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Flagship Pioneering is an American founder of life sciences companies. In the past, Flagship sometimes funded outside ventures. The firm focuses on businesses in health and environmental sustainability. It was founded by Noubar Afeyan and Edwin Kania Jr.

History
Noubar Afeyan founded NewCoGen in 1999. Initially, NewCoGen shared office space with OneLiberty Ventures and the two firms collaborated closely. In 2000, NewCoGen became a subsidiary of Flagship Ventures, founded by Afeyan and Edwin Kania Jr. of OneLiberty. As of January 2002, NewCoGen and OneLiberty had raised $400 million in capital.

In 2015, Flagship Ventures raised $537 million for its Fund V. The amount raised was notable due to the relative scarcity of venture capital funding available for life sciences then. As of March 2015, eight of Flagships portfolio companies had gone public in just the past two years. As of the same date, those companies had a total market capitalization of about $10 billion. As of March 2017, Moderna had a market capitalization of about $5 billion. As of early 2019, Rubius had a market capitalization of more than $1 billion.

In 2016, Flagship Ventures changed its name to Flagship Pioneering. In a statement explaining the change, the firm said it “reflects the distinctive nature of its enterprise: systematically conceiving, creating, resourcing and growing first-in-category ventures to transform human health and sustainability.”

As of 2016, Flagship Pioneering was one of the biggest and most prominent life-science focused investment firms in Massachusetts. That year the firm conducted a $285-million raise for a "special opportunities fund."

As of 2017, Flagship had around $2.3 billion in funds under management.

Investing style and corporate culture
Flagship Pioneering originates its own start-ups. It provides seed-stage capital, and also makes early, later, and growth stage investments. Unlike private equity and venture capital firms, the science behind most of the companies in Flagship's portfolio came from the firm's in-house Flagship Labs, formerly know as VentureLabs..

Flagship Pioneering's culture combines a willingness to experiment tempered with strict discipline. The firm's business model is based on creating and funding new companies that monetize original scientific research. Instead of soliciting and evaluating business plans from outside entrepreneurs, Flagship has internal teams of scientists who research subjects of economic importance in an initially unconstrained manner. Team members then come up with testable hypotheses that could be the basis for new ventures. Flagship then subjects these hypotheses to rigorous experimentation that results in their being discarded, reformulated, and refined.

Flagship does not, at least initially, run experiments to confirm hypotheses. Its teams run rigorous experiments with the deliberate purpose of finding all the flaws lurking in an idea or falsifying it outright. These experiments are generally designed to take less than six months and cost less than $1 million. This approach allows research teams to cycle through many ideas quickly while making it easier psychologically to walk away from research that lacks potential. The goal of "killer experiments" is to learn what you have gotten wrong while moving on to more promising prospects as quickly as possible.

Flagship's culture regards experimental data as sacred. If an experiment nullifies a hypothesis, teams are expected to either kill that line of inquiry or reformulate in light of the data. Many companies have cultures that make it tempting to "spin" bad data. There is no such pressure at Flagship which regards ignoring experimental data as unacceptable. Flagship's researchers have a strong incentive to be disciplined about discarding "loser" ideas. They reap no rewards from holding on to unpromising ideas and miss out on the lucrative opportunities to develop winning ideas into new enterprises.

Flagship generally makes initial investments between $500,000 and $5 million, with a typical total investment between $7 million and $15 million during the life of a venture. Flagship generally forms syndicates with other firms. Flagship prefers to be the lead investor and to take seats on the boards of its portfolio companies. It generally targets 20% to 30% equity stakes in its portfolio companies but usually invests less in later stage companies. As of the end of 2016, Flagship had funded about 75 companies, including 45 start-ups launched on the basis of in-house scientific research.

Noubar Afeyan
As of 2019, Noubar Afeyan was Senior Managing Partner and CEO of Flagship Pioneering.

Afeyan started PerSeptive Biosystems, a bio-instrumentation company that was purchased by PerkinElmer in 1998 for $360 million. After founding PerSeptive Biosystems, Afeyan became a senior executive at Applera where he oversaw the founding of Celera Genomics, the first firm to sequence the human genome.

As PerSeptive Biosystems matured, Afeyan started to work on multiple start-ups at the same time. In 1995, he started ChemGenics Pharmaceuticals. This company merged the staff and assets of Myco Pharmaceuticals with a research team from PerSeptive Biosystems. Chemgenics created a novel approach to genomic drug discovery. ChemGenics validated its approach to drug discovery through two partnerships with major pharmaceutical companies. It was acquired by Millennium Pharmaceuticals in 1996. From 1995 to 1997, Afeyan co-founded Antigenics (later Agenus), which researched cancer vaccines; Exact Sciences, which developed molecular diagnostics for colon cancer; and Color Kinetics, an early maker of color-LED lighting. Each of these firms eventually went public. Color Kinetics was acquired by Royal Dutch Philips in 2007.

