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The Stanley Institute for Cognitive Genomics is dedicated to genetics and neuroscience research that will enhance our understanding of schizophrenia, bipolar disorder, major depression and other cognitive disorders. The goal is to improve the diagnosis and treatment of these disorders.

Work at the Stanley Institute for Cognitive Genomics at CSHL is funded by gifts from Theodore and Vada Stanley and grants from the
National Institute of Mental Health.

Stanley InstituteSchizophrenia, bipolar disorder and major recurrent depression are cognitive disorders that create an enormous burden on patients, their families and our health care system.

Because vulnerability to these disorders tends to run in families, genetics is a factor; however the specific genetic components involved and how they impact symptoms or treatments of these disorders has yet to be fully worked out.  With recent advances in genomic technologies, CSHL is now poised to unravel the genetic complexity of cognitive disorders. Simultaneously, advanced technologies in neuroscience are allowing CSHL researchers to understand how the brain assembles neural circuits to control behaviors and cognitive processes like attention and decision-making. At the CSHL Stanley Institute for Cognitive Genomics, these two approaches – genetics and neuroscience – are integrated to form a dual-strategy aimed at improving the diagnosis and treatment of schizophrenia, bipolar disorder, depression and other cognitive disorders.

    Detailed images of NMDA receptor show how zinc and a potential drug affect its function

    Detailed images of NMDA receptor show how zinc and a potential drug affect its function

    December 1, 2016

    Drugs precisely targeting portions of this receptor may have applications in Alzheimer’s, depression and schizophrenia Cold Spring Harbor, NY — The difference between mental health and mental illness can turn on changes in brain cells and their connections that are almost incomprehensibly tiny, at least in physical terms. This irony is brought to light by...


    Was it better or worse than you expected? Your basal ganglia know – so you can act accordingly

    Was it better or worse than you expected? Your basal ganglia know – so you can act accordingly

    September 21, 2016

    Identifying a neural circuit that processes evaluations, with implications for understanding depression Cold Spring Harbor, NY — You make reservations at a restaurant, expecting the food to be good. If the meal turns out to be superb—even better than expected—that’s information you will want to remember, so you can go back again. The reverse applies...


    Innovative tools will shed clarifying light on inhibitory neurons

    Innovative tools will shed clarifying light on inhibitory neurons

    September 21, 2016

    Cold Spring Harbor, NY — Imagine if every time you got in your car, you fired it up, put it in drive, slammed on the gas, and didn’t let up until you reached your destination. Now imagine every driver on the road did the same thing. It would be pile up after pile up. A...


    Our brain uses statistics to calculate confidence, make decisions

    Our brain uses statistics to calculate confidence, make decisions

    May 4, 2016

    The brain produces feelings of confidence that inform decisions the same way statistics pulls patterns out of noisy data Cold Spring Harbor, NY — The directions, which came via cell phone, were a little garbled, but as you understood them: “Turn left at the 3rd light and go straight; the restaurant will be on your...


    First structural views of the NMDA receptor in action will aid drug development

    First structural views of the NMDA receptor in action will aid drug development

    May 2, 2016

    Cold Spring Harbor, NY – Structural biologists at Cold Spring Harbor Laboratory (CSHL) and Janelia Research Campus/HHMI, have obtained snapshots of the activation of an important type of brain-cell receptor. Dysfunction of the receptor has been implicated in a range of neurological illnesses, including Alzheimer’s disease, Parkinson’s disease, depression, seizure, schizophrenia, autism, and injuries related...


    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards

    April 12, 2016

    Cold Spring Harbor, NY – Two scientists, both leaders of research labs at Cold Spring Harbor Laboratory (CSHL), are among 25 teams that have won Human Frontier Science Program (HFSP) Research Program Grants for 2016. The awards were announced by the International Human Frontier Science Program Organization (HFSPO), based in Strasbourg, France. The two CSHL...


