2012 ANNUAL REPORT ­ Using big science to answer big questions.

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Back cover Front cover Our Team

Founders Marc Tessier-Lavigne, Ph.D. David Tank, Ph.D. The Rockefeller University Princeton University Paul G. Allen David Van Essen, Ph.D. Giulio Tononi, M.D., Ph.D. Jody Allen Washington University University of Wisconsin, Madison Doris Tsao, Ph.D. California Institute of Technology Leadership Additional Scientific Advisors Christopher Walsh, M.D., Ph.D. Allan Jones, Ph.D. Harvard Medical School Chief Executive Officer Larry Abbott, Ph.D. Columbia University Chinh Dang Chief Technology Officer Yang Dan, Ph.D. Past Scientific Advisors University of California, Berkeley Christof Koch, Ph.D. Gregor Eichele, Ph.D. Chief Scientific Officer Michael Elowitz, Ph.D. Max Planck Institute for California Institute of Technology Biophysical Chemistry David Poston Chief Operating Officer Adrienne Fairhall, Ph.D. Eberhard Fetz, Ph.D. University of Washington University of Washington Anne Claude Gavin, Ph.D. Joshua Huang, Ph.D. Board of Directors European Molecular Cold Spring Harbor Laboratory Biology Laboratory Jody Allen Edward Jones, M.D., Ph.D. President and Board Chair, Richard Gibbs, Ph.D. University of California, Davis Allen Institute for Brain Science Baylor College of Medicine What makes us President and CEO, Vulcan Inc. Alexandra Joyner, Ph.D. Patrick Hof, M.D. New York University Nathaniel T. Brown Mount Sinai School of Medicine School of Medicine Senior Vice President, Finance and Financial Strategy, The Seattle Times Arnold Kriegstein, M.D., Ph.D. Sacha Nelson, M.D., Ph.D. University of California, University of California, San Diego Susan M. Coliton San Francisco human? Steven Paul, M.D. Vice President, Foundation and Collections, Vulcan Inc. John H.R. Maunsell, Ph.D. Weill Cornell Medical College Harvard Medical School The power of the human brain is unmatched even by Thomas Daniel, Ph.D. Luis Puelles, M.D., Ph.D. Professor of Biology, Neurobiology David McCormick, Ph.D. University of Murcia today’s most advanced computing technologies. Decoding Yale University and Behavior, Komen Endowed Larry Swanson, Ph.D. the brain’s mysteries is essential to understanding the Chair, University of Washington Markus Meister, Ph.D. University of Southern California Harvard University Stephen Hall Joseph Takahashi, Ph.D. human condition and to improving human health. Managing Director, Venture Randall Moon, Ph.D. University of Texas Southwestern Capital, Vulcan Inc. University of Washington Medical Center Allen D. Israel Jeffrey Nye, M.D., Ph.D. Arthur Toga, Ph.D. Member, Foster Pepper PLLC Janssen Pharmaceutical Companies University of California, Los Angeles of Johnson & Johnson Phyllis Wise, Ph.D. Pasko Rakic, M.D., Ph.D. University of Washington Scientific Advisory Board Yale School of Medicine David Anderson, Ph.D. Sharad Ramanathan, Ph.D. California Institute of Technology Harvard University Staff György Buzsáki, M.D., Ph.D. Botond Roska, M.D., Ph.D. More than 200 dedicated employees Rutgers University Friedrich Miescher Institute Approved 10-year for Biomedical Research More than 55 researchers plan for expansion and Edward Callaway, Ph.D. with Ph.D. degrees new scientific initiatives, Salk Institute for Biological Studies John Rubenstein, M.D., Ph.D. and received a new Thomas Daniel, Ph.D. University of California, $300M commitment from Published landmark University of Washington San Francisco Paul G. Allen to support study on the human brain Clifford Saper, M.D., Ph.D. Follow us on Twitter Phase I of the plan in Nature Catherine Dulac, Ph.D. @Allen_Institute Harvard University Harvard Medical School Daniel Geschwind, M.D., Ph.D. Eric Schadt, Ph.D. Like us on Facebook Mount Sinai School of Medicine Allen Institute for Brain Science Expanded scientific Generated ~1 petabyte University of California, Los Angeles leadership and team with of new data on the human Increased usage of the Lorenz Studer, M.D. Michael Stryker, Ph.D. Subscribe to us on YouTube 14 Ph.D.-level scientists brain, neural circuitry, Allen Brain Atlas resources Sloan-Kettering Institute University of California, AllenInstitute from Harvard, Stanford and brain development to more than 1 million San Francisco 2012 and other world-class for our online public visits from more than Karel Svoboda, Ph.D. institutions resources 125 countries Howard Hughes Medical Institute, Highlights Janelia Farm Research Campus

