Different subpopulations of neurons in the dorsal raphe region of the mouse brain. Image by Daniel Cardozo Pinto, Lammel lab, from research published in Nature Communications.

The Neuroscience PhD Program at UC Berkeley offers intensive training in neuroscience research through a combination of coursework, research training, mentoring, and professional development. More than 60 program faculty from many departments provide broad expertise from molecular and cellular neuroscience to systems and computational neuroscience, to human cognitive neuroscience. (For detailed information on faculty research interests, see the Faculty page.)

A unique feature of the neuroscience training at Berkeley is the highly multidisciplinary research environment. For instance, neuroscientists work side-by-side in the lab with engineers and roboticists to study motor control, with bioengineers to grow stem cells for regenerative medicine and tissue engineering, and with chemists to develop new reagents for optical monitoring and control of neural activity. Neuroscience PhD Program students are trained at these intersections between fields and help drive scientific and technological advances.

The Neuroscience PhD Program trains a select group of students (about 10 entering students per year) in an intellectually stimulating and supportive environment. Since its official launch in 2000, the program has trained more than 100 students. Our applicants have outstanding undergraduate records in both research and scholarship from diverse academic disciplines, including biology, chemistry, psychology, physics, engineering, and computer science. We carefully select students with the expectation that, given strong graduate training, they will develop into tomorrow’s leaders in the field of neuroscience. We welcome you to apply to our program.

Apply Here

How to Apply

Application deadline: November 16.

Applications are accepted from the beginning of September through November 16th for admission the following year. Complete applications include transcripts, test scores (if applicable), and recommendation letters. Late applications are not accepted or reviewed. We do not accept applications for spring semester. The entire application process is online, and it includes uploading transcripts, Personal History Statement and Statement of Purpose, registration numbers for the TOEFL and/or GRE (submission of GRE scores is optional in our program) and contact information for at least three recommenders. *It is the responsibility of the applicant to ensure that all materials, including recommendation letters, are submitted by the deadline.

For general questions about graduate admissions or technical problems with the online application:

Email

For comprehensive information on university-wide graduate application and admissions processes:

More Info

Neuroscience PhD Program, UC Berkeley
444 Li Ka Shing, MC#3370
Berkeley, CA 94720

Get in Touch

Steps to a PhD

Neuroscience PhD Program students (left to right) Greg Telian, Charles Garfinkle and Jocelyn Breton.

Neuroscience is a broad field that requires multidisciplinary training as well as intensive study of specific concepts and techniques related to each student’s primary research focus. The Neuroscience PhD Program is designed to provide highly individualized, flexible training that fulfills both these needs. Our PhD training program has a standard completion time of 5 to 5.5 years. The program is PhD-granting only, there is no master’s degree program. The following is a general overview of the steps to a Neuroscience PhD at UC Berkeley. For detailed policies, see Resources For Current Students.

Neuroscience Boot Camp

First-year students begin the program with an intensive, 10-day “Boot Camp” course held just prior to the official start of fall semester classes. The course features lectures on key neuroscience concepts and on classical and emerging experimental techniques and evening research seminars by Berkeley Neuroscience faculty. In addition, hands-on research projects in faculty laboratories cover techniques ranging from molecular neuroscience to neurophysiology and optogenetics to fMRI. The goal is to provide an immersive introduction to multiple disciplines and experimental approaches within neuroscience. Our Boot Camp unites neuroscience-oriented students from multiple PhD programs.

Image of a section from a human brain organoid showing patches of developing neural progenitor cells (green and red). Cell nuclei are labeled in blue. Bateup lab.

Laboratory Rotations

During Year 1, each student spends three 10-week periods performing research projects in different faculty laboratories. The choice of laboratories is based on student preference. The goal is to expose students to different techniques and approaches in neuroscience and to provide training in experimental design, critical analysis of data, and presentation of research findings. Performance in rotations is evaluated and graded. Rotations also allow students to identify the laboratory in which their thesis research will be performed. Students formally present results from the laboratory rotations in a dedicated course designed to instruct students in clear, effective presentation of scientific findings.

Irene Grossrubatscher
Neuroscience PhD student Irene Grossrubatscher.

Coursework

The program has highly flexible course requirements. These are designed to provide students with sufficiently broad training in all areas of neuroscience, while allowing focus in the area of primary research interest.

During the first two years of the program, each student is required to take one course in each of three broad areas: (A) Cellular, Molecular & Developmental Neuroscience; (B) Systems and Computational Neuroscience; and (C) Cognitive and Behavioral Neuroscience. Each student consults with faculty advisers to determine the most appropriate individual courses within these areas.

Students must also complete a one-semester course in Applied Statistics in Neuroscience, or an equivalent approved course in statistics or quantitative analysis methods.

For additional details, see the Neuroscience Course Curriculum.

Training in Teaching

Effective teaching is a critical skill required in most academic and research careers. Students are required to serve as Graduate Student Instructors (GSIs; equivalent to Teaching Assistants) for two semesters. GSI teaching occurs during Years 2 and 3 and provides supervised teaching experience in laboratory and discussion settings. Teaching is evaluated, and outstanding teaching is rewarded with annual Outstanding Graduate Student Instructor Awards. One to three of our students typically win this award each year.

Qualifying Examination

Students complete an Oral Qualifying Exam during the spring semester of Year 2. This exam is structured around a written thesis proposal and oral examination on this proposal, related research areas, and foundational questions in neuroscience. During the exam, a faculty committee tests the student’s knowledge of these areas and general neuroscience. Students must demonstrate the ability to recognize important research problems, propose relevant experimental approaches, and display comprehensive knowledge of relevant subjects. Students must pass the qualifying examination before advancing to doctoral candidacy.

Neuroscience PhD student Timothy Day and faculty member John Flannery.

Thesis Research

Thesis research begins after the completion of rotations in spring or summer of Year 1. During Year 2, students conduct thesis research while completing required coursework and GSI teaching. Years 3 to 5 are spent primarily on thesis research. Progress on thesis research is evaluated by the student, the thesis adviser, and a Thesis Committee of three additional faculty members.

Thesis research is expected to lead to publication in top-ranked, refereed scientific journals. Students are strongly encouraged to present posters and speak at scientific meetings and conferences. During Year 4, they make a formal presentation of their research progress to their peers. Completion of thesis research is determined by the Thesis Committee. While there is no formal thesis defense, students present a formal thesis seminar to the neuroscience community in their last semester of candidacy.

Neuroscience PhD student Emily Jacobs.

Other Program Activities

During training, students are expected to participate in a range of activities to increase their exposure to neuroscience research within and outside their specialty areas. These include the annual Neuroscience Retreat, the Neuroscience Seminar Series, as well as other affiliated seminar series and lectures. Students also participate in journal clubs, lab meetings, and multi-laboratory special interest group meetings focused on specific scientific topics. See Program Activities for a comprehensive list.

Neuroscience PhD Program students (left to right) Greg Telian, Charles Garfinkle and Jocelyn Breton.

Neuroscience is a broad field that requires multidisciplinary training as well as intensive study of specific concepts and techniques related to each student’s primary research focus. The Neuroscience PhD Program is designed to provide highly individualized, flexible training that fulfills both these needs. Our PhD training program has a standard completion time of 5 to 5.5 years. The program is PhD-granting only, there is no master’s degree program. The following is a general overview of the steps to a Neuroscience PhD at UC Berkeley. For detailed policies, see Resources For Current Students.

Neuroscience Boot Camp

First-year students begin the program with an intensive, 10-day “Boot Camp” course held just prior to the official start of fall semester classes. The course features lectures on key neuroscience concepts and on classical and emerging experimental techniques and evening research seminars by Berkeley Neuroscience faculty. In addition, hands-on research projects in faculty laboratories cover techniques ranging from molecular neuroscience to neurophysiology and optogenetics to fMRI. The goal is to provide an immersive introduction to multiple disciplines and experimental approaches within neuroscience. Our Boot Camp unites neuroscience-oriented students from multiple PhD programs.

Image of a section from a human brain organoid showing patches of developing neural progenitor cells (green and red). Cell nuclei are labeled in blue. Bateup lab.

Laboratory Rotations

During Year 1, each student spends three 10-week periods performing research projects in different faculty laboratories. The choice of laboratories is based on student preference. The goal is to expose students to different techniques and approaches in neuroscience and to provide training in experimental design, critical analysis of data, and presentation of research findings. Performance in rotations is evaluated and graded. Rotations also allow students to identify the laboratory in which their thesis research will be performed. Students formally present results from the laboratory rotations in a dedicated course designed to instruct students in clear, effective presentation of scientific findings.

Irene Grossrubatscher
Neuroscience PhD student Irene Grossrubatscher.

Coursework

The program has highly flexible course requirements. These are designed to provide students with sufficiently broad training in all areas of neuroscience, while allowing focus in the area of primary research interest.

During the first two years of the program, each student is required to take one course in each of three broad areas: (A) Cellular, Molecular & Developmental Neuroscience; (B) Systems and Computational Neuroscience; and (C) Cognitive and Behavioral Neuroscience. Each student consults with faculty advisers to determine the most appropriate individual courses within these areas.

Students must also complete a one-semester course in Applied Statistics in Neuroscience, or an equivalent approved course in statistics or quantitative analysis methods.

For additional details, see the Neuroscience Course Curriculum.

Training in Teaching

Effective teaching is a critical skill required in most academic and research careers. Students are required to serve as Graduate Student Instructors (GSIs; equivalent to Teaching Assistants) for two semesters. GSI teaching occurs during Years 2 and 3 and provides supervised teaching experience in laboratory and discussion settings. Teaching is evaluated, and outstanding teaching is rewarded with annual Outstanding Graduate Student Instructor Awards. One to three of our students typically win this award each year.

Qualifying Examination

Students complete an Oral Qualifying Exam during the spring semester of Year 2. This exam is structured around a written thesis proposal and oral examination on this proposal, related research areas, and foundational questions in neuroscience. During the exam, a faculty committee tests the student’s knowledge of these areas and general neuroscience. Students must demonstrate the ability to recognize important research problems, propose relevant experimental approaches, and display comprehensive knowledge of relevant subjects. Students must pass the qualifying examination before advancing to doctoral candidacy.

Neuroscience PhD student Timothy Day and faculty member John Flannery.

Thesis Research

Thesis research begins after the completion of rotations in spring or summer of Year 1. During Year 2, students conduct thesis research while completing required coursework and GSI teaching. Years 3 to 5 are spent primarily on thesis research. Progress on thesis research is evaluated by the student, the thesis adviser, and a Thesis Committee of three additional faculty members.

Thesis research is expected to lead to publication in top-ranked, refereed scientific journals. Students are strongly encouraged to present posters and speak at scientific meetings and conferences. During Year 4, they make a formal presentation of their research progress to their peers. Completion of thesis research is determined by the Thesis Committee. While there is no formal thesis defense, students present a formal thesis seminar to the neuroscience community in their last semester of candidacy.

Neuroscience PhD student Emily Jacobs.

Other Program Activities

During training, students are expected to participate in a range of activities to increase their exposure to neuroscience research within and outside their specialty areas. These include the annual Neuroscience Retreat, the Neuroscience Seminar Series, as well as other affiliated seminar series and lectures. Students also participate in journal clubs, lab meetings, and multi-laboratory special interest group meetings focused on specific scientific topics. See Program Activities for a comprehensive list.

Leadership

Berkeley Neuroscience PhD Program Director

Michael Silver, PhD

Professor of Optometry and Vision Science and Neuroscience

Graduate Program Manager

Candace Groskreutz

For questions about the PhD Program, please contact Candace at candaceg@berkeley.edu; voice 510.642.8915; fax 510.643.4966

Past PhD Program Directors

This past year was an exciting and productive one for our program. In 2019, the Helen Wills Neuroscience Institute (HWNI) celebrated its twentieth birthday. In the 1990s, Carla Shatz and Corey Goodman carried out much of the foundational work to unify the neuroscientists on our campus, culminating in the founding of HWNI and the Berkeley Neuroscience PhD Program.

Although Corey has since moved out of his lab and into the world of venture capital, he remains an active member of the Berkeley Neuroscience community as an Adjunct Professor in HWNI. Last year, Corey and his partner, Marcia Barinaga, announced their plans to bequeath a substantial portion of their estate to HWNI, with half of this donation dedicated for support of our graduate students. We are profoundly grateful to Corey and Marcia for this transformative gift, which will create an endowment that will benefit the students in our program for many generations.

