• About Me

    Clinical Psychology | Developmental Neuroscience

    I study how neurobiological development influences mental and physical health trajectories. I am particularly interested in understanding how sensitive periods of neurobiological development create both vulnerabilities to environmental adversity as well as opportunities for prevention and intervention. To do so, I take an interdisciplinary approach across neural, hormonal, microbial, and psychosocial indices to assess the emergence of mental health symptoms and health-risk behaviors during adolescence.


    Recent News and Updates


    Beginning July 2020, I will start my post doctoral fellowship with Eva Telzer and Mitch Prinstein at UNC Chapel Hill!


    I joined the University of Washington Clinical Psychology Internship as part of the Child Track in July 2019!


    I successfully defended my dissertation in May 2019! You can check it out at the link above!


    Check Out my TedX talk "Teen Behavior: What's The Gut Got to Do With It?" !


  • Research

    Developmental Social & Affective Neuroscience

    How does social and affective brain function and functional connectivity influence

    mental health and health-risk behavior during adolescence?


    I study these questions using task-based functional magnetic resonance imaging (fMRI) and resting state functional connectivity MRI. I am a member of the Developmental Social Neuroscience Lab, led by Dr. Jennifer Pfeifer and

    an affiliated member of the Brain in Context Lab, led by Dr. Kathryn Mills.

    Taxonomic & Functional Gut Microbiome

    How do the bacteria and functional capacity of these microbes in our large intestines influence our

    mood and brain function during development?


    I study these questions using 16sr RNA microbial sequencing to identify "who is there" and shotgun metagenomics to identify "what they are doing." I work in close collaboration and under the advisement of microbiologist, Dr. Thomas Sharpton.

    Psychosocial Environment

    How do social and cultural environments influence the development of mental health and health risk behaviors,

    such as depression and risk-taking behaviors?


    How can these psychosocial environments alter the trajectory of developing neurobiology, including brain, neuroendocrine, and microbiome function -- for better or for worse?


    I study these questions by studying children with a history of foster care or child welfare involvement. More recently, I have extended these questions to see how a range of early and chronic childhood adversity, including poor economic and social environments can influence the trajectory of behavioral and neurobiological development. I am a member of the Stress Neurobiology and Prevention Lab, led by Dr. Philip Fisher.


    Previously, I worked under Dr. Nim Tottenham at the University of California Los Angeles (UCLA) to study social and emotional brain and hormonal development of children that had been institutionalized abroad (orphaned) and are now adopted into the USA.

  • Clinical Experience

    My clinical training focuses on pediatric populations with a history of early life adversity. I am currently completing my psychology residency at Seattle Children's Hospital / University of Washington's School of Medicine. Here, my training includes a broad range of child and adolescent psychiatric and medical disorders in the context of outpatient neuropsychological assessments, outpatient child therapy and parent management training, as well as inpatient child psychiatry behavioral medical unit therapy and inpatient psychology consult & liason. Previously, I primarily used neuropsychological assessments with children and adolescents displaying complex social, cognitive, and medical life histories, as well as mild traumatic brain injuries. My theoretical orientation integrates cognitive behavioral and biopsychosocial (integrative) approaches.

    Pediatric Neuropsychology & Psychological Assessment


    I trained in general pediatric psychological evaluations and in pediatric neuropsychological evaluations with children 4-18 years old in an outpatient clinic. Training occurred in the context of a multidisciplinary team, including a psychologist, social worker, speech language pathologist, occupational therapist, and developmental pediatrician. Neuropsychological evaluations occurred in the context of a multidisciplinary team and full-day single team evaluations.

    I am currently training in pediatric neuropsychology at a sports medicine outpatient clinic, specifically focused on concussions and mild traumatic brain injuries.
    Assessment training includes:

    -Wechsler Adult Intelligence Scale (WAIS)

    -Wechsler Intelligence Scale for Children (WISC)

    -Wechsler Abbreviated Scale of Intelligence (WASI-II)

    -Wechsler Preschool and Primary Scale of Intelligence (WPPSI)

    -Wechsler Memory Scale (WMS)

    -California Verbal Learning Test (CVLT)

    -California Verbal Learning Test- Child (CVLT-C)

    -Wide Range Assessment of Memory and Learning (WRAML)

    -A Developmental Neuropsychological Assessment (NEPSY), Memory for Designs subscale

    -Test of Memory Malingering (TOMM)

    -Delis-Kaplan Executive Function System (D-KEFS)

    -Wechsler Individual Achievement Test (WIAT)

    -Conners Continuous Performance Test (CPT)

    Social Learning & Behaviorally-Based Interventions


    I trained in a community mental health agency, as part of the Early Intervention Foster Care (EIFC) team. I was specifically trained in the intervention, Multidimensional Treatment Foster Care- Preschool (MTFC-P). Theoretical orientation was centered in social learning and behavioral theory and Parent Management Training Oregon (PMTO). I worked as an individual child therapist and group therapy leader for children 3-8 years old.


