ReproNim

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ReproNim Publications

  1. Esteban O, Ciric R, Finc K, Blair R, Markiewicz CJ, Moodie CA, Kent JD, Goncalves M, DuPre E, Gomez EP, Ye Z, Salo T, Valabregue R, Amlien IK, Liem F, Jacoby N, Stojic H, Cieslak M, Urchs S, Halchenko YO, Ghosh SS, De La Vega A, Yarkoni T, Wright J, Thompson WH, Poldrack RA, Gorgolewski KJ. (2020). Analysis of task-based functional mri data preprocessed with fmriprep. BioRxiv doi: 10.1101/694364. Accepted: Nature Protocols (in press).
     
  2. Botvinik-Nezer R, Holameister F, [...], Schonberg T. (2020 May 20). Variability in the analysis of a single neuroimaging dataset by many teams. Nature. doi: 10.1038/s41586-020-2314-9.
     
  3. Lin D, Crabtree J, Dillo I, Downs RR, Edmunds R, Giaretta D, De Giusti M, L’Hours H, Hugo W, Jenkyns R, Khodiyar V, Martone ME, Mokrane M, Navale V, Petters J, SIerman B, Sokolova M, Westbrook J. (2020 May 14). The TRUST Principles for Digital Repositories. Scientific data, 7(1):144. doi: 10.1038/s41597-020-0486-7. PubMed PMID: 32409645; PubMed Central PMCID:PMC7224370.
     
  4. Charles AS, Falk B, Turner N, Pereira TD, Tward D, Pedigo BD, Chung J, Burns R, Ghosh SS, Kebschull JM, Silversmith W, Vogelstein JT. (2020 Apr 13). Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics. Annual Rev Neurosci.doi: 10.1146/annurev-neuro-100119-110036. [Epub ahead of print] PubMed PMID:32283996.
     
  5. Siless V, Hubbard NA, Jones R, Wang J, Lo N, Bauer CCC, Goncalves M, Frosch I, Norton D, Vergara G, Conroy K, De Souza FV, Rosso IM, Wickham AH, Cosby EA, Pinaire M, Hirshfeld-Becker D, Pizzagalli DA, Henin A, Hofmann SG, Auerbach RP, Ghosh S, Gabrieli J, Whitfield-Gabrieli S, Yendiki A. (2020 Mar 19). Image acquisition and quality assurance in the Boston Adolescent Neuroimaging of Depression and Anxiety study.Neuroimage Clin. 26:102242. doi: 10.1016/j.nicl.2020.102242. [Epub ahead of print] PubMed PMID:32339824; PubMed Central PMCID: PMC7184183.
     
  6. Hubbard NA, Siless V, Frosch IR, Goncalves M, Lo N, Wang J, Bauer CCC, Conroy K, Cosby E, Hay A, Jones R, Pinaire M, Vaz De Souza F, Vergara G, Ghosh S, Henin A, Hirshfeld-Becker DR, Hofmann SG, Rosso IM, Auerbach RP, Pizzagalli DA, Yendiki A, Gabrieli JDE, Whitfield-Gabrieli S. (2020 Mar 12). Neuroimage Clin. 7:102240. doi:10.1016/j.nicl.2020.102240. [Epub ahead of print] PubMed PMID: 32361633; PubMed Central PMCID: PMC7199015.
     
  7. Sitek KR, Gulban OF, Calabrese E, Johnson GA, Lage-Castellanos A, Moerel M, Ghosh SS, De Martino F. (2019 Aug 1). Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T. eLife, 8. doi: 10.7554/eLife.48932
     
  8. Poline JB. (2019). From data sharing to data publishing [version 2; peer review: 2 approved, 1 approved with reservations]. MNI open research, 2. doi: 10.12688/mniopenres.12772.2
     
  9. Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. (2019 Apr 10). A data citation roadmap for scholarly data repositories. Scientific data, 6(1), 28. doi: 10.1038/s41597-019-0031-8
     
  10. Keshavan A, Poline JB. (2019). From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research. Frontiers in neuroinformatics, 13, 3. doi: 10.3389/fninf.2019.00003
     
  11. Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. (2019). Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. Frontiers in neuroinformatics, 13, 1. doi: 10.3389/fninf.2019.00001
     
  12. Guell X, Goncalves M, Kaczmarzyk JR, Gabrieli JDE, Schmahmann JD, Ghosh SS. (2019). LittleBrain: A gradient-based tool for the topographical interpretation of cerebellar neuroimaging findings. PloS one, 14(1), e0210028. doi: 10.1371/journal.pone.0210028
     
  13. Ozyurt IB, Grethe JS. (2018 Jan 1). Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database : the journal of biological databases and curation, 2018. doi: 10.1093/database/bay130
     
  14. Millman KJ, Brett M, Barnowski R, Poline JB. (2018). Teaching Computational Reproducibility for Neuroimaging. Frontiers in neuroscience, 12, 727. doi: 10.3389/fnins.2018.00727
     
  15. Guell X, Schmahmann JD, Gabrieli J, Ghosh SS. (2018 Aug 14). Functional gradients of the cerebellum. eLife, 7. doi: 10.7554/eLife.36652
     
