Pioneering the Future
PIONEERING THE FUTURE
Annual Report 2014

Annual Report 2014 From Our President

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The Transformative Power of Philanthropy


This year’s annual report features Bill Bowes, a San Francisco venture capitalist and philanthropist, and one of ISB’s biggest supporters. Bill has been a valued colleague and a good friend for many years – we started Amgen and Applied Biosystems together in the 1980s. He’s a true Renaissance man.

My colleagues and I are incredibly grateful for his extraordinary generosity to the Institute. His support has allowed us to hire new faculty which, along with his unwavering commitment for our pioneering approaches to research, is enabling us to lead the way in transforming medicine. It is unique individuals like Bill that present ISB with the resources we need to “invent the future of medicine.”

Optimizing Wellness and Minimizing Disease

While the American healthcare system continues to focus almost entirely on diagnosing and treating disease instead of keeping people well, ISB continues to make great strides in disrupting that system. In fact, we are at the forefront of establishing an entirely new healthcare sector – scientific wellness.

As always, my colleagues across ISB have made notable discoveries to advance the study of cancers, post-traumatic stress, tuberculosis, malaria, rare diseases (e.g. Adams-Oliver syndrome and peroxisomal disorders), ocean acidification, and various aspects of the microbial genome. We share some research highlights from 2014 later in this report.

But 2014 was particularly exciting because we brought the 100K Wellness Project to life. This Framingham-like study for the digital age was launched with a 10-month pilot study of 107 well individuals through the Hundred Person Wellness Project. The goals of this pilot were to:

  • Present actionable recommendations to the participants that could improve their health
  • Potentially identify transitions from disease-to-wellness, and wellness-to-disease
  • Document changes in health and wellness
  • Create a framework for establishing early transition markers and scientifically validated metrics for wellness
  • Develop a framework for scaling the project cost-effectively, including methodologies for real-world application

As discussed in detail in the Vision for the Future of Health Care section of this annual report, ISB made significant progress in each of these goals. We have also developed a pathway to scale the project from 100 to 100,000, with ISB focusing on its core scientific strengths and engaging with partners to recruit and directly engage with participants. Our first major partner is Arivale, the spin-out company that grew out of the pilot study. We believe that ISB and Arivale will together present the opportunity to transform the American healthcare system – moving it toward scientific wellness - and eventually bringing wellness potentially to all Americans, letting them optimize their human potential and avoid disease.

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

A Vision of the
Future of Healthcare

By Lee Hood, MD, PhD, President
Nathan Price, PhD, Associate Director
Sui Huang, MD, PhD, Professor

In this article we provide the background and a concise summary of the pathway the Institute for Systems Biology (ISB) followed to execute the Hundred Person Wellness Project – a longitudinal, pilot study on 107 well individuals in 2014 that created a dense and dynamical data cloud of billions of data points for each participant.

During the short duration of this pilot study, many of the participants made life-altering changes to improve their health and wellbeing, and ISB made some profound discoveries. In fact, what ISB learned far exceeded its expectations.

This pilot study was strikingly successful in:

  • Uncovering the potential for optimizing individual wellness.
  • Driving forward new scientific discoveries.
  • Document changes in health and wellness
  • Creating unique new partnership and other opportunities for ISB.

In the grander scheme, this is one key to the transformation of contemporary healthcare in that the adoption of scientific wellness throughout the system over time – will eventually create a medicine that is predictive, preventive, personalized and participatory (P4 medicine).

Introduction

Today, we spend more than 17% of the US GDP on healthcare – far more than any other country – and yet by many measures we are ranked near the bottom of the top 20 developed countries of the world in the quality of our healthcare. Over the past 15 years, ISB has pioneered a series of systems-driven (global) advances that have defined systems medicine (a systems or global approach to disease) and have begun to delineate P4 medicine. Indeed, over the past few years there has been a convergence of four major scientific and social thrusts to more completely define P4 medicine: systems medicine, big data/analytics, digital quantified-self measurements, and consumer/patient-activated social networks.

P4 Medicine

P4 medicine differs from contemporary medical practice in numerous ways:

  • It is proactive rather than reactive, addressing underlying issues that affect health before symptoms arise.
  • It focuses on parameters specific to individuals rather than relying on averages based on unstratified populations of patients.
  • It focuses on the importance of addressing wellness and disease rather than primarily disease.
  • It generates dense (billions of data points) and dynamical (repeated measurements over time) individual data clouds (high-dimensional “big” data, i.e., genomes, proteomes, metabolomes, gut microbiomes, clinical chemistry and quantified-self measurements). These dense and dynamical data clouds capture the key elements of health: genetics and environment.
  • These data can be integrated to identify the biological networks that govern development, physiology and aging. Determining how these networks are altered in diseases and how these “disease-perturbed networks” differ from their normal counterparts allow fundamental insights into disease mechanisms. Further, it becomes possible to design new strategies for identifying disease biomarkers and delineating leverage points for intervention, such as drug targets.
  • For clinical trials, P4 medicine highlights the importance of gathering large numbers of individuals with dense and dynamical data clouds for each participant and then segregating them according to the traits of interest (e.g., response to a drug, or adverse reactions to a drug). This view also showcases the importance of “N-of-one” (N=1) studies of clinical processes to gain deep insights into wellness or disease.
  • Importantly, whole genome sequencing coupled with these longitudinal data sets allows us to make predictions contextualized for each individual in order to specifically interpret dynamic measurements and networks that vary between individuals. Contemporary medicine uses large cohorts of individuals and treats them as uniform – even though each individual is genetically and environmentally unique. This averaging over highly heterogeneous populations obscures information on the individual that is relevant for personalized medicine and suffers from the problem of low signal-to-noise ratio, as exemplified by the failure of randomized clinical drug trials to predict drug effects on specific, individual patients.
  • Online social networks are important for educating patients (and physicians), about this emerging P4 medicine. They also help build community and create relationship-based accountability, which increases motivation for long-term lifestyle change. Crowdsourcing provides individuals the opportunity to discover and share new ways to improve their own health through aggregated – but not averaged, knowledge. It also provides individuals with a means to persuade their own physicians (sometimes conservative or reluctant) to embrace and understand the new concept of scientific wellness and the power of P4 medicine – and it creates change agents in the often rigid current system.

Scientific Wellness: A New Industry and an Untapped Market

P4 medicine has two central thrusts – improving wellness and helping to avoid disease. Perhaps 97% of society’s healthcare resources are spent on disease and very few on wellness. Accordingly, wellness – and how to enhance it and extend it – has not been studied very thoroughly by scientists. ISB proposes to change this by taking a systems – approach to understanding wellness – and thereby make it scientific. For example, we will establish quantitative metrics that will allow us to evaluate both the physiological and psychological aspects of wellness.

