Peer-reviewed journal articles

2018 Buttigieg P.L., Fadeev E., Bienhold C., Hehemann L., *Offre P., Boetius A. (2018) Marine microbes in 4D – using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Current Opinion in Microbiology 43: 169–185 doi:10.1016/j.mib.2018.01.015
  Chafee M., Fernàndez-Guerra A., Buttigieg P.L., Gerdts G., Eren A.M., Teeling H., Amann R.I. (2018) Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME Journal 12, 237–252. doi:10.1038/ismej.2017.165
2017 Stec K.F., Caputi L., Buttigieg P.L., D'Alelio D., Ibarbalz F.M., Sullivan M.B., Chaffron S., Bowler C., d'Alcala' M.R., Iudicone D. (2017) Modeling plankton interactions in the meta-omics era. Are we ready? Marine Genomics 32: 1-17. doi:10.1016/j.margen.2017.02.006
2016 Schnetzer J., Kopf A., Bietz M. J., Buttigieg P. L., Fernandez-Guerra A., Pop Ristova P., Glöckner F. O., Kottmann R. (2016) MyOSD 2014: Evaluating oceanographic measurements contributed by citizen scientists in support of Ocean Sampling Day. Journal of Microbiology & Biology Education. 17(1), 163.
  Pafilis E., Buttigieg P. L., Ferrel B.l, Pereira E., Schnetzer J., Arvanitidis C., Jensen L. J. (2016) EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database.
  Koureas D, Hardisty A, Vos R, Agosti D, Arvanitidis C, Bogatencov P, Buttigieg P.L., et al. (2016) Unifying European Biodiversity Informatics (BioUnify). Research Ideas and Outcomes 2: e7787.
  ten Hoopen P., Amid C., Buttigieg P. L., Pafilis E., et al. (2016) Value, but high costs in post-deposition data curation. Database. bav126.
  Fernández-Méndez M., Turk-Kubo K. A., Rapp J. Z., Buttigieg P. L., Krumpen T., Zehr J. P., Boetius A. (2016) Diazotroph diversity in the sea ice, melt ponds and water column of the Central Arctic Ocean. Frontiers in Aquatic Microbiology 7:1884

Buttigieg P.L., Pafilis E., Lewis S.E., Schildhauer M.P., Walls R.L., Mungall C.J. (2016) The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. Journal of Biomedical Semantics 7 (1), 57.


Thessen A. E., Bunker D. E., Buttigieg P. L., et al. (2015) Emerging semantics to link phenotypes and environment. PeerJ. 3:e1470

  Buttigieg PL and Ramette A. (2015) Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (Hausgarten, Fram Strait). Front. Microbiol. 5: 660.

Buttigieg PL and Ramette A. (2014) A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. FEMS Microbiology Ecology, 90: 543–550.


Ramette A and Buttigieg PL. (2014) The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data. Microbiol. 5:601.

  Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, et al. (2014) Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE. 9(3): e89606.

Walls R.L., Guralnick R., Deck J., Buntzman A., Buttigieg P.L., et al. (2014) Meeting report: advancing practical applications of biodiversity ontologies. Stand Genomic Sci. 9:17


Wörmer L., Elvert M., Fuchser J., Lipp J.S., Buttigieg P.L., Zabel M. and Hinrichs K.-U. (2014) Ultra-high-resolution paleoenvironmental records via direct laser-based analysis of lipid biomarkers in sediment core samples. Proc Natl Acad Sci. 111: 15669-15674.

  Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, et al. (2014) BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semant. 5:5.
2013 Buttigieg PL, Morrison N, Smith B,Mungall CJ, Lewis SE, the ENVO Consortium (2013) The environment ontology: contextualising biological and biomedical entities. J Biomed Semant. 4(43).
  Deck J, Barker K, Beaman R, Buttigieg PL, Dröge G, et al. (2013) Clarifying Concepts and Terms in Biodiversity Informatics. Stand Genomic Sci. 8(2): 352–359.
  Buttigieg PL, Hankeln W, Kostadinov I, Kottmann, R., Yilmaz, P., Duhaime MB, Glöckner FO (2013) Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes. PLoS ONE. 8(3): e50869.
2011 Hankeln W, Wendel NJ, Gerken J, Waldmann J, Buttigieg PL, Kostadinov I, Kottmann R, Yilmaz P, Glöckner FO (2011) CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data. PLoS ONE, 6(9): e24797.
  Kostadinov I, Kottmann R, Ramette A, Waldmann J, Buttigieg PL, Glöckner FO (2011) Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. Microb Inform Exp. 1: 9.
  Yilmaz P, Kottmann R, Field D, et al. (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol.29(5): 415–420.
2010 Buttigieg PL (2010). Perspectives on presentation and pedagogy in aid of bioinformatics education. Brief Bioinform. 11(6): 587–597.
  Hankeln W, Buttigieg PL, Fink D, Kottmann R, Yilmaz P, Glöckner FO(2010) MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. BMC Bioinformatics. 11: 358.
  Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldemann J, Glöckner FO(2010) integrated database resource for marine ecological genomics. Nucleic Acids Res. 38 (Database issue): D391–395.
2007 Büth H, Buttigieg PL, Ostafe R, Rehders M, Dannenmann SR, Schaschke N, Stark HJ, Boukamp P, Brix K(2007) Cathepsin B is essential for regeneration of scratch-wounded normal human epidermal keratinocytes. Eur J Cell Biol. 86(11-12): 747–761.


Textbook chapters

2012 Zhurina D, Srivastava A, Weingart H, Buttigieg PL, Ullrich M. (2008). Regulation of the Levansucrase Genes from Pseudomonas syringae pv. glycinea at the Level of Transcription. In M. Fatmi, A. Collmer, N. S. Iacobellis, J. W. Mansfield, J. Murillo, N. W. Schaad, & M. Ullrich (Eds.), Pseudomonas syringae Pathovars and Related Pathogens – Identification, Epidemiology and Genomics (pp. 265–69). Dordrecht: Springer Netherlands.


Presentations and posters

2014 Buttigieg PL (2014) Meaningfully mobilising genomic information with environmental descriptors. Presented at: Phenotype RCN. Biosphere 2, AZ, USA.
  Buttigieg PL (2014) An Introduction to the Environment Ontology. Presented at: The Biocollections Ontology / Population and Community Ontology Workshop. Tucson AZ, USA.
2012 Buttigieg PL (2012) Introducing the Environment Ontology: A community tool for semantically controlled environmental description. Presented at: NBDC/DBCLS BioHackathon 2012. Toyama, Japan.
  Buttigieg PL (2012) An Introduction to the Environment Ontology. Presented at: From Signals to Environmentally Tagged Sequences (Workshop). Heraklion, Greece.
2011 Buttigieg PL, Kottmann R, Pommier T, Glöckner FO (2011). Exploring niche specialisation in marine microbes by context-