Publications

@article{Verzelli2024_editorial,

title = {Editorial overview: Computational neuroscience as a bridge between artificial intelligence, modeling and data},

author = {Pietro Verzelli and Tatjana Tchumatchenko and J Hellgren Kotaleski},

year  = {2024},

date = {2024-01-01},

journal = {Current Opinion in Neurobiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nikbakht2024_aversive,

title = {Efficient encoding of aversive location by CA3 long-range projections},

author = {N Nikbakht and M Pofahl and A Miguel-Lopez and F Kamali and Tatjana Tchumatchenko and H Beck},

doi = {10.1016/j.celrep.2024.113957},

year  = {2024},

date = {2024-01-01},

journal = {Cell Reports},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Squadrani2024_astrocytes,

title = {Astrocytes enhance plasticity response during reversal learning},

author = {Lorenzo Squadrani and Carlos Wert-Carvajal and Daniel Mueller-Komorowska and Kirsten Bohmbach and Christian Henneberger and Pietro Verzelli and Tatjana Tchumatchenko},

doi = {10.1038/s42003-024-06540-8},

year  = {2024},

date = {2024-01-01},

journal = {Communications Biology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chater2024_competitive,

title = {Competitive processes shape multi-synapse plasticity along dendritic segments},

author = {Thomas E. Chater and Maximilian F. Eggl and Yukiko Goda and Tatjana Tchumatchenko},

doi = {10.1038/s41467-024-51919-0},

year  = {2024},

date = {2024-01-01},

journal = {Nature Communications},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chung2023,

title = {Myomatrix arrays for high-definition muscle recording},

author = {Bryce Chung and Muneeb Zia and Kyle A Thomas and Jonathan A Michaels and Amanda Jacob and Andrea Pack and Matthew J Williams and Kailash Nagapudi and Lay Heng Teng and Eduardo Arrambide and Logan Ouellette and Nicole Oey and Rhuna Gibbs and Philip Anschutz and Jiaao Lu and Yu Wu and Mehrdad Kashefi and Tomomichi Oya and Rhonda Kersten and Alice C Mosberger and Sean O'Connell and Runming Wang and Hugo Marques and Ana Rita Mendes and Constanze Lenschow and Gayathri Kondakath and Jeong Jun Kim and William Olson and Kiara N Quinn and Pierce Perkins and Graziana Gatto and Ayesha Thanawalla and Susan Coltman and Taegyo Kim and Trevor Smith and Ben Binder-Markey and Martin Zaback and Christopher K Thompson and Simon Giszter and Abigail Person and Martyn Goulding and Eiman Azim and Nitish Thakor and Daniel O'Connor and Barry Trimmer and Susana Q Lima and Megan R Carey and Chethan Pandarinath and Rui M Costa and J Andrew Pruszynski and Muhannad Bakir and Samuel J Sober},

url = {https://www.biorxiv.org/content/10.1101/2023.02.21.529200v1 https://www.biorxiv.org/content/10.1101/2023.02.21.529200v1.abstract},

doi = {10.7554/elife.88551.3},

year  = {2023},

date = {2023-02-01},

journal = {eLife},

volume = {12},

pages = {2023.02.21.529200},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous system's actual motor output – the activation of muscle fibers by motor neurons – typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices (‘Myomatrix arrays') that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a ‘motor unit,' during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous system's motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and identifying pathologies of the motor system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hayashi2023,

title = {A spinal synergy of excitatory and inhibitory neurons coordinates ipsilateral body movements},

author = {Marito Hayashi and Miriam Gullo and Gokhan Senturk and Stefania Di Costanzo and Shinji C. Nagasaki and Ryoichiro Kageyama and Itaru Imayoshi and Martyn Goulding and Samuel L. Pfaff and Graziana Gatto},

