemokine Gene Cluster That Modifies Age at Onset in Familial Alzheimer’s Disease.” Molecular Psychiatry 20 (November): 1294–1300. http://doi.org/10.1038/mp.2015.131.
  • Lee, J. M., K. H. Kim, A. Shin, M. J. Chao, K. Abu Elneel, T. Gillis, J. S. Mysore, et al. 2015. “Sequence-Level Analysis of the Major European Huntington Disease Haplotype.” American Journal of Human Genetics 97 (September): 435–44. http://doi.org/10.1016/j.ajhg.2015.07.017.
  • Lee, H. J., J. M. Kim, K. H. Kim, J. I. Heo, S. J. Kwak, and J. A. Han. 2015. “Genotoxic stress/p53-Induced DNAJB9 Inhibits the pro-Apoptotic Function of p53.” Cell Death and Differentiation 22 (1): 86–95.
  • Lee, Ming-Jen, Ya-Fang Chen, Pi-Chuan Fan, Kuo-Chuan Wang, Kai Wang, Jinyuan Wang, and Meng-Fai Kuo. 2015. “Mutation Genotypes of RNF213 Gene from Moyamoya Patients in Taiwan.” J Neurol Sci 353 (June): 161–65. http://doi.org/10.1016/j.jns.2015.04.019.
  • Li, X., Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, et al. 2015. “Two Mature Products of MIR-491 Coordinate to Suppress Key Cancer Hallmarks in Glioblastoma.” Oncogene 34 (March): 1619–28. http://doi.org/10.1038/onc.2014.98.
  • Lin, B., H. Lee, J. G. Yoon, A. Madan, E. Wayner, S. Tonning, P. Hothi, et al. 2015. “Global Analysis of H3K4me3 and H3K27me3 Profiles in Glioblastoma Stem Cells and Identification of SLC17A7 as a Bivalent Tumor Suppressor Gene.” Oncotarget, January.
  • Liu, Y., M. Yasukawa, K. Chen, L. Hu, R. R. Broaddus, L. Ding, E. R. Mardis, et al. 2015. “Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma.” JAMA Oncology 1 (July): 486–94. http://doi.org/10.1001/jamaoncol.2015.1432.
  • Liu, Guoyan, Da Yang, Rajesha Rupaimoole, Chad V. Pecot, Yan Sun, Lingegowda S. Mangala, Xia Li, et al. 2015. “Augmentation of Response to Chemotherapy by microRNA-506 Through Regulation of RAD51 in Serous Ovarian Cancers.” J Natl Cancer Inst 107 (July). http://doi.org/10.1093/jnci/djv108.
  • Lopez Garcia de Lomana, A., S. Schauble, J. Valenzuela, S. Imam, W. Carter, D. D. Bilgin, C. B. Yohn, et al. 2015. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels 8: 207. http://doi.org/10.1186/s13068-015-0391-z.
  • Ludwig, Claudia, Monica Orellana, DeVault, Megan, Zac Simon, and Nitin Baliga. 2015. “Ocean Acidification.” The Science Teacher 082 (06). http://doi.org/10.2505/4/tst15_082_06_41.
  • Luo, J., P. Cimermancic, S. Viswanath, C. C. Ebmeier, B. Kim, M. Dehecq, V. Raman, et al. 2015. “Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.” Molecular Cell 59 (September): 794–806. http://doi.org/10.1016/j.molcel.2015.07.016.
  • Ma, Shuyi, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, and Nathan D. Price. 2015. “Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium Tuberculosis.” PLoS Computational Biology 11 (11): e1004543. http://doi.org/10.1371/journal.pcbi.1004543.
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