Scientific wellness will emerge as a new sector in healthcare. Our prediction is that within a 10-15 year period the wellness industry will promote such a dramatic shift in healthcare dollars from the disease to the wellness sectors that the scientific wellness industry will exceed the “disease” industry in market cap. ISB, being at the source of the first dense and dynamical data clouds, is well positioned to catalyze companies that will populate this new arena of scientific wellness – and perhaps even create the Google of this emerging industry.

Bringing P4 Medicine to the Healthcare System

A critical question has always been how to bring P4 medicine to the healthcare system. In ISB’s 2012 annual report, one of us (LH) first suggested a longitudinal Framingham-like study for the digital age that would include 100,000 well individuals and would delineate a dense and dynamical data cloud for every participant.

In 2014, Lee Hood and Nathan Price and other ISB colleagues initiated the Hundred Person Wellness Project – a 10-month pilot study with 107 individuals. This project has been extremely valuable for both the participants – and the study team for the deep science we have learned. The Hundred Person Wellness Project is the first real-world test of Hood’s P4 medicine paradigm – that is, using a systems approach to ultimately transform healthcare. The pilot study focused on optimizing wellness through longitudinal data collection from whole-genome sequencing, clinical laboratory tests (3x), gut microbiome (3x), and quantified-self measurements (diet, exercise, sleep, etc.) from each individual. These dense and dynamical individual data clouds have revealed multiple “actionable possibilities” for each participant -- that if acted upon either improved their wellness or helped them to prevent a disease. Each of the participants was aided in interpreting their data by a wellness coach who played a critical role in bringing the actionable possibilities to the individuals’ attention and in guiding them on how to change their behaviors by acting on the actionable possibilities.

At the individual level, participants had an opportunity to get a snapshot of what it truly means to begin to optimize their health and hopefully avoid disease. Most of them established a new and very personalized baseline for their own health and 70% of them acted on the coaching recommendations provided. Continued measurements also allowed participants to observe firsthand the responses to their behavior changes, which further motivated them over the course of the study. They also realized that new actionable possibilities will emerge over time with changes to their individual environment and lifestyle.

These data have opened up exciting new opportunities for examining the dark matter of human biology and disease, areas that no one has ever traversed before by creating more than 35,000 fascinating data correlations. Strikingly powerful analytical tools have been developed in the course of analyzing this first-of-its-kind data set. This effort has resulted in a rich database of results, which is poised to expand dramatically in the years ahead.

When ISB launched this study in 2014, it hoped to develop a series of stories about how actionable opportunities have changed the wellness of the participants – or made them aware of how they can avoid disease in the future. The pilot study results greatly exceeded ISB’s expectations and below are a few examples from the participants:

  • One participant that was homozygous (inherits one bad copy of a gene from each parent) for a gene that can cause hereditary hemochromatosis, a condition of excess iron absorption. He also had very high iron biomarkers from the first blood draw lab results, showing that the disease he was at genetic risk for had manifested itself. The individual was referred to his physician and was diagnosed with hemochromatosis and treatment was initiated. If untreated, hemochromatosis leads to joint degeneration, liver fibrosis, heart failure and diabetes – and chronic disease. With proper treatment, which this individual received, all of this can be avoided.
  • Forty-three participants entered the study meeting diagnostic criteria for pre-diabetes. By the end of the study, seven individuals had completely normalized blood sugar and many others had favorable improvements in their pre-diabetes markers.
  • Another individual had been working with her physician because of unexplained high levels of inflammation. The Study Team discovered that the individual had an abnormal microbe in her gut microbiome and so was started on prebiotic and probiotic supplements. After three months the inflammatory markers in the blood had normalized.

Scientific wellness will emerge as a new sector in healthcare. Our prediction is that within a 10-15 year period the wellness industry will promote such a dramatic shift in healthcare dollars from the disease to the wellness sectors that the scientific wellness industry will exceed the “disease” industry in market cap. ISB, being at the source of the first dense and dynamical data clouds, is well positioned to catalyze companies that will populate this new arena of scientific wellness – and perhaps even create the Google of this emerging industry.

  • A number of the 107 participants viewed this study as the experience of a lifetime.
  • Many realized that given the proper information, they could make decisions for themselves to improve their health in ways they didn’t previously appreciate. Over time, this can have enormous effects on reducing risk for downstream debilitating and expensive chronic and other diseases. This is central to reducing the cost of healthcare.
  • Most came to realize that genetics do not determine their destiny, but rather their potential for wellness or disease. With appropriate changes in behavior and lifestyle, one can circumvent many genetic limitations.
  • Almost all individuals came to the study with the view that they were (for the most part) well. However, the study exposed for all individuals multiple actionable possibilities that could be acted upon to improve their wellness. This illustrated that most of us have unrealized potential for optimizing our wellness. Ongoing access to data measuring our individual state of wellness is critical for taking advantage of this potential. The fact that we will continue to discover new actionable possibilities as we integrate more data from such studies suggests that scientific wellness will be a lifelong journey of wellness opportunities.
  • All individuals were convinced that the coach played a key role in achieving a 70% compliance to actionable possibilities – a remarkable accomplishment.
  • Finally, most individuals wanted to go on to the next stage of the study.

ISB is moving forward with this study in two distinct directions.

Because of the remarkable advances in scientific wellness and ISB’s unique role in this nascent area, we are strategically positioned to catalyze the adoption of P4 medicine by the US healthcare system. In fact, we are seeking out clinical and academic partners that will enable the many different possibilities outlined in this document – and are exploring a number of exciting opportunities in this arena.

Strategic Partnerships

We are seeking out strategic partners, both national and international, both industry and academia, to identify relevant populations of individuals to interrogate for wellness or in which the transition from wellness to disease (or the inverse) can be identified in real-time. This is why expanding disease monitoring to encompass the wellness time period is critical. Such longitudinal data at the individual level allows for the new dimension of dynamics in the dense data clouds. Examples of partnerships that we are exploring include the following:

  • A scientific wellness study of individuals from the Aboriginal tribes of Australia is being organized. This will demonstrate that scientific wellness studies can be carried out for the poor as well as the rich or the middle class.
  • A study of individuals that have gone through the difficult treatment of breast cancer. This will demonstrate the power of scientific wellness to transform the post-treatment lives of cancer patients.
  • A study of middle class Indians (country) that is focused on wellness in conjunction with diabetes. This is an important study as diabetes is a disease that we know how to address and it would tackle a major healthcare issue for India (and most other developed, as well as developing countries) with the power of scientific wellness.
  • A scientific wellness study of 100-200 individuals with new types of assays with powerful new microfluidic approaches that measure complex phenotypes, epigenetics, and many immunological parameters. This parallels efforts at ISB to miniaturize, automate, integrate and parallelize relevant wellness assays. Efforts like these are leading to the digitization of medicine – with potential impact like that of the digitization of communication (smart phones) that greatly reduce the costs, while opening up previously unfathomable new forms of services. Digitization of medicine is critical to strikingly reduce the cost of healthcare – democratizing scientific wellness to benefit the poor as well the rich.
  • International partnerships to extend P4 medicine. ISB is also exploring the possibility of bringing scientific wellness to the healthcare systems of several countries, moving beyond the US to catalyze impact around the world.
  • Transforming medical education and bringing it into the 21st century. ISB is currently exploring this opportunity with a number of existing medical schools, although it would be ideal to launch this with a new medical school to avoid the conservative constraints of the past.

