Publications

• Imam, F. T., Gillespie, T. H., Ziogas, I., Surles-Zeigler, M. C., Tappan, S., Ozyurt, B. I., Boline, J., de Bono, B., Grethe, J. S., & Martone, M. E. (2025).Developing a multiscale neural connectivity knowledgebase of the autonomic nervous system. Frontiers in Neuroinformatics, 19. doi: 10.3389/fninf.2025.1541184

• Pelot NA, Wang B, Marshall DP, Hussain MA, Musselman ED, Yu GJ, Dale J, Baumgart IW, Dardani D, Zamani PT, Chang Villacreses D, Wagenaar JB, Grill WM. Guidance for sharing computational models of neural stimulation: from project planning to publication. J Neural Eng. 2025 Mar 13;22(2). doi: 10.1088/1741-2552/adb997. PMID: 39993327.

• Fasse, A., Newton, T., Liang, L., Agbor, U., Rowland,R., Kuster, N., Gaunt, R., Pirondini, E., and Neufeld, E. A Novel CNN-Based Image Segmentation Pipeline for Individualized Feline Spinal Cord Stimulation Modeling, Journal of Neural Engineering, 21(3):036032, June 2024, doi: 10.1088/1741-2552/ad4e6b

• Bizanti A, Zhang Y, Toledo Z, Bendowski KT, Harden SW, Mistareehi A, Chen J, Gozal D, Heal M, Christie R, Hunter PJ, Paton JFR, Cheng ZJ. Chronic intermittent hypoxia remodels catecholaminergic nerve innervation in mouse atria. J Physiol. 2024 Jan;602(1):49-71. doi: 10.1113/JP284961. Epub 2023 Dec 29.

• Cruz-Almeida, Y., Mehta, B., Haelterman, N. A., Johnson, A. J., Heiting, C., Ernberg, M., ... & RE-JOIN Consortium Investigators. (2024). Clinical and biobehavioral phenotypic assessments and data harmonization for the RE-JOIN research consortium: Recommendations for common data element selection. Neurobiology of Pain, 16, doi: 100163.10.1016/j.ynpai.2024.100163.

• Goldblum, Z., Xu, Z., Shi, H., Orzechowski, P., Spence, J., Davis, K. A., ... & Wagenaar, J. (2024). Pennsieve: A Collaborative Platform for Translational Neuroscience and Beyond. arXiv preprint arXiv:2409.10509.

• Marroquin et al., (2024). SODA: Software to Support the Curation and Sharing of FAIR Autonomic Nervous System Data. Journal of Open Source Software, 9(100), 6140, doi: 10.21105/joss.06140.

• Martone, M. E. (2024). The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR. Frontiers in Neuroinformatics, 17, 1276407.doi: 10.3389/fninf.2023.1276407.

• Ma J, Nguyen D, Madas J, Bizanti A, Mistareehi A, Kwiat AM, Chen J, Lin M, Christie R, Hunter P, Heal M, Baldwin S, Tappan S, Furness JB, Powley TL, Cheng ZJ. Organization and morphology of calcitonin gene-related peptide-immunoreactive axons in the whole mouse stomach. J Comp Neurol. 2023 Nov;531(16):1608-1632. doi: 10.1002/cne.25519. Epub 2023 Sep 11.

• Sullivan, A.E., Tappan, S.J., Angstman, P.J. et al. A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling. Neuroinform 20, 221–240 (2022). doi: /10.1007/s12021-021-09530-x.

• Surles-Zeigler, M. C., Sincomb, T., Gillespie, T. H., de Bono, B., Bresnahan, J., Mawe, G. M., Grethe, J. S., Tappan, S., Heal, M., and Martone, M. E. (2022). Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Front. Neuroinform. 0, 80. doi: 10.3389/fninf.2022.819198.

• Kokash N, de Bono B. Knowledge representation for multi-scale physiology route modeling. Front Neuroinform. 2021;15: 560050. doi: 10.3389/fninf.2021.560050.

• Leung C, Robbins S, Moss A, Heal M, Osanlouy M, Christie R, Farahani N, Monteith C, Chen J, Hunter P, Tappan S, Vadigepalli R, Cheng ZJ, Schwaber JS. 3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system. iScience. 2021 Jul 19;24(7):102795. doi: 10.1016/j.isci.2021.102795.

• Osanlouy, M., Bandrowski, A., Bono, B. de, Brooks, D., Cassarà, A.M., Christie, R., Ebrahimi, N., Gillespie, T., Grethe, J.S., Guercio, L.A., et al. (2021). The SPARC DRC: Building a resource for the autonomic nervous system community. Frontiers in Physiology 0, 929. doi: 10.3389/fphys.2021.693735.

