Neural circuits of cognition – Marie Carlén group

Our group researches on the prefrontal cortex and the cellular logic of cognition.

Latest research news

New light on mental disorders

Research focus

Room with multiple colours representing lasers used within the group, as a signature.
CarlenLab signature. Photo: CarlenLab.

The prefrontal cortex (PFC) in the frontal lobes integrates internally generated information with information from the external world. Prefrontal processing is most important when behavior must be guided by internal intentions (often referred to as goal-directed behavior), and in line with this proper PFC functioning is essential to cognitive processes such as attention, working memory, planning, and decision-making.

In the lab we use systems neuroscience approaches to elucidate how neurons and circuits modulate network activity in the encoding and causation of behavior. We have a strong focus on the prefrontal cortex (PFC) and studies in rodents (mus musculus and rattus norvegicus).

Most projects involve electrophysiological recordings (tetrodes or silicon probes, including Neuropixels) or imaging (microendoscopes, fiber photometry, or 2-photon microscopy) of neuronal activity in behaving animals (head-fixed or freely moving) in combination with circuit tracing and cell-type specific manipulations (optogenetics, genetic). Slice electrophysiology and voltage imaging are used for detailed ex vivo circuit studies.

Our research is rooted in the firm belief that only experiments in relation to behavioral functions can directly address when and how the brain’s circuits exert their unique actions.

The prefrontal cortex

The PFC still lacks a conclusive definition, and the structure and function of this brain area across species remain unresolved. The PFC is implicated in perceptual, emotional, social, motivational, and numerous other brain processes, and is considered to enable cognition and flexible behavior. In following, disturbed PFC functioning has been connected to most, if not all, mental disorders, including drug addiction. Naturally, deciphering of the structure and function(s) of the PFC is of great importance to medicine.

Present-day preclinical researchers increasingly utilize mice (Mus musculus) as model animals. However, lack of understanding of the structure and function of the brain hampers the understanding of which findings are transferable between species. While class-common functions and class-common behaviors involving the PFC have been firmly established, effort must also be put into clarifying dissociations and differences between species. Ultimately, understanding of what makes the human PFC unique will build on comparative studies in different species.

We are utilizing the unique technological toolbox available to studies in mice, with the aim to provide a comprehensive view of the structure and function of the mouse PFC. A blueprint of the mammalian PFC could serve as a source for investigation of homologies between species and shed light on the translational value of studies in distinct species. 

The mouse PFC

Large-scale mappings of the connectivity of the mouse cortex indicates the presence of a prefrontal module. Regions within a cortical module display particularly high interconnectivity and are suggested to be dedicated to similar functions. Hodology thus gives support for the presence of a distinct prefrontal region in the mouse brain. However, how hodology and cytoarchitectural features relate to functional features is highly unclear.

The connectivity indicates that the prefrontal module in mice sits on the top of the cortical hierarchy. Further, there is also hodological support for the presence of functional subnetworks within the moue PFC, each being defined by its specific brain connectivity. The presence of subnetworks, high interconnectivity, and a location on the top of the cortical hierarchy collectively strongly suggest that the mouse prefrontal module has a prominent role in feedback and holds both distributed and integrated information processing. These findings align with the theories on what the mammalian PFC is and does.

Our research

Using large-scale Neuropixels recordings in head-fixed mice we are mapping neuronal and network signatures across the layers and subregions of the suggested prefrontal module in a series of tasks engaging distinct brain states and cognitive processes. Our ultimate goal is to characterize neuronal and network activities that define the functional features of the mouse PFC. We have a specific interest in the circuit functions of inhibition and GABA-ergic interneurons, particularly the parvalbumin (PV)-expressing interneurons, and as in our previous work neuronal oscillations are included in our analyses.

Our work also involves long-term electrophysiological recordings of prefrontal activity in freely moving rats. For this we are employing tetrode recordings and optogenetic tagging of select prefrontal cell-types using microdrives and transgenic Cre rats developed in the lab. This enables probing of cognitive processing in conjunction with motoric processing in the PFC. 