Inside front cover Inside back cover We are dedicated to accelerating brain research, using How do we big science to drive the field forward. Our success enables scientists around the world to answer critical questions about the development, structure, and function of the brain, enable others? and to use those answers to improve human health. Our groundbreaking discoveries and research tools provide brain researchers around the world with truly innovative ways to ask and answer big questions in brain science.

In 2004 we launched Since then, we have built With more than 4 million the first of our a highly valuable suite visits to date, our online “The Allen Institute open public approach Allen Brain Atlas of publicly available, resources have supported is transforming brain that thousands of resources, forever web-based research tools many thousands of science around the scientists use to advance changing the way encompassing multiple experiments and are cited world. In the last their research every day. in which brain decade, the Institute I am excited to help the research could species, developmental routinely in peer-reviewed has successfully Institute build on these be conceptualized stages, anatomical struc- publications. Our sought-after tackled industrial- achievements and tures, and brain-related transgenic mouse lines are and conducted. scale science projects, expand the scale and Allan Jones, Ph.D. diseases. Any researcher also publicly available, and delivering massive scope of its impact.” Chief Executive Officer with an Internet connection we are generating additional databases with an can access these resources resources to support a freely through a single variety of laboratory and “In 2012, we turned our focus data portal. Our tools computational studies from our achievements to enable scientists to work that have not previously date to the opportunities more quickly and make been feasible. that lie ahead. The launch more effective decisions, of our ambitious 10-year allowing them to focus plan sets us on a course on their most promising to further transform brain discoveries. research, both within our own walls and in collabo- ration with the global brain science community.” Paul G. Allen Founder Page 12 Page 1 ’03 ’04 ’05 ’06 ’07 ’08

>25,000 >250,000 visits to Allen visits to Allen Brain Atlas Brain Atlas resources resources (all 2005) (all 2008) Expense COMMUNITY Distribution 8% 10% 8% ALLEN Spinal Employees Cord Atlas created in response to Outside Services requests from the 3% Lab Supplies research commu- 12% nity and funded Depreciation by a consortium of Occupancy 8% contributors includ- Human Cortex ing foundations, Tools & Equipment Study, the Allen individuals, disease Other Institute’s first organizations, and 2012 human project ALLEN Mouse corporate entities. Sleep Study and a critical Brain Atlas [Completed 2009] [Completed 2008] foundation for [Completed 2006] generating the Allen Human Brain Atlas. [Completed 2009] ALLEN Developing

ONLINE PUBLIC RESOURCES Mouse Brain Atlas [Completed 2010]

Transgenic Mouse 51% Study Received $100M seed commitment from Paul G. Allen 9% 9% BUSINESS 8% Reached 100 Employees 2% Launched 16% operations 7%

2011

Where do we begin? 49%

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Financial Information >500,000 Held the >750,000 >1,000,000 visits to Allen First Annual visits to Allen visits to Allen Brain Atlas Allen Institute Brain Atlas Brain Atlas resources Symposium resources resources This new model of (all 2009) symposium engages top (all 2011) (all 2012) experts in discussions Allen Institute for Brain Science of diverse topics to stimulate collaborative First Allen Summary Statements of Financial Position As of December 31, and forward-thinking outlooks. Distribution Brain Atlas (in thousands) 2012 2011 of videos publicly Hackathon Current Assets online extends benefit brings programmers Cash and cash equivalents $ 18,267 $ 55, 1 1 5 to the global research and informatics experts Restricted cash 573 212 community. together to collaborate Federal grants receivable 1,217 406 on developing new data analysis strategies and Pledges receivable 47,000 100 tools based on the Allen Other current assets 2, 1 3 1 2,219 ALLEN Human Brain Atlas resources. Brain Atlas Total current assets 69,276 57,964 Mouse Diversity Study Restricted cash 1,082 1,073 [Completed 2009] Approval of Other non-current assets 400 Property and equipment, net 11,11 0 10,562 BrainSpan Atlas ALLEN Mouse 10-year plan of the Developing Brain Connectivity sets the course for Total assets $ 81,468 $ 69,999 Human Brain Atlas expanded opportunities NIH Blueprint and scientific endeavors. Non-Human New initiatives launched Current Liabilities Primate (NHP) in neural coding, Accounts payable $ 2,758 $ 1,580 Atlas molecular networks, Accrued expenses 1,479 1, 2 1 1 Ivy Glioblastoma and characterization of Atlas Project different brain cell types. Total liabilities 4,237 2,791