For example, we could enroll a freshman class of medical students in a program similar to the Hundred Person Wellness Project for all four years of their education. Each year, we would design courses of increasing sophistication to enable them to learn about systems medicine, emerging technologies, systems-driven strategies and P4 medicine. This would recast classical medical school topics as they would be viewed through the lens of system thinking, combined with the integration and analysis of their own data. Four authors at ISB are just finishing a textbook on systems biology and systems medicine that could be instrumental in initiating this effort.

Arivale – A Scientific wellness company

We launched a scientific wellness company, Arivale, directed at bringing scientific wellness to the consumer in a way that will emulate the strategy of the Hundred Person Wellness Project described above. This is an attractive opportunity because it will permit us to generate 5,000 - 10,000 dense and dynamical data clouds in the next 18 months – optimizing wellness and minimizing disease for 100 times more individuals than in the Hundred Person Wellness Project.

This provides a scalable model to ultimately bring scientific wellness to vast numbers of individuals. With data from these individuals we can drive the scientific discoveries forward to move this field ahead and provide individuals with vastly expanded actionable possibilities to enhance their wellness and minimize their risk for disease.

ISB has an agreement with Arivale to analyze all of these data for consenting participants – opening up new opportunities for understanding human wellness and disease transitions, as well as exploring the dark matter of human biology and disease. The Arivale data will create possibilities for exciting new industrial strategic partnerships.

Our Vision for the Future of Healthcare

  • P4 medicine will play a central role in healthcare of the future and in increasing wellness. Medicine will truly achieve the 4 Ps (participatory, the 4th P – means that the individual is at the center of his / her own healthcare).
  • The health and disease states are assessed by evaluating both the genetics and the environments of each individual. Analyzing the dense and dynamical data clouds provides a powerful approach to assessing these two components and identifying actionable possibilities.
  • Scientific wellness plays two important roles:
    • It maximizes human potential by optimizing both physiological and psychological possibilities.
    • With sufficient numbers of participating individuals, the data clouds allow us to define the signatures of wellness-to-disease transitions for all of the major diseases. We can then identify the earliest signs of an impending disease transition and use systems approaches to delineate the disease-perturbed networks--and thus develop the diagnostic and therapeutic reagents necessary to reverse the disease at the earliest possible stage. Such preemptive action across the spectrum of diseases will save the healthcare system billions of dollars.
  • The scientific wellness industry will open tremendous opportunities for innovation and company creation. This will be a major driving force for the creation of cheaper and better assays that will lead to the digitalization of medicine. This will drastically reduce its cost – to the point where the rich as well as the poor can be served. This, in turn, will lead to a democratization of healthcare unimaginable even a few years ago.
  • Tens of thousands of dense and dynamical data clouds will provide the information necessary to fundamentally change how pharmaceutical, biotechnology, nutrition and diagnostic companies practice their science. Longitudinal dynamical studies on tens of thousands of individuals from genetically stratified populations will transform how we understand early disease mechanisms, identify novel panels of biomarkers and drug candidates and come to understand nutrition in an increasingly sophisticated manner.

In the context of these observations, suppose that we could elevate normal individuals to the status of the wellderly by having them participate in a scientific wellness study and respond to all of their emerging actionable possibilities throughout their entire lives. If so, one could lead a mentally and physically active life far into the 90s. If scientific wellness can bring you to 100 as an effectively functioning individual, when you die it will most likely happen very quickly. This also suggests that scientific wellness must be a lifelong journey.

Looking Ahead

This is a unique time in the history of ISB. We need to go forward boldly to “invent the future” of healthcare. In E. O. Wilson’s terms we are witnessing for healthcare a “consilience” or grand unification of science, the social sciences and the humanities – that extends far beyond the conventional cross-disciplinary nature of systems approaches to science itself, which ISB has pioneered. Together, systems medicine, P4 medicine and the opportunities that have been created as a result of the Hundred Person Wellness Project will lead the way for a transformation of US and international healthcare.

Headlines 2014Click on any of the images to learn more.

FinancialsFor the Year Ending December 31, 2014

5-Year Overview
Research Operating Expenses vs. Total Revenue

Statement of Activities
Dollars in Thousands

Revenues
$
%
Grants & Contract Revenue
23,244
65.7
Contributions
7,896
22.3
Investment & Other Income
4,260
12.0
Total Revenues
35,400
100.0
Expenditures
$
Research & Other Direct Costs
24,322
Management & General
11,460
Fundraising & Other
188
Total Expenditures
35,970
Decrease in Net Assets
(570)

Balance Sheet
Dollars in Thousands

Assets
$
Cash & Investments
18,427
Other Assets
13,549
Property & Equipment (Net)
10,578
Total Assets
42,554
Liabilities
$
Accounts Payable & Accrued Expenses
14,825
Deferred Revenues
3,731
Notes Payable
7,782
Total Liabilities
26,338
Net Assets
$
Unrestricted Net Assets
(197)
Temporarily Restricted Net Assets
7,741
Permanently Restricted Net Assets
8,672
Total Net Assets
16,216
bowes

 

Bill Bowes:
A Quiet Force For Social Good
By Gene Stout


When Bill Bowes and Dr. Lee Hood met in 1980, they began a business relationship and friendship that was sealed over a clunker of a machine hiding in a basement at Caltech. Hood had invented a device that automated protein sequencing that he believed would transform biology.

“It was completely unmanufacturable,” says Bowes. “But it was potentially useful.”

Indeed, Hood had presented his prototype to 19 medical device companies and was rejected 19 times. But Bowes recognized Hood’s “imaginative inventiveness” and agreed to invest $2 million to develop this sequencer.

“This was a machine that really took a lot of ingenious thinking to come up with,” Bowes says. “Lee had a this-is-going-to-change-the-world kind of attitude and he was a good salesman (full of) rambunctiousness.”

Bowes, who received a BA in economics from Stanford University and an MBA from Harvard Business School, began his career as an investment banker in the 1950s. In 1980, he launched U.S. Venture Partners and then shifted his efforts to philanthropy in 1992 with the founding of the William K. Bowes Jr. Foundation. The Foundation boasts more than $400 million in assets and grants nearly $40 million per year to nonprofits focused on medical research (stem cells and cancers), college access, arts, and higher education.