The generation of complex behaviors depends on the integration of top-down signals from the PFC with action-selection programs in the striatum. How projections from different types of PFC output neurons target and control the striatal circuitry to support cognitive control and decision-making remains unknown. The PFC-Striatum pathway has been implicated as a primary site of circuit imbalance in cognitive and emotional disorders, notably autism spectrum disorder (ASD). In a large-scale project conducted in collaboration with the laboratory of Konstantinos Meletis, KI, we are characterizing PFCs interactions with the striatum, focusing on processing involved in decision-making. This work involves whole-brain circuit tracing, genetic targeting, and registration of neuronal activities using imaging and electrophysiology in behaving mice. 

Our behavior needs to dynamically change to adapt to ever-shifting environmental affordances – a process described as learning. An influential theory in both neuroscience and computer science known as reinforcement learning postulates that actions with a positive outcome (e.g., reward) are reinforced, while outcomes with a negative outcome (e.g., punishment) are devalued. The neuronal basis of effective and complex learning in brain-wide circuits remains to be established. One current proposal states that the PFC through its widespread and reciprocal connectivity directs the dynamic and long-term adaptions in synaptic transmission underlying learning processes. Using circuit tracing, 2-photon imaging and Neuropixels recordings in head-fixed mice we are investigating signatures of learning in the mouse PFC and their transmission to downstream sensory cortical areas. The involvement of dopamine signaling is also investigated. This project, as the PFC-striatum project, is part of our efforts to establish how information from the PFC is utilized in downstream brain regions.


Selected publications

Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed reinoic acid delivery
Alekseenko Z, Dias JM, Adler AF, Kozhevnikova M, van Lunteren JA, Nolbrant S, Jeggari A, Vasylovska S, Yoshitake T, Kehr J, Carlén M, Alexyenko A, Parmar M, Ericson J.
(2022), Nature Communications, 13:3046,

Reducing pericyte-derived scarring promotes recovery after spinal cord injury.
Dias DO, Kim H, Holl D, Solnestam BW, Lundeberg J, Carlén M, Göritz C*/Frisén J*.
(2018) Cell. Mar 22;173(1):153-165.e22.

An interactive framework for whole-brain maps at cellular resolution.
Fürth D, Vaissière T, Tzortzi O, Xuan Y, Lazaridis I, Spigolon G, Fisone G, Tomer R, Deissoerth K, Carlén M, Miller C, Rumbaugh G. Meletis K.
(2018) Nature Neuroscience. Jan;21(1):139-149

What constitutes the prefrontal cortex? Review
Carlén, M.
(2017) Science. Oct 27; 285(6362):478-82.

Prefrontal parvalbumin neurons in control of attention.
Kim H, Ährlund-Richter S, Wang X, Deisseroth K, Carlén M.
(2016) Cell. Jan 14:164(1-2):208-218

Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity.
Berndt A, Lee SY, Wietek J, Ramakrishnan C, Steinberg EE, Rashid AJ, Kim H, Park S, Santoro A, Frankland PW, Iyer SM, Pak S, Ährlund-Richter S, Delp SL, Malenka RC, Josselyn SA, Carlén M, Hegemann P, Deisseroth K.
(2016) Proc Natl Acad Sci U S A. Jan 26;113(4):822-9

The Diameter of Cortical Axons and Their Relevance to Neural Computing. Book chapter
Innocenti GM, Carlén M, Dyrby TB.
(2015) Axons and Brain Architecture. Dec 15. ISBN: 978-0-12-801393-9. Elsevier Inc.

Loss of cyclin-dependent kinase 5 from parvalbumin interneurons leads to hyperinhibition, decreased anxiety, and memory impairment.
Rudenko A, Seo J, Hu J, Su SC, de Anda FC, Durak o, Ericsson m, Carlén M, Tsai L-H.
(2015) Journal of Neuroscience. Feb 11;35(6):2372-83.

A whole-brain atlas of inputs to serotonergic neurons of the dorsal and median raphe nuclei.
Pollak Dorocic I, Fürth D, Xuan Y, Johansson Y, Pozzi L, Silberberg G, Carlén M, Meletis K.
(2014) Neuron. Aug 6;83(3):663-78.