Net Assets Unrestricted 75,521 14,023 Reached 200 Temporarily restricted 1,710 53,185 Employees Received largest Christof Koch, Ph.D. Total net assets 77,231 67,208 federal grant named CSO award to date following a highly Total liabilities and net assets $ 81,468 $ 69,999 ($16.2M) successful 25-year career Received $300M at the California Institute commitment of Technology. Initiates expansion of the Institute’s from Paul G. scientific team by recruiting Allen for the Allen Institute for Brain Science top scientists from around next four years, the world. Summary Statements of Activities bringing his total commitment to Year Ended December 31, date to $500M. (in thousands) 2012 2011 Support and Revenue Contributions $ 47,000 $ 70,400 Federal and other grants 4,888 9,732 Other revenue 195 248 Total support and revenue 52,083 80,380

Expenses Launched in 2003, the Allen Institute has forever changed Program services 35,303 28,942 Management and general 6,757 5,671 the trajectory of brain research in less than 10 years. Total expenses 42,060 34,613 We intend to build on this successful foundation to catalyze Change in net assets $ 10,023 $ 45,767 breakthrough discoveries and accelerate knowledge This information was derived from the Allen Institute for Brain Science’s annual audited financial statements. acquisition in brain science in the years ahead.

Page 10 Page 3 Our top-notch scientific team works

Christof Koch, Ph.D. collaboratively to Chief Scientific Officer “The Allen Institute offers answer the most an absolutely unique opportunity to do something on a scale and with a complex questions in ruthless focus unheard of in a traditional research setting. The opportunity brain research to participate in such a transformative effort drives world-class scientists to join our organization.” Why do we need Clay Reid, M.D., Ph.D. Hanchuan Peng, Ph.D. Degree: Cornell University, Degree: Southeast University, The Rockefeller University Nanjing, China Prior Affilliation: Prior Affilliation: Harvard Janelia Farm Research Campus, University Program Area: HHMI Program Area: Neural big science? Neural Coding Coding, Cell Types Deciphering the complexity of the human brain is a tremendous challenge, one that cannot be solved by any single experiment or individual laboratory.

Thomas Keenan, Ph.D. Stefan Mihalas, Ph.D. Severine Durand, Ph.D. Nicholas Cain, Ph.D. Degree: University of Washington Degree: Caltech Prior Degree: University of Zurich, Degree: University of Prior Affilliation: University of Affilliation: Johns Hopkins Switzerland Prior Affilliation: Washington Prior Affilliation: Our approach to brain share data on an individual experiments Wisconsin Program Area: University Program Area: Harvard University Program University of Washington Molecular Networks, Cell Types, Neural Coding, Cell Types Area: Neural Coding Program Area: Neural Coding research is as big as the unprecedented scale. that we enable. The Neural Coding challenge itself, combining Our commitment to ongoing financial support our internal expertise and making our innovations of our founder, Paul G. capabilities with global publicly available is a Allen, and leading grant collaboration to enable catalyst for advancing organizations, including problem solving among diverse areas of brain the National Institutes of researchers around the research. The whole of Health, validates our big world. We are innovating the knowledge base that science approach and tools and techniques that is being built on the provides critical funding Saskia de Vries, Ph.D. Michael Buice, Ph.D. Lu Li, Ph.D. Kenji Mizuseki, M.D., Ph.D. can be used to generate, foundation of our work for making our impact Degree: Harvard University Degree: University of Chicago Degree: Vanderbilt University Degree: Kyoto University, Prior Affilliation: Stanford Prior Affilliation: University of Prior Affilliation: UC Berkeley Japan Prior Affilliation: capture, analyze, and is greater than the even greater. University Program Area: Texas at Austin Program Area: Program Area: Cell Types New York University Neural Coding Neural Coding Program Area: Neural Coding