While Bowes focuses most of his philanthropy on causes based in his native San Francisco (such as the Exploratorium – a sprawling educational facility with 500 interactive science exhibits that Bowes suggests the wearing of “track shoes” is necessary to explore), he has contributed a total of $18 million to Institute for Systems Biology during his tenure of more than a decade on ISB’s board of directors. ISB is one of the top beneficiaries of the William K. Bowes Jr. Foundation.

“Bill is really interested in first-class science,” says Hood, who co-founded ISB in 2000 and serves as its president. “But he has many talents and great dimensionality, with broad interest in the arts, music and civics. He’s really an exceptional person.”

Bowes, now in his late 80s, is a kindly and soft-spoken World War II veteran who followed his instinct to champion biomedical research, education and social good. He made shrewd investments in biotechnology and high tech companies, notably Amgen, Applied Biosystems and Sun Microsystems, which helped him accumulate a fortune that he is now leveraging to make long-lasting improvements in society and the lives of others.

In an interview at his foundation headquarters at One Maritime Plaza in San Francisco, Bowes shared his story and why he’s been such an ardent supporter of ISB.

Q: As a member of the board of directors of ISB, what goals do you support for the organization?

Bowes: To change the way medicine is done. Cheaper and better. Simple as that.

Q: What inspired you to become a venture capitalist?

Bowes: One of the real pioneers of venture capital was a guy named Georges Doriot, who was in Boston and taught a class at Harvard Business School. It was a very popular and inspiring class. I guess that kind of got me started, even though I didn’t go into venture capital for another few decades. But when I started investment banking, venture capital didn’t really exist.

Q: What motivates you as a venture capitalist and philanthropist with a passion for scientific advancement?

Bowes: I guess medical research. I support individual scientists who are young and terrific and they’re in those particular years when money’s hard to come by. They’re not eligible for grants yet. So that’s where I come in at various institutions.

Q: How did you meet Dr. Hood?

Bowes: I had made an informal but pretty intensive survey of southern California scientists. We were going to place Amgen in southern California because of the excellence of the science there that had not yet been spoken for by a company. And after getting to know Lee Hood at Caltech, I learned that he had a machine down in the basement which was useful.

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Lee Hood with his protein sequencer at Caltech in the 1980s.

 

Q: The protein sequencer?

Bowes: Yes. So I went over to see him. He was in his office and wearing Lederhosen, which appealed to me. And his machine looked really good. Completely unmanufacturable. Sort of a clunker. But potentially useful. What took a lot of time was to get the intellectual property problems resolved with Caltech. They were business-unfriendly in those days. But they finally said, ‘OK.’ We sort of wore them down.

Q: What was the next step in the development of the protein sequencer?

Bowes: We found a guy at Hewlett-Packard, Sam Eletr, and his job was to take products like Lee Hood’s that had been tossed over the wall, and he would product-tize them. That was his job. He was a brilliant engineer.

Q: This led to the launch of Applied Biosystems?

Bowes: Yes. We moved the company up here to the Bay Area. And put Sam in charge of it. And we financed the company by getting big companies to put in deposits for early machines, which was very non-dilutive financing. We had venture capital in there too, of course. The company just did extremely well. And after a number of years, it was bought by another big company, Life Technologies.

Q: You have a knack for recruiting and hiring people to run new companies, such as George Rathmann at Amgen. What did you see in his leadership abilities at the time you were launching the company?

Bowes: George was a proven leader. He had a big job at 3M, and he had a big job at Abbott Laboratories. He ran diagnostics. He got interested in the new biology and he took a sabbatical from Abbott and spent a year at UCLA in a lab there. So he was the perfect guy. He had executive experience, and he was interested in the new biology. And he was willing to leave a lush life on the North Shore of Chicago and come live in Ventura, Calif., and start with three other people from scratch. Dead scratch. That’s the kind of guy you want.

Q: You also serve on the boards of the Asian Art Museum, Grace Cathedral and the Hoover Institution at Stanford. And you’re also a jazz fan. Is there an entity here in San Francisco that you support?

Bowes: SF Jazz. Just last year they finished their new building. They’ve been in venues all over the city, and now they have their own place. The only other one in the country like it is in New York.

Q: What role did you have in the construction of that building?

Bowes: I was a contributor. I was on the campaign committee, and I did some individual investing. I helped choose the architect and so forth. I’m really proud of how it turned out. It’s probably got the best sound in San Francisco.

Q: Did your interest in jazz begin in the ‘40s?

Bowes: Yeah

Q: Anyone in particular?

Bowes: Louis. Louis Armstrong. He used to come to town with his gang twice a year. I never missed it. I love the way he played the trumpet. And he could sing a little too. Or growl. And Jack Teagarden. He was local. And Earl “Fatha” Hines. The whole gamut.

Q: Were there other people in American culture and society that you admired? Musicians, artists, scholars?

Bowes: Maybe Mike (John Michael) Bishop, who was a Nobel Laureate at UCSF. And Stan Prusiner, same thing. And I’m a great admirer of John Hennessey, the president of Stanford University. There’s a real long list, I guess.

Q: You’re a member of the executive committee of the San Francisco Conservatory of Music. What are their objectives?

Bowes: It’s an absolutely first-class conservatory. The plan now is to have student living quarters right there because it’s been a big competitive disadvantage for them compared to other schools where the students can live in a nice apartment right on the grounds. Their students are scattered around the city. So we bought two buildings, and we’re going to transform them into student housing. We think that’s going to make a huge difference in the quality of students we attract. Everyone wants to come to San Francisco, but not everyone wants to scramble for housing.

Q: What do you do for the Environmental Defense Fund?

Bowes: What I like about EDF is that you can invest in individual projects there and not throw money into the pot. So I have some individual initiatives inside EDF that suit me better than just putting money in.

Q: What for example?

Bowes: Bringing back the fisheries of the world. We started in Alaska with halibut. The halibut were getting less and less populous in the sea, and all the authorities could think of was to shorten the season. So they got down to three weeks in a season and mayhem on the water as everyone was trying to get their fish all at one time. And the fish were rapidly piling up on the docks and becoming unsalable.

Q: What was your solution?

Bowes: And so we instituted a program that was experimental at first. A program called “catch share,” which determined scientifically how much fish a body of water could sustainably produce and then divide it among the local fishermen to get their share of the catch. They can do it any time of the year they want, and that’s what they have, no more and no less. They find that their share increased over the years as the fish population increased. And they’re finding that their fish are more valuable because they’re not being caught all at once, they’re being caught through the year. And they get down to the market in prime shape.