Afeyan earned a PhD in Biochemical Engineering from the Massachusetts Institute of Technology in 1987. Afeyan has been a Senior Lecturer at MIT's Sloan School of Management since 2000.

In 2008, Afeyan received the Ellis Island Medal of Honor. Afeyan received a Technology Pioneer 2012 award from the World Economic Forum for his work on solar cell technology developed at Joule Unlimited. In 2016, the Carnegie Corporation named Afeyan a Great Immigrant.

Stephen Berenson
As of 2017, Stephen Berenson was a Managing Partner at Flagship Pioneering. He worked at JPMorgan for 30 years and eventually rose to the position of vice chairman for investment banking.

Berenson holds an SB in Mathematics from the Massachusetts Institute of Technology.

David Epstein
As of 2017, David Epstein was an Executive Partner at Flagship Pioneering. Epstein was immediately made Chairman of Rubius Therapeutics, a venture founded by Flagship VentureLabs.

Epstein was CEO of Novartis for six years.

Epstein earned an undergraduate degree of the Rutgers University College of Pharmacy in 1984 and an MBA from the Columbia University Graduate School of Business in 1987.

David Berry
David Berry became a General Partner at Flagship Ventures in 2015.

Berry joined Flagship Pioneering in 2005. Berry has been described as "a rising star of the Boston-area venture capital scene," and as one of its most brilliant thinkers." Berry has founded over 20 companies at Flagship including Seres Therapeutics, Evelo Biosciences, Joule Unlimited, Axcella Health, Eleven Biotherapeutics, Indigo Agriculture, and LS9. Berry also helped launch companies including T2 Biosystems, Seventh Sense Biosystems, and KSQ Therapeutics.

Berry graduated with an SB from the Massachusetts Institute of Technology in 2000. He earned his MD from Harvard Medical School and his PhD from the Massachusetts Institute of Technology. He completed his dual degree through the Harvard-MIT Program of Health Sciences and technology.

Jason Pontin
Jason Pontin is a Senior Partner at Flagship Pioneering.

From 1996 to 2002, Pontin edited Red Herring, a business and technology publication. From 2002 to 2004, he was the editor of The Acumen Journal, a now-defunct magazine he founded about the life sciences.

He was hired as the editor of Technology Review in July 2004, and in August 2005 was named publisher. Pontin engaged in what The Boston Globe has described as a "strategic overhaul" of Technology Review, whose goal is to make the magazine into a largely electronic publishing company. In October 2012, he renamed the organization MIT Technology Review and relaunched it as a "digital-first enterprise". AdWeek commented that "Pontin and MIT Technology Review could set the standard for the transition to a digital future for legacy media." Pontin was Chairman of the MIT Enterprise Forum, MIT's global organization of technology entrepreneurs.

Pontin has written for national and international magazines and newspapers, including The New York Times, The Economist, The Financial Times, The Boston Globe, The Believer Magazine, and Wired. He writes a bi-weekly column for Wired in the publication’s “IDEAS” channel and contributes to the magazine.

Pontin is an alumnus of Oxford University.

BG Medicine
Beyond Genomics, now BG Medicine, was founded in 2000 by Afeyan and Mike Masterson and raised $15 million from Flagship Ventures to fund development of biomarker-based diagnostic tests for cardiovascular problems.

As of 2015, BG Medicine was commercializing two diagnostic tests. The first is the BGM Galectin-3 test, a novel assay for measuring galectin-3 levels in blood plasma or serum to be used in assessing the prognosis of patients diagnosed with heart failure. BG Medicine's second diagnostic test is the CardioSCORE, which is designed to identify individuals at high risk for near-term, significant cardiovascular events, such as heart attacks and strokes.

Acceleron Pharma
Acceleron Pharma is a public American "clinical stage biopharmaceutical company" based in Boston, Massachusetts with a broad focus on developing medicines that regulate the transforming growth factor beta (TGF-β) superfamily of proteins, which play fundamental roles in the growth and repair of cells and tissues such as red blood cells, muscle, bone, and blood vessels. Acceleron Pharma was founded in 2003 as Phoenix Pharma.

Accuri
Accuri was founded in 2005 to make smaller and cheaper flow cytometers than those commonly used at present. Flow cytometers are used by scientists to count and categorize large numbers of cell types from tissue samples. Accuri's C6 Flow Cytometer System weights about 30 pounds and covers about two square feet of counter space. A competing tool from Becton Dickinson weights about ten times as much and occupies 13 square feet of counter space. Accuri's machine sells for less than one-third the price of Becton Dickinson's instrument.