url = {https://elifesciences.org/reviewed-preprints/89362},

doi = {10.7554/ELIFE.89362},

year  = {2023},

date = {2023-01-01},

journal = {eLife},

volume = {12},

publisher = {eLife Sciences Publications Limited},

abstract = {Innate and goal-directed movements require a high-degree of trunk and appendicular muscle coordination to preserve body stability while ensuring the correct execution of the motor action. The spinal neural circuits underlying motor execution and postural stability are finely modulated by propriospinal, sensory and descending feedback, yet how distinct spinal neuron populations cooperate to control body stability and limb coordination remains unclear. Here, we identified a spinal microcircuit composed of V2 lineage-derived excitatory (V2a) and inhibitory (V2b) neurons that together coordinate ipsilateral body movements during locomotion. Inactivation of the entire V2 neuron lineage does not impair intralimb coordination but destabilizes body balance and ipsilateral limb coupling, causing mice to adopt a compensatory festinating gait and be unable to execute skilled locomotor tasks. Taken together our data suggest that during locomotion the excitatory V2a and inhibitory V2b neurons act antagonistically to control intralimb coordination, and synergistically to coordinate forelimb and hindlimb movements. Thus, we suggest a new circuit architecture, by which neurons with distinct neurotransmitter identities employ a dual-mode of operation, exerting either synergistic or opposing functions to control different facets of the same motor behavior.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{arican2023mushroom,

title = {The mushroom body output encodes behavioral decision during sensory-motor transformation},

author = {Cansu Arican and Felix Johannes Schmitt and Wolfgang Rössler and Martin Fritz Strube-Bloss and Martin Paul Nawrot},

year  = {2023},

date = {2023-01-01},

journal = {Current Biology},

volume = {33},

number = {19},

pages = {4217–4224},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Eggl2023_linking,

title = {Linking spontaneous and stimulated spine dynamics},

author = {Maximilian F. Eggl and Janko Petkovic and Thomas E. Chater and Yukiko Goda and Tatjana Tchumatchenko},

doi = {10.1038/s42003-023-05303-1},

year  = {2023},

date = {2023-01-01},

journal = {Communications Biology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{morales2023ubiquitous,

title = {Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex},

author = {Aitor Morales-Gregorio and Alexander Meegen and Sacha J. Albada},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Cereb Cortex},

volume = {33},

number = {16},

pages = {9439–9449},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wagle2023_computational,

title = {Computational insights into mRNA and protein dynamics underlying synaptic plasticity rules},

author = {Surbhit Wagle and Nataliya Kraynyukova and Anne-Sophie Hafner and Tatjana Tchumatchenko},

doi = {10.1016/j.mcn.2023.103846},

year  = {2023},

date = {2023-01-01},

journal = {Molecular and Cellular Neuroscience},

volume = {125},

pages = {103846},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Timón2022How,

title = {How to incorporate biological insights into network models and why it matters},

author = {Laura Bernáez Timón and Pierre Ekelmans and Nataliya Kraynyukova and Tobias Rose and Laura Busse and Tatjana Tchumatchenko},

url = {https://doi.org/10.1113/JP282755},

doi = {10.1113/JP282755},

year  = {2022},

date = {2022-09-01},

journal = {The Journal of Physiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weiler2022Functional,

title = {Functional and structural features of L2/3 pyramidal cells continuously covary with pial depth in mouse visual cortex},

author = {Simon Weiler and Drago Guggiana Nilo and Tobias Bonhoeffer and Mark Hübener and Tobias Rose and Volker Scheuss},

url = {https://doi.org/10.1093/cercor/bhac303},

doi = {10.1093/cercor/bhac303},

year  = {2022},

date = {2022-08-01},

journal = {Cerebral Cortex},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weiler2022Orientation,

title = {Orientation and direction tuning align with dendritic morphology and spatial connectivity in mouse visual cortex},

author = {Simon Weiler and Drago Guggiana Nilo and Tobias Bonhoeffer and Mark Hübener and Tobias Rose and Volker Scheuss},