Mice lacking NMDA receptors in parvalbumin neurons display normal depression-related behavior and response to antidepressant action of NMDAR antagonists.
Pozzi L, Dorocic IP, Wang X, Carlén M, Meletis K.
(2014) PLoS One. Jan 16;9(1):e83879.

Target selectivity of feedforward inhibition by striatal fast-spiking interneurons.
Szydlowski SN, Pollak Dorocic I, Planert H, Carlén M, Meletis K*/Silberberg G*.
(2013) Journal of Neuroscience. Jan 23;33(4):1678-83.

A critical role for NMDA receptors in parvalbumin interneurons for gamma rhythm induction and behavior.
Carlén M*/Meletis K*, Siegle J, Cardin J, Futai K, Vierling-Claasen D, Ruhlmann C, Jones S, Deisseroth K, Sheng M, Moore C, Tsai LH.
(2012) Molecular Psychiatry. May; 17(5)537-48

Optogenetic dissection of cortical information processing – shining light on schizophrenia. Review
Wang X, Carlén M.
(2012) Brain Research. Oct 2; 1476: 31-7. 

Chronically implanted hyperdrive for cortical recording and optogenetic control in behaving mice.
Siegle JH, Carlén M, Meletis K, Tsai LH, Moore CI, Ritt J.
(2011) Conf Proc IEEE Eng Med Biol Soc.:7529-32.

Efficient reprogramming of adult neural stem cells to monocytes by ectopic expression of a single gene.
Forsberg M*/Carlén M*, Meletis K, Yeung MS, Barnabé-Heider F, Persson MA, Aarum J, Frisén J.
(2010) Proc Natl Acad Sci U S A. Aug 17;107(33):14657-61.

Targeted optogenetic stimulation and recording of neurons in vivo using cell-type-specific expression of Channelrhodopsin-2.
Cardin JA*/Carlén M*, Meletis K, Knoblich U, Zhang F, Deisseroth K, Tsai LH, Moore C.
(2010) Nature Protocols. Jan 21 5(2):247-254

Neocortical Interneurons: From Diversity, Strength. Review
Moore CI, Carlén M, Knoblich U, Cardin J.
(2010) Cell. Jul 21; 142(2):184-88. 

Driving fast-spiking cells induces gamma rhythm and controls sensory responses.
Cardin JA*/Carlén M*, Meletis K, Knoblich U, Zhang F, Deisseroth K, Tsai LH, Moore C.
(2009) Nature. Jun 4;459(7247):663-7.

Forebrain ependymal cells are Notch-dependent and generate neuroblasts and astrocytes after stroke.
Carlén M, Meletis K, Göritz C, Darsalia V, Evergren E, Tanigaki K, Amendola M, Barnabé-Heider F, Yeung MSY, Naldini L, Honjo T, Kokaia Z, Shupliakov O, Cassidy RM, Lindvall O, Frisén J.
(2009) Nature Neuroscience. Mar;12(3):259-67.

Spinal Cord Injury Reveals Multilineage Differentiation of Ependymal Cells.
Meletis K*/Barnabé-Heider F*/Carlén M*, Evergren E, Tomilin N, Shupliakov O, Frisén J.
(2008) PLoS Biology. Jul 22;6(7)

Genetic visualization of neurogenesis.
Carlén M, Meletis K, Barnabé-Heider F, Frisén J.
(2006) Exp Cell Res. Sep 10;312(15):2851-9.

Evidence for neurogenesis in the adult mammalian substantia nigra.
Zhao M*/Momma S*, Delfani K, Carlén M, Cassidy RM, Johansson CB, Brismar H, Shupliakov O, Frisen J, Janson AM.
(2003) Proc Natl Acad Sci U S A. Jun 24;100(13): 7925-30.

Gene delivery to adult neural stem cells.
Falk A*/Holmström N*, Carlén M, Cassidy R, Lundberg C, Frisén J.
(2002) Exp Cell Res. Sep 10; 279(1): 34-9.

Functional integration of adult born neurons.
Carlén M*/Cassidy RM*, Brismar H, Smith GA, Enquist LW, Frisén J.
(2002) Current Biology. Apr 2, 12(7): 606-08

Staff and contact

Group leader

All members of the group

Contact and visit us

Contact information for the CarlenLab at the Department of Neuroscience, Karolinska Institutet.