• Achanta S, Gorky J, Leung C, Moss A, Robbins S, Eisenman L, Chen J, Tappan S, Heal M, Farahani N, Huffman T, England S, Cheng ZJ, Vadigepalli R, Schwaber JS. A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System. iScience. 2020 Jun 26;23(6):101140. doi: 10.1016/j.isci.2020.101140. Epub 2020 May 26. PMID: 32460006; PMCID: PMC7327996.

• Lloyd, B., Farcito, S., Cassara, A., Zhuang, K., Neufeld, E., & Kuster, N. (2020). SPARC: Development of Human and Rodent Neuro‐Functionalized Computational Anatomical Models with Detailed Mapping of Peripheral Nervous System. The FASEB Journal, 34(S1), 1-1. doi: 10.1096/fasebj.2020.34.s1.07492.

• Neufeld, E., Chavannes, N., Zhuang, K. Z., Cassara, A., Lloyd, B., Crespo-Valero, P., ... & Kuster, N. (2020). SPARC’s Open Online Simulation Platform for Computational Modeling of the ANS’s Physiological Role and its Modulation by Electroceutical Devices: o2S2PARC. The FASEB journal, 34(S1), 1-1. doi: 10.1096/fasebj.2020.34.s1.07491.

• Neufeld, E., Lloyd, B., Schneider, B., Kainz, W., & Kuster, N. (2018). Functionalized anatomical models for computational life sciences. Frontiers in physiology, 9, 1594. doi: 10.3389/fphys.2018.01594.

Codeathon papers:

• Shahidi N, Athavale O, Munarko Y et al. A tutorial hub for realising the potential of tools within the SPARC ecosystem [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:45 (https://doi.org/10.12688/f1000research.138059.1)

• Ben Aribi H, Ding M and Kiran A. Gene expression data visualization tool on the o²S²PARC platform [version 2; peer review: 2 approved]. F1000Research 2023, 11:1267 (https://doi.org/10.12688/f1000research.126840.2)

• Soundarajan S, Kuruppu S, Singh A et al. SPARClink: an interactive tool to visualize the impact of the SPARC program [version 1; peer review: 2 approved, 1 approved with reservations]. F1000Research 2022, 11:124 (https://doi.org/10.12688/f1000research.75071.1)

• Shahidi N, Lin X, Munarko Y et al. AQUA: an Advanced QUery Architecture for the SPARC Portal [version 1; peer review: 1 approved with reservations, 1 not approved]. F1000Research 2021, 10:930 (https://doi.org/10.12688/f1000research.73018.1)

White papers:

• Neuron Phenotype white paper

Gillespie, T.H., Tripathy, S., Sy, M.F., Martone, M.E., and Hill, S.L. (2020). The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. BioRxiv 2020.09.01.278879. https://doi.org/10.1101/2020.09.01.278879

• SDS whitepaper

Bandrowski, A., Grethe, J.S., Pilko, A., Gillespie, T., Pine, G., Patel, B., Surles-Zeigler, M., and Martone, M.E. (2021). SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data. BioRxiv 2021.02.10.430563. https://doi.org/10.1101/2021.02.10.430563

Zenodo entities:

• SCKAN Curation manual

Ziogas, I., Imam, F., Gillespie, T., Tappan, S., Boline, J., de Bono, B., & Martone, M. E. (2025). SPARC Connectivity Knowledge base of the Autonomic Nervous System (SCKAN) Curation Manual. Zenodo. https://doi.org/10.5281/zenodo.14774195

• RE-JOIN metadata standard

Ziogas, I., Maryann E, M., & RE-JOIN: Restoring Joint Health and Function to Reduce Pain Consortium. (2025). RE-JOIN Minimal Metadata Standards (MMS), Data Dictionary, Data Templates, and Protocol Guidelines. Zenodo. https://doi.org/10.5281/zenodo.14725464

• The SPARC Minimal Information Standard (MIS) (Version 1)

Gillespie, T. H., de Bono, B., Boline, J., & Martone, M. E. (2021). The SPARC Minimal Information Standard (MIS) (Version 1). Zenodo. https://doi.org/10.5281/zenodo.5348190

• SCKAN release Tom Gillespie, Bernard de Bono, Monique Surles-Zeigler, Natallia Kokash, Fahim Imam, Ziogas, I., Susan Tappan, Jyl Boline, Jeffrey Grethe, & Maryann Martone. (2024). SPARC Connectivity Knowledge base of the Autonomic Nervous System (2024-09-21) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14042929

• SPARC Minimum Microscopy Image metadata Tappan, S., & Martone, M. (2021). SPARC Optical Microscopy Imaging Data and Imaging Metadata Standard (1.0). Zenodo. https://doi.org/10.5281/zenodo.5347993

• Terms from SPARC Term Request Pipeline SPARC K-Core. (2021). Terms from the SPARC Term Request Pipeline (Oct 2019 - Aug 2021) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5703661

Interviews:

“SPARC Data and Resource Center Aims to Accelerate Research with Open Science”