url = {https://doi.org/10.1016/j.cub.2022.02.048},

doi = {10.1016/j.cub.2022.02.048},

year  = {2022},

date = {2022-04-01},

journal = {Current Biology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Obenhaus2022Functional,

title = {Functional network topography of the medial entorhinal cortex},

author = {Horst A. Obenhaus and Weijian Zong and R. Irene Jacobsen and Tobias Rose and Flavio Donato and Liangyi Chen and Heping Cheng and Tobias Bonhoeffer and May-Britt Moser and Edvard I. Moser},

url = {https://doi.org/10.1073/pnas.2121655119},

doi = {10.1073/pnas.2121655119},

year  = {2022},

date = {2022-02-01},

journal = {Proceedings of the National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Senk22_e1010086,

title = {Connectivity Concepts in Neuronal Network Modeling},

author = {Johanna Senk and Birgit Kriener and Mikael Djurfeldt and Nicole Voges and Han-Jia Jiang and Lisa Schüttler and Gabriele Gramelsberger and Markus Diesmann and Hans E. Plesser and Sacha J. Albada},

doi = {10.1371/journal.pcbi.1010086},

year  = {2022},

date = {2022-01-01},

journal = {PLOS Comput Biol},

volume = {18},

number = {9},

pages = {e1010086},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WertCarvajal2022_dopamine,

title = {Dopamine and serotonin interplay for valence-based spatial learning},

author = {C Wert-Carvajal and Melissa Reneaux and Tatjana Tchumatchenko and Claudia Clopath},

year  = {2022},

date = {2022-01-01},

journal = {Cell Reports},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BernaezTimon2022_population,

title = {Synaptic plasticity controls the emergence of population-wide invariant representations in balanced network models},

author = {L Bernaez Timon and P Ekelmans and N Kraynyukova and S Konrad and A Nold and Tatjana Tchumatchenko},

year  = {2022},

date = {2022-01-01},

journal = {Physical Review Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kraynyukova2022_V1,

title = {In vivo extracellular recordings of thalamic and cortical visual responses reveal V1 connectivity rules},

author = {N Kraynyukova and S Renner and G Born and Y Bauer and M. A. Spacek and G Tushev and L Busse and Tatjana Tchumatchenko},

year  = {2022},

date = {2022-01-01},

journal = {Proceedings of the National Academy of Sciences (PNAS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Peirs2021,

title = {Mechanical Allodynia Circuitry in the Dorsal Horn Is Defined by the Nature of the Injury},

author = {Cedric Peirs and Sean Paul G. Williams and Xinyi Zhao and Cynthia M Arokiaraj and David W Ferreira and Myung Noh and Kelly M Smith and Priyabrata Halder and Kelly A Corrigan and Jeremy Y Gedeon and Suh Jin Lee and Graziana Gatto and David Chi and Sarah E Ross and Martyn Goulding and Rebecca P Seal},

url = {http://www.ncbi.nlm.nih.gov/pubmed/33181066},

doi = {10.1016/j.neuron.2020.10.027},

issn = {10974199},

year  = {2021},

date = {2021-11-01},

journal = {Neuron},

volume = {109},

number = {1},

pages = {73–90.e7},

publisher = {Elsevier},

abstract = {The spinal dorsal horn is a major site for the induction and maintenance of mechanical allodynia, but the circuitry that underlies this clinically important form of pain remains unclear. The studies presented here provide strong evidence that the neural circuits conveying mechanical allodynia in the dorsal horn differ by the nature of the injury. Calretinin (CR) neurons in lamina II inner convey mechanical allodynia induced by inflammatory injuries, while protein kinase C gamma (PKCγ) neurons at the lamina II/III border convey mechanical allodynia induced by neuropathic injuries. Cholecystokinin (CCK) neurons located deeper within the dorsal horn (laminae III–IV) are important for both types of injuries. Interestingly, the Maf+ subset of CCK neurons is composed of transient vesicular glutamate transporter 3 (tVGLUT3) neurons, which convey primarily dynamic allodynia. Identification of an etiology-based circuitry for mechanical allodynia in the dorsal horn has important implications for the mechanistic and clinical understanding of this condition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gatto2020,

