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How We Began

The Allen Institute was founded in 2003 by Microsoft co-founder and philanthropist Paul G. Allen, who sought to push the limits of human exploration in science.

Initially founded to map gene activity in the mouse brain, the Institute’s work quickly expanded to catalogue the constellation of cells and their connections in the mouse and human brain, along with deep research into the human immune system; inner workings of our cells; and identifying transformative, paradigm-shifting science around the world.

Today, our multidisciplinary approach at tackling large-scale, foundational research serves as the bedrock for scientific discovery and continues to advance the frontiers of bioscience.

Our Founders

Investor and philanthropist Paul G. Allen spent his career tackling some of the world’s biggest challenges and pushing the boundaries of what is possible. Allen, who co-founded Microsoft in 1975, mapped new frontiers and fueled exploration across a broad range of areas as the chairman of Vulcan, the Seattle-based company that he co-founded with his sister, Jody Allen, to oversee his business and philanthropic portfolio. With lifetime giving totaling over $2.65 billion, Allen is included among the world’s leading philanthropists who, through the Giving Pledge, dedicated the majority of their fortunes to charity.

Jodie and Paul Allen
Jody and Paul Allen

Allen, who died in 2018, was a visionary who sparked important developments and innovations in science, technology, education, conservation, and the arts. His desire to accelerate understanding of the human brain in health and disease led him to start the Allen Institute for Brain Science in 2003, which ultimately expanded to include the Allen Institute for Cell Science, The Paul G. Allen Frontiers Group, the Allen Institute for Immunology, and the Allen Institute for Neural Dynamics. Today, Paul Allen’s sister, Jody Allen, honors his legacy as Board Chair of the Allen Institute, helping direct our mission to transform human health through science for generations to come.

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Portrait of Allen Institute founder Paul G. Allen in a research lab.

A tribute to our founder, Paul G. Allen

The Allen Institute began as a technology pioneer's dream to change the landscape of neuroscience and genomics. Paul Allen's bold ambitions taught all of us to think bigger and reach higher—but with achievable goals.

Ed Lein Headshot

History and Accomplishments

Since 2003, we’ve been focused on accelerating foundational research and cultivating new ideas to make a transformational impact on science. Our greatest discoveries and accomplishments so far include:

  • September 16, 2003: Our beginnings. Investor and philanthropist Paul G. Allen committed $100M in seed money to launch the Allen Institute for Brain Science. The Institute launched with a single ambitious project: the Allen Mouse Brain Atlas.
  • September 26, 2006: A map completed. The Allen Mouse Brain Atlas, a map of genome-wide gene expression over the entire brain of the adult laboratory mouse, was released to the public.
  • July 17, 2008: Charting the spinal cord. Following on the success of the Allen Mouse Brain Atlas, our researchers completed the Allen Spinal Cord Atlas, the world’s first genome-wide map of gene expression in the mouse spinal cord. The atlas aimed to fill a gap in the scientific community focused on spinal cord disease and injuries.
  • April 2011: Human brain mapped. Four years in the works, a precise map of the human brain, the Allen Human Brain Atlas, is released. The most comprehensive characterization of the human brain at the time, the atlas marries precise gene expression with anatomical information.
  • March 2012: 10-Year Plan launched. Founder Paul Allen commits an additional $300m to expand the Allen Institute for Brain Science, setting it on a new 10-year course to tackle the most challenging questions facing the field of brain science.
  • October 2013: Groundbreaking for Future Discovery. Construction began on the Allen Institute’s new state-of-the-art headquarters in the heart of the South Lake Union, a neighborhood that was quickly becoming a hub for biotechnology and scientific research in Seattle.