    I was trained and served as an intervention coach for the strength-based parenting intervention for parents of low socioeconomic status, led by Dr. Philip Fisher, Filming Interactions to Nurture Development (FIND).


    I additionally served as an intervention coach for a pilot parenting intervention for depressed mothers of adolescents, led by Dr. Nicholas Allen and Dr. Lisa Sheeber.


    I am currently involved in a longitudinal study of adolescent girls and serve as both an MRI operator and semi-structured intake interviewer.


    Pediatric diagnostic training includes:

    Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS)

    Cognitive Behavioral Therapy


    I trained in Cognitive Behavioral Therapy (CBT). This included individual therapy with adults 18- 25 years old for anxiety and mood-related disorders.


    Adult diagnostic training includes:

    Structural Clinical Interview for DSM IV, V (SCID I).

    Mindfulness-Based Therapies


    I trained in Mindfulness-Based Cognitive Therapy (MBCT) and Mindfulness Based Stress Reduction (MBSR). This included group therapy with adults 18-70 years old.

  • Publications

    Google Scholar Profile

    Note: *denotes shared first authorship



    Flannery JE*, Stagaman K*, Burns AR, Hickey RJ, Roos LE, Giuliano RJ, Fisher PA, Sharpton TJ (2020). Gut feelings begin in childhood: the gut metagenome correlates with early environment, caregiving, and behavior. mBio 


    Barendse, M., Vijayakumar, N., Byrne, M., Flannery, J., Cheng, T., Flournoy, J., Nelson, B., Cosme, D., Mobasser, A., Chavez, S., Hval, L., Brady, B., Nadel, H., Helzer, A., Shirtcliff, E., Nick Allen, N., Pfeifer J. (2020) Study protocol: Transitions in Adolescent Girls (TAG).


    Vijayakumar, N., Flournoy, J., Mills, K., Cheng, T., Mobasser, A., Flannery, J., Allen, N., Pfeifer J., Getting to know me better: (2020). An fMRI study of intimate and superficial self-disclosure to friends during adolescence.


    Callaghan, B., Fields, A., Gee, D.G., Gabard-Durnam, L., Caldera, C., Humphreys, K., Goff, B., Flannery, J., Telzer, E., Shapiro, M., Tottenham, N. (2020). Mind and gut: associations between mood and gastrointestinal distress in children exposed to adversity. Development and Psychopathology.



    Humphreys, K., Gabard-Durnam, L., Goff, B., Telzer, E., Flannery, J., Gee, D., Park, V., Lee, S., Tottenham, N. (2019) Friendship and social functioning following early institutional rearing: The role of ADHD symptoms. Development and Psychopathology.


    Tottenham, N., Shapiro, M., Flannery, J.,Caldera, C., & Sullivan, R.M. (2019). Parental presence switches avoidance to attraction learning in children. Nature Human Behaviour.


    Flannery, J., Callaghan, B., Sharpton, T., Fisher, P., Pfeifer, J., (2019). Is adolescence the missing developmental link in gut-brain axis communication? Developmental Psychobiology.


    Alba, L., Flannery, J., Shapiro, M., & Tottenham, N. (2019). Working Memory Moderates the Association Between Early Institutional Care and Separation Anxiety Symptoms in Late Childhood and Adolescence. Development and Psychopathology.


    Callaghan, B., Gee, D., Gabard-Durnam, L.J., Telzer, E., Humphreys, K., Goff, B., Shapiro, M., Flannery, J., Lumian, D., Fareri, D., Caldera, C., Tottenham, N. (2019). Decreased amygdala reactivity to parent cues protects against anxiety following early adversity: an examination across 3 years. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging.



    Op de Macks, Z.,* Flannery, J.,* Peake, S., Flournoy, J.C., Mobasser, A., Alberti, S., Fisher, P., Pfeifer, J. (2018). Novel insights from the Yellow Light Game: Safe and risky decisions differentially impact adolescent outcome-related brain function. Neuroimage.


    Humphreys, K.L., Gabard-Durnam, L., Goff, B., Telzer, E.H., Flannery, J., Gee, D.G., Park, V., Lee, S.S., Tottenham, N. (2018). Friendship and social functioning following early institutional rearing: The role of ADHD symptoms. Development and Psychopathology.


    Horn., S.R., Roos, L.E., Beauchamp, K.G., Flannery, J.E., Fisher, P.A. (2018). Polyvictimization and externalizing symptoms in foster care children: the moderating role of executive function. Journal of Trauma & Dissociation.


    Roos, L., Beauchamp, K.,Flannery, J., Fisher, P. (2018). Cultural contributions to executive function. Journal of Cognition and Culture.