In 2012 we welcomed Jim Berg, Ph.D. Chaoyang Ye, Ph.D. Aleena Garner, Ph.D. Corinne Teeter, Ph.D. Degree: Harvard Medical Degree: University of Missouri, Degree: UC San Diego Degree: UC San Diego 14 world-class School Prior Affilliation: Columbia Prior Affilliation: Prior Affilliation: UC San Prior Affilliation: Sandia UC San Francisco Program University of Pennsylvania Diego Program Area: National Laboratories scientists to Area: Cell Types Program Area: Molecular Neural Coding Program Area: Neural Networks Coding, Cell Types our team

Page 4 Page 9 John Phillips, Ph.D. Executive Director, Structured Science

“We are using an We believe that providing The resources that we have industrial model of researchers around the created to date are tangible cross-disciplinary world with ready access to evidence of our ability to problem solving our data and online tools innovate new technologies. Where do we go to answer critical is the most effective way Today we are developing questions in brain to spur progress in brain new cell lines, transgenic research, and to science. Our commitment tools, models, methods, and develop cutting- to making our resources computer algorithms that edge technologies available to the research will allow scientists around from here? that overcome new community establishes a the world to ask and answer research challenges.” benchmark for open and wholly new questions in Our initial achievements have allowed us collaborative science. brain science. to attract an exceptional roster of scientific leaders in a variety of disciplines.

Combined with the In 2012 we implemented Our ongoing commitment new $300 million a 10-year plan that will to innovating cutting-edge commitment from our expand the scale of our technologies and sharing founder, Paul G. Allen, efforts, the scope of our our unique resources and financial support impact, and our physical with the global scientific “Our structured from federal funding infrastructure. In 2013 we community should enable agencies and other expect to break ground wholly new endeavors granting institutions, on a new building that in brain science. We look approach to we have the critical will consolidate all of our forward to answering Amy Bernard, Ph.D. Director, Structured Science intellectual and capital personnel into a single important questions, and resources we need for space that will enhance to asking even bigger ones. brain science success in our second our multidisciplinary decade. approach to brain research. differentiates us The key How does the brain drive from conventional initiatives of the physiology and behavior? 10-year plan “We pursue defined projects, research setting goals and developing encompass What drives neural What roles do different an execution plan to answer three critical development and disease neural components play the most challenging processes? in health and disease? questions: organizations.” questions in brain research.”