Q: How did your childhood shape you? Your father was a businessman and your mother a physician. What did you learn from them that was helpful later on?

Bowes: Nothing specific. But it was a very nice combination of parents to be brought up around.

Q: Your mother was one of the first two women to graduate from Stanford School of Medicine. Was she also an exceptional parent?

Bowes: She was a fantastic person. I was impressed that she went back to teaching at Stanford Medical School when the war broke out. She did that for two or three years. It was hard work. But it kept her on her toes.

2014 ContributorsSpecial thanks to the following believers in the promise of systems biology

$100,000+
Mark Ashida and Lisbet Nilson
William K. Bowes, Jr. Foundation
Fenwick & West LLP
Lee Hood and Valerie Logan
Roger M. Perlmutter
Dave and Sandra Sabey
Sabey Corporation
Wilke Family Foundation
$25,000 - $99,999
Douglas Howe and Robin DuBrin
Craig and Marie Mundie
Gil Omenn and Martha Darling
$10,000 - $24,999
Amgen Foundation
David Barker and Jeanne Loring
Timothy and Irene Kilgallon
Louis G. Lange
Clayton Lewis and Tom Rasmussen
Dan Ling and Lee Obrzut
Rob Lipshutz and Nancy Wong
M.J. Murdock Charitable Trust
Muckleshoot Charity Fund
Sciex LLC
Dan Ling and Lee Obrzut
Doug and Maggie Walker
Robert and Joan Wallace
Tayloe Washburn and Deborah Winter
$2,500 - $9,999
Agilent Technologies, Inc.
Amy and Matt Rudolf
Aron and Sara Thompson
Bevan J. Annaloro
Brian and Carrie Chee
Carole Ellison
Complete Genomics, Inc.
David S. Anderson
Dee Dickinson
Douglas C. Fisher
Ed Lazowska
Edward Lin
Exiqon, Inc.
Gregory T. Lucier
Ian Tolmie and Jennifer Black
Integrated Diagnostics, Inc.
Jason and Amanda Stoffer
JKW Medical Group LLC
John C. Rudolf
Kilroy Realty Corporation
Kim P. Kamdar
Larry L. Smarr
Life Technologies Corporation
Michael R. Flory
MNX
Nina S. Kjellson
Robert J. Martin
Ron and Darlene Howell
Ron and Sara Seubert
Russ and Gemma Daggatt
Salal Credit Union
Scott W. Daggatt
Short-Dooley Family Foundation
Steve and Kathanne Moore
TD's of Clemson, Inc.
The Boeing Company
The Greer/Solien Fund
The Myhrvold Family Charitable Fund
The Senyei Family Foundation
Touchstone Corporation
Tulalip Tribes Charitable Contributions
Washington Research Foundation
Wells Fargo Insurance Services USA, Inc.
$1,000 - $2,499
John and Leslie Aitchison
Marne Anderson
Ray and Edith Aspiri
Nitin Baliga and Janet Ceballos
Robert and Beatrice Bast
Terry Bergeson
Sissy and Tom Bouchard
Bristol-Myers Squibb Company
Carolynne Bryant-Dowdy
Suzanne Burke
Tom and Barbara Cable
Jane and Terry Chadsey
Peter and Susan Cheney
Ellison Foundation
Myron and Sue Hood
Floyd U. Jones
Kim and Ralph Klinke
Jim and Sherry Ladd
Nick Newcombe
Don and Melissa Nielsen Family Foundation
Patti Payne
Carl and Carole Scandella
Erich C. Strauss
Sheryl and Pack Suchoknand
$500 - $999
Arne and Mary Anderson
Katherine Barnett and David Badders
Inyoul Lee and Myungkee Min
Cammi Libby
B Lippit
Lisa Mayfield
Nicholas Naylor-Leyland
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To demonstrate your belief in the promise of systems biology in 2015:

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
Mark Ashida
CEO
Symform
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
Robert T. Nelson
Co-founder and
Managing Director
ARCH Venture Partners
Roger Perlmutter, MD, PhD
Executive Vice President and President
Merck Research Laboratories
Louis G. Lange, MD, PhD
Senior Advisor
Gilead
Drew Senyei, MD
Managing Director
Enterprise Partners Venture Capital
J. Leighton Read, MD
General Partner Alloy Ventures

Senior Leadership

President and Co-Founder
Senior Vice President and Director
Associate Director
Chief Operating Officer & Treasurer
Chief Legal Officer, Chief Compliance Officer & Secretary

Faculty

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

Principal Scientist

Kai Wang, PhD

Senior Research Scientists

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

Senior Research Scientists (continued)

