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A Digital Atlas to Characterize the Mouse Brain Transcriptome

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Morphological multiscale decomposition of connected regions with emphasis on cell clusters

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Radial symmetries based decomposition of cell clusters in binary and gray level images

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Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

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Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

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Uniformity, specificity and variability of corticocortical connectivity

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Reconstructing networks of pathways via significance analysis of their intersections

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Matching Spatial with Ontological Brain Regions using Java Tools for Visualization, Database Access, and Integrated Data Analysis

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Online workbenches for neural network connections

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An evaluation of the use of multidimensional scaling for understanding brain connectivity

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Integrating Databases and Expert Systems for the Analysis of Brain Structures: Connections, Similarities, and Homologies

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Causal localization of neural function: the Shapley value method

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Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualization, and comparison of spatial distribution data

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A Complex Network Approach to the Determination of Functional Groups in the Neural System of C. Elegans

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Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and Examples

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Mining Bridge and Brick Motifs From Complex Biological Networks for Functionally and Statistically Significant Discovery

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On the Decomposition of Cell Clusters

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Toward a workbench for rodent brain image data systems architecture and design

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Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data.

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Extracting Data Records from Unstructured Biomedical Full Text

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NeuroTerrain – a client-server system for browsing 3D biomedical image data sets

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Computational Intelligence in Medical Informatics

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LONI Visualization Environment

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Neuroanatomical Affiliation Visualization-Interface System

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BacGrid: simulations of bacteria using the grid

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Comparison of semi-automatic and automatic data acquisition methods for studying three-dimensional distributions of large neuronal populations and axonal plexuses

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Internet Image Viewer (iiV)

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Mesencephalic Human Neural Progenitor Cells Transplanted into the Adult Hemiparkinsonian Rat Striatum Lack Dopaminergic Differentiation but Improve Motor Behavior

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Optimal sparse coding of song in a size-constrained auditory system?

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The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data

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Parallelized segmentation of a serially sectioned whole human brain

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A first principles approach to differential expression in microarray data analysis

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Modelling the connectivity between terms in the neuroscience literature

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A hybrid approach to quantify lamination of the cerebral cortex

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The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content

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CoCoMac 2.0 and the future of tract-tracing databases

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A systematic review on the quantitative relationship between structural and functional network connectivity strength in mammalian brains

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Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON

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The connectome of the basal ganglia

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VisNEST — Interactive analysis of neural activity data

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Network models to enhance the translational impact of cross-species studies

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The Intrinsic Connectome of the Rat Amygdala

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Norepinephrine is a negative regulator of the adult periventricular neural stem cell niche

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Scalable Interactive Visualization for Connectomics

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Subthalamic nucleus deep brain stimulation induces sustained neurorestoration in the mesolimbic dopaminergic system in a Parkinson's disease model

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Brain-Wide Mapping of Axonal Connections: Workflow for Automated Detection and Spatial Analysis of Labeling in Microscopic Sections

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Building the Ferretome

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Pathological changes of brain oscillations following ischemic stroke

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2

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Subthalamic nucleus deep brain stimulation induces nigrostriatal dopaminergic plasticity in a stable rat model of Parkinson’s disease

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Towards Differential Connectomics with NeuroVIISAS

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Connectomes: from a sparsity of networks to large-scale databases

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Šanda, P., Hlinka, J., van den Berg, M., Škoch, A., Bazhenov, M., Keliris, G. A., & Krishnan, G. P. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012099 · Cited by 9 · see citing works

Olfactory Bulb D2/D3 Receptor Availability after Intrastriatal Botulinum Neurotoxin-A Injection in a Unilateral 6-OHDA Rat Model of Parkinson’s Disease

Alberts, T., Antipova, V., Holzmann, C., Hawlitschka, A., Schmitt, O., Kurth, J., Stenzel, J., Lindner, T., Krause, B. J., Wree, A., et al. (2022) · Toxins · doi:10.3390/toxins14020094 · Cited by 8 · see citing works

Changing Connectomes

Kaiser, M. (2020) · The MIT Press eBooks · doi:10.7551/mitpress/11980.001.0001 · Cited by 25 · see citing works

The Mind-Brain Relationship as a Mathematical Problem

Ascoli, G. A. (2013) · ISRN Neuroscience · doi:10.1155/2013/261364 · Cited by 7 · see citing works

Golgi: Interactive Online Brain Mapping

Brown, R. A., & Swanson, L. W. (2015) · Frontiers in Neuroinformatics · doi:10.3389/fninf.2015.00026 · Cited by 7 · see citing works

Direct comparisons of neural activity during placebo analgesia and nocebo hyperalgesia between humans and rats

Boorman, D. C., Crawford, L., Henderson, L. A., & Keay, K. A. (2025) · Communications Biology · doi:10.1038/s42003-025-07993-1 · Cited by 7 · see citing works

Modeling and simulation for prediction of multiple sclerosis progression

Prathapan, V., Eipert, P., Wigger, N., Kipp, M., Appali, R., & Schmitt, O. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108416 · Cited by 6 · see citing works

Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity

Schmitt, O., Eipert, P., Schwanke, S., Leßmann, F., Jennifer, M., Beier, J., Kadir, K., Karnitzki, A., Sellner, L., Klünker, A.-C., et al. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby048 · Cited by 6 · see citing works