    Discovery of a new X-linked intellectual disability syndrome is aided by web communication tools

    Discovery of a new X-linked intellectual disability syndrome is aided by web communication tools

    December 3, 2015

    Cold Spring Harbor, NY — It’s a genetic detective story with a distinct 21st-century flavor. A geneticist from Cold Spring Harbor Laboratory (CSHL) in the United States has used powerful internet and social media tools to find doctors and researchers in nine U.S. states and eight other nations to help him confirm, document and describe in...


    Surprised? Cholinergic neurons send brain-wide broadcasts enabling us to learn from the unexpected

    Surprised? Cholinergic neurons send brain-wide broadcasts enabling us to learn from the unexpected

    August 25, 2015

    Cold Spring Harbor, NY — When a large combat unit, widely dispersed in dense jungle, goes to battle, no single soldier knows precisely how his actions are affecting the unit’s success or failure. But in modern armies, every soldier is connected via an audio link that can instantly receive broadcasts—reporting both positive and negative surprises—based...


    Drs. Kepecs and Li honored with 2015 NARSAD Independent Investigator grant awards

    Drs. Kepecs and Li honored with 2015 NARSAD Independent Investigator grant awards

    May 12, 2015

    Cold Spring Harbor, NY — Two neuroscientists at Cold Spring Harbor Laboratory (CSHL) have been awarded prestigious NARSAD Independent Investigator grants. The announcement was made by the New York City-based Brain and Behavior Research Foundation (BBRF). Adam Kepecs, Ph.D., and Bo Li, Ph.D., both CSHL associate professors, were among 40 mid-career scientists from 30 institutions in...


    Scientists discover important communication mechanism between two brain areas implicated in schizophrenia

    Scientists discover important communication mechanism between two brain areas implicated in schizophrenia

    April 7, 2015

    Disruptions in an inhibitory brain circuit between the thalamus and prefrontal cortex may underlie cognitive disorders such as schizophrenia Cold Spring Harbor, NY — The prefrontal cortex (PFC) plays an important role in cognitive functions such as attention, memory and decision-making. Faulty wiring between PFC and other brain areas is thought to give rise to...


    A new brain circuit that controls fear is identified

    A new brain circuit that controls fear is identified

    January 19, 2015

    Researchers discover a pathway in that mouse brain that regulates fear memory and behavior Cold Spring Harbor, NY — Some people have no fear, like that 17-year-old kid who drives like a maniac. But for the nearly 40 million adults who suffer from anxiety disorders, an overabundance of fear rules their lives. Debilitating anxiety prevents...


    Imaging method linking brainwide cell activation & behavior shows what it means for mice to have sex in mind

    Imaging method linking brainwide cell activation & behavior shows what it means for mice to have sex in mind

    January 5, 2015

    Automated method detects activity of neurons during specific behaviors, brain-wide, at cellular resolution Cold Spring Harbor, NY — Most people have seen fMRI scans of the human brain. These use a technology called functional magnetic resonance imaging to identify portions of the brain that are active while a subject is being scanned. Fuzzy, ill-defined areas...


    Neuronal circuits filter out distractions in the brain

    Neuronal circuits filter out distractions in the brain

    December 15, 2014

    Scientists identify a neural pathway that controls attention, with implications for psychiatric disorders Cold Spring Harbor, NY — The next time you are in a crowded room, or a meeting, or even at the park with your kids, take a look around. How many people are on their phone? Distractions invade every aspect of our...


    4 CSHL scientists will contribute to President’s BRAIN Initiative under new NIH grants

    4 CSHL scientists will contribute to President’s BRAIN Initiative under new NIH grants

    September 30, 2014

    Cold Spring Harbor, NY — Four scientists at Cold Spring Harbor Laboratory (CSHL) will perform research in President Obama’s BRAIN Initiative under two new CSHL grants announced in Washington today. The CSHL grants are among more than 100 issued by the National Institutes of Health (NIH), totaling $46 million for the 2014-15 fiscal year. They...