Equity, Diversity, and Inclusion

UC Berkeley has a history of embracing diversity. The Neuroscience PhD Program at UC Berkeley seeks to recruit and train the very best young neuroscientists, including historically underrepresented students. We see a direct connection between diversity and excellence. Explore the videos below to hear faculty and student reflections on the strengths of the PhD Program, with an emphasis on equity and inclusion.

Keven LaBoy
Alum, Feldman lab

Sam Israel
Alum, Feldman lab, Ngai lab

Daniela Kaufer
Professor of Neuroscience and Integrative Biology

PhD Program Students

Entering Class of 2019

Adrian Alejandro, 2019

Giovanni Anthony, 2019

Karina Bistrong, 2019

Julian Dishart, 2019

Yanabah Jaques, 2019

Leana King, 2019

Emily Meschke, 2019

Nathan Munet, 2019

Lucia Rodriguez, 2019

Brooke Staveland, 2019

Kaeli Vandemark, 2019

Jacob Ziontz, 2019

Entering Class of 2018

Entering class of 2018. Top row (left to right): Matt David, Erin Aisenberg, Marisa Becerra, Julia Bleier, Brett Nelson, Mark Gorenstein. Bottom row (left to right): Katie Cording, Madeline Klinger, Sonali Mali, Azure Grant.

Erin Aisenberg, 2018
Bateup Lab

Marisa Becerra, 2018
Jagust Lab

Julia Bleier, 2018
Isacoff Lab

Katie Cording, 2018
Bateup Lab

Matt Davis, 2018
Saijo Lab

Mark Gorenstein, 2018
Piantadosi Lab

Azure Grant, 2018
Kriegsfeld/Wilbrecht Lab

Madeline Klinger, 2018
Wilbrecht/Landry Lab

Sonali Mali, 2018
Bautista Lab

Brett Nelson, 2018
Bouchard Lab

Entering Class of 2017

Entering class of 2017 (left to right): Ryan Schultz, Ellen Zippi, Christiane Voufo, Molly LaPoint, Lily Gong, Hayley Bounds, Celia Ford, Sylvia Madhow, Dariya Bakshinskaya

Dariya Bakshinskaya, 2017
Isacoff Lab

Hayley Bounds, 2017
National Science Foundation Graduate Fellow, Adesnik Lab

Celia Ford, 2017
National Science Foundation Graduate Fellow, Wallis Lab

Lily Gong, 2017
Theunissen Lab

Molly LaPoint, 2017
Jagust Lab

Sylvia Madhow, 2017
Bouchard Lab

Ryan Schultz, 2017
Isacoff Lab

Christiane Voufo, 2017
Feller Lab

Ellen Zippi, 2017
National Science Foundation Graduate Fellow, Carmena Lab

Entering Class of 2016

Zuzanna Balewski, 2016
Wallis Lab

Bill Croughan, 2016
Foster Lab

Vael Gates, 2016
Griffiths Lab

Holly Gildea, 2016
National Science Foundation Graduate Fellow
Dillin Lab

Carson McNeil, 2016
Gallant Lab

Jacob Miller, 2016
D’Esposito Lab

Tobias Schmid, 2016
National Science Foundation Graduate Fellow
Yartsev Lab

Christine Tseng, 2016
Gallant Lab

Kevin Yu, 2016
National Science Foundation Graduate Fellow
Theunissen Lab

Entering Class of 2015

Jenna Adams, 2015, Jagust Lab
“Associations between tau spread and functional connectivity in cognitively normal older adults”

Krisha Aghi, 2015, Isacoff Lab
“Synaptic homeostasis and heterogeneity in vivo at the Drosophila larval neuromuscular junction”

Joseph Aman, 2015, National Science Foundation Graduate Fellow, Feldman Lab
“Rapid homeostatic plasticity in somatosensory cortex”

Zeke Barger, 2015, National Science Foundation Graduate Fellow, Dan Lab
“Medullary control of sleep”

Ruairidh Battleday, 2015, Griffiths/Olshausen Labs
“Probabilistic models of cognition”

Althea Cavanaugh, entered 2017, National Science Foundation Graduate Fellow, Foster Lab
“Dynamics of Spatial Coding Along the Dorsoventral Axis of the Hippocampus”

Adam Eichenbaum, 2015, Berkeley Fellow
National Defense Science and Engineering Graduate Fellow, D’Esposito Lab
“Mechanisms of human learning and plasticity”

Malak El-Quessny, 2015, Chancellor’s Fellow, Feller Lab
“How visual experience shapes the interplay of dendritic form and circuit function in the developing retina”

Irene Grossrubatscher, 2015, Isacoff Lab
“Setting thresholds for behavior: How does internal state modulate prey capture?”

Arjun Mukerji, 2015, Silver Lab
“Parallel Visual Processing Streams in Thalamus and Cortex”

Sara Popham, 2015, Gallant Lab
“Investigating multimodal semantic representations in the human brain”

Maimon Rose, 2015, Yartsev Lab
“Tracking the development of neural dynamics in a vocal learning mammal”

Daniel Toker, 2015, National Science Foundation Graduate Fellow, D’Esposito Lab
“Sensory information transmission in oscillatory networks”

Amanda Tose, 2015, National Science Foundation Graduate Fellow, Lammel Lab
“Role of dorsal raphe input to the lateral hypothalamus in behavior with in vivo calcium imaging”

Entering Class of 2014

Jocelyn Breton, 2014
Fields/Lammel Labs
“The role of mesocortical projections in anxiety and alcohol consumption”

Franklin Caval-Holme, 2014
National Research Service Award Fellow
Feller Lab
“Dissecting a microcircuit that regulates the earliest light responses in the retina”

Charles Frye, 2014
Berkeley Fellow
National Science Foundation Graduate Fellow
Sommer Lab
“Extending Minimum Probability Flow to models with hidden variables”

Colin Hoy, 2014
National Science Foundation Graduate Fellow
Knight Lab
“The role of surprise in error signals”

Christine Liu, 2014
National Science Foundation Graduate Fellow
Lammel Lab
“Elucidating the neural circuitry underlying nicotine-related behaviors”

Ben Shababo, 2014
Hertz Foundation Fellow
Adesnik Lab
“High-throughput, cellular resolution mapping of neural circuits”

Emilio Soto-Soto, 2014
National Science Foundation Graduate Fellow
Kriegsfeld Lab
“The Impact of Early Life Circadian Disruption on Neural Development and Cognitive Flexibility”

Greg Telian, 2014
Chancellor’s Fellow
Howard Hughes Medical Institute Gilliam Fellow
Adesnik Lab
“Sensorimotor cortical representations in vM1 and vS1 during active sensation”

Entering Class of 2013

Charles Garfinkle, 2013
Sommer Lab
“Identifiability in Sparse Dictionary Learning with Applications to Neuroscience”

Sean Mackesey, 2013
Sommer Lab
“The role of hippocampal field potentials in memory / Neuroinformatics infrastructure for electrophysiology”

Entering Class of 2012

Melissa Newton, 2012
Kayser Lab
“Neural representations of sensory evidence accumulation during abstract decisions”

Eric Weiss, 2012
Olshausen Lab
“3D visual perception in humans and the computational role of eye movements”

Entering class of 2019. Top row (left to right): Emily Meschke, Karina Bistrong, Jacob Ziontz, Julian Dishart, Adrian Alejandro, Kaeli Vandemark, Lucia Rodriguez. Bottom row (left to right): Yanabah Jaques, Giovanni Anthony, Brooke Staveland, Nathan Munet, Leana King.

Complete Alumni List

View a one-page summary of the current positions held by all Neuroscience PhD Program alumni.
*Last updated January 2018

In-depth Alumni Profiles

Our PhD Program alumni have gone on to a variety of careers in academia and industry. Read what they have to say about their personal and professional paths.

Q&A with the Graduates

We have a tradition of asking our graduating students to answer several questions about their PhD studies and future plans. The resulting Q&A articles are filled with reflections and words of advice.

Neuroscientist Portrait Project

This project takes a look at the lives of neuroscientists, with an emphasis on those who are underrepresented in science. Created by PhD student Christine Liu and sponsored by Berkeley Neuroscience.

Selected Student Publications

Adams JN, Maass A, Harrison TM, Baker SL, Jagust WJ (2019) Cortical tau deposition follows patterns of entorhinal functional connectivity in aging. eLife 8:e49132

Barger Z, Frye CG, Liu D, Dan Y, Bouchard KE (2019) Robust, automated sleep scoring by a compact neural network with distributional shift correction. PLoS ONE 14:e0224642

Breton JM, Charbit AR, Snyder BJ, Fong PTK, Dias EV, Himmels P, Lock H, Margolis EB (2019) Relative contributions and mapping of ventral tegmental area dopamine and GABA neurons by projection target in the rat. Journal of Comparative Neurology 526:916-941

Caval-Holme F, Zhang Y, Feller MB (2019) Gap junction coupling shapes the encoding of light in the developing retina. Current Biology 29:4024-4035

Cerniauskas I, Winterer J, …, Lammel S (2019) Chronic stress induces activity, synaptic, and transcriptional remodeling of the lateral habenula associated with deficits in motivated behaviors. Neuron 104:899-915

Kobayashi K, Hsu M (2019) Common neural code for reward and information value. Proceedings of the National Academy of Sciences USA 26:13061-13066

Naka A, Veit J, Shababo B, …, Ngai J, Adesnik H (2019) Complementary networks of cortical somatostatin interneurons enforce layer specific control. eLife 8:e43696

Senatorov VV Jr., Friedman AR, …, Kaufer D (2019) Blood-brain barrier dysfunction in aging induces hyperactivation of TGF-beta signaling and chronic yet reversible dysfunction. Science Translational Medicine 11:521

Toker D, Sommer FT (2019) Information integration in large brain networks. PLoS Computational Biology 15:e1006807

Isett BR, Feasel SH, Lane MA, Feldman DE (2018) Slip-based coding of local shape and texture in mouse S1. Neuron 97:418-33.

Day TP, Byrne LC, Flannery JG, Schaffer DV (2018) Screening for neutralizing antibodies against natural and engineered AAV capsids in nonhuman primate retinas. Methods Mol Biol 1715:239-49.

Gaub BM, Berry MH, Visel M, Holt A, Isacoff EY, Flannery JG. (2018) Optogenetic Retinal Gene Therapy with the Light Gated GPCR Vertebrate Rhodopsin. Methods Mol Biol. 1715:177-189.

Adams JN, Lockhart SN, Li L, Jagust WJ. (2018) Relationships between tau and glucose metabolism reflect Alzheimer’s disease pathology in cognitively normal older adults. Cereb Cortex, in press.

Neely RM, Koralek AC, Athalye VR, Costa RM, Carmena JM. (2018) Volitional modulation of primary visual cortex activity requires the basal ganglia. Neuron 97:1356-1368.

Liberman A, Manassi M, Whitney D. (2018) Serial dependence promotes the stability of perceived emotional expression depending on face similarity. Atten Percept Psychophys 80:1461-1473.

Lieder F, Shenhav A, Musslick S, Griffiths TL. (2018) Rational metareasoning and the plasticity of cognitive control. PLoS Comput Biol 14:e1006043.

Lorenc ES, Sreenivasan KK, Nee DE, Vandenbroucke ARE, D’Esposito M. (2018) Flexible coding of visual working memory representations during distraction. J Neurosci 38:5267-5276.

Haller M, Case J, Crone NE, Chang EF, King-Stephens D, Laxer KD, Weber PB, Parvizi J, Knight RT, Shestyuk AY. (2018) Persistent neuronal activity in human prefrontal cortex links perception and action. Nat Hum Behav 2:80-91

Bliss DP, D’Esposito M. (2017) Synaptic augmentation in a cortical circuit model reproduces serial dependence in visual working memory. PLoS One. 12(12):e0188927.

Goldstein-Piekarski AN, Greer SM, Saletin JM, Harvey AG, Williams LM, Walker MP. (2017) Sex, Sleep Deprivation, and the Anxious Brain. J Cogn Neurosci.Dec 15:1-14.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB. (2017) Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities. Cell Stem Cell. pii: S1934-5909(17)30452-6.

