User:Daniel Mietchen/Publications

Paratype of the centipede Eupolybothrus cavernicolus, a species described with its full transcriptome, micro CT and DNA barcoding, in addition to a morphological description.

Play media

The Asian Elephant Koshik mimicking human speech.

Magnetic resonance microscopy of an Epiblema scudderiana larva at different temperatures.

3D Magnetic resonance microscopy of a Belemnopsis guard.

3D MRI of a pathological Gonioteuthis quadrata - fracture of the rostrum

Below is a list of my publications in scholarly journals, sorted in reverse chronological order, along with links to Wikipedia articles on related subjects. The list is manually curated, so usually incomplete. A more complete list can be found at my Scholia profile.

See also my open-access pledge, my ORCID record, my Google Scholar profile as well as my contributions at Zenodo, arXiv or Nature Precedings and videos on Vimeo. For a biographical sketch, see here.

General keywords: Biophysics, Magnetic Resonance Imaging, Biodiversity, Cognitive evolution, Vocal learning, Palaeopathology, Cryobiology, Embryology, Open research, Academic publishing, Data publishing, Wikis, Markup

Specific keywords are given along with the individual articles

• Simms, Stephanie; Jones, Sarah; Mietchen, Daniel; Miksa, Tomasz (2017). "Machine-actionable data management plans (maDMPs)". Research Ideas and Outcomes. 3: e13086. doi:10.3897/rio.3.e13086.
  • data management plan, research data management, data discovery
• Littler, Katherine; Boon, Wee-Ming; Carson, Gail; Depoortere, Evelyn; Mathewson, Sophie; Mietchen, Daniel; Moorthy, Vasee S; O’Connor, Denise; Roth, Cathy; Segovia, Carlos (2017). "Progress in promoting data sharing in public health emergencies". Bulletin of the World Health Organization. 95 (4): 243–243. doi:10.2471/BLT.17.192096.
  • data sharing, public health emergency
• Finn Årup Nielsen; Mietchen, Daniel; Willighagen, Egon (2017). "Scholia and scientometrics with Wikidata". arXiv:1703.04222 [cs.DL].
  • Wikidata, LaTeX, bibliometrics, scientometrics, Python
• Penev, Lyubomir; Mietchen, Daniel; Chavan, Vishwas; Hagedorn, Gregor; Smith, Vincent; Shotton, David; Ó Tuama, Éamonn; Senderov, Viktor; Georgiev, Teodor; Stoev, Pavel; Groom, Quentin; Remsen, David; Edmunds, Scott (2017). "Strategies and guidelines for scholarly publishing of biodiversity data". Research Ideas and Outcomes. 3: e12431. doi:10.3897/rio.3.e12431.
  • data publishing, biodiversity data, biodiversity, open research data, open data, data repository, data citation