    A shift in the code: new method reveals hidden genetic landscape

    A shift in the code: new method reveals hidden genetic landscape

    August 18, 2014

    Scientists develop algorithm to uncover genomic insertions and deletions involved in autism, OCD Cold Spring Harbor, NY — With three billion letters in the human genome, it seems hard to believe that adding a DNA base here or removing a DNA base there could have much of an effect on our health. In fact, such...


    Unprecedented detail of intact neuronal receptor offers blueprint for drug developers

    Unprecedented detail of intact neuronal receptor offers blueprint for drug developers

    May 29, 2014

    NMDA receptor malfunction is implicated in Alzheimer’s, Parkinson’s, depression, schizophrenia, autism, and stroke Cold Spring Harbor, NY — Biologists at Cold Spring Harbor Laboratory (CSHL) report today that they have succeeded in obtaining an unprecedented view of a type of brain-cell receptor that is implicated in a range of neurological illnesses, including Alzheimer’s disease, Parkinson’s...


    Dealing with stress—to cope or to quit?

    Dealing with stress—to cope or to quit?

    May 27, 2014

    Researchers identify neurons that determine whether an individual will be depressed or resilient Cold Spring Harbor, NY — We all deal with stress differently.  For many of us, stress is a great motivator, spurring a renewed sense of vigor to solve life’s problems. But for others, stress triggers depression. We become overwhelmed, paralyzed by hopelessness...


    Research sees overlap in altered genes found in schizophrenia, autism and intellectual disability

    Research sees overlap in altered genes found in schizophrenia, autism and intellectual disability

    April 28, 2014

    Dublin, Ireland and Cold Spring Harbor, NY — In research published today in Molecular Psychiatry, a multinational team of scientists presents new evidence supporting the theory that in at least some cases of schizophrenia, autism and intellectual disability (ID), malfunctions in some of the same genes are contributing to pathology. The team, the product of...


    Scientists discover a new pathway for fear deep within the brain

    Scientists discover a new pathway for fear deep within the brain

    February 12, 2014

    ‘Far-reaching’ neurons connect the amygdala with fear response center to control behavior Cold Spring Harbor, NY — Fear is primal. In the wild, it serves as a protective mechanism, allowing animals to avoid predators or other perceived threats. For humans, fear is much more complex. A normal amount keeps us safe from danger. But in...


    Team demonstrates power of precision medicine in successful treatment of patient with disabling OCD

    Team demonstrates power of precision medicine in successful treatment of patient with disabling OCD

    October 3, 2013

    Cold Spring Harbor, NY — A multidisciplinary team led by a geneticist and psychiatrist from Cold Spring Harbor Laboratory’s (CSHL) Stanley Institute for Cognitive Genomics today publish a paper providing a glimpse of both the tremendous power and the current limitations of what is sometimes called “precision medicine.” Precision medicine is an approach to diagnosis...


    CSHL’s sequencing power gets a fresh boost

    CSHL’s sequencing power gets a fresh boost

    August 12, 2011

    LabDish blog At CSHL’s Woodbury Genome Center a decade ago, it took 12 technicians working in two shifts and six “first generation” sequencing machines to sequence 70 million bases of DNA—repeats of A, T, G, C—in a single month. By 2007, as the Center began to acquire “second generation” machines, the output jumped up to...


    Collaboration column: SMA therapeutics and potential drug target for schizophrenia

    Collaboration column: SMA therapeutics and potential drug target for schizophrenia

    March 11, 2011

    LabDish blog CSHL researchers are part of two highly successful, multi-institutional collaborations that report exciting advances in developing therapeutics for a devastating neuromuscular disorder and in finding a ‘druggable’ target for schizophrenia. For several years now, CSHL’s Adrian Krainer has devoted his expertise in alternative splicing—a cellular process for editing RNA—towards fixing the genetic glitch that underlies...


Researchers at CSHL began working on the genetics of cognitive disorders in 2005 following a generous gift from Ted and Vada Stanley. Under the leadership of James Watson, this effort grew substantially in 2007 with a gift from the Stanley’s to establish the Stanley Institute for Cognitive Genomics. At that time, new DNA sequencing technologies, called “Next Generation Sequencing” were being developed. CSHL Professor and sequencing pioneer W. Richard McCombie was one of the first to apply this technology to study the genetics of cognitive disorders putting the Stanley Institute on the map.