Postal address

Karolinska Institutet
Department of Neuroscience
171 77 Stockholm

Visiting address (visitors, couriers, etc.)

Karolinska Institutet
Biomedicum, Quarter B4, Room B0477
Solnavägen 9
171 65 Solna

Delivery address (goods, parcels, etc.)

Tomtebodavägen 16
171 65 Solna

Map to Karolinska Institutet, Biomedicum, Solnavägen 9

Defended PhD students

Xinming Wang


28 April 2017: "Neuronal circuit mechanisms in decision-making"


Yang Xuan


27 April 2018: "Mapping brain circuits: anatomy, connectivity and function"

Sofie Ährlund-Richter


24 January 2020: "On the neuronal basis of cognition: cell-type specific circuitry and functions of the prefrontal cortex"

Nicolas Guyon


21 May 2021: "On the role of parvalbumin interneurons in neuronal network activity in the prefrontal cortex"

Josina van Lunteren


3 December 2021: "Inhibition in cognition: neurophysiology and connectivity of GABAergic interneurons in the prefrontal cortex"


Members of the CarlenLab walking on the beach.
CarlenLab team. Photo: CarlenLab.

Visiting researchers

  • Cleiton Lopez Aguiar, PhD, University of São Paolo, Brazil
  • Leonardo Rakauskas Zacharias, University of São Paolo, Brazil


  • Charlotte Alme, PhD
  • Anna Paula Crestani, PhD
  • Ziauddin Darokhan, PhD
  • Martin Hägglund, PhD
  • Daniel Kaping, PhD
  • Åsa Konradsson-Geuken, PhD
  • Calvin Young, PhD

Research assistants

  • Linn Andréasson, 2023
  • Loran Heymans, 2023
  • Eleni Moysiadou, 2023
  • Sabine Gnodde, 2022
  • Angelo Guadagno, 2021
  • Cantin Ortiz, 2019
  • Fredrik Wernstål, 2019

Master / bachelor students


  • Eleni Moysiadou, Stockholm University
  • Loran Heymans, Stockholm University


  • Gabrielle Dolisie, ENS Lyon, France
  • Simon Mayer, Technical University of Munich, Germany
  • Mariam Shahata, KI, Sweden
  • Moritz Stingl, University of Heidelberg, Germany


  • Gregor Ehmer, Stockholm University, Sweden
  • Karyn Lewis, KI, Sweden
  • Ram Yahya, Stockhom University, Sweden


  • Laura Heezen, University of Utrecht, The Netherlands
  • Jana Immenschuh, Stockholm University, Sweden
  • Agnieszska Limiszewska, Stockholm University, Sweden
  • Hyunsoo Park, KI


  • Emily Cox, University of Calgary, Canada
  • Cantin Ortiz, Royal Institute of Technology (KTH), Sweden
  • Leonardo Rakauskas, University of São Paolo, Brazil
  • Yicheng Wu, KI, Sweden


  • Joseph Clerke, University of Glasgow, Scottland
  • Lovisa Franzén, Stockholm University, Sweden
  • Michal Miazga, University of Warsaw, Poland


  • Leonidas Georgiu, University of Glasgow, Scottland
  • Laura Heikkinen, KI, Sweden
  • Solmaz Yazdani, KI, Sweden


  • Charlotta Henningson, University of Edingburgh, Scotland


  • Marieke Oudelaar, KI, Sweden


  • Cilla Gottfries, KI, Sweden
  • John-Peter Vinnars, KI, Sweden
  • Chan Shi Yu, National University of Singapore, Singapore

Work with us

Marie Carlén in a telephone booth, reading a magazine. The telephone booth is a library filled with books.
Marie Carlén reading a magazine in a telephone booth. Photo: N/A

Work with us

We are always looking to extend our team!

If you are interested in joining the CarlenLab, please send an email to Marie Carlén at with a cover letter describing your education, experience, and expertise relevant to the lab’s research. Please also let us know what your career goals are and what you hope to achieve in the CarlenLab.

Name and full contact information for 2-3 references ready to submit reference letters upon request is also highly appreciated.

Applications at all levels are welcome!