Page 8 Page 5 Our resources can “What’s most gratifying to me when I train >4 million visits to Allen Brain scientists to use our resources is enable advances in helping them find new features that can all aspects of brain Atlas resources to date, with significantly speed their research. I love nearly 50,000 individuals at seeing that light bulb go on.” research, including — Terri Gilbert, Ph.D., Application Scientist, Allen behavior, anatomy, academic, corporate, government Institute for Brain Science and nonprofit organizations from “This will likely become the reference atlas for physiology, and molecular and cellular neuroscientists.” brain disorders. more than 100 countries across — Thomas R. Insel, M.D., Director, National Institute of Mental Health, in Nature six continents visiting our online GREENLAND Addiction resources each month. ICELAND SWEDEN ADHD FINLAND Alzheimer’s Disease NORWAY RUSSIA Autism ESTONIA LATVIA Avian Influenza H5N1 “By using the Allen Spinal Cord Atlas, we CANADA DENMARK LITHUANIA were able to discover a brand- Bipolar Disorder IRELAND NETHERLANDS new cell type that has previously been overlooked and that could be Brain Development UNITED KINGDOM POLAND GERMANY an important player in all manner BELGIUM Brain Evolution KAZAKHSTAN of spinal cord injury and disease, LUXEMBOURG CZECH REPUBLIC UKRAINE including multiple sclerosis and ALS.” Cancer SLOVAK REPUBLIC LIECHTENSTEIN AUSTRIA MOLDOVA — Jane Roskams, Ph.D., Professor of Zoology, Depression SWITZERLAND HUNGARY University of British Columbia SLOVENIA CROATIA ROMANIA Diabetes BOSNIA & HERZEGOVINA REPUBLIC OF SERBIA BULGARIA GEORGIA UZBEKISTAN SPAIN MONTENEGRO MACEDONIA AZERBAIJAN Epilepsy “I use the Allen Mouse Brain Atlas in my ALBANIA TURKEY ARMENIA UNITED STATES PORTUGAL ITALY Huntington’s Disease work every day. We’ve conducted GREECE JAPAN POLYNESIA (FRENCH) CHINA phenotypic analysis of mouse mutants, MALTA SOUTH KOREA Hypomyelination/Myelin Deficiencies which have identified epilepsy genes in CYPRUS SYRIA LEBANON Hypothyroidism 20 mouse models.” JORDAN IRAN BERMUDA MOROCCO PALESTINIAN TERRITORIES — Jeffrey Noebels, M.D., Ph.D., Professor of ISRAEL Infantile Encephalopathy Neurology, Neuroscience, and Molecular and Human Genetics, Vice Chair for Research, EGYPT PAKISTAN NEPAL Intellectual Disability Department of Neurology, Baylor College of SAUDI ARABIA BAHRAIN MEXICO BAHAMAS Medicine Metabolic Disorders UNITED ARAB EMIRATES INDIA TAIWAN CUBA HONG KONG Multiple Sclerosis BANGLADESH DOMINICAN REPUBLIC Neuroinflammation VIRGIN ISLANDS (USA) ANTIGUA AND BARBUDA Obesity GUATEMALA YEMEN THAILAND PHILIPPINES Pain NICARAGUA ARUBA CAMBODIA VIETNAM TRINIDAD AND TOBAGO Parkinson’s Disease COSTA RICA VENEZUELA Psychiatric & Neurological Diseases IVORY COAST GHANA SRI LANKA (COTE D’IVOIRE) COLOMBIA MALAYSIA Schizophrenia Training programs span the globe BRUNEI DARUSSALAM SINGAPORE Spinal Cord Injury KENYA ECUADOR BRITISH Spinocerebellar Ataxia Type 3 UNITED STATES Princeton University University of North Carolina UNITED KINDOM GERMANY INDIAN WEBINAR TRAINING INDONESIA OCEAN ATTENDEES Stroke TERRITORY Baylor College of Medicine Salk Institute for University of Southern California Cambridge ASCENSION ISLAND Center for Regenerative Biological Studies University Therapies Dresden Belgium Traumatic Brain Injury California Institute of Technology University of Texas at Austin Brazil Stanford University PERU BRAZIL King’s College Humboldt Universitat Williams-Beuren Syndrome Columbia University University of Texas London Canada COCOS (KEELING) ISLANDS The Scripps Research Institute Southwestern Medical Center Max Planck Institute for China And More... TUVALU Duke University University of Human Cognitive and Colombia University of California, Berkeley Genentech Oxford Brain Sciences Denmark University of California, Davis BOLIVIA Finland Georgetown University France FIJI University of California, Irvine Harvard University SWEDEN JAPAN MAURITIUS India University of California, Israel NEW CALEDONIA NIUE Massachusetts Institute PARAGUAY Karolinska Institutet Okinawa Institute (FRENCH) Los Angeles for Science and Italy of Technology Korea University of California, NAMIBIA Technology AUSTRALIA Icahn School of Medicine Lebanon San Diego FINLAND New Zealand at Mount Sinai SOUTH AFRICA University of California, CHILE University of Helsinki Singapore National Institutes of Health San Francisco LESOTHO Sweden URUGUAY United Kingdom United States ARGENTINA

NEW ZEALAND

Our publicly available resources have a truly In 2012 alone, we generated nearly one petabyte (PB) of data — that is 1,000 terabytes, the equivalent of 60,000 HD global impact on brain research. Around the movies. Since 2005, we have generated 230 million human microarray data world and across multiple disease areas, our points, and generated and processed Who benefits from more than 2PB of data. An end-to-end stack of the slides containing the nearly data and tools make a difference. And we are 2 million tissue sections that we have collected to date would span 42 miles. The combined thickness of the tissue leading the charge to gather, analyze, and sections collected in 2012 alone is 30.9 feet — just slightly less than the average our work? share brain research data on a massive scale. length of a Tyrannosaurus rex.

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