Bliss DP, Sun JJ, D’Esposito M. (2017) Serial dependence is absent at the time of perception but increases in visual working memory. Sci Rep. 7(1):14739.

Holdgraf CR, Rieger JW, Micheli C, Martin S, Knight RT, Theunissen FE. (2017) Encoding and Decoding Models in Cognitive Electrophysiology. Front Syst Neurosci. Sep 26;11:61

Moorman HG, Gowda S, Carmena JM. (2017) Control of Redundant Kinematic Degrees of Freedom in a Closed-Loop Brain-Machine Interface. IEEE Trans Neural Syst Rehabil Eng. 25(6):750-760.

Gratton C, Yousef S, Aarts E, Wallace DL, D’Esposito M, Silver MA. (2017) Cholinergic, But Not Dopaminergic or Noradrenergic, Enhancement Sharpens Visual Spatial Perception in Humans. J Neurosci. 37(16):4405-4415.

Kim H, Kirkhart C, Scott K. Long-range projection neurons in the taste circuit of Drosophila. Elife. 2017 6. pii: e23386.

Pluta SR, Lyall EH, Telian GI, Ryapolova-Webb E, Adesnik H. (2017) Surround Integration Organizes a Spatial Map during Active Sensation. Neuron. 94(6):1220-1233.e5.

Kobayashi K, Hsu M. (2017) Neural mechanisms of updating under reducible and irreducible uncertainty. J Neurosci. Jun 16. pii: 0535-17.

Marks SM, Lockhart SN, Baker SL, Jagust WJ. (2017) Tau and β-Amyloid Are Associated with Medial Temporal Lobe Structure, Function, and Memory Encoding in  Normal Aging. J Neurosci. 37(12):3192-3201.

Slama SJK, Helfrich RF. (2017) How Does Expectation Shape Object-Based Attentional  Selection? J Neurosci. 37(17):4427-4429.

de Heer WA, Huth AG, Griffiths TL, Gallant JL, Theunissen FE. (2017) The hierarchical cortical organization of human speech processing. J Neurosci. Jun 6. pii: 3267-16.

Seo D, Neely RM, Shen K, Singhal U, Alon E, Rabaey JM, Carmena JM, Maharbiz MM.  (2016) Wireless Recording in the Peripheral Nervous System with Ultrasonic Neural Dust. Neuron 91(3):529-39.

McGuire LM, Telian G, Laboy-Juárez KJ, Miyashita T, Lee DJ, Smith KA, Feldman DE. (2016) Short Time-Scale Sensory Coding in S1 during Discrimination of Whisker Vibrotactile Sequences. PLoS Biol. 14(8):e1002549.

Holdgraf CR, de Heer W, Pasley B, Rieger J, Crone N, Lin JJ, Knight RT, Theunissen FE. (2016) Rapid tuning shifts in human auditory cortex enhance speech intelligibility. Nat Commun. 7: 13654.

Langberg T. (2016) Thalamic Bursts and Single Spikes Evoke Distinct Inhibitory States in the Primary Sensory Cortex. J Neurosci. 36(45): 11496-11497.

Huth AG, de Heer WA, Griffiths TL, Theunissen FE, Gallant JL. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex.  Nature.  532: 453-8.

Vlasits AL, Morrie RD, Tran-Van-Minh A, Bleckert A, Gainer CF, DiGregorio DA, Feller MB. (2016) A Role for Synaptic Input Distribution in a Dendritic Computation of Motion Direction in the Retina.  Neuron. 89: 1317-30.

Greer SM, Goldstein AN, Knutson B, Walker MP. (2016) A Genetic Polymorphism of the Human Dopamine Transporter Determines the Impact of Sleep Deprivation on Brain Responses to Rewards and Punishments.  J Cogn Neurosci. 28: 803-10. doi: 10.1162/jocn_a_00939.

Hillenbrand SF, Ivry RB, Schlerf JE. (2016)  Impact of task-related changes in heart rate on estimation of hemodynamic response and model fit.  Neuroimage. 132: 455-68.

Cox J, Pinto L, Dan Y. (2016)  Calcium imaging of sleep-wake related neuronal activity in the dorsal pons. Nat Commun. 7: 10763.

Merel J, Shababo B, Naka A, Adesnik H, Paninski L. (2016) Bayesian methods for event analysis of intracellular currents.  J Neurosci Methods. 269: 21-32.

Fonken YM, Rieger JW, Tzvi E, Crone NE, Chang E, Parvizi J, Knight RT, Krämer UM (2016)  Frontal and motor cortex contributions to response inhibition: evidence from electrocorticography. J Neurophysiol. 115: 2224-36.

Muroy SE, Long KL, Kaufer D, Kirby ED. (2016)  Moderate Stress-Induced Social Bonding and Oxytocin Signaling are Disrupted by Predator Odor in Male Rats.  Neuropsychopharmacology. 41: 2160-70.

Thomas AW, Caporale N, Wu C, Wilbrecht L. (2016) Early maternal separation impacts cognitive flexibility at the age of first independence in mice.  Dev Cogn Neurosci. 18: 49-56.

Cano ME, Knight RT. (2016)  Behavioral and EEG Evidence for Auditory Memory Suppression. Front Hum Neurosci. 10: 133.

Gallen CL, Turner GR, Adnan A, D’Esposito M. (2016) Reconfiguration of brain network architecture to support executive control in aging.  Neurobiol Aging. 44: 42-52.

Kallman BR, Kim H, Scott K. (2015)  Excitation and inhibition onto central courtship neurons biases Drosophila mate choice.  Elife. 4: e11188.

Voytek B, Kayser AS, Badre D, Fegen D, Chang EF, Crone NE, Parvizi J, Knight RT, D’Esposito M. (2015) Oscillatory dynamics coordinating human frontal networks in support of goal maintenance. Nat Neurosci. 18: 1318-24. doi: 10.1038/nn.4071.

Pinto L, Dan Y. (2015) Cell-Type-Specific Activity in Prefrontal Cortex during Goal-Directed Behavior. Neuron. 87(2): 437-50.

Fegen D, Buchsbaum BR, D’Esposito M. (2015) The effect of rehearsal rate and memory load on verbal working memory. Neuroimage. 105: 120-31.

Gaub BM, Berry MH, Holt AE, Isacoff EY, Flannery JG (2015) Optogenetic Vision Restoration Using Rhodopsin for Enhanced Sensitivity.  Mol Therapy. 23: 1562-71.

Pluta S, Naka A, Veit J, Telian G, Yao L, Hakim R, Taylor D, Adesnik H. (2015)  A direct translaminar inhibitory circuit tunes cortical output.  Nat Neurosci. 18: 1631-40.

Arnemann KL, Chen AJ, Novakovic-Agopian T, Gratton C, Nomura EM, D’Esposito M. (2015)  Functional brain network modularity predicts response to cognitive training after brain injury.  Neurology 84: 1568-74.

Mander BA, Marks SM, Vogel JW, Rao V, Lu B, Saletin JM, Ancoli-Israel S, Jagust WJ, Walker MP. (2015)  β-amyloid disrupts human NREM slow waves and related hippocampus-dependent memory consolidation.  Nat Neurosci. 18: 1051-7.

Flinker A, Korzeniewska A, Shestyuk AY, Franaszczuk PJ, Dronkers NF, Knight RT, Crone NE. (2015) Redefining the role of Broca’s area in speech.  Proc Natl Acad Sci U S A. 112: 2871-5.

Gao JS, Huth AG, Lescroart MD, Gallant JL. (2015)  Pycortex: an interactive surface visualizer for fMRI.  Front Neuroinform. 9: 23. doi: 10.3389/fninf.2015.00023.

Mackey AP, Miller Singley AT, Wendelken C, Bunge SA. (2015)  Characterizing Behavioral and Brain Changes Associated with Practicing Reasoning Skills.  PLoS One. 10(9):e0137627.

Naka A.  (2015) Cell-Type-Specific Manipulation Reveals New Specificity in the Neocortical Microcircuit.  J Neurosci. 35: 8976-8.

Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG. (2015) The expression pattern of systemically injected AAV9 in the developing mouse retina is determined by age. Mol Ther. 23(2):290-6.

Kirkhart C, Scott K. (2015) Gustatory learning and processing in the Drosophila mushroom bodies. J Neurosci. 2015 35: 5950-8.

Forster S, Nunez Elizalde AO, Castle E, Bishop SJ. (2015) Unraveling the anxious mind: anxiety, worry, and frontal engagement in sustained attention versus off-task processing. Cereb Cortex. 25: 609-18.

Griffiths TL, Lieder F, Goodman ND. (2015) Rational use of cognitive resources: levels of analysis between the computational and the algorithmic. Topics in Cognitive Science 7: 217-29.

Goldstein-Piekarski AN, Greer SM, Saletin JM, Walker MP (2015)  Sleep Deprivation Impairs the Human Central and Peripheral Nervous System Discrimination of Social Threat.  J Neurosci. 35: 10135-45.

Lara AH, Wallis JD. (2014) Executive control processes underlying multi-item working memory. Nat Neurosci. 17: 876-83.

Agarwal G, Stevenson IH, Berényi A, Mizuseki K, Buzsáki G, Sommer FT. (2014) Spatially distributed local fields in the hippocampus encode rat position. Science 344: 626-30.

Liberman A, Fischer J, Whitney D. (2014) Serial dependence in the perception of faces. Curr Biol. 24: 2569-74.

Gaub BM, Berry MH, Holt AE, Reiner A, Kienzler MA, Dolgova N, Nikonov S, Aguirre GD, Beltran WA, Flannery JG, Isacoff EY. (2014) Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells. Proc Natl Acad Sci U S A. 111: E5574-83.

Pool AH, Kvello P, Mann K, Cheung SK, Gordon MD, Wang L, Scott K (2014). Four GABAergic interneurons impose feeding restraint in Drosophila. Neuron 83: 164-77.

Rodgers CC, DeWeese MR (2014) Neural correlates of task switching in prefrontal cortex and primary auditory cortex in a novel stimulus selection task for rodents. Neuron 82: 1157-70.

Vlasits AL, Bos R, Morrie RD, Fortuny C, Flannery JG, Feller MB, Rivlin-Etzion M. (2014) Visual Stimulation Switches the Polarity of Excitatory Input to Starburst Amacrine Cells. Neuron. 83: 1172-84.

Clancy KB, Koralek AC, Costa RM, Feldman DE, Carmena JM (2014) Volitional modulation of optically recorded calcium signals during neuroprosthetic learning.  Nat Neurosci. 17: 807-9.

Chetty S, Friedman AR, Taravosh-Lahn K, Kirby ED, Mirescu C, Guo F, Krupik D, Nicholas A, Geraghty AC, Krishnamurthy A, Tsai MK, Covarrubias D, Wong AT, Francis DD, Sapolsky RM, Palmer TD, Pleasure D, Kaufer D (2014) Stress and glucocorticoids promote oligodendrogenesis in the adult hippocampus. Mol Psychiatry. 19: 1275-83.

Day TP, Byrne LC, Schaffer DV, Flannery JG (2014) Advances in AAV vector development for gene therapy in the retina. Adv Exp Med Biol. 801: 687-93.

Blumenfeld RS, Bliss DP, Perez F, D’Esposito M (2014) CoCoTools: open-source software for building connectomes using the CoCoMac anatomical database. J Cogn Neurosci. 26: 722-45.

Orsborn AL, Moorman HG, Overduin SA, Shanechi MM, Dimitrov DF, Carmena JM (2014) Closed-loop decoder adaptation shapes neural plasticity for skillful neuroprosthetic control. Neuron 82: 1380-93.

Denison RN, Vu AT, Yacoub E, Feinberg DA, Silver MA (2014) Functional mapping of the magnocellular and parvocellular subdivisions of human LGN. Neuroimage 102P2:358-369.

Goldstein AN, Walker MP. (2014) The role of sleep in emotional brain function. Annu Rev Clin Psychol. 10: 679-708.

Sreenivasan KK, Gratton C, Vytlacil J, D’Esposito M (2014) Evidence for working memory storage operations in perceptual cortex. Cogn Affect Behav Neurosci. 14: 117-28.

Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG (2014) Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse. Gene Therapy 21: 585-92.