• Chodacki, John; Lemberger, Thomas; Lin, Jennifer; Martone, Maryann; Mietchen, Daniel; Polka, Jessica; Sever, Richard; Strasser, Carly (2017). "Technical aspects of preprint services in the life sciences: a workshop report". Research Ideas and Outcomes. 3: e11825. doi:10.3897/rio.3.e11825.
  • preprints, life sciences, science policy, ASAPbio
• Koureas, Dimitrios; Arvanitidis, Christos; Belbin, Lee; Berendsohn, Walter; Damgaard, Christian; Groom, Quentin; Güntsch, Anton; Hagedorn, Gregor; Hardisty, Alex; Hobern, Donald; Marcer, Arnald; Mietchen, Daniel; Morse, David; Obst, Matthias; Penev, Lyubomir; Pettersson, Lars; Sierra, Soraya; Smith, Vincent; Vos, Rutger (2016). "Community engagement: The 'last mile' challenge for European research e-infrastructures". Research Ideas and Outcomes. 2: e9933. doi:10.3897/rio.2.e9933.
  • Virtual Research Environment, data infrastructure, open science, Horizon 2020, science policy
• Welch, Lonnie; Brooksbank, Cath; Schwartz, Russell; Morgan, Sarah L.; Gaeta, Bruno; Kilpatrick, Alastair M.; Mietchen, Daniel; Moore, Benjamin L.; Mulder, Nicola; Pauley, Mark; Pearson, William; Radivojac, Predrag; Rosenberg, Naomi; Rosenwald, Anne; Rustici, Gabriella; Warnow, Tandy (2016). "Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee)". PLOS Computational Biology. 12 (5): e1004943. doi:10.1371/journal.pcbi.1004943. PMID 27175996.
  • computational biology, curriculum development
• Penev, Lyubomir; Egloff, Willi; Agosti, Donat; Patterson, David; Hoffmann, Anke; Mietchen, Daniel; Kishor, Puneet (2016). "Data Policy Recommendations for Biodiversity Data. EU BON Project Report". Research Ideas and Outcomes. 2: e8458. doi:10.3897/rio.2.e8458.
  • data sharing, biodiversity, science policy, Framework Programmes for Research and Technological Development
• Ekins, Sean; Mietchen, Daniel; Coffee, Megan; Stratton, Thomas; Freundlich, Joel; Freitas-Junior, Lucio; Muratov, Eugene; Siqueira-Neto, Jair; Williams, Antony; Andrade, Carolina (2016). "Open drug discovery for the Zika virus". F1000Research. 5: 150. doi:10.12688/f1000research.8013.1. PMC 4841202. PMID 27134728.
  • Zika virus, Zika fever, Zika virus outbreak (2015–present), drug discovery, open science, Dengue fever, Ebola virus
• Mietchen, Daniel; Hagedorn, Gregor; Willighagen, Egon; Rico, Mariano; Gómez-Pérez, Asunción; Aibar, Eduard; Rafes, Karima; Germain, Cécile; Dunning, Alastair; Pintscher, Lydia; Kinzler, Daniel (2015). "Enabling Open Science: Wikidata for Research (Wiki4R)". Research Ideas and Outcomes. 1: e7573. doi:10.3897/rio.1.e7573.
  • Wikidata, open research, open science, peer review, virtual research environment, research funding, Horizon 2020, citizen science