Reaction-diffusion models in weighted and directed connectomes

Schmitt, O., Nitzsche, C., Eipert, P., Prathapan, V., Hütt, M. ‐., & Hilgetag, C. C. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010507 · Cited by 6 · see citing works

Distribution of Cleaved SNAP-25 in the Rat Brain, following Unilateral Injection of Botulinum Neurotoxin-A into the Striatum

Schümann, F., Schmitt, O., Wree, A., & Hawlitschka, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021685 · Cited by 5 · see citing works

Photonics meets connectomics: case of diffuse, long-range horizontal projections in rat cortex

Johnson, B. A., & Frostig, R. D. (2015) · Neurophotonics · doi:10.1117/1.nph.2.4.041403 · Cited by 5 · see citing works

Relationships and representations of brain structures, connectivity, dynamics and functions

Schmitt, O. (2025) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2025.111332 · Cited by 4 · see citing works

Connectome-based prediction of functional impairment in experimental stroke models

Schmitt, O., Eipert, P., Wang, Y., Kanoke, A., Rabiller, G., & Liu, J. (2024) · PLoS ONE · doi:10.1371/journal.pone.0310743 · Cited by 4 · see citing works

Subthalamic nucleus deep brain stimulation does not alter growth factor expression in a rat model of stable dopaminergic deficiency

Statz, M., Schleuter, F., Weber, H., Kober, M., Plocksties, F. V., Timmermann, D., Storch, A., & Fauser, M. (2023) · Neuroscience Letters · doi:10.1016/j.neulet.2023.137459 · Cited by 4 · see citing works

The brainstem connectome database

Schmitt, O., Eipert, P., Ruß, F., Beier, J., Kadir, K., & Horn, A. K. E. (2022) · Scientific Data · doi:10.1038/s41597-022-01219-3 · Cited by 4 · see citing works

Basal Ganglia

Wree, A., & Schmitt, O. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-397025-1.00215-3 · Cited by 3 · see citing works

neuroVIISAS-based construction of a stereotactic rhesus monkey brain atlas for connectome research

Kohnen, K., Eipert, P., Budde, L., & Schmitt, O. (2025) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2025.110656 · Cited by 1 · see citing works

MRI-based Measurement of Structural and Functional Connectivity in Health and Disease

Sinke, M. R. T. (2020) · doi:10.33540/77

Connecting the dots: Structural and functional connections in healthy and diseased brain

Straathof, M. (2021) · doi:10.33540/877

Subthalamic nucleus deep brain stimulation induces functional deficits in norepinephrinergic neurotransmission in a Parkinson’s disease model

Statz, M., Weber, H., Weis, F., Kober, M., Bathel, H., Plocksties, F. V., van Rienen, U., Timmermann, D., Storch, A., & Fauser, M. (2024) · Brain Research · doi:10.1016/j.brainres.2024.149128

Critical Regions and Connections Form Pathways and Clusters in the Mouse Brain

Hotama, C. F., Kralik, J. D., & Jeong, J. (2025) · European Journal of Neuroscience · doi:10.1111/ejn.16673

Proteomic Characterization of Spinal Cord Myelin in the Mouse

Schmitt, O., Kaddatz, H., Mikkat, S., Kipp, M., Schümann, A., & Joost, S. (2025) · ASN NEURO · doi:10.1080/17590914.2025.2595945

The Cerebellar Connectome

Schmitt, O., Morawska, P., Prathapan, V., & Eipert, P. (2026) · The Cerebellum · doi:10.1007/s12311-026-02042-x

Deciphering nervous systems wiring: Tract-tracing and complementary methods

Schmitt, O., Eipert, P., Maestro, R. T., Bellmann, M., Haase, S., Morawska, P., & Prathapan, V. (2026) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2026.106943

FAIRsharing record for: Brainstem Connectome

FAIRsharing Team, & Schmitt, O. (2018) · FAIRsharing.org · doi:10.25504/fairsharing.hd7sxq

neuroVIISAS: The Integration of Atlases and Connectomes for Modeling

Eipert, P., & Oliver, S. (2013) · Frontiers in Neuroinformatics · doi:10.3389/conf.fninf.2013.09.00016

Integration neuronaler Modalitäten für Konnektomanalysen und populationsbasierte Simulationen

Eipert, P. (2015) · Ros Dok Rostocker Dokumentenserver (Universitätsbibliothek Rostock) · doi:10.18453/rosdok_id00001629

The connectome of the rat central nervous system in neuroVIISAS

Schmitz, K. (2011) · Frontiers in Neuroinformatics · doi:10.3389/conf.fninf.2011.08.00025

Towards an Explorative Visual Analysis of Cortical Neuronal Network Simulations

Kuhlen, T., & Hentschel, B. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-12084-3_14 · Cited by 6 · see citing works

The Virtual Brain: a simulator of primate brain network dynamics

Sanz‐Leon, P., Knock, S. A., Woodman, M., Domide, L., Mersmann, J., McIntosh, A. R., & Jirsa, V. (2013) · Frontiers in Neuroinformatics · doi:10.3389/fninf.2013.00010 · Cited by 516 · see citing works