Whitaker KJ, Kang X, Herron TJ, Woods DL, Robertson LC, Alvarez BD (2014) White matter microstructure throughout the brain correlates with visual imagery in grapheme-color synesthesia. Neuroimage 90:52-9.

Pinto L, Goard MJ, Estandian D, Xu M, Kwan AC, Lee SH, Harrison TC, Feng G, Dan Y. (2013) Fast modulation of visual perception by basal forebrain cholinergic neurons. Nat Neurosci. 16: 1857-63.

Hamilton LS, Sohl-Dickstein J, Huth AG, Carels VM, Deisseroth K, Bao S. (2013) Optogenetic activation of an inhibitory network enhances feedforward functional connectivity in auditory cortex. Neuron 80: 1066-76.

Moore RC, Lee T, Theunissen FE. (2013) Noise-invariant neurons in the avian auditory cortex: hearing the song in noise. PLoS Comput Biol. 9(3):e1002942.

Çukur T, Huth AG, Nishimoto S, Gallant JL. (2013) Functional subdomains within human FFA. J Neurosci. 33: 16748-66.

Koralek AC, Costa RM, Carmena JM. (2013) Temporally precise cell-specific coherence develops in corticostriatal networks during learning. Neuron 79: 865-72.

Kim H, Gibboni R, Kirkhart C, Bao S. (2013) Impaired critical period plasticity in primary auditory cortex of fragile X model mice. J Neurosci. 33: 15686-92.

Shao YR, Isett BR, Miyashita T, Chung J, Pourzia O, Gasperini RJ, Feldman DE. (2013) Plasticity of recurrent L2/3 inhibition and gamma oscillations by whisker experience. Neuron 80: 210-22.

Kauwe G, Isacoff EY. (2013) Rapid feedback regulation of synaptic efficacy during high-frequency activity at the Drosophila larval neuromuscular junction. Proc Natl Acad Sci U S A. 110: 9142-7.

Voytek B, D’Esposito M, Crone N, Knight RT. (2013) A method for event-related phase/amplitude coupling. Neuroimage. 64: 416-24.

Long JD 2nd, Carmena JM. (2013) Dynamic changes of rodent somatosensory barrel cortex are correlated with learning a novel conditioned stimulus. J Neurophysiol. 109: 2585-95.

Mann K, Gordon MD, Scott K. (2013) A Pair of Interneurons Influences the Choice between Feeding and Locomotion in Drosophila. Neuron. 79: 754-65.

Kirby ED, Muroy SE, Sun WG, Covarrubias D, Leong MJ, Barchas LA, Kaufer D. Acute stress enhances adult rat hippocampal neurogenesis and activation of newborn neurons via secreted astrocytic FGF2. Elife. 2:e00362.

Greer SM, Goldstein AN, Walker MP. (2013) The impact of sleep deprivation on food desire in the human brain. Nat Commun. 4:2259.

Goldstein AN, Greer SM, Saletin JM, Harvey AG, Nitschke JB, Walker MP. (2013) Tired and apprehensive: anxiety amplifies the impact of sleep loss on aversive brain anticipation. J Neurosci. 33: 10607-15.

Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. (2013) In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 5: 189ra76.

Köver H, Gill K, Tseng YT, Bao S. (2013) Perceptual and neuronal boundary learned from higher-order stimulus probabilities. J Neurosci. 33: 3699-705.

Mackey AP, Miller Singley AT, Bunge SA. (2013) Intensive reasoning training alters patterns of brain connectivity at rest. J Neurosci. 33: 4796-803.

Gratton C, Sreenivasan KK, Silver MA, D’Esposito M. (2013) Attention selectively modifies the representation of individual faces in the human brain. J Neurosci. 33: 6979-89.

Denison RN, Driver J, Ruff CC. (2013) Temporal structure and complexity affect audio-visual correspondence detection. Front Psychol. 3: 619.

Li L, Gratton C, Fabiani M, Knight RT. (2013) Age-related frontoparietal changes during the control of bottom-up and top-down attention: an ERP study. Neurobiol Aging. 34: 477-88.

Moore RC, Lee T, Theunissen FE. (2013) Noise-invariant neurons in the avian auditory cortex: hearing the song in noise. PLoS Comput Biol. 2013;9(3):e1002942.

Amin N, Gastpar M, Theunissen FE. (2013) Selective and efficient neural coding of communication signals depends on early acoustic and social environment. PLoS One. 2013 8(4):e61417.

Miyakawa A, Gibboni R, Bao S. (2013) Repeated exposure to a tone transiently alters spectral tuning bandwidth of neurons in the central nucleus of inferior colliculus in juvenile rats. Neuroscience 230: 114-20.

Published in 2012

Huth AG, Nishimoto S, Vu AT, Gallant JL. (2012) A continuous semantic space describes the representation of thousands of object and action categories across the human brain. Neuron. 76: 1210-24.

Mackey AP, Whitaker KJ, Bunge SA. (2012) Experience-dependent plasticity in white matter microstructure: reasoning training alters structural connectivity. Front Neuroanat. 6: 32.

Kirby ED, Friedman AR, Covarrubias D, Ying C, Sun WG, Goosens KA, Sapolsky RM, Kaufer D. (2012) Basolateral amygdala regulation of adult hippocampal neurogenesis and fear-related activation of newborn neurons. Mol Psychiatry. 17: 527-36.

Voytek B, D’Esposito M, Crone N, Knight RT. (2013) A method for event-related phase/amplitude coupling. Neuroimage. 64: 416-24.

Dang LC, O’Neil JP, Jagust WJ. (2012) Dopamine supports coupling of attention-related networks. J Neurosci. 32: 9582-7.

Cadieu CF, Olshausen BA. (2012) Learning intermediate-level representations of form and motion from natural movies. Neural Comput. 24: 827-66.

Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, Isacoff EY. (2012) Emergence of patterned activity in the developing zebrafish spinal cord. Curr Biol. 22: 93-102.

Mormino EC, Brandel MG, Madison CM, Marks S, Baker SL, Jagust WJ. (2012) Aβ Deposition in aging is associated with increases in brain activation during successful memory encoding. Cereb Cortex. 22: 1813-23.

Gratton C*, Nomura EM*, Perez F, D’Esposito M. (2012) Focal brain lesions disrupt modular organization throughout the brain. Journal of Cognitive Neuroscience, 24, 1275-1285 (*Equal contribution)

Koralek AC, Jin X, Long JD, Costa RM, Carmena JM. (2012) Corticostriatal plasticity is necessary for learning intentional neuroprosthetic skills. Nature, 483: 331-335.

Denison RN, Silver MA. (2012) Distinct contributions of the magnocellular and parvocellular visual streams to perceptual selection. Journal of Cognitive Neuroscience. 24: 246-59.

Held RT, Cooper EA, Banks MS. (2012) Blur and Disparity are Complementary Cues to Depth. Current Biology, 22: 426-31.

Marella S, Mann K, Scott K. (2012) Dopaminergic modulation of sucrose acceptance behavior in Drosophila. Neuron. 2012 73: 941-50.

Published in 2011

Kirby, E.D., Friedman, A.R., Covarrubias, D., Ying, C., Grant, W.G., Goosens, K.A., Sapolsky, R.M., & Kaufer, D. (2011). Basolateral amygdala regulation of adult hippocampal neurogenesis and fear-related activation of newborn neurons. Molecular Psychiatry, In Press.

Perrotin A, Mormino EC, Madison CM, Hayenga AO, Jagust WJ. Subjective cognition and amyloid deposition imaging. A PiB PET study in normal elderly individuals. Arch Neurol. In Press.

Mormino EC, Smiljic A, Hayenga AO, Onami S, Greicius MD, Rabinovici GD, Janabi M, Baker SL, Yen I, Madison CM, Miller BL, Jagust WJ. Relationships between beta-amyloid and functional connectivity in different components of the default mode network in aging. Cerebral Cortex. In Press.

Rosenbloom MH, Alkalay A, Agerwal N, Baker SL, O’Neill JP, Janabi M, Yen IV, Growdon M, Jung J, Madison C, Mormino EC, Rosen HJ, Gorno-Tempini ML, Miller BL, Jagust WJ, Rabinovici GD. Distinct clinical and metabolic deficits in posterior cortical atrophy and Alzheimer’s disease are not related to amyloid distribution. Neurology. In Press.

Oh H, Mormino EC, Madison C, Hayenga A, Smiljic A, Jagust WJ. β-amyloid affects frontal and posterior brain networks in normal aging. 2011. Neuroimage. 54, 1887-95.

Emily Jacobs and Mark D’Esposito, Estrogen Shapes Dopamine-Dependent Cognitive Processes: Implications for Women’s Health, The Journal of Neuroscience, April 6, 2011 • 31(14):5286 –5293

E.A. Cooper, U. Hasson, and S.L. Small. Interpretation-Mediated Changes in Neural Activity During Language Comprehension. NeuroImage, 55(3), 1314-1323, 2011.

E.A. Cooper, J. Burge, and M.S. Banks. The Vertical Horopter is not Adaptable, but It may be Adaptive. Journal of Vision, 11(3):20, 1-19, 2011.

Flinker, A., Chang, E.F., Barbaro, N.M., Berger, M.S., Knight, R.T. (2011) Sub-centimeter language organization in the human temporal lobe. Brain and Language 117 pp. 103-109

Published in 2010

Rabinovici GD, Furst AJ, Alkalay A, Racine CA, O’Neil JP, Janabi M, Baker SL, Agarwal N, Karydas A, Bonasera SJ, Mormino EC, Madison CM, Weiner MW, Gorno-Tempini ML, Rosen HJ, Miller BL, Jagust WJ. Increased Metabolic Vulnerability in Early-Onset Alzheimer’s Disease is Not Related to Amyloid Burden. 2010. Brain, 133, 512-28.

Furst AJ and Mormino E. A BOLD move: clinical application of functional magnetic resonance imaging (fMRI) in aging. 2010. Neurology. 74, 1940-1.

Marta E. Soden and Lu Chen. Fragile X Protein FMRP Is Required for Homeostatic Plasticity and Regulation os Synaptic Strength by Retinoic Acid. The Journal of Neuroscience, December 15, 2010, 30(50):16910-16921; doi:10.1523/JNEUROSCI.3660-10.2010

Flinker, A., Chang, F.E., Kirsch, H.E., Barbaro N.M., Crone, N.E., Knight, R.T. (2010) “Single-Trial Speech Suppression of Auditory Cortex Activity in Humans.” Journal of Neuroscience vol. 30 (49) pp. 16643.

Hania Köver, Shaowen Bao. (2010) Cortical plasticity as a mechanism for storing Bayesian priors in sensory perception. PLoS One, Vol 5, Issue 5, e1049

Nomura, E. M., Gratton, C., Visser, R. M., Kayser, A., Perez, F., & D’Esposito, M. (2010). Double dissociation of two cognitive control networks in patients with focal brain lesions. Proceedings of the National Academy of Sciences of the United States of America, 107(26), 12017-12022

Voytek B. & Knight RT (2010). Prefrontal cortex and basal ganglia contributions to visual working memory. Proc Natl Acad Sci USA 107(42), 18167-18172.

Voytek B, Davis M., Yago E, Barceló F, Vogel EK, Knight RT (2010). Dynamic neuroplasticity after human prefrontal cortex damage. Neuron 68(3), 401-408.

Voytek B, Secundo L, Bidet-Caulet A, Scabini D, Stiver S, Gean AD, Manley G, Knight RT. Hemicraniectomy: A New Model for Human Electrophysiology with High Spatio-Temporal Resolution. J. Cogn Neurosci 22(11), 2491-2502.

R. Held, E.A. Cooper, J. O’Brien, and M.S. Banks. Using Blur to Affect Perceived Distance and Size. ACM Transactions on Graphics, 29(2):1-16, 2010

Insanally MN, Albanna BF, Bao S. Pulsed Noise Experience Disrupts Complex Sound Representations.J Neurophysiol. 2010 Mar 3. PMID: 20200123

Mormino EC, Kluth JT, Madison CM, Rabinovici GD, Baker SL, Miller BL, Koeppe RA, Mathis CA, Weiner MW, Jagust WJ. Episodic memory loss is related to hippocampal-mediated beta-amyloid deposition in elderly subjects. Brain, 132:1310-1323, 2009.

