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We are celebrating 20 years of science impact


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

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

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.

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.

With a focus on impact, and years of pharmaceutical industry experience, Jones developed an organizational culture that brought dedicated scientists from multiple disciplines together to conquer scientific challenges at scale. Under his leadership, the Allen Institute grew to include the Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, Allen Institute for Neural Dynamics, and the Paul G. Allen Frontiers Group.

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.

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.

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.

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.

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.

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.

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.

Allen Institute staff move from several different buildings around Seattle to their new dedicated facility in Seattle’s South Lake Union neighborhood.

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.

The Allen Brain Observatory, the first tool of its kind to capture standardized data about cellular activity of the mouse visual system, launches.

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.

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.

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.

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.

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.

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.

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.

Cell Types and MindScope research programs to enter new stages of resource generation and discovery; another neuroscience division to launch in 2022.

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.

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.

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.

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.

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.

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.

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.

The 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.

Large group photos of Allen Institute Staff - Allenites
2023 All-Allenite photo