  • April 2014: Wiring diagram of the brain published. The Allen Institute completes and publishes the Allen Mouse Brain Connectivity Atlas, a “connectome” map of the mouse brain, the most comprehensive wiring diagram of a mammalian brain to date.
  • April 2014: The BrainSpan Atlas of the Developing Human Brain debuted. Developed by a consortium of research organizations, including the Allen Institute for Brain Science, the atlas revealed how genes are turned on and off in the developing human brain during pregnancy –shedding light on how developmental disorders arise at their earliest stages.
  • December 2014: A new institute for cell science is born. Mr. Allen commits $100M to launch the Allen Institute for Cell Science, dedicated to creating integrated, predictive models of the human cell and sharing tools and data publicly.
  • May 2015: The first data from the Allen Cell Types Database is released. This census of cell types in the mouse brain is an ongoing project that aims to better understand the brain by characterizing its base elements, the cells.
  • December 2015: A new home. Allen Institute staff move from several different buildings around Seattle to their new dedicated facility in Seattle’s South Lake Union neighborhood.
  • March 2016: New frontiers. Mr. Allen launches the Frontiers Group with a commitment of $100m to identify and fund pioneering, transformative bioscience around the world. At the launch, the Frontiers Group also announced the first two Allen Discovery Centers, new collaborative research groups headquartered at Standford University and Tufts University.
  • July 2016: The Brain in Action. The Allen Brain Observatory, the first tool of its kind to capture standardized data about cellular activity of the mouse visual system, launches.
  • November 30, 2016: Glowing cells for science. The Allen Cell Collection is announced, giving researchers around the world access to the Allen Institute for Cell Science’s gene-edited, fluorescently tagged human stem cell lines.
  • July 2017: New Centers of Discovery. Two new Allen Discovery Centers are announced: The Allen Discovery Center at Boston Children’s Hospital and Harvard Medical School studies the evolution of the human brain, and the Allen Discovery Center at UW Medicine creates global maps of cell lineage.
  • October 2017: Human data shared. The first data from live human nerve cells was added to the Allen Cell Types Database, a publicly available tool for researchers to explore the building blocks of the human brain.
  • April 2018: An integrated human cell. The Allen Institute for Cell Science announced the Allen Integrated Cell, the first predictive and comprehensive 3D model of a live human stem cell, allowing researchers to see multiple structures inside living cells at the same time.
  • December 12, 2018: The Allen Institute for Immunology launches. Seeded by a $125 million commitment by the late Paul G. Allen, this new division of the Allen Institute will study human immune health, cancer, and autoimmune diseases.
  • May 2019: The first comprehensive view of human stem cell division. The Integrated Mitotic Stem Cell, a data-driven model and visualization tool captured — for the first time — a holistic view of human stem cell division.
  • August 21, 2019: Brain discovery lays roadmap to better treatments. In a study published in the journal Nature, scientists found crucial differences found in human and mice brain cells could explain why many drugs that work in the lab don’t work in us.
  • April 6, 2020: A new phase of neuroscience research. Cell Types and MindScope research programs to enter new stages of resource generation and discovery; another neuroscience division to launch in 2022.
  • June 2020: A high-resolution map of Alzheimer’s disease. We launched the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD), a collaborative effort with the University of Washington Medicine and Kaiser Permanente to catalogue the cell types and genetic profile of the Alzheimer’s brain.
  • July 2021: Detailed map of mouse brain released. Neuroscientists and engineers from the Allen Institute, Princeton University, and Baylor College of Medicine came together to map the fine structures and connectivity of 200,000 brain cells and close to half a billion synapses in just one cubic millimeter of mouse brain – the largest dataset of its kind to date.
  • October 2021: Mapping the cells that make up the mammalian brain. Hundreds of neuroscientists, brought together by the National Institutes of Health’s BRAIN Initiative, built the first “parts list” of the motor cortex in humans, mice and monkeys, laying the groundwork to map the whole brain and better understand brain diseases.
  • November 2021: The Allen Institute for Neural Dynamics launches. The fifth division of the Allen Institute aims to uncover the mammalian brain’s computations that give rise to complex behaviors like decision making, learning and memory.
  • December 2021: Rui Costa named next President and Chief Executive Officer of the Allen Institute. Neuroscientist Rui Costa, D.V.M., Ph.D., is a renowned expert in the brain circuitry that underlies movement and joined the Allen Institute from the Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University, where he served as CEO since 2017.
  • June 2022: Releasing an open-access portal for human immunology data. Researchers at the Allen Institute launched the Human Immune System Explorer, a portal for sharing de-identified and anonymized data with the broader scientific community. The platform provides a secure and collaborative environment for scientists to answer complex questions of human health and immune-related disease.
  • July 2022: Alzheimer’s brain cells mapped. The SEA-AD team released their first dataset comparing brain cell types in Alzheimer’s patients to those of a healthy human brain. The high-resolution dataset of 1.2 million cells sheds new light on the disease’s cellular roots.

Hundreds of men and women standing in the halls and staircases of the Allen Institute posing for an all-staff photoThe Allen Institute Today

The Allen Institute’s scientific mission has grown beyond the Allen Institute for Brain Science to include the Allen Institute for Cell Science, The Paul G. Allen Frontiers Group, the Allen Institute for Immunology, and the Allen Institute for Neural Dynamics — all working to unlock the complexities of bioscience and advance our knowledge to improve human health.

From a small but mighty team of four in 2003, the Allen Institute is now more than 700 strong, has been cited thousands of times in scientific papers, and shares dozens of petabytes of open data with the world.