With the goal of improving diagnosis and the potential for personalized therapy, the Stanley Center began applying state-of-the-art genomics technologies to identify genetic variants contributing to schizophrenia, bipolar disorder and major depression. Together with collaborators in the U.S., Scotland, Ireland, Pakistan and Australia, CSHL focused first on sequencing the complete genomes or protein coding regions of the genomes of families that had many members suffering from mental illness. One of the key findings demonstrated an overlap among genes contributing to schizophrenia and autism. CSHL also showed a link between the genes involved in the modification of chromatin structure and schizophrenia.

In 2014, with continuing support from Ted and Vada Stanley, the Stanley Institute incorporated the efforts of CSHL neuroscientists focused on understanding how brain circuits assemble and function. Like the genetics group, neuroscientists are developing and applying new technologies, including sophisticated brain mapping technologies and novel behavioral paradigms for studying decision making, attention and other processes. Stanley Institute neuroscientists are now studying the function of genes that have been implicated in cognitive disorders.

Building publication list.
Hiro Furukawa

Hiro Furukawa

The nervous system transmits information by passing chemical signals from one nerve cell to the others. This signal transmission relies on a variety of proteins to receive and transmit the chemical signals. My group studies the structure and function of neurotransmitter receptors and ion channels that regulate fundamental neuronal activities.

Jesse Gillis

Jesse Gillis

Of the tens of thousand of protein-coding genes in the human genome, only a small portion have an experimentally defined function. For the rest, how can we determine what they do? My lab develops computational predictions based on co-expression networks. We are applying our predictions to understand neuropsychiatric disorders.

Z. Josh Huang

Z. Josh Huang

Studies the development and organization of neural circuits in the mouse cerebral cortex. His team uses an integrated approach to identify neuronal cell types and discover how they interact to process information and guide behavior, focusing on the motor cortex that controls forelimb movement. His studies of inhibitory interneurons, such as chandelier cells, have implications for understanding schizophrenia and autism.

Adam Kepecs

Adam Kepecs

My lab studies the neurobiological principles underlying cognition and decision-making. Using state-of-the-art technologies, we interrogate neural circuits in rodents as they perform a task. We validate our findings with analogous tasks in humans. We hope to define the neural circuits underlying decisions that will inform the development of new therapies for psychiatric diseases.

Bo Li

Bo Li

My group studies the neural circuits underlying cognitive function and dysfunction as they relate to anxiety, depression, schizophrenia and autism. We use sophisticated technologies to manipulate specific neural circuits in the rodent brain to determine their role in behavior. We are interested in changes in synaptic strength that may underlie mental disorders.

W. Richard McCombie

W. Richard McCombie

Over the last two decades, revolutionary improvements in DNA sequencing technology have made it faster, more accurate, and much cheaper. We are now able to sequence up to 10 trillion DNA letters in just one month. I harness these technological advancements to assemble genomes for a variety of organisms and probe the genetic basis of neurological disorders, including autism and schizophrenia, better understand cancer progression and understand the complex structures of the genomes of higher plants.

Alea A. Mills

Alea A. Mills

Cells employ stringent controls to ensure that genes are turned on and off at the correct time and place. Accurate gene expression relies on several levels of regulation, including how DNA and its associated molecules are packed together. I study the diseases arising from defects in these control systems, such as aging and cancer.

Pavel Osten

Pavel Osten

To understand what’s going wrong in illnesses like autism and schizophrenia, we need to know more about how neural circuits are connected in the healthy brain. We’ve developed advanced imaging methods to draw the first whole-brain activation map in the mouse. Now we’re applying that technology to study changes in brain activity in mice whose behavior models human autism and schizophrenia.

Jessica Tollkuhn

Jessica Tollkuhn

I am interested in how transient events during development program neurons to take on a specific identity and function. More specifically, I am studying how estrogen and testosterone generate sex differences in the brain and behavior.