title = {A Functional Topographic Map for Spinal Sensorimotor Reflexes},

author = {Graziana Gatto and Steeve Bourane and Xiangyu Ren and Stefania Di Costanzo and Peter K. Fenton and Priyabrata Halder and Rebecca P. Seal and Martyn D. Goulding},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627320307716},

doi = {10.1016/j.neuron.2020.10.003},

issn = {10974199},

year  = {2021},

date = {2021-11-01},

journal = {Neuron},

volume = {109},

number = {1},

pages = {91–104.e5},

publisher = {Elsevier},

abstract = {Cutaneous somatosensory modalities play pivotal roles in generating a wide range of sensorimotor behaviors, including protective and corrective reflexes that dynamically adapt ongoing movement and posture. How interneurons (INs) in the dorsal horn encode these modalities and transform them into stimulus-appropriate motor behaviors is not known. Here, we use an intersectional genetic approach to functionally assess the contribution that eight classes of dorsal excitatory INs make to sensorimotor reflex responses. We demonstrate that the dorsal horn is organized into spatially restricted excitatory modules composed of molecularly heterogeneous cell types. Laminae I/II INs drive chemical itch-induced scratching, laminae II/III INs generate paw withdrawal movements, and laminae III/IV INs modulate dynamic corrective reflexes. These data reveal a key principle in spinal somatosensory processing, namely, sensorimotor reflexes are driven by the differential spatial recruitment of excitatory neurons.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bauer2021Limited,

title = {Limited functional convergence of eye-specific inputs in the retinogeniculate pathway of the mouse},

author = {Joel Bauer and Simon Weiler and Martin H. P. Fernholz and David Laubender and Volker Scheuss and Mark Hübener and Tobias Bonhoeffer and Tobias Rose},

url = {https://doi.org/10.1016/j.neuron.2021.05.036},

doi = {10.1016/j.neuron.2021.05.036},

year  = {2021},

date = {2021-08-01},

journal = {Neuron},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rapp2020spiking,

title = {A spiking neural program for sensorimotor control during foraging in flying insects},

author = {Hannes Rapp and Martin Paul Nawrot},

year  = {2020},

date = {2020-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {117},

number = {45},

pages = {28412–28421},

publisher = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tchumatchenko2020_statistical,

title = {Statistical Laws of Protein Motion in Neuronal Dendritic Trees},

author = {F Sartori and Anne-Sophie Hafner and A Karimi and A Nold and Y Fonkeu and E. M. Schuman and Tatjana Tchumatchenko},

year  = {2020},

date = {2020-01-01},

journal = {Cell Reports},

volume = {33},

number = {7},

pages = {108391},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gatto2019,

title = {Neuronal diversity in the somatosensory system: bridging the gap between cell type and function},

author = {Graziana Gatto and Kelly Megan Smith and Sarah Elizabeth Ross and Martyn Goulding},

url = {http://www.ncbi.nlm.nih.gov/pubmed/30953870 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6583900},

doi = {10.1016/j.conb.2019.03.002},

issn = {18736882},

year  = {2019},

date = {2019-06-01},

journal = {Current Opinion in Neurobiology},

volume = {56},

pages = {167–174},

publisher = {Elsevier Ltd},

abstract = {A recent flurry of genetic studies in mice have provided key insights into how the somatosensory system is organized at a cellular level to encode itch, pain, temperature, and touch. These studies are largely predicated on the idea that functional cell types can be identified by their unique developmental provenance and gene expression profile. However, the extent to which gene expression profiles can be correlated with functional cell types and circuit organization remains an open question. In this review, we focus on recent progress in characterizing the sensory afferent and dorsal horn neuron cell types that process cutaneous somatosensory information and ongoing circuit studies that are beginning to bridge the divide between cell type and function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}