    Flannery, J., Gabard-Durnam, L., Shapiro, M., Goff, B., Caldera, C., Louie, J., Gee, D., Telzer, E., Humphreys, K., Lumian, D., Tottenham, N. (2017). Diurnal cortisol after early institutional care - age matters. Developmental Cognitive Neuroscience, 25:160-166.PMID: 28442223 PMCID: PMC5520669


    Flannery, J.E., Giuliani, N.R., Flournoy, J., Pfeifer, J.H. (2017). Neurodevelopmental changes across adolescence in viewing and labeling dynamic peer emotions. Developmental Cognitive Neuroscience, 25:113-127.PMID: 28262423 PMCID: PMC5764159


    Fareri D., Laurel Gabard-Durnam. L., Goff, B., Flannery, J., Gee., B., Lumian, D., Caldera, C., Tottenham, N. (2017). Altered ventral striatal-medial prefrontal cortex resting-state connectivity mediates adolescent social problems after early institutional care. Development and Psychopathology, 29(5):1865-1876. PMID: 29162189 PMCID: PMC5957481


    Flannery, J.E., Beauchamp, K.G., Fisher, P.A. (2017). The role of social buffering on chronic disruptions in quality of care: evidence from caregiver-based interventions in foster children. Social Neuroscience, 12(1), 86-91. PMID: 27021231 PMCID: PMC5372832



    Silvers, J.A., Lumian, D.S., Gabard-Durnam, L., Gee, D.G., Goff, B., Fareri, D.S., Caldera, C., Flannery, J., Telzer, E., Humphreys, K., Tottenham, N. (2016). Previous institutionalization is followed by broader amygdala-hippocampal-PFC network connectivity during aversive learning in human development. Journal of Neuroscience, 36(24), 6420-6430. PMID: 27307231 PMCID: PMC5015779


    Gabard-Durnam, L.J., Gee, D. G., Goff, B., Flannery, J., Telzer, E., Humphreys, K.L., Lumian, D., Fareri, D., Caldera, C., Tottenham, N. (2016). Stimulus-elicited connectivity influences resting-state connectivity years later in human development: A prospective study. Journal of Neuroscience, 36(17), 4771-4784. PMID: 27122035 PMCID: PMC4846673


    Green, S.A., Goff, G., Gee, D.G., Gabard-Durnam, L., Flannery, J., Telzer, E.H., Humphreys, K., Louie, J., Tottenham, N. (2016). Discrimination of amygdala response predicts future separation anxiety in youth with early deprivation. Journal of Child Psychology and Psychiatry, 57(10), 1135-1144. PMID: 27260337 PMCID: PMC5030125


    Fisher, P.A., Beauchamp, K.G., Roos, L.E., Noll, L.K., Flannery, J., Delker, B.C. (2016). The Neurobiology of Intervention and Prevention in Early Adversity. Annual Review of Clinical Psychology, 12, 331-357. PMID: 26666968



    Humphreys, K.L., Telzer, E.H., Flannery, J., Goff, B., Gabard-Durnam, L., Gee, D.G., Lee, S.S., Tottenham, N. (2015). Risky decision making from childhood through adulthood: Contributions of learning and sensitivity to negative feedback. Emotion, 16(1), 101. PMID: 26389647 PMCID: PMC4718882


    Fareri D.S., Gabard-Durnam .L, Goff B., Flannery J., Gee D.G., Lumian D.S., Caldera C., Tottenham, N. (2015). Normative development of ventral striatal resting state connectivity in humans. Neuroimage, 118, 422-437. PMID: 26087377 PMCID: PMC5553607


    Telzer, E.H., Flannery, J., Humphreys, K.L., Goff, B., Gabard-Durman, L., Gee, D.G., Tottenham, N. (2015). “The Cooties Effect”: Amygdala reactivity to opposite- versus same-sex faces declines from childhood to adolescence. Journal of Cognitive Neuroscience, 7(9):1685-96. PMID:25848681 PMCID: PMC5723398


    Humphreys, K.L., Lee, S.S., Telzer, E.H., Gabard‐Durnam, L.J., Goff, B., Flannery, J., Tottenham, N. (2015). Exploration – Exploitation strategy is dependent on early experience. Developmental Psychobiology, 57(3), 313-321. PMID: 25783033 PMCID: PMC5934758



    Gee*, D., Gabard-Durnam*, L., Telzer, E., Humphreys, K., Goff, B., Shapiro, M., Flannery, J., Lumian, D., Fareri, D., Caldera, C., Tottenham, N. (2014). Maternal buffering of human amygdala–prefrontal circuitry during childhood but not adolescence. Psychological Science, 25(11): 2067–2078. PMID: 25280904 PMCID: PMC4377225