John E. Schlerf, Timothy D. Verstynen, Richard B Ivry, and Rebecca M. C. Spencer. Evidence of a novel somatopic map in the human neocerebellum during complex actions. J Neurophysiol, Apr 2010; doi:10.1152/jn.01117.2009

Mathevon, N., Koralek, A., Weldele, M., Glickman, S.E., & Theunissen, F.E. (2010). What the hyena’s laugh tells: sex, age, dominance and individual identity in the giggling call of Crocuta Crocuta. BMC Ecology, 10(1):9. PMID: 20353550

Published in 2009

Bunge, S.A., Mackey, A., & Whitaker, K. Neurodevelopmental changes in cognitive control and fluid reasoning over childhood. The Cognitive Neurosciences III, edited by Michael Gazzaniga.

Ganguly K, Secundo L, Ranade G, Orsborn A, Chang EF, Dimitrov DF, Wallis JD, Barbaro NM, Knight RT, Carmena JM. Cortical representation of ipsilateral arm movements in monkey and man.J Neurosci. 2009 Oct 14;29(41):12948-56.

Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, Isacoff EY. 2009. Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature. 461, 407-10.

Lu, H., Lim, B., and Poo, M. M. (2009). Cocaine exposure in utero alters synaptic plasticity in the medial prefrontal cortex of postnatal rats. J Neurosci 29, 12664-12674.

Goard M and Dan Y (2009). Basal forebrain activation enhances cortical coding of natural scenes. Nature Neuroscience. Nov; 12(11):1444-9.

Cacheaux LP, Ivens S, David Y, Lakhter AJ, Bar-Klein G, Shapira M, Heinemann U, Friedman A, Kaufer D. Transcriptome profiling reveals TGF-beta signaling involvement in epileptogenesis. J Neurosci. 2009 Jul 15;29(28):8927-35.

Rokem A, Silver MA. A model of encoding and decoding in V1 and MT accounts for motion perception anisotropies in the human visual system. Brain Res. 2009 Nov 24;1299:3-16

David Y, Cacheaux LP, Ivens S, Lapilover E, Heinemann U, Kaufer D, Friedman A. (2009) Astrocytic dysfunction in epileptogenesis: consequence of altered potassium and glutamate homeostasis J. Neuroscience, 29, 10588-99.

Antonio H. Lara, Steven W. Kennerley, and Jonathan D. Wallis. Encoding of Gustatory Working Memory by Orbitofrontal Neurons. J. Neurosci. 2009;29 765-774

Heesoo Kim and Shaowen Bao. Selective Increase in Representations of Sounds Repeated at an Ethological Rate. J. Neurosci. 2009; 29: 5163Ð5169

Beery AK, Routman DM, Zucker I. Same-sex social bond formation in meadow voles: multiple and rapid formation of attachments. Physiology and Behavior 2009 97: 52-57.

Pasley, B.N.*, Allen, E.A.*, & Freeman, R.D. State-dependent variability of neuronal responses to transcranial magnetic stimulation of the visual cortex. Neuron 2009 62: 291-303. (*Equal contributions)

A. Rokem and M. Ahissar. Interactions of cognitive and auditory abilities in congenitally blind individuals. Neuropsychologia 2009 47: 843-848

Venkatraman, S., Elkabany, K., Long, J.D., Yao, Yimin, and Carmena, J.M. A System for Neural Recording and Closed-Loop Intracortical Microstimulation in Awake Rodents. IEEE Transactions on Biomedical Engineering 2009 56: 15-22.

Huberman A*, Wei W*, Elstrott J*, Stafford B, Feller MB, Barres B. Genetic identification of On-Off direction selective retinal ganglion cells reveals a layer specific subcortical map of posterior motion. Neuron 2009 62: 327-334. (* = equal contribution)

Kirby, E.D., Geraghty, A.G., Ubuka, T., Bentley, G.E., & Kaufer, D. Stress increases putative gonadotropin inhibitory hormone and decreases luteinizing hormone in male rats. Proc Natl Acad Sci. 2009, 106, 11324-9.

Michele N. Insanally, Hania Köver, Heesoo Kim, and Shaowen Bao. Feature-Dependent Sensitive Periods in the Development of Complex Sound Representation. J. Neurosci. 2009 29: 6567-6562.

C. Cadieu and B. Olshausen. Learning transformational invariants from natural movies. In D. Koller, D. Schuurmans, Y. Bengio, and L. Bottou, Eds., Advances in Neural Information Processing Systems 21, pages 209-216. MIT Press, 2009.

Luk, C.-H., Wallis, J. D. Dynamic encoding of responses and outcomes by neurons in medial prefrontal cortex. J. Neurosci. 2009 29: 7526-7539.

Published in 2008

Beery AK, Lacey EA, Francis DD. Oxytocin and vasopressin receptor distributions in a solitary and a social species of tuco-tuco (Ctenomys haigi and Ctenomys sociabilis). J Comp Neurol. 2008 507: 1847-59.

Caporale N, Dan Y. Spike timing-dependent plasticity: a hebbian learning rule. Annu Rev Neurosci. 2008 31: 25-46.

Ivry RB, Schlerf JE. Dedicated and intrinsic models of time perception. Trends in Cognitive Sciences, in press 2008.

Kim H, Bao S. Distributed representation of perceptual categories in the auditory cortex. J Comput Neurosci. 2008; 24: 277-290.

Karns CM, Knight RT. Intermodal Auditory, Visual, and Tactile Attention Modulates Early Stages of Neural Processing. J Cogn Neurosci. 2008 Jun 19.

Miller BT, Verstynen T, Johnson MK, D‘Esposito M. Prefrontal and parietal contributions to refreshing: an rTMS study. Neuroimage. 2008 39: 436-40.

Mormino EC, Kluth JT, Madison CM, Rabinovici GD, Baker SL, Miller BL, Koeppe RA, Mathis CA, Weiner MW, Jagust WJ; Alzheimer’s Disease Neuroimaging Initiative. Episodic memory loss is related to hippocampal-mediated beta-amyloid deposition in elderly subjects. Brain. 2009 132: 1310-23.

Pan CL, Garriga G. Fresh air is good for nerves: hypoxia disturbs axon guidance. Nat Neurosci. 2008 11: 859-61.

Pan CL, Baum PD, Gu M, Jorgensen EM, Clark SG, Garriga G. C. elegans AP-2 and retromer control Wnt signaling by regulating mig-14/Wntless. Dev Cell. 2008 14: 132-9.

Published in 2007

Allen EA, Pasley BN, Duong T, Freeman RD. Transcranial magnetic stimulation elicits coupled neural and hemodynamic consequences. Science. 2007 317: 1918-21.

Amin N, Doupe A, Theunissen FE. Development of selectivity for natural sounds in the songbird auditory forebrain. J Neurophysiol. 2007 97: 3517-31.

Cadieu C, Kouh M, Pasupathy A, Connor CE, Riesenhuber M, Poggio T. A model of V4 shape selectivity and invariance. J Neurophysiol. 2007 98: 1733-50.

Canolty, RT, Soltani, M, Dalal, SS, Edwards, E, Dronkers, NF, Nagarajan, SS, Kirsch, HE, Barbaro, NM, Knight, RT. Spatiotemporal dynamics of word processing in the human brain. Frontiers in Neuroscience 2007 1: 185-196.

Chen L, Tracy T, Nam CI. Dynamics of postsynaptic glutamate receptor targeting. Curr Opin Neurobiol. 2007 17: 53-8.

Cools R, Sheridan M, Jacobs E, D‘Esposito M. Impulsive personality predicts dopamine-dependent changes in frontostriatal activity during component processes of working memory. J Neurosci 2007; 27:5506-5514.

Han YK, Köver H, Insanally MN, Semerdjian JH, Bao S. Early experience impairs perceptual discrimination. Nat Neurosci. 2007 10: 1191-7.

Khan, R. M., Luk, C. H., Flinker, A., Aggarwal, A., Lapid, H., Haddad, R., Sobel, N. (2007) . Predicting odor pleasantness from odorant structure: pleasantness as a reflection of the physical world. J Neurosci 27: 10015-10023.

Pasley BN, Inglis BA, Freeman RD. Analysis of oxygen metabolism implies a neural origin for the negative BOLD response in human visual cortex. Neuroimage. 2007 36: 269-76.

Pathak MM, Yarov-Yarovoy V, Agarwal G, Roux B, Barth P, Kohout S, Tombola F, Isacoff EY. Closing in on the resting state of the
Shaker K(+) channel. Neuron. 2007 56: 124-40.

Yao H, Shi L, Han F, Gao H & Dan Y, Rapid Learning in Visual Cortical Coding of Natural Scenes. Nature Neuroscience 2007 10: 772-778.

Published in 2006

Allen EA, Freeman RD. Dynamic spatial processing originates in early visual pathways. J Neurosci. 2006 26: 11763-74.

Canolty, RT, Edwards, E, Dalal, SS, Soltani, M, Nagarajan, SS, Kirsch, HE, Berger, MS, Barbaro, NM, Knight, RT. High gamma power is phase-locked to theta oscillations in human neocortex. Science 2006 313 (5793) : 1626-1628.

Gilbert AL, Regier T, Kay P, Ivry RB. Whorf hypothesis is supported in the right visual field but not the left. Proc Natl Acad Sci U S A. 2006 103: 489-94.

Münch TA, Werblin FS. Symmetric interactions within a homogeneous starburst cell network can lead to robust asymmetries in dendrites of starburst amacrine cells. J Neurophysiol. 2006 96: 471-7.

Pan CL, Howell JE, Clark SG, Hilliard M, Cordes S, Bargmann CI, Garriga G. Multiple Wnts and frizzled receptors regulate anteriorly directed cell and growth cone migrations in Caenorhabditis elegans. Dev Cell. 2006 10: 367-77.

Published in 2005

Fried SI, Münch TA, Werblin FS. Directional selectivity is formed at multiple levels by laterally offset inhibition in the rabbit retina. Neuron. 2005 46: 117-27.

Guerrero G, Reiff DF, Agarwal G, Ball RW, Borst A, Goodman CS, Isacoff EY. Heterogeneity in synaptic transmission along a Drosophila larval motor axon. Nat Neurosci. 2005 8: 1188-96.

Mainland JD, Johnson BN, Khan R, Ivry RB, Sobel N. Olfactory impairments in patients with unilateral cerebellar lesions are selective to inputs from the contralesional nostril. J Neurosci. 2005 25: 6362-71.

Miller BT, D‘Esposito M. Searching for “the top” in top-down control. Neuron. 2005 48: 535-8.

Zelano C, Bensafi M, Porter J, Mainland J, Johnson B, Bremner E, Telles C, Khan R, Sobel N. Attentional modulation in human primary olfactory cortex . Nat Neurosci. 2005 8: 114-20.

Selected Student Publications

Adams JN, Maass A, Harrison TM, Baker SL, Jagust WJ (2019) Cortical tau deposition follows patterns of entorhinal functional connectivity in aging. eLife 8:e49132

Barger Z, Frye CG, Liu D, Dan Y, Bouchard KE (2019) Robust, automated sleep scoring by a compact neural network with distributional shift correction. PLoS ONE 14:e0224642

Breton JM, Charbit AR, Snyder BJ, Fong PTK, Dias EV, Himmels P, Lock H, Margolis EB (2019) Relative contributions and mapping of ventral tegmental area dopamine and GABA neurons by projection target in the rat. Journal of Comparative Neurology 526:916-941

Caval-Holme F, Zhang Y, Feller MB (2019) Gap junction coupling shapes the encoding of light in the developing retina. Current Biology 29:4024-4035

Cerniauskas I, Winterer J, …, Lammel S (2019) Chronic stress induces activity, synaptic, and transcriptional remodeling of the lateral habenula associated with deficits in motivated behaviors. Neuron 104:899-915

Kobayashi K, Hsu M (2019) Common neural code for reward and information value. Proceedings of the National Academy of Sciences USA 26:13061-13066

Naka A, Veit J, Shababo B, …, Ngai J, Adesnik H (2019) Complementary networks of cortical somatostatin interneurons enforce layer specific control. eLife 8:e43696

Senatorov VV Jr., Friedman AR, …, Kaufer D (2019) Blood-brain barrier dysfunction in aging induces hyperactivation of TGF-beta signaling and chronic yet reversible dysfunction. Science Translational Medicine 11:521

Toker D, Sommer FT (2019) Information integration in large brain networks. PLoS Computational Biology 15:e1006807

Isett BR, Feasel SH, Lane MA, Feldman DE (2018) Slip-based coding of local shape and texture in mouse S1. Neuron 97:418-33.