Flagship Ventures and Fidelity Biosciences led Accuri's third round of funding in 2008 that raised $13 million.

Evelo Biosciences
In early 2016, Flagship launched Evelo Biosciences with $35 million of funding.

In mid-2017, Evelo Biosciences raised another $50 million to take monoclonal microbial drugs designed to fight cancer and auto-immune disease into the first phase of clinical trials. Flagship invested yet more money in the series B. Other investors in this round included GV, formerly known as Google Ventures, Celgene, Alexandria Venture Investments, and the Mayo Clinic.

Moderna Therapeutics
Flagship Ventures founded Moderna Therapeutics, a messenger RNA drug developer. AstraZeneca, Alexion Pharmaceuticals, Merck, and other investors gave Moderna more than $1 billion in funding. As of March 2015, Flagship remained the firm's largest shareholder.

In 2017 Science published an article describing Moderna's platform, which was the result of several months of discussions with Moderna employees. Moderna had made the strategic decision to disclose some of its approach to break the hype cycle into which it was getting locked. The Science piece disclosed that Moderna was delivering some of its mRNA therapeutic candidates in liposomes, that they were using modified uridine nucleosides based on work done by Katalin Karikó on avoiding immune responses to mRNA drugs, that the company was using mRNAs with modified sequences to improve folding and translation efficiency, and that their mRNA drug candidates were modified on each end, outside the coding region, to target them to specific cell types.

Rubius Therapeutics
Rubius Therapeutics is a small, early-stage Cambridge, Massachussetts-based firm. It is developing enucleated cell-based therapies that could treat a wide variety of problems such as cancer autoimmune, metabolic, and hematologic diseases.

Joule Unlimited
Joule Unlimited was founded in 2007 to develop a process for making renewable liquid fuels and chemicals without using biomass feedstock from agriculture. After exploring several possible paths, VentureLabs focused on applying synthetic biology to the genomic engineering of photosynthetic bacteria. Joule uses engineered cyanobacteria to convert solar energy and carbon dioxide into ethanol, diesel, jet fuel, and gasoline.

When Joule started to develop its technology, the highest land productivity for algal production of liquid fuels reported was 500 to 1,500 gallons per acre per year. Productivity of 15,000 to 25,000 gallons per acre per year would be needed to produce fuels at unsubsidized costs below the equivalent $50 per barrel of crude oil, a level that could compete with fossil fuels over the long term.

This level of productivity could only be reached if the carbon and photon conversion wasted on growing biomass were minimized in favor of the end product. Biochemical engineering principles suggested that a semi-continuous conversion process that could convert feedstock carbon dioxide into a secreted fuel molecule for several weeks after a short period of cell growth. Joule developed a growth switch to redirect the metabolism of the cyanobacteria from growth into product formation. The cells were engineered with synthetic metabolic pathways to convert carbon either into ethanol or into long and mid-range alkanes. Mid-range alkanes can be used as diesel fuel or as blend stock for jet fuel or gasoline. Joule called this production process Helioculture.

Axcella Health
Axcella Health was originally known as Pronutria. Pronutria originally planned to develop medical foods and dietary supplements based on information from a library of DNA sequences when it emerged from stealth in 2013. Pronutria went on to focus mainly on developing new drugs.

Immediately after raising $39 million in May 2015, Pronutria's CEO announced that the company was focusing on treating serious diseases with limited or non-existent therapies. In 2016, the company changed its name to Axcella Health to better reflect its mission. It is developing oral protein-based drugs designed to restore homeostasis in diseased cells. The company has four areas of focus: muscular dystrophy, drug-resistant epileptic seizures, the liver conditions nonalcoholic steatohepatitis and nonalcoholic fatty liver disease, and sarcopenia. Axcella Health formed a wholly-owned subsidiary, Acora Nutrition, to focus on medical foods. As of June 2016, Axcella said it had three "clinical-stage candidates."

Nestle Health invested $42.5 million into Axcella Health in February 2016. As of June 2016, Axcella had raised a total of $112 million. It was founded by Flagship Ventures in 2011.

Cygnal Therapeutics
Cygnal Therapeutics was founded by Flagship Pioneering based on research from its Labs division. As of 2019, Cygnal was developing drugs to treat cancer and other diseases that target the peripheral nervous system (PNS). Based on the principle that the PNS affects non-neuronal processes, Cygnal has linked PNS targets to non-neurological disease.

Cygnal hired Pearl Huang, a former senior executive at Roche, as CEO in January of 2019. Huang also became a partner at Flagship Pioneering.

Investors
Flagship's investors include the Alaska Permanennt Fund, the Investment Corporation of Dubai, Baillie Gifford, and many other institutional investors with long time horizons.