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

Senior Research Engineer

Chris Lausted

Senior Software Engineers

Ryan Bressler
Dick Kreisberg
Bill Longabaugh
Hector Rovira
Natalie Tasman

Senior IT Analyst

Kerry Deutsch, PhD

Publications2014 Aggregate

  • Bundgaard, Louise, Stine Jacobsen, Mette Aamand Sørensen, Zhi Sun, Eric W. Deutsch, R. L. Moritz, and Emøke Bendixen. 2014. “The Equine PeptideAtlas–a Resource for Developing Proteomics-Based Veterinary Research.” Proteomics.
  • Brownstein, Catherine A., Alan H. Beggs, Nils Homer, Barry Merriman, Timothy W. Yu, Katherine C. Flannery, Elizabeth T. DeChene, et al. 2014. “An International Effort towards Developing Standards for Best Practices in Analysis, Interpretation and Reporting of Clinical Genome Sequencing Results in the CLARITY Challenge.” Genome Biol 15: R53. doi:10.1186/gb-2014-15-3-r53.
  • Benedict, M. N., J. R. Henriksen, W. W. Metcalf, R. J. Whitaker, and N. D. Price. 2014. “ITEP: An Integrated Toolkit for Exploration of Microbial Pan-Genomes.” BMC Genomics 15 (1): 8.
  • Bai, Jane PF, Robert J. Fontana, Nathan D. Price, and Vineet Sangar. 2014. “Systems Pharmacology Modeling: An Approach to Improving Drug Safety.” Biopharmaceutics & Drug Disposition 35 (1): 1–14.
  • Ekici, Seda, Serdar Turkarslan, Grzegorz Pawlik, Andrew Dancis, Nitin S. Baliga, Hans-Georg Koch, and Fevzi Daldal. 2014. “Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production.” mBio 5 (1): e01055–13.
  • Gierman, Hinco J., Kristen Fortney, Jared C. Roach, Natalie S. Coles, Hong Li, G. Glusman, Glenn J. Markov, et al. 2014. “Whole-Genome Sequencing of the World’s Oldest People.” PLoS One 9: e112430. doi:10.1371/journal.pone.0112430.
  • Hu, Zhiyuan, Christopher Lausted, Hyuntae Yoo, Xiaowei Yan, Amy Brightman, Jiankui Chen, Weizhi Wang, Xiangli Bu, and Leroy Hood. 2014. “Quantitative Liver-Specific Protein Fingerprint in Blood: A Signature for Hepatotoxicity.” Theranostics 4: 215–28. doi:10.7150/thno.7868.
  • Chiang, Jung-Hsien, Wan-Shu Cheng, Leroy Hood, and Qiang Tian. 2014. “An Epigenetic Biomarker Panel for Glioblastoma Multiforme Personalized Medicine through DNA Methylation Analysis of Human Embryonic Stem Cell-like Signature.” Omics: A Journal of Integrative Biology.
  • Carr, S. A. et al. Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach. Molecular & Cellular Proteomics mcp. M113. 036095 (2014).
  • Garmendia-Torres, C. et al. Unidirectional P-Body Transport during the Yeast Cell Cycle. PLoS ONE 9, e99428 (2014).
  • Guo, Fei, Brittany C. Parker Kerrigan, Da Yang, Limei Hu, Ilya Shmulevich, Anil K. Sood, Fengxia Xue, and Wei Zhang. 2014. “Post-Transcriptional Regulatory Network of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions.” J Hematol Oncol 7: 19. doi:10.1186/1756-8722-7-19.
  • Ghaffarizadeh, A., Podgorski, G. J. & Flann, N. S. Modeling and visualizing cell type switching. Computational and mathematical methods in medicine 2014, 293980 (2014).
  • Glusman, G., Cox, H. C. & Roach, J. C. Whole-genome haplotyping approaches and genomic medicine. Genome Med 6, 73 (2014).
  • Chevillet, J. R., Lee, I., Briggs, H. A., He, Y. & Wang, K. Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules 19, 6080–105 (2014).
  • Krishna, Abhimanyu, Maria Biryukov, Christophe Trefois, Paul M. A. Antony, Rene Hussong, Jake Lin, Merja Heinäniemi, et al. 2014. “Systems Genomics Evaluation of the SH-SY5Y Neuroblastoma Cell Line as a Model for Parkinson’s Disease.” BMC Genomics 15: 1154. doi:10.1186/1471-2164-15-1154.
  • Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research 42, D231–9 (2014).
  • Lopes, M., B. Kutlu, M. Miani, C. H. Bang-Berthelsen, J. Storling, F. Pociot, N. Goodman, et al. 2014. “Temporal Profiling of Cytokine-Induced Genes in Pancreatic Beta-Cells by Meta-Analysis and Network Inference.” Genomics, January.
  • Turkarslan, S., E. J. Wurtmann, W. J. Wu, N. Jiang, J. C. Bare, K. Foley, D. J. Reiss, P. Novichkov, and N. S. Baliga. 2014. “Network Portal: A Database for Storage, Analysis and Visualization of Biological Networks.” Nucleic Acids Res 42 (1): D184–90.
  • Vialas, V., Z. Sun, Y. Penha C. V. Loureiro, M. Carrascal, J. Abian, L. Monteoliva, E. W. Deutsch, R. Aebersold, R. L. Moritz, and C. Gil. 2014. “A Candida Albicans PeptideAtlas.” Journal of Proteomics 97 (January): 62–68.
  • Lausted, C., I. Lee, Y. Zhou, S. Qin, J. Sung, N. D. Price, L. Hood, and K. Wang. 2014. “Systems Approach to Neurodegenerative Disease Biomarker Discovery.” Annual Review of Pharmacology and Toxicology 54 (January): 457–81.
  • Surmann, Kristin, Stephan Michalik, Petra Hildebrandt, Philipp Gierok, Maren Depke, Lars Brinkmann, Jörg Bernhardt, et al. 2014. “Comparative Proteome Analysis Reveals Conserved and Specific Adaptation Patterns of Staphylococcus Aureus after Internalization by Different Types of Human Non-Professional Phagocytic Host Cells.” Front Microbiol 5: 392. doi:10.3389/fmicb.2014.00392.
  • Rustad, Tige R., Kyle J. Minch, Shuyi Ma, Jessica K. Winkler, Samuel Hobbs, Mark Hickey, William Brabant, et al. 2014. “Mapping and Manipulating the Mycobacterium Tuberculosis Transcriptome Using a Transcription Factor Overexpression-Derived Regulatory Network.” Genome Biol 15: 502. doi:10.1186/PREACCEPT-1701638048134699.
  • Hu, Z., C. Lausted, H. Yoo, X. Yan, A. Brightman, J. Chen, W. Wang, X. Bu, and L. Hood. 2014. “Quantitative Liver-Specific Protein Fingerprint in Blood: A Signature for Hepatotoxicity.” Theranostics 4 (2): 215–28.
  • Richards, Matthew A., Victor Cassen, Benjamin D. Heavner, Nassim E. Ajami, Andrea Herrmann, Evangelos Simeonidis, and Nathan D. Price. 2014. “MediaDB: A Database of Microbial Growth Conditions in Defined Media.” PLoS One 9: e103548. doi:10.1371/journal.pone.0103548.
  • Lausted, Christopher, Inyoul Lee, Yong Zhou, Shizhen Qin, Jaeyun Sung, Nathan D. Price, Leroy Hood, and Kai Wang. 2014. “Systems Approach to Neurodegenerative Disease Biomarker Discovery.” Annu Rev Pharmacol Toxicol 54: 457–81. doi:10.1146/annurev-pharmtox-011613-135928.
  • Laczny, C. C., Pinel, N., Vlassis, N. & Wilmes, P. Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction. Scientific reports 4, 4516 (2014).
  • Li, H., G. Glusman, H. Hu, Shankaracharya, J. Caballero, R. Hubley, D. Witherspoon, et al. 2014. “Relationship Estimation from Whole-Genome Sequence Data.” PLoS Genetics 10 (1): e1004144.