Day TP, Byrne LC, Flannery JG, Schaffer DV (2018) Screening for neutralizing antibodies against natural and engineered AAV capsids in nonhuman primate retinas. Methods Mol Biol 1715:239-49.

Gaub BM, Berry MH, Visel M, Holt A, Isacoff EY, Flannery JG. (2018) Optogenetic Retinal Gene Therapy with the Light Gated GPCR Vertebrate Rhodopsin. Methods Mol Biol. 1715:177-189.

Adams JN, Lockhart SN, Li L, Jagust WJ. (2018) Relationships between tau and glucose metabolism reflect Alzheimer’s disease pathology in cognitively normal older adults. Cereb Cortex, in press.

Neely RM, Koralek AC, Athalye VR, Costa RM, Carmena JM. (2018) Volitional modulation of primary visual cortex activity requires the basal ganglia. Neuron 97:1356-1368.

Liberman A, Manassi M, Whitney D. (2018) Serial dependence promotes the stability of perceived emotional expression depending on face similarity. Atten Percept Psychophys 80:1461-1473.

Lieder F, Shenhav A, Musslick S, Griffiths TL. (2018) Rational metareasoning and the plasticity of cognitive control. PLoS Comput Biol 14:e1006043.

Lorenc ES, Sreenivasan KK, Nee DE, Vandenbroucke ARE, D’Esposito M. (2018) Flexible coding of visual working memory representations during distraction. J Neurosci 38:5267-5276.

Haller M, Case J, Crone NE, Chang EF, King-Stephens D, Laxer KD, Weber PB, Parvizi J, Knight RT, Shestyuk AY. (2018) Persistent neuronal activity in human prefrontal cortex links perception and action. Nat Hum Behav 2:80-91

Bliss DP, D’Esposito M. (2017) Synaptic augmentation in a cortical circuit model reproduces serial dependence in visual working memory. PLoS One. 12(12):e0188927.

Goldstein-Piekarski AN, Greer SM, Saletin JM, Harvey AG, Williams LM, Walker MP. (2017) Sex, Sleep Deprivation, and the Anxious Brain. J Cogn Neurosci.Dec 15:1-14.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB. (2017) Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities. Cell Stem Cell. pii: S1934-5909(17)30452-6.

Bliss DP, Sun JJ, D’Esposito M. (2017) Serial dependence is absent at the time of perception but increases in visual working memory. Sci Rep. 7(1):14739.

Holdgraf CR, Rieger JW, Micheli C, Martin S, Knight RT, Theunissen FE. (2017) Encoding and Decoding Models in Cognitive Electrophysiology. Front Syst Neurosci. Sep 26;11:61

Moorman HG, Gowda S, Carmena JM. (2017) Control of Redundant Kinematic Degrees of Freedom in a Closed-Loop Brain-Machine Interface. IEEE Trans Neural Syst Rehabil Eng. 25(6):750-760.

Gratton C, Yousef S, Aarts E, Wallace DL, D’Esposito M, Silver MA. (2017) Cholinergic, But Not Dopaminergic or Noradrenergic, Enhancement Sharpens Visual Spatial Perception in Humans. J Neurosci. 37(16):4405-4415.

Kim H, Kirkhart C, Scott K. Long-range projection neurons in the taste circuit of Drosophila. Elife. 2017 6. pii: e23386.

Pluta SR, Lyall EH, Telian GI, Ryapolova-Webb E, Adesnik H. (2017) Surround Integration Organizes a Spatial Map during Active Sensation. Neuron. 94(6):1220-1233.e5.

Kobayashi K, Hsu M. (2017) Neural mechanisms of updating under reducible and irreducible uncertainty. J Neurosci. Jun 16. pii: 0535-17.

Marks SM, Lockhart SN, Baker SL, Jagust WJ. (2017) Tau and β-Amyloid Are Associated with Medial Temporal Lobe Structure, Function, and Memory Encoding in  Normal Aging. J Neurosci. 37(12):3192-3201.

Slama SJK, Helfrich RF. (2017) How Does Expectation Shape Object-Based Attentional  Selection? J Neurosci. 37(17):4427-4429.

de Heer WA, Huth AG, Griffiths TL, Gallant JL, Theunissen FE. (2017) The hierarchical cortical organization of human speech processing. J Neurosci. Jun 6. pii: 3267-16.

Seo D, Neely RM, Shen K, Singhal U, Alon E, Rabaey JM, Carmena JM, Maharbiz MM.  (2016) Wireless Recording in the Peripheral Nervous System with Ultrasonic Neural Dust. Neuron 91(3):529-39.

McGuire LM, Telian G, Laboy-Juárez KJ, Miyashita T, Lee DJ, Smith KA, Feldman DE. (2016) Short Time-Scale Sensory Coding in S1 during Discrimination of Whisker Vibrotactile Sequences. PLoS Biol. 14(8):e1002549.

Holdgraf CR, de Heer W, Pasley B, Rieger J, Crone N, Lin JJ, Knight RT, Theunissen FE. (2016) Rapid tuning shifts in human auditory cortex enhance speech intelligibility. Nat Commun. 7: 13654.

Langberg T. (2016) Thalamic Bursts and Single Spikes Evoke Distinct Inhibitory States in the Primary Sensory Cortex. J Neurosci. 36(45): 11496-11497.

Huth AG, de Heer WA, Griffiths TL, Theunissen FE, Gallant JL. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex.  Nature.  532: 453-8.

Vlasits AL, Morrie RD, Tran-Van-Minh A, Bleckert A, Gainer CF, DiGregorio DA, Feller MB. (2016) A Role for Synaptic Input Distribution in a Dendritic Computation of Motion Direction in the Retina.  Neuron. 89: 1317-30.

Greer SM, Goldstein AN, Knutson B, Walker MP. (2016) A Genetic Polymorphism of the Human Dopamine Transporter Determines the Impact of Sleep Deprivation on Brain Responses to Rewards and Punishments.  J Cogn Neurosci. 28: 803-10. doi: 10.1162/jocn_a_00939.

Hillenbrand SF, Ivry RB, Schlerf JE. (2016)  Impact of task-related changes in heart rate on estimation of hemodynamic response and model fit.  Neuroimage. 132: 455-68.

Cox J, Pinto L, Dan Y. (2016)  Calcium imaging of sleep-wake related neuronal activity in the dorsal pons. Nat Commun. 7: 10763.

Merel J, Shababo B, Naka A, Adesnik H, Paninski L. (2016) Bayesian methods for event analysis of intracellular currents.  J Neurosci Methods. 269: 21-32.

Fonken YM, Rieger JW, Tzvi E, Crone NE, Chang E, Parvizi J, Knight RT, Krämer UM (2016)  Frontal and motor cortex contributions to response inhibition: evidence from electrocorticography. J Neurophysiol. 115: 2224-36.

Muroy SE, Long KL, Kaufer D, Kirby ED. (2016)  Moderate Stress-Induced Social Bonding and Oxytocin Signaling are Disrupted by Predator Odor in Male Rats.  Neuropsychopharmacology. 41: 2160-70.

Thomas AW, Caporale N, Wu C, Wilbrecht L. (2016) Early maternal separation impacts cognitive flexibility at the age of first independence in mice.  Dev Cogn Neurosci. 18: 49-56.

Cano ME, Knight RT. (2016)  Behavioral and EEG Evidence for Auditory Memory Suppression. Front Hum Neurosci. 10: 133.

Gallen CL, Turner GR, Adnan A, D’Esposito M. (2016) Reconfiguration of brain network architecture to support executive control in aging.  Neurobiol Aging. 44: 42-52.

Kallman BR, Kim H, Scott K. (2015)  Excitation and inhibition onto central courtship neurons biases Drosophila mate choice.  Elife. 4: e11188.

Voytek B, Kayser AS, Badre D, Fegen D, Chang EF, Crone NE, Parvizi J, Knight RT, D’Esposito M. (2015) Oscillatory dynamics coordinating human frontal networks in support of goal maintenance. Nat Neurosci. 18: 1318-24. doi: 10.1038/nn.4071.

Pinto L, Dan Y. (2015) Cell-Type-Specific Activity in Prefrontal Cortex during Goal-Directed Behavior. Neuron. 87(2): 437-50.

Fegen D, Buchsbaum BR, D’Esposito M. (2015) The effect of rehearsal rate and memory load on verbal working memory. Neuroimage. 105: 120-31.

Gaub BM, Berry MH, Holt AE, Isacoff EY, Flannery JG (2015) Optogenetic Vision Restoration Using Rhodopsin for Enhanced Sensitivity.  Mol Therapy. 23: 1562-71.

Pluta S, Naka A, Veit J, Telian G, Yao L, Hakim R, Taylor D, Adesnik H. (2015)  A direct translaminar inhibitory circuit tunes cortical output.  Nat Neurosci. 18: 1631-40.

Arnemann KL, Chen AJ, Novakovic-Agopian T, Gratton C, Nomura EM, D’Esposito M. (2015)  Functional brain network modularity predicts response to cognitive training after brain injury.  Neurology 84: 1568-74.

Mander BA, Marks SM, Vogel JW, Rao V, Lu B, Saletin JM, Ancoli-Israel S, Jagust WJ, Walker MP. (2015)  β-amyloid disrupts human NREM slow waves and related hippocampus-dependent memory consolidation.  Nat Neurosci. 18: 1051-7.

Flinker A, Korzeniewska A, Shestyuk AY, Franaszczuk PJ, Dronkers NF, Knight RT, Crone NE. (2015) Redefining the role of Broca’s area in speech.  Proc Natl Acad Sci U S A. 112: 2871-5.

Gao JS, Huth AG, Lescroart MD, Gallant JL. (2015)  Pycortex: an interactive surface visualizer for fMRI.  Front Neuroinform. 9: 23. doi: 10.3389/fninf.2015.00023.

Mackey AP, Miller Singley AT, Wendelken C, Bunge SA. (2015)  Characterizing Behavioral and Brain Changes Associated with Practicing Reasoning Skills.  PLoS One. 10(9):e0137627.

Naka A.  (2015) Cell-Type-Specific Manipulation Reveals New Specificity in the Neocortical Microcircuit.  J Neurosci. 35: 8976-8.

Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG. (2015) The expression pattern of systemically injected AAV9 in the developing mouse retina is determined by age. Mol Ther. 23(2):290-6.

Kirkhart C, Scott K. (2015) Gustatory learning and processing in the Drosophila mushroom bodies. J Neurosci. 2015 35: 5950-8.

Forster S, Nunez Elizalde AO, Castle E, Bishop SJ. (2015) Unraveling the anxious mind: anxiety, worry, and frontal engagement in sustained attention versus off-task processing. Cereb Cortex. 25: 609-18.

Griffiths TL, Lieder F, Goodman ND. (2015) Rational use of cognitive resources: levels of analysis between the computational and the algorithmic. Topics in Cognitive Science 7: 217-29.

Goldstein-Piekarski AN, Greer SM, Saletin JM, Walker MP (2015)  Sleep Deprivation Impairs the Human Central and Peripheral Nervous System Discrimination of Social Threat.  J Neurosci. 35: 10135-45.

Lara AH, Wallis JD. (2014) Executive control processes underlying multi-item working memory. Nat Neurosci. 17: 876-83.

Agarwal G, Stevenson IH, Berényi A, Mizuseki K, Buzsáki G, Sommer FT. (2014) Spatially distributed local fields in the hippocampus encode rat position. Science 344: 626-30.

Liberman A, Fischer J, Whitney D. (2014) Serial dependence in the perception of faces. Curr Biol. 24: 2569-74.

Gaub BM, Berry MH, Holt AE, Reiner A, Kienzler MA, Dolgova N, Nikonov S, Aguirre GD, Beltran WA, Flannery JG, Isacoff EY. (2014) Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells. Proc Natl Acad Sci U S A. 111: E5574-83.