• Mietchen, Daniel; Mounce, Ross; Penev, Lyubomir (2015). "Publishing the research process". Research Ideas and Outcomes. 1: e7547. doi:10.3897/rio.1.e7547.
  • open research, open science, peer review, academic journal, research funding, collaborative writing, sustainable development

• Mietchen D, McEntyre J, Beck J, Maloney C; Force11 Data Citation Implementation Group (2015) Adapting JATS to support data citation. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). Available from: http://www.ncbi.nlm.nih.gov/books/NBK280240/
  • JATS, data citation, open data, PubMed Central

• Beck J, Chodacki J, Eaton A, Evans M, Gatti R, Gilbert J, Harrison M, Maloney C, Mietchen D, Mowlam T; JATS4R Working Group (2015) Improving the reusability of JATS. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). Available from: http://www.ncbi.nlm.nih.gov/books/NBK279901/
  • XML, JATS, PubMed Central, Open access, open licensing, Wikimedia Commons, equation, Open Access Media Importer
• Mietchen, D. (2014). "The Transformative Nature of Transparency in Research Funding". PLoS Biology. 12 (12): e1002027. doi:10.1371/journal.pbio.1002027. PMC 4280101. PMID 25549343.
  • research funding, open science, peer review
• Biserkov, J.; Vos, R.; Balech, B.; Beard, N.; Blissett, M.; Brenninkmeijer, C.; Van Dooren, T.; Eades, D.; Gosline, G.; Groom, Q.; Hamann, T.; Hettling, H.; Hoehndorf, R.; Holleman, A.; Hovenkamp, P.; Kelbert, P.; King, D.; Kirkup, D.; Lammers, Y.; Demeulemeester, T.; Mietchen, D.; Miller, J.; Mounce, R.; Nicolson, N.; Page, R.; Pawlik, A.; Pereira, S.; Penev, L.; Richards, K.; et al. (2014). "Enriched biodiversity data as a resource and service". Biodiversity Data Journal. 2: e1125. doi:10.3897/BDJ.2.e1125.
  • hackathon, biodiversity, taxonomy, ontologies
• Stoev, P.; Komerički, A.; Akkari, N.; Liu, S.; Zhou, X.; Weigand, A. M.; Hostens, J.; Hunter, C. I.; Edmunds, S. C.; Porco, D.; Zapparoli, M.; Georgiev, T.; Mietchen, D.; Roberts, D.; Faulwetter, S.; Smith, V.; Penev, L. (2013). "Eupolybothrus cavernicolus Komerički & Stoev sp. N. (Chilopoda: Lithobiomorpha: Lithobiidae): The first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data". Biodiversity Data Journal. 1: e1013. doi:10.3897/BDJ.1.e1013.
  • Eupolybothrus cavernicolus, taxonomy, data publishing, morphology, transcriptome, µCT, DNA barcoding, speleology
• Mietchen, D.; Maloney, C.; and Moskopp, N. D. (2013) Inconsistent XML as a Barrier to Reuse of Open Access Content. Journal Article Tag Suite Conference (JATS-Con) Proceedings 2013.
  • XML, JATS, PubMed Central, Open access, open licensing, Wikimedia Commons, media type, Open Access Media Importer
• Bateman, A.; Kelso, J.; Mietchen, D.; MacIntyre, G.; Di Domenico, T. S.; Abeel, T.; Logan, D. W.; Radivojac, P.; Rost, B. (2013). "ISCB Computational Biology Wikipedia Competition". PLOS Computational Biology. 9 (9): e1003242. doi:10.1371/journal.pcbi.1003242. PMC 3777890. PMID 24068913.
  • computational biology, Wikipedia, International Society for Computational Biology, WikiProject Computational Biology, ISCB competition announcement 2013
• Smith, V.; Georgiev, T.; Stoev, P.; Biserkov, J.; Miller, J.; Livermore, L.; Baker, E.; Mietchen, D.; Couvreur, T. L. P.; Mueller, G.; Dikow, T.; Helgen, K. M.; Frank, J. I.; Agosti, D.; Roberts, D.; Penev, L. (2013). "Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal". Biodiversity Data Journal. 1: e995. doi:10.3897/BDJ.1.e995.
  • biodiversity, open data, data publishing, academic publishing, open access, collaborative authoring, peer review
• Stoev, P.; Penev, L.; Akkari, N.; Koon-Bong Cheung, D.; Enghoff, H.; Brunke, A.; Souza, C. M.; Pape, T.; Mietchen, D.; Erwin, T. (2013). "Revolving images and multi-image keys open new horizons in descriptive taxonomy: ZooKeys working examples". ZooKeys. 328: 1. doi:10.3897/zookeys.328.6171.