  • Beer, K. D., E. J. Wurtmann, N. Pinel, and N. S. Baliga. 2014. “Model Organisms Have Memory of Complex Ecologically-Relevant Environmental Variation.” Applied and Environmental Microbiology, January.
  • Hao, D. et al. Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. European journal of human genetics : EJHG (2014).
  • Kusebauch, U., E. W. Deutsch, D. S. Campbell, Z. Sun, T. Farrah, and R. L. Moritz. 2014. “Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics.” Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.] 46: 13 25 1–13 25 28.
  • Randhawa, M., Sangar, V., Tucker-Samaras, S. & Southall, M. Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway. PLoS ONE 9, e90367 (2014).
  • Li, H., Glusman, G., Huff, C., Caballero, J. & Roach, J. C. Accurate and robust prediction of genetic relationship from whole-genome sequences. PloS one 9, e85437 (2014).
  • Qi, L. et al. Contemporary avian influenza A virus subtype H1, H6, H7, H10, and H15 hemagglutinin genes encode a mammalian virulence factor similar to the 1918 pandemic virus H1 hemagglutinin. MBio 5, e02116 (2014).
  • Rosenberger, George, Ching Chiek Koh, Tiannan Guo, Hannes L. Röst, Petri Kouvonen, Ben C. Collins, Moritz Heusel, et al. 2014. “A Repository of Assays to Quantify 10,000 Human Proteins by SWATH-MS.” SCIENTIFIC DATA 1.
  • Ruusuvuori, P., J. Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, and A. M. Dudley. 2014. “Quantitative Analysis of Colony Morphology in Yeast.” BioTechniques 56 (1): 18–27.
  • Schoggins, J. W., D. A. Macduff, N. Imanaka, M. D. Gainey, B. Shrestha, J. L. Eitson, K. B. Mar, et al. 2014. “Pan-Viral Specificity of IFN-Induced Genes Reveals New Roles for cGAS in Innate Immunity.” Nature 505 (7485): 691–95.
  • Labhsetwar, Piyush, John Cole, Nathan Price, and Zaida Luthey-Schulten. 2014. “Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression.” Biophysical Journal 106 (2): 644a.
  • Stolyar, S. et al. Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a. Genome Announc 2, (2014).
  • Westerhoff, H. V. et al. Macromolecular networks and intelligence in microorganisms. Front Microbiol 5, 379 (2014).
  • Kash, J. C. et al. Treatment with the reactive oxygen species scavenger EUK-207 reduces lung damage and increases survival during 1918 influenza virus infection in mice. Free radical biology & medicine 67, 235–47 (2014).
  • Wang, Yi, Holger Janssen, Caroline B. Milne, Andrew T. Magis, Yong-Su Jin, Nathan D. Price, and Hans P. Blaschek. 2014. “136. Understanding Fundamental Aspects of Butanol Production by Clostridium Beijerinckii.” 2014 Genomic Science Contractor-Grantee Meeting XII, 234.
  • Muller, Emilie E. L., Nicolás Pinel, Cedric C. Laczny, Michael R. Hoopmann, Shaman Narayanasamy, Laura A. Lebrun, Hugo Roume, et al. 2014. “Community-Integrated Omics Links Dominance of a Microbial Generalist to Fine-Tuned Resource Usage.” Nat Commun 5: 5603. doi:10.1038/ncomms6603.
  • Galhardo, M. et al. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Res 42, 1474–96 (2014).
  • Huang, S. 2014. “When Correlation and Causation Coincide.” Bioessays 36 (January): 1–2. doi:10.1002/bies.201370003.
  • Lindner, Scott E., Mark J. Sartain, Kiera Hayes, Anke Harupa, R. L. Moritz, Stefan H. I. Kappe, and Ashley M. Vaughan. 2014. “Enzymes Involved in Plastid-Targeted Phosphatidic Acid Synthesis Are Essential for Plasmodium Yoelii Liver-Stage Development.” Mol Microbiol 91 (February): 679–93. doi:10.1111/mmi.12485.
  • Danziger, S. A., A. V. Ratushny, J. J. Smith, R. A. Saleem, Y. Wan, C. E. Arens, A. M. Armstrong, et al. 2014. “Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data.” Nucleic Acids Research 42 (3): 1442–60.
  • Thyme, S. B. et al. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic acids research 42, 2564–76 (2014).
  • Silva, R. R. et al. ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics (2014).
  • Cho, J. H., I. Lee, R. Hammamieh, K. Wang, D. Baxter, K. Scherler, A. Etheridge, et al. 2014. “Molecular Evidence of Stress-Induced Acute Heart Injury in a Mouse Model Simulating Posttraumatic Stress Disorder.” Proceedings of the National Academy of Sciences of the United States of America 111 (8): 3188–93.
  • Hood, L., and N. D. Price. 2014. “Demystifying Disease, Democratizing Health Care.” Science Translational Medicine 6 (225): 225ed5.
  • Cermelli, S., Jang, I. S., Bernard, B. & Grandori, C. Synthetic lethal screens as a means to understand and treat MYC-driven cancers. Cold Spring Harb Perspect Med 4, (2014).
  • Christian, N. et al. Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. Journal of theoretical biology 343, 102–12 (2014).
  • Liu, G., Y. Sun, P. Ji, X. Li, D. Cogdell, D. Yang, B. C. Parker Kerrigan, et al. 2014. “MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer.” The Journal of Pathology 233 (3): 308–18.
  • Knijnenburg, Theo A., Stephen A. Ramsey, Benjamin P. Berman, Kathleen A. Kennedy, Arian F. A. Smit, Lodewyk F. A. Wessels, Peter W. Laird, Alan Aderem, and Ilya Shmulevich. 2014. “Multiscale Representation of Genomic Signals.” Nature Methods 11 (June): 689–94. doi:10.1038/nmeth.2924.
  • Goldberg, R., Kauffman, S. & Topol, E. J. Study design and the drug development process. JAMA : the journal of the American Medical Association 311, 2023 (2014).
  • Mast, F. D., Barlow, L. D., Rachubinski, R. A. & Dacks, J. B. Evolutionary mechanisms for establishing eukaryotic cellular complexity. Trends in cell biology (2014).
  • Craig, Theodore A., Yuji Zhang, Andrew T. Magis, Cory C. Funk, Nathan D. Price, Stephen C. Ekker, and Rajiv Kumar. 2014. “Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing.” Zebrafish, March. doi:10.1089/zeb.2013.0899.
  • Cary, G. A. et al. Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae. Yeast 31, 167–78 (2014).
  • Daugherty, M. D., Young, J. M., Kerns, J. A. & Malik, H. S. Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLoS genetics 10, e1004403 (2014).
  • Sperber, H. et al. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure. RNA 20, 621–31 (2014).
  • Holden, J. M., L. Koreny, S. Obado, A. V. Ratushny, W. M. Chen, J. H. Chiang, S. Kelly, et al. 2014. “Nuclear Pore Complex Evolution: A Trypanosome Mlp Analogue Functions in Chromosomal Segregation but Lacks Transcriptional Barrier Activity.” Molecular Biology of the Cell 25 (9): 1421–36.