Pool AH, Kvello P, Mann K, Cheung SK, Gordon MD, Wang L, Scott K (2014). Four GABAergic interneurons impose feeding restraint in Drosophila. Neuron 83: 164-77.

Rodgers CC, DeWeese MR (2014) Neural correlates of task switching in prefrontal cortex and primary auditory cortex in a novel stimulus selection task for rodents. Neuron 82: 1157-70.

Vlasits AL, Bos R, Morrie RD, Fortuny C, Flannery JG, Feller MB, Rivlin-Etzion M. (2014) Visual Stimulation Switches the Polarity of Excitatory Input to Starburst Amacrine Cells. Neuron. 83: 1172-84.

Clancy KB, Koralek AC, Costa RM, Feldman DE, Carmena JM (2014) Volitional modulation of optically recorded calcium signals during neuroprosthetic learning.  Nat Neurosci. 17: 807-9.

Chetty S, Friedman AR, Taravosh-Lahn K, Kirby ED, Mirescu C, Guo F, Krupik D, Nicholas A, Geraghty AC, Krishnamurthy A, Tsai MK, Covarrubias D, Wong AT, Francis DD, Sapolsky RM, Palmer TD, Pleasure D, Kaufer D (2014) Stress and glucocorticoids promote oligodendrogenesis in the adult hippocampus. Mol Psychiatry. 19: 1275-83.

Day TP, Byrne LC, Schaffer DV, Flannery JG (2014) Advances in AAV vector development for gene therapy in the retina. Adv Exp Med Biol. 801: 687-93.

Blumenfeld RS, Bliss DP, Perez F, D’Esposito M (2014) CoCoTools: open-source software for building connectomes using the CoCoMac anatomical database. J Cogn Neurosci. 26: 722-45.

Orsborn AL, Moorman HG, Overduin SA, Shanechi MM, Dimitrov DF, Carmena JM (2014) Closed-loop decoder adaptation shapes neural plasticity for skillful neuroprosthetic control. Neuron 82: 1380-93.

Denison RN, Vu AT, Yacoub E, Feinberg DA, Silver MA (2014) Functional mapping of the magnocellular and parvocellular subdivisions of human LGN. Neuroimage 102P2:358-369.

Goldstein AN, Walker MP. (2014) The role of sleep in emotional brain function. Annu Rev Clin Psychol. 10: 679-708.

Sreenivasan KK, Gratton C, Vytlacil J, D’Esposito M (2014) Evidence for working memory storage operations in perceptual cortex. Cogn Affect Behav Neurosci. 14: 117-28.

Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG (2014) Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse. Gene Therapy 21: 585-92.

Whitaker KJ, Kang X, Herron TJ, Woods DL, Robertson LC, Alvarez BD (2014) White matter microstructure throughout the brain correlates with visual imagery in grapheme-color synesthesia. Neuroimage 90:52-9.

Pinto L, Goard MJ, Estandian D, Xu M, Kwan AC, Lee SH, Harrison TC, Feng G, Dan Y. (2013) Fast modulation of visual perception by basal forebrain cholinergic neurons. Nat Neurosci. 16: 1857-63.

Hamilton LS, Sohl-Dickstein J, Huth AG, Carels VM, Deisseroth K, Bao S. (2013) Optogenetic activation of an inhibitory network enhances feedforward functional connectivity in auditory cortex. Neuron 80: 1066-76.

Moore RC, Lee T, Theunissen FE. (2013) Noise-invariant neurons in the avian auditory cortex: hearing the song in noise. PLoS Comput Biol. 9(3):e1002942.

Çukur T, Huth AG, Nishimoto S, Gallant JL. (2013) Functional subdomains within human FFA. J Neurosci. 33: 16748-66.

Koralek AC, Costa RM, Carmena JM. (2013) Temporally precise cell-specific coherence develops in corticostriatal networks during learning. Neuron 79: 865-72.

Kim H, Gibboni R, Kirkhart C, Bao S. (2013) Impaired critical period plasticity in primary auditory cortex of fragile X model mice. J Neurosci. 33: 15686-92.

Shao YR, Isett BR, Miyashita T, Chung J, Pourzia O, Gasperini RJ, Feldman DE. (2013) Plasticity of recurrent L2/3 inhibition and gamma oscillations by whisker experience. Neuron 80: 210-22.

Kauwe G, Isacoff EY. (2013) Rapid feedback regulation of synaptic efficacy during high-frequency activity at the Drosophila larval neuromuscular junction. Proc Natl Acad Sci U S A. 110: 9142-7.

Voytek B, D’Esposito M, Crone N, Knight RT. (2013) A method for event-related phase/amplitude coupling. Neuroimage. 64: 416-24.

Long JD 2nd, Carmena JM. (2013) Dynamic changes of rodent somatosensory barrel cortex are correlated with learning a novel conditioned stimulus. J Neurophysiol. 109: 2585-95.

Mann K, Gordon MD, Scott K. (2013) A Pair of Interneurons Influences the Choice between Feeding and Locomotion in Drosophila. Neuron. 79: 754-65.

Kirby ED, Muroy SE, Sun WG, Covarrubias D, Leong MJ, Barchas LA, Kaufer D. Acute stress enhances adult rat hippocampal neurogenesis and activation of newborn neurons via secreted astrocytic FGF2. Elife. 2:e00362.

Greer SM, Goldstein AN, Walker MP. (2013) The impact of sleep deprivation on food desire in the human brain. Nat Commun. 4:2259.

Goldstein AN, Greer SM, Saletin JM, Harvey AG, Nitschke JB, Walker MP. (2013) Tired and apprehensive: anxiety amplifies the impact of sleep loss on aversive brain anticipation. J Neurosci. 33: 10607-15.

Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. (2013) In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 5: 189ra76.

Köver H, Gill K, Tseng YT, Bao S. (2013) Perceptual and neuronal boundary learned from higher-order stimulus probabilities. J Neurosci. 33: 3699-705.

Mackey AP, Miller Singley AT, Bunge SA. (2013) Intensive reasoning training alters patterns of brain connectivity at rest. J Neurosci. 33: 4796-803.

Gratton C, Sreenivasan KK, Silver MA, D’Esposito M. (2013) Attention selectively modifies the representation of individual faces in the human brain. J Neurosci. 33: 6979-89.

Denison RN, Driver J, Ruff CC. (2013) Temporal structure and complexity affect audio-visual correspondence detection. Front Psychol. 3: 619.

Li L, Gratton C, Fabiani M, Knight RT. (2013) Age-related frontoparietal changes during the control of bottom-up and top-down attention: an ERP study. Neurobiol Aging. 34: 477-88.

Moore RC, Lee T, Theunissen FE. (2013) Noise-invariant neurons in the avian auditory cortex: hearing the song in noise. PLoS Comput Biol. 2013;9(3):e1002942.

Amin N, Gastpar M, Theunissen FE. (2013) Selective and efficient neural coding of communication signals depends on early acoustic and social environment. PLoS One. 2013 8(4):e61417.

Miyakawa A, Gibboni R, Bao S. (2013) Repeated exposure to a tone transiently alters spectral tuning bandwidth of neurons in the central nucleus of inferior colliculus in juvenile rats. Neuroscience 230: 114-20.

Published in 2012

Huth AG, Nishimoto S, Vu AT, Gallant JL. (2012) A continuous semantic space describes the representation of thousands of object and action categories across the human brain. Neuron. 76: 1210-24.

Mackey AP, Whitaker KJ, Bunge SA. (2012) Experience-dependent plasticity in white matter microstructure: reasoning training alters structural connectivity. Front Neuroanat. 6: 32.

Kirby ED, Friedman AR, Covarrubias D, Ying C, Sun WG, Goosens KA, Sapolsky RM, Kaufer D. (2012) Basolateral amygdala regulation of adult hippocampal neurogenesis and fear-related activation of newborn neurons. Mol Psychiatry. 17: 527-36.

Voytek B, D’Esposito M, Crone N, Knight RT. (2013) A method for event-related phase/amplitude coupling. Neuroimage. 64: 416-24.

Dang LC, O’Neil JP, Jagust WJ. (2012) Dopamine supports coupling of attention-related networks. J Neurosci. 32: 9582-7.

Cadieu CF, Olshausen BA. (2012) Learning intermediate-level representations of form and motion from natural movies. Neural Comput. 24: 827-66.

Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, Isacoff EY. (2012) Emergence of patterned activity in the developing zebrafish spinal cord. Curr Biol. 22: 93-102.

Mormino EC, Brandel MG, Madison CM, Marks S, Baker SL, Jagust WJ. (2012) Aβ Deposition in aging is associated with increases in brain activation during successful memory encoding. Cereb Cortex. 22: 1813-23.

Gratton C*, Nomura EM*, Perez F, D’Esposito M. (2012) Focal brain lesions disrupt modular organization throughout the brain. Journal of Cognitive Neuroscience, 24, 1275-1285 (*Equal contribution)

Koralek AC, Jin X, Long JD, Costa RM, Carmena JM. (2012) Corticostriatal plasticity is necessary for learning intentional neuroprosthetic skills. Nature, 483: 331-335.

Denison RN, Silver MA. (2012) Distinct contributions of the magnocellular and parvocellular visual streams to perceptual selection. Journal of Cognitive Neuroscience. 24: 246-59.

Held RT, Cooper EA, Banks MS. (2012) Blur and Disparity are Complementary Cues to Depth. Current Biology, 22: 426-31.

Marella S, Mann K, Scott K. (2012) Dopaminergic modulation of sucrose acceptance behavior in Drosophila. Neuron. 2012 73: 941-50.

Published in 2011

Kirby, E.D., Friedman, A.R., Covarrubias, D., Ying, C., Grant, W.G., Goosens, K.A., Sapolsky, R.M., & Kaufer, D. (2011). Basolateral amygdala regulation of adult hippocampal neurogenesis and fear-related activation of newborn neurons. Molecular Psychiatry, In Press.

Perrotin A, Mormino EC, Madison CM, Hayenga AO, Jagust WJ. Subjective cognition and amyloid deposition imaging. A PiB PET study in normal elderly individuals. Arch Neurol. In Press.

Mormino EC, Smiljic A, Hayenga AO, Onami S, Greicius MD, Rabinovici GD, Janabi M, Baker SL, Yen I, Madison CM, Miller BL, Jagust WJ. Relationships between beta-amyloid and functional connectivity in different components of the default mode network in aging. Cerebral Cortex. In Press.

Rosenbloom MH, Alkalay A, Agerwal N, Baker SL, O’Neill JP, Janabi M, Yen IV, Growdon M, Jung J, Madison C, Mormino EC, Rosen HJ, Gorno-Tempini ML, Miller BL, Jagust WJ, Rabinovici GD. Distinct clinical and metabolic deficits in posterior cortical atrophy and Alzheimer’s disease are not related to amyloid distribution. Neurology. In Press.

Oh H, Mormino EC, Madison C, Hayenga A, Smiljic A, Jagust WJ. β-amyloid affects frontal and posterior brain networks in normal aging. 2011. Neuroimage. 54, 1887-95.

Emily Jacobs and Mark D’Esposito, Estrogen Shapes Dopamine-Dependent Cognitive Processes: Implications for Women’s Health, The Journal of Neuroscience, April 6, 2011 • 31(14):5286 –5293

E.A. Cooper, U. Hasson, and S.L. Small. Interpretation-Mediated Changes in Neural Activity During Language Comprehension. NeuroImage, 55(3), 1314-1323, 2011.

E.A. Cooper, J. Burge, and M.S. Banks. The Vertical Horopter is not Adaptable, but It may be Adaptive. Journal of Vision, 11(3):20, 1-19, 2011.

Flinker, A., Chang, E.F., Barbaro, N.M., Berger, M.S., Knight, R.T. (2011) Sub-centimeter language organization in the human temporal lobe. Brain and Language 117 pp. 103-109

Published in 2010

Rabinovici GD, Furst AJ, Alkalay A, Racine CA, O’Neil JP, Janabi M, Baker SL, Agarwal N, Karydas A, Bonasera SJ, Mormino EC, Madison CM, Weiner MW, Gorno-Tempini ML, Rosen HJ, Miller BL, Jagust WJ. Increased Metabolic Vulnerability in Early-Onset Alzheimer’s Disease is Not Related to Amyloid Burden. 2010. Brain, 133, 512-28.