  • taxonomy, identification keys, 3D imaging, Portable Document Format
• Schmidt, S.; Broad, G.; Stoev, P.; Mietchen, D.; Penev, L. (2013). "The move to open access and growth: Experience from Journal of Hymenoptera Research". Journal of Hymenoptera Research. 30: 1. doi:10.3897/JHR.30.4733.
  • open access journals, scholarly societies, hymenoptera
• Fitch WT, Mietchen D (2013) Convergence and deep homology in the evolution of spoken language. In: Bolhuis JJ, Everaert M, editors. Birdsong, speech, and language: exploring the evolution of mind and brain. Cambridge, MA: MIT Press. pp. 45–62.
  • vocal learning, speech, vocal production, vocal tract, deep homology, birdsong, FOXP2
• Stoeger, A. S.; Mietchen, D.; Oh, S.; De Silva, S.; Herbst, C. T.; Kwon, S.; Fitch, W.  T. (2012). "An Asian Elephant Imitates Human Speech". Current Biology. 22 (22): 2144. doi:10.1016/j.cub.2012.09.022. PMID 23122846.
  • vocal learning, speech, vocal production, vocal tract, Elephas maximus, Koshik, Batyr, proboscis
• Wodak, S. J.; Mietchen, D.; Collings, A. M.; Russell, R. B.; Bourne, P. E. (2012). "Topic Pages: PLoS Computational Biology Meets Wikipedia". PLoS Computational Biology. 8 (3): e1002446. doi:10.1371/journal.pcbi.1002446. PMC 3315447. PMID 22479174.
  • Computational biology, review articles, Wikipedia, open access, Creative Commons licenses
• Hagedorn, G.; Mietchen, D.; Morris, R.; Agosti, D.; Penev, L.; Berendsohn, W.; Hobern, D. (2011). "Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information". ZooKeys. 150 (150): 127–149. doi:10.3897/zookeys.150.2189. PMC 3234435. PMID 22207810.
  • Creative Commons licenses, non-commercial, biodiversity
• Daniel Mietchen, Gregor Hagedorn, Konrad U. Förstner, M. Fabiana Kubke, Claudia Koltzenburg, Mark Hahnel, Lyubomir Penev (2011). "Wikis in scholarly publishing". Information Services and Use. 31 (1–2): 53–59. doi:10.3233/ISU-2011-0621.CS1 maint: Multiple names: authors list (link)
  • wikis, science communication, scientific method, open research
• Mietchen, D. (2011). "Peer reviews: Make them public". Nature. 473 (7348): 452. doi:10.1038/473452b.
  • peer review, public peer review, open peer review
• Penev, L.; Hagedorn, G.; Mietchen, D.; Georgiev, T.; Stoev, P.; Sautter, G.; Agosti, D.; Plank, A.; Balke, M. (2011). "Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID". ZooKeys. 90 (90): 1–12. doi:10.3897/zookeys.90.1369. PMC 3084489. PMID 21594104.
  • wikis, version control, biodiversity
• Ziegler, A.; Mietchen, D.; Faber, C.; Von Hausen, W.; Schöbel, C.; Sellerer, M.; Ziegler, A. (2011). "Effectively incorporating selected multimedia content into medical publications". BMC Medicine. 9: 17. doi:10.1186/1741-7015-9-17. PMC 3040697. PMID 21329532.
  • multimedia, academic publishing, Portable Document Format, supplementary materials, brain morphometry, Doppler ultrasound, sleep apnoea,
• Mietchen, D.; Gaser, C. (2009). "Computational morphometry for detecting changes in brain structure due to development, aging, learning, disease and evolution". Frontiers in Neuroinformatics. 3. doi:10.3389/neuro.11.025.2009.
  • brain morphometry, brain evolution, brain development, brain disease, brain aging
• Mietchen, D.; Manz, B.; Volke, F.; Storey, K. (2008). Sinclair, Brent (ed.). "In Vivo Assessment of Cold Adaptation in Insect Larvae by Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy". PLoS ONE. 3 (12): e3826. doi:10.1371/journal.pone.0003826. PMC 2586655. PMID 19057644.
  • Magnetic resonance microscopy, chemical-shift imaging, cold hardiness, Epiblema scudderiana, Eurosta solidaginis, Solidago, supercooling, glycerol, sorbitol
• Mietchen, D.; Aberhan, M.; Manz, B.; Hampe, O.; Mohr, B.; Neumann, C.; Volke, F. (2008). "Three-dimensional Magnetic Resonance Imaging of fossils across taxa". Biogeosciences. 5: 25. doi:10.5194/bg-5-25-2008.