    Gabard-Durnam, L., Flannery, J., Goff, B., Gee, D., Humphreys, K., Telzer, E., Hare, T., Tottenham, N. (2014). The development of human amygdala functional connectivity at rest from 4 to 23years: A cross-sectional study. Neuroimage, 95, 193-207. PMID: 24662579 PMCID: PMC4305511



    Gee, D., Gabard-Durnam, L., Flannery, J., Goff, B., Humphreys, K., Telzer, E., Hare, T., Bookheimer, S., Tottenham, N. (2013). Early developmental emergence of human amygdala-prefrontal connectivity after maternal deprivation. Proceedings of the National Academy of Sciences, 110(39), 15638-15643. PMID: 24019460 PMCID: PMC3785723

    Goff, B., Gee, D.G., Telzer, E.H., Humphreys, K.L., Gabard-Durnam, L., Flannery, J., Tottenham, N. (2013). Reduced nucleus accumbens reactivity and adolescent depression following early-life stress. Neuroscience, 249, 129-138. PMID: 23262241 PMCID: PMC3646076

    Gee, D., Humphreys, K., Flannery, J., Goff, B., Telzer, E., Shapiro, M., Bookheimer, S., Tottenham, N. (2013). A developmental shift from positive to negative connectivity in human amygdala-prefrontal circuitry. Journal of Neuroscience, 33(10), 4584-4593. PMID: 23467374 PMCID: PMC3670947


    Telzer, E.H., Flannery, J., Shapiro, M., Humphreys, K., Goff, B., Gabard-Durman, L., Gee, D.G., Tottenham, N. (2013). Early experience shapes amygdala sensitivity to race: An international adoption design. Journal of Neuroscience, 33(33), 13484-13488. PMID: 23946406 PMCID: PMC3742934


    Olsavsky, A.K., Telzer, E.H., Shapiro, M., Humphreys, K.L., Flannery, J., Goff, B., Tottenham, N. (2013). Indiscriminate amygdala response to mothers and strangers after early maternal deprivation. Biological Psychiatry, 74(11), 853-860.PMID: 23810622 PMCID: PMC3818506


    Tottenham, N., Phuong, J., Flannery, J., Gabard-Durnam, L., Goff, B. (2013). A negativity bias for ambiguous facial-expression valence during childhood: Converging evidence from behavior and facial corrugator muscle responses. Emotion, 13(1), 92.

    PMID: 22906084 PMCID: PMC4006094


    Book Chapters

    Roos, L., Beauchamp, K., Flannery, J., Horn, S., Fisher, P. (2018). Interventions, stress during development, and psychosocial adjustment. International Handbook of Social Neuroendocrinology.


  • Open science contributions

    Flannery, J., (2019, November). Preregistration: updated challenges and solutions for complex study design. Presented at BrainHack Global, Eugene Chapter.


    Flannery, J. (2018, October). Flannery Dissertation Preregistration: The “Depressed” Gut-Brain Axis during Adolescence. Retrieved from osf.io/cb7ys


    Flannery, J., (2018, May). Preregistration: Challenges and Solutions for fMRI.

    Presented at BrainHack Global, Eugene Chapter.


    Flannery, J. (2018, May). fMRI Preregistration Template. Retrieved from osf.io/6juft

  • Science Communication Blog

    Thoughts, musings, and ruminations.

    Try these 8 tips to reduce parenting stress during the coronavirus pandemic "Parenting can be tough at the best of times, but family life has changed dramatically during social isolation that’s been mandated by COVID-19...Here are a few research-based strategies to make this unprecedented time...
    As the new wave of anxiety rides over the next year's clinical internship matching class, I want to share some of my experiences with the process. In an attempt to avoid my survivorship-biased responses to internship tips, I tried to write the majority of these notes during the process of...
    I started this resource page for myself awhile back when I was feeling overwhelmed with work and I wanted to learn new habits to work more efficiently. I recently started sharing it with other lab members who expressed similar roadblocks. Now I hope others can find it useful too! The goal of...
    More Posts
  • Social Me

    Media engagement


    Roos, L., Flannery, J., (April, 2020) “Try these 8 tips to reduce parenting stress during the coronavirus pandemicThe Conversation


    Radio interview "A Possible Link Between Gut Bacteria And Kids’ Behavior” (January, 2020) Think Out Loud. Oregon Public Broadcasting.


    TEDxUOregon “Teen Behaviors—What’s the gut got to do with it?” (March, 2019)


    Radio interview on teenage risk-taking. (March, 2018) BYU Radio, Matt Townsend Show.


    Flannery, J., Berkman, E., & Pfeifer, J., (Feb, 2018) “Teens aren’t just risk machines- there’s a method to their madnessThe Conversation


    I Study Poop – Adventures from Researchers on the Front Line (Feb, 2017) The Two Brains Blog

  • Contact me

    Let's grab a cup and collaborate!

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