Furst AJ and Mormino E. A BOLD move: clinical application of functional magnetic resonance imaging (fMRI) in aging. 2010. Neurology. 74, 1940-1.

Marta E. Soden and Lu Chen. Fragile X Protein FMRP Is Required for Homeostatic Plasticity and Regulation os Synaptic Strength by Retinoic Acid. The Journal of Neuroscience, December 15, 2010, 30(50):16910-16921; doi:10.1523/JNEUROSCI.3660-10.2010

Flinker, A., Chang, F.E., Kirsch, H.E., Barbaro N.M., Crone, N.E., Knight, R.T. (2010) “Single-Trial Speech Suppression of Auditory Cortex Activity in Humans.” Journal of Neuroscience vol. 30 (49) pp. 16643.

Hania Köver, Shaowen Bao. (2010) Cortical plasticity as a mechanism for storing Bayesian priors in sensory perception. PLoS One, Vol 5, Issue 5, e1049

Nomura, E. M., Gratton, C., Visser, R. M., Kayser, A., Perez, F., & D’Esposito, M. (2010). Double dissociation of two cognitive control networks in patients with focal brain lesions. Proceedings of the National Academy of Sciences of the United States of America, 107(26), 12017-12022

Voytek B. & Knight RT (2010). Prefrontal cortex and basal ganglia contributions to visual working memory. Proc Natl Acad Sci USA 107(42), 18167-18172.

Voytek B, Davis M., Yago E, Barceló F, Vogel EK, Knight RT (2010). Dynamic neuroplasticity after human prefrontal cortex damage. Neuron 68(3), 401-408.

Voytek B, Secundo L, Bidet-Caulet A, Scabini D, Stiver S, Gean AD, Manley G, Knight RT. Hemicraniectomy: A New Model for Human Electrophysiology with High Spatio-Temporal Resolution. J. Cogn Neurosci 22(11), 2491-2502.

R. Held, E.A. Cooper, J. O’Brien, and M.S. Banks. Using Blur to Affect Perceived Distance and Size. ACM Transactions on Graphics, 29(2):1-16, 2010

Insanally MN, Albanna BF, Bao S. Pulsed Noise Experience Disrupts Complex Sound Representations.J Neurophysiol. 2010 Mar 3. PMID: 20200123

Mormino EC, Kluth JT, Madison CM, Rabinovici GD, Baker SL, Miller BL, Koeppe RA, Mathis CA, Weiner MW, Jagust WJ. Episodic memory loss is related to hippocampal-mediated beta-amyloid deposition in elderly subjects. Brain, 132:1310-1323, 2009.

John E. Schlerf, Timothy D. Verstynen, Richard B Ivry, and Rebecca M. C. Spencer. Evidence of a novel somatopic map in the human neocerebellum during complex actions. J Neurophysiol, Apr 2010; doi:10.1152/jn.01117.2009

Mathevon, N., Koralek, A., Weldele, M., Glickman, S.E., & Theunissen, F.E. (2010). What the hyena’s laugh tells: sex, age, dominance and individual identity in the giggling call of Crocuta Crocuta. BMC Ecology, 10(1):9. PMID: 20353550

Published in 2009

Bunge, S.A., Mackey, A., & Whitaker, K. Neurodevelopmental changes in cognitive control and fluid reasoning over childhood. The Cognitive Neurosciences III, edited by Michael Gazzaniga.

Ganguly K, Secundo L, Ranade G, Orsborn A, Chang EF, Dimitrov DF, Wallis JD, Barbaro NM, Knight RT, Carmena JM. Cortical representation of ipsilateral arm movements in monkey and man.J Neurosci. 2009 Oct 14;29(41):12948-56.

Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, Isacoff EY. 2009. Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature. 461, 407-10.

Lu, H., Lim, B., and Poo, M. M. (2009). Cocaine exposure in utero alters synaptic plasticity in the medial prefrontal cortex of postnatal rats. J Neurosci 29, 12664-12674.

Goard M and Dan Y (2009). Basal forebrain activation enhances cortical coding of natural scenes. Nature Neuroscience. Nov; 12(11):1444-9.

Cacheaux LP, Ivens S, David Y, Lakhter AJ, Bar-Klein G, Shapira M, Heinemann U, Friedman A, Kaufer D. Transcriptome profiling reveals TGF-beta signaling involvement in epileptogenesis. J Neurosci. 2009 Jul 15;29(28):8927-35.

Rokem A, Silver MA. A model of encoding and decoding in V1 and MT accounts for motion perception anisotropies in the human visual system. Brain Res. 2009 Nov 24;1299:3-16

David Y, Cacheaux LP, Ivens S, Lapilover E, Heinemann U, Kaufer D, Friedman A. (2009) Astrocytic dysfunction in epileptogenesis: consequence of altered potassium and glutamate homeostasis J. Neuroscience, 29, 10588-99.

Antonio H. Lara, Steven W. Kennerley, and Jonathan D. Wallis. Encoding of Gustatory Working Memory by Orbitofrontal Neurons. J. Neurosci. 2009;29 765-774

Heesoo Kim and Shaowen Bao. Selective Increase in Representations of Sounds Repeated at an Ethological Rate. J. Neurosci. 2009; 29: 5163Ð5169

Beery AK, Routman DM, Zucker I. Same-sex social bond formation in meadow voles: multiple and rapid formation of attachments. Physiology and Behavior 2009 97: 52-57.

Pasley, B.N.*, Allen, E.A.*, & Freeman, R.D. State-dependent variability of neuronal responses to transcranial magnetic stimulation of the visual cortex. Neuron 2009 62: 291-303. (*Equal contributions)

A. Rokem and M. Ahissar. Interactions of cognitive and auditory abilities in congenitally blind individuals. Neuropsychologia 2009 47: 843-848

Venkatraman, S., Elkabany, K., Long, J.D., Yao, Yimin, and Carmena, J.M. A System for Neural Recording and Closed-Loop Intracortical Microstimulation in Awake Rodents. IEEE Transactions on Biomedical Engineering 2009 56: 15-22.

Huberman A*, Wei W*, Elstrott J*, Stafford B, Feller MB, Barres B. Genetic identification of On-Off direction selective retinal ganglion cells reveals a layer specific subcortical map of posterior motion. Neuron 2009 62: 327-334. (* = equal contribution)

Kirby, E.D., Geraghty, A.G., Ubuka, T., Bentley, G.E., & Kaufer, D. Stress increases putative gonadotropin inhibitory hormone and decreases luteinizing hormone in male rats. Proc Natl Acad Sci. 2009, 106, 11324-9.

Michele N. Insanally, Hania Köver, Heesoo Kim, and Shaowen Bao. Feature-Dependent Sensitive Periods in the Development of Complex Sound Representation. J. Neurosci. 2009 29: 6567-6562.

C. Cadieu and B. Olshausen. Learning transformational invariants from natural movies. In D. Koller, D. Schuurmans, Y. Bengio, and L. Bottou, Eds., Advances in Neural Information Processing Systems 21, pages 209-216. MIT Press, 2009.

Luk, C.-H., Wallis, J. D. Dynamic encoding of responses and outcomes by neurons in medial prefrontal cortex. J. Neurosci. 2009 29: 7526-7539.

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Beery AK, Lacey EA, Francis DD. Oxytocin and vasopressin receptor distributions in a solitary and a social species of tuco-tuco (Ctenomys haigi and Ctenomys sociabilis). J Comp Neurol. 2008 507: 1847-59.

Caporale N, Dan Y. Spike timing-dependent plasticity: a hebbian learning rule. Annu Rev Neurosci. 2008 31: 25-46.

Ivry RB, Schlerf JE. Dedicated and intrinsic models of time perception. Trends in Cognitive Sciences, in press 2008.

Kim H, Bao S. Distributed representation of perceptual categories in the auditory cortex. J Comput Neurosci. 2008; 24: 277-290.

Karns CM, Knight RT. Intermodal Auditory, Visual, and Tactile Attention Modulates Early Stages of Neural Processing. J Cogn Neurosci. 2008 Jun 19.

Miller BT, Verstynen T, Johnson MK, D‘Esposito M. Prefrontal and parietal contributions to refreshing: an rTMS study. Neuroimage. 2008 39: 436-40.

Mormino EC, Kluth JT, Madison CM, Rabinovici GD, Baker SL, Miller BL, Koeppe RA, Mathis CA, Weiner MW, Jagust WJ; Alzheimer’s Disease Neuroimaging Initiative. Episodic memory loss is related to hippocampal-mediated beta-amyloid deposition in elderly subjects. Brain. 2009 132: 1310-23.

Pan CL, Garriga G. Fresh air is good for nerves: hypoxia disturbs axon guidance. Nat Neurosci. 2008 11: 859-61.

Pan CL, Baum PD, Gu M, Jorgensen EM, Clark SG, Garriga G. C. elegans AP-2 and retromer control Wnt signaling by regulating mig-14/Wntless. Dev Cell. 2008 14: 132-9.

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Allen EA, Pasley BN, Duong T, Freeman RD. Transcranial magnetic stimulation elicits coupled neural and hemodynamic consequences. Science. 2007 317: 1918-21.

Amin N, Doupe A, Theunissen FE. Development of selectivity for natural sounds in the songbird auditory forebrain. J Neurophysiol. 2007 97: 3517-31.

Cadieu C, Kouh M, Pasupathy A, Connor CE, Riesenhuber M, Poggio T. A model of V4 shape selectivity and invariance. J Neurophysiol. 2007 98: 1733-50.

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Chen L, Tracy T, Nam CI. Dynamics of postsynaptic glutamate receptor targeting. Curr Opin Neurobiol. 2007 17: 53-8.

Cools R, Sheridan M, Jacobs E, D‘Esposito M. Impulsive personality predicts dopamine-dependent changes in frontostriatal activity during component processes of working memory. J Neurosci 2007; 27:5506-5514.

Han YK, Köver H, Insanally MN, Semerdjian JH, Bao S. Early experience impairs perceptual discrimination. Nat Neurosci. 2007 10: 1191-7.

Khan, R. M., Luk, C. H., Flinker, A., Aggarwal, A., Lapid, H., Haddad, R., Sobel, N. (2007) . Predicting odor pleasantness from odorant structure: pleasantness as a reflection of the physical world. J Neurosci 27: 10015-10023.

Pasley BN, Inglis BA, Freeman RD. Analysis of oxygen metabolism implies a neural origin for the negative BOLD response in human visual cortex. Neuroimage. 2007 36: 269-76.

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Yao H, Shi L, Han F, Gao H & Dan Y, Rapid Learning in Visual Cortical Coding of Natural Scenes. Nature Neuroscience 2007 10: 772-778.

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Allen EA, Freeman RD. Dynamic spatial processing originates in early visual pathways. J Neurosci. 2006 26: 11763-74.

Canolty, RT, Edwards, E, Dalal, SS, Soltani, M, Nagarajan, SS, Kirsch, HE, Berger, MS, Barbaro, NM, Knight, RT. High gamma power is phase-locked to theta oscillations in human neocortex. Science 2006 313 (5793) : 1626-1628.

Gilbert AL, Regier T, Kay P, Ivry RB. Whorf hypothesis is supported in the right visual field but not the left. Proc Natl Acad Sci U S A. 2006 103: 489-94.

Münch TA, Werblin FS. Symmetric interactions within a homogeneous starburst cell network can lead to robust asymmetries in dendrites of starburst amacrine cells. J Neurophysiol. 2006 96: 471-7.

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Published in 2005

Fried SI, Münch TA, Werblin FS. Directional selectivity is formed at multiple levels by laterally offset inhibition in the rabbit retina. Neuron. 2005 46: 117-27.

Guerrero G, Reiff DF, Agarwal G, Ball RW, Borst A, Goodman CS, Isacoff EY. Heterogeneity in synaptic transmission along a Drosophila larval motor axon. Nat Neurosci. 2005 8: 1188-96.

Mainland JD, Johnson BN, Khan R, Ivry RB, Sobel N. Olfactory impairments in patients with unilateral cerebellar lesions are selective to inputs from the contralesional nostril. J Neurosci. 2005 25: 6362-71.

Miller BT, D‘Esposito M. Searching for “the top” in top-down control. Neuron. 2005 48: 535-8.

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