  16. Solo V, Poline JB, Lindquist MA, Simpson SL, Bowman FD, Chung MK, Cassidy B. (2018 Jul). Connectivity in fMRI: Blind Spots and Breakthroughs. IEEE transactions on medical imaging, 37(7), 1537-1550. doi: 10.1109/TMI.2018.2831261
     
  17. Kim YM, Poline JB, Dumas G. (2018 Jul 1). Experimenting with reproducibility: a case study of robustness in bioinformatics. GigaScience, 7(7). doi: 10.1093/gigascience/giy077
     
  18. Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. (2018 May 8). Uniform resolution of compact identifiers for biomedical data. Scientific data, 5, 180029. doi: 10.1038/sdata.2018.29
     
  19. Kennedy DN. (2018 Apr). Neuroimaging Neuroinformatics: Sample Size and Other Evolutionary Topics. Neuroinformatics, 16(2), 149-150. doi: 10.1007/s12021-018-9379-8
     
  20. Ghosh SS, Poline JB, Keator DB, Halchenko YO, Thomas AG, Kessler DA, Kennedy DN. (2017). A very simple, re-executable neuroimaging publication. F1000Research, 6, 124. doi: 10.12688/f1000research.10783.2
     
  21. Irimia A, Wei S, Lu N, Moore CM, Kennedy DN. (2017 Jul). Mobile Monitoring of Traumatic Brain Injury in Older Adults: Challenges and Opportunities. Neuroinformatics, 15(3), 227-230. doi: 10.1007/s12021-017-9335-z
     
  22. Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L. (2017 Jun 6). DATS, the data tag suite to enable discoverability of datasets. Scientific data, 4, 170059. doi: 10.1038/sdata.2017.59
     
  23. Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline JB. (2017 May 25). Toward standard practices for sharing computer code and programs in neuroscience. Nature neuroscience, 20(6), 770-773. doi: 10.1038/nn.4550
     
  24. Kennedy DN. (2017 Apr). The Information Sharing Statement Grows Some Teeth. Neuroinformatics, 15(2), 113-114. doi: 10.1007/s12021-017-9331-3
     
  25. Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Chakravarty MM, Churchill NW, Cohen AL, Craddock RC, Devenyi GA, Eklund A, Esteban O, Flandin G, Ghosh SS, Guntupalli JS, Jenkinson M, Keshavan A, Kiar G, Liem F, Raamana PR, Raffelt D, Steele CJ, Quirion PO, Smith RE, Strother SC, Varoquaux G, Wang Y, Yarkoni T, Poldrack RA. (2017 Mar). BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS computational biology, 13(3), e1005209. doi: 10.1371/journal.pcbi.1005209
     
  26. Nichols TE, Das S, Eickhoff SB, Evans AC, Glatard T, Hanke M, Kriegeskorte N, Milham MP, Poldrack RA, Poline JB, Proal E, Thirion B, Van Essen DC, White T, Yeo BT. (2017 Feb 23). Best practices in data analysis and sharing in neuroimaging using MRI. Nature neuroscience, 20(3), 299-303. doi: 10.1038/nn.4500
     
  27. Huntenburg JM, Bazin PL, Goulas A, Tardif CL, Villringer A, Margulies DS. (2017 Feb 1). A Systematic Relationship Between Functional Connectivity and Intracortical Myelin in the Human Cerebral Cortex. Cerebral cortex (New York, N.Y. : 1991), 27(2), 981-997. doi: 10.1093/cercor/bhx030
     
  28. James EG, Leveille SG, Hausdorff JM, Travison T, Kennedy DN, Tucker KL, Al Snih S, Markides KS, Bean JF. (2017 Aug 1). Rhythmic Interlimb Coordination Impairments and the Risk for Developing Mobility Limitations. The journals of gerontology. Series A, Biological sciences and medical sciences, 72(8), 1143-1148. doi: 10.1093/gerona/glw236
     
  29. Maumet C, Auer T, Bowring A, Chen G, Das S, Flandin G, Ghosh S, Glatard T, Gorgolewski KJ, Helmer KG, Jenkinson M, Keator DB, Nichols BN, Poline JB, Reynolds R, Sochat V, Turner J, Nichols TE. (2016 Dec 6). Sharing brain mapping statistical results with the neuroimaging data model. Scientific data, 3, 160102. doi: 10.1038/sdata.2016.102
     
  30. Margulies DS, Ghosh SS, Goulas A, Falkiewicz M, Huntenburg JM, Langs G, Bezgin G, Eickhoff SB, Castellanos FX, Petrides M, Jefferies E, Smallwood J. (2016 Nov 1). Situating the default-mode network along a principal gradient of macroscale cortical organization. Proceedings of the National Academy of Sciences of the United States of America, 113(44), 12574-12579. doi: 10.1073/pnas.1608282113
     
  31. Honor LB, Haselgrove C, Frazier JA, Kennedy DN. (2016). Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution. Frontiers in neuroinformatics, 10, 34. doi: 10.3389/fninf.2016.00034
     
  32. Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline JB, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. (2016 Jun 21). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific data, 3, 160044. doi: 10.1038/sdata.2016.44
     
  33. Bandrowski AE, Martone ME. (2016 May 4). RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods. Neuron, 90(3), 434-6. doi: 10.1016/j.neuron.2016.04.030