  • Magnetic resonance microscopy, permineralization, diagenesis, biomineralization, crystal water, Magic angle spinning, Atocetus, Gonioteuthis, Belemnitella, Araucaria, Pararaucaria patagonica, Isselicrinus buchii
• Koelsch, S.; Remppis, A.; Sammler, D.; Jentschke, S.; Mietchen, D.; Fritz, T.; Bonnemeier, H.; Siebel, W. A. (2007). "A cardiac signature of emotionality". European Journal of Neuroscience. 26 (11): 3328–3338. doi:10.1111/j.1460-9568.2007.05889.x. PMID 18028117.
  • emotion, personality, ECG
• Koelsch, S.; Jentschke, S.; Sammler, D.; Mietchen, D. (2007). "Untangling syntactic and sensory processing: An ERP study of music perception". Psychophysiology. 44 (3): 476–490. doi:10.1111/j.1469-8986.2007.00517.x. PMID 17433099.
  • music perception, ERP, musical syntax, auditory perception, auditory system, auditory processing, sensory information,
• Lee, S. C.; Mietchen, D.; Cho, J. H.; Kim, Y. S.; Kim, C.; Hong, K. S.; Lee, C.; Kang, D.; Lee, W.; Cheong, C. (2007). "In vivo magnetic resonance microscopy of differentiation in Xenopus laevis embryos from the first cleavage onwards". Differentiation. 75 (1): 84–92. doi:10.1111/j.1432-0436.2006.00114.x. PMID 17244024.
  • Magnetic resonance microscopy, embryonic development, cell division, fate map, gastrulation, oocyte, Xenopus laevis
• Lee, S. C.; Cho, J. H.; Mietchen, D.; Kim, Y. S.; Hong, K. S.; Lee, C.; Kang, D.; Park, K. D.; Choi, B. S.; Cheong, C. (2006). "Subcellular in Vivo 1H MR Spectroscopy of Xenopus laevis Oocytes". Biophysical Journal. 90 (5): 1797–1803. doi:10.1529/biophysj.105.073502. PMC 1367328. PMID 16361348.
  • Magnetic resonance spectroscopy, localized spectroscopy, Berenil, oocyte, Xenopus laevis
• Müller, W. E. G.; Kaluzhnaya, O. V.; Belikov, S. I.; Rothenberger, M.; Schröder, H. C.; Reiber, A.; Kaandorp, J. A.; Manz, B.; Mietchen, D.; Volke, F. (2006). "Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis". Journal of Structural Biology. 153 (1): 31–41. doi:10.1016/j.jsb.2005.09.008. PMID 16364658.
  • Magnetic resonance microscopy, biomineralization, Lubomirskia baicalensis
• Mietchen, D.; Jakobi, J. R.; Richter, H. P. (2005). "Cortex reorganization of Xenopus laevis eggs in strong static magnetic fields". BioMagnetic Research and Technology. 3: 2. doi:10.1186/1477-044X-3-2. PMC 1326199. PMID 16351729.
  • Magnetic field, gastrulation, oocyte, Xenopus laevis
• Mainguy, G.; Motamedi, M. R.; Mietchen, D. (2005). "Peer Review—The Newcomers' Perspective". PLoS Biology. 3 (9): e326. doi:10.1371/journal.pbio.0030326. PMC 1201308. PMID 16149851.
  • peer review, single-blind peer review, double-blind peer review, researchers
• Mietchen, D.; Keupp, H.; Manz, B.; Volke, F. (2005). "Non-invasive diagnostics in fossils - Magnetic Resonance Imaging of pathological belemnites". Biogeosciences. 2 (2): 133. doi:10.5194/bg-2-133-2005.
  • Magnetic resonance microscopy, palaeopathology, Gonioteuthis quadrata, Neoclavibelus subclavatus, Hibolithes jaculoides, biomineralization
• Vella, F.; Mietchen, D.; Gabaldón, T.; Eurodoc, C. (2004). "Perceptions about postdocs". EMBO Reports. 5 (12): 1104. doi:10.1038/sj.embor.7400304. PMC 1299198. PMID 15577920.
  • postdoc, researchers, Torsten Wiesel, Eurodoc
• Urani, A.; Tan, R.; Rubele, R.; Mietchen, D. (2004). "Scientists & Societies: Giving young European students a voice". Nature. 427 (6972): 378. doi:10.1038/nj6972-378b.
  • researchers, science policy, Eurodoc, European Research Area
• Mietchen, D.; Schnelle, T.; Müller, T.; Hagedorn, R.; Fuhr, G. N. (2002). "Automated dielectric single cell spectroscopy - temperature dependence of electrorotation". Journal of Physics D: Applied Physics. 35 (11): 1258. doi:10.1088/0022-3727/35/11/324.
  • Dielectric spectroscopy, electrorotation, Chlamydomonas nivalis, automation