  • Kusebauch, U., C. Ortega, A. Ollodart, R. S. Rogers, D. R. Sherman, R. L. Moritz, and C. Grundner. 2014. “Mycobacterium Tuberculosis Supports Protein Tyrosine Phosphorylation.” Proceedings of the National Academy of Sciences of the United States of America, June.
  • Vizcaino, J. A. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature biotechnology 32, 223–6 (2014).
  • Hu, Hao, Jared C. Roach, Hilary Coon, Stephen L. Guthery, Karl V. Voelkerding, Rebecca L. Margraf, Jacob D. Durtschi, et al. 2014. “A Unified Test of Linkage Analysis and Rare-Variant Association for Analysis of Pedigree Sequence Data.” Nat Biotechnol 32 (July): 663–69. doi:10.1038/nbt.2895.
  • Sun, Bingyun, and Leroy Hood. 2014. “Protein-Centric N-Glycoproteomics Analysis of Membrane and Plasma Membrane Proteins.” J Proteome Res, May. doi:10.1021/pr500187g.
  • Kauffman, S. A. Prolegomenon to patterns in evolution. Bio Systems (2014).
  • Romagnoli, G. et al. Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose. Yeast (2014). doi:10.1002/yea.3015
  • Carpp, L. N., R. S. Rogers, R. L. Moritz, and J. D. Aitchison. 2014. “Quantitative Proteomic Analysis of Host-Virus Interactions Reveals a Role for GBF1 in Dengue Infection.” Molecular & Cellular Proteomics : MCP, May.
  • Ptak, C., J. D. Aitchison, and R. W. Wozniak. 2014. “The Multifunctional Nuclear Pore Complex: A Platform for Controlling Gene Expression.” Current Opinion in Cell Biology 28C (March): 46–53.
  • Wu, X., Hasan, M. A. & Chen, J. Y. Pathway and network analysis in proteomics. Journal of theoretical biology (2014).
  • Wurtmann, E. J., A. V. Ratushny, M. Pan, K. D. Beer, J. D. Aitchison, and N. S. Baliga. 2014. “An Evolutionarily Conserved RNase-Based Mechanism for Repression of Transcriptional Positive Autoregulation.” Molecular Microbiology 92 (2): 369–82.
  • Shaw, S. et al. Discovery and characterization of olokizumab: A humanized antibody targeting interleukin-6 and neutralizing gp130-signaling. mAbs 6, 773–81 (2014).
  • Caballero, Juan, Arian F. A. Smit, Leroy Hood, and G. Glusman. 2014. “Realistic Artificial DNA Sequences as Negative Controls for Computational Genomics.” Nucleic Acids Res 42 (July): e99. doi:10.1093/nar/gku356.
  • Hu, H., J. C. Roach, H. Coon, S. L. Guthery, K. V. Voelkerding, R. L. Margraf, J. D. Durtschi, et al. 2014. “A Unified Test of Linkage Analysis and Rare-Variant Association for Analysis of Pedigree Sequence Data.” Nature Biotechnology, May.
  • Kemp, C. J., J. M. Moore, R. Moser, B. Bernard, M. Teater, L. E. Smith, N. A. Rabaia, et al. 2014. “CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer.” Cell Reports, April.
  • Liu, X. et al. Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development. Nature 507, 513–8 (2014).
  • Omenn, G. S. Plasma proteomics, the human proteome project, and cancer-associated alternative splice variant proteins. Biochimica et biophysica acta 1844, 866–73 (2014).
  • Li, X., Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, et al. 2014. “Two Mature Products of MIR-491 Coordinate to Suppress Key Cancer Hallmarks in Glioblastoma.” Oncogene, April.
  • Hillesland, K. L., S. Lim, J. J. Flowers, S. Turkarslan, N. Pinel, G. M. Zane, N. Elliott, et al. 2014. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America, September.
  • Sangar, Vineet, Cory C. Funk, Ulrike Kusebauch, David S. Campbell, R. L. Moritz, and Nathan D. Price. 2014. “Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-Promoting Proteins Secreted by Glioblastoma Cells.” Mol Cell Proteomics 13 (October): 2618–31. doi:10.1074/mcp.M114.040428.
  • Liu, Yuexin, Lalit Patel, Gordon B. Mills, Karen H. Lu, Anil K. Sood, Li Ding, Raju Kucherlapati, et al. 2014. “Clinical Significance of CTNNB1 Mutation and Wnt Pathway Activation in Endometrioid Endometrial Carcinoma.” J Natl Cancer Inst 106 (September). doi:10.1093/jnci/dju245.
  • Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202–9 (2014).
  • Peterson, Eliza J. R., David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher L. Plaisier, William J. R. Longabaugh, David R. Sherman, and Nitin S. Baliga. 2014. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Res, September. doi:10.1093/nar/gku777.
  • Lehman, A. et al. Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations. Am J Med Genet A 164A, 2656–62 (2014).
  • Kang, Seunghwa, Simon Kahan, Jason McDermott, Nicholas Flann, and Ilya Shmulevich. 2014. “Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models.” Bioinformatics, July. doi:10.1093/bioinformatics/btu498.
  • Stittrich, A.-B. et al. Mutations in NOTCH1 cause Adams-Oliver syndrome. Am J Hum Genet 95, 275–84 (2014).
  • Wang, Weizhi, Zewen Wei, Di Zhang, Huailei Ma, Zihua Wang, Xiangli Bu, Menglin Li, et al. 2014. “Rapid Screening of Peptide Probes through in Situ Single-Bead Sequencing Microarray.” Anal Chem 86 (December): 11854–59. doi:10.1021/ac503454z.
  • Lalli, Matthew A., Hannah C. Cox, Mary L. Arcila, Liliana Cadavid, Sonia Moreno, Gloria Garcia, Lucia Madrigal, et al. 2014. “Origin of the PSEN1 E280A Mutation Causing Early-Onset Alzheimer’s Disease.” Alzheimers Dement 10 (October): S277–83.e10. doi:10.1016/j.jalz.2013.09.005.
  • Zhu, Ling, Kun Wang, Jian Cui, Huan Liu, Xiangli Bu, Huailei Ma, Weizhi Wang, et al. 2014. “Label-Free Quantitative Detection of Tumor-Derived Exosomes through Surface Plasmon Resonance Imaging.” Anal Chem 86 (September): 8857–64. doi:10.1021/ac5023056.
  • Schubert, Julian, Aleksandra Siekierska, Mélanie Langlois, Patrick May, Clément Huneau, Felicitas Becker, Hiltrud Muhle, et al. 2014. “Mutations in STX1B, Encoding a Presynaptic Protein, Cause Fever-Associated Epilepsy Syndromes.” Nat Genet 46 (December): 1327–32. doi:10.1038/ng.3130.
  • Tien, Jerry F., Neil T. Umbreit, Alex Zelter, Michael Riffle, Michael R. Hoopmann, Richard S. Johnson, Bryan R. Fonslow, et al. 2014. “Kinetochore Biorientation in Saccharomyces Cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex.” Genetics, September. doi:10.1534/genetics.114.167775.
  • He, Yuqing, Kang Zeng, Xibao Zhang, Qiaolin Chen, Jiang Wu, Hong Li, Yong Zhou, et al. 2014. “A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family.” J Invest Dermatol, October. doi:10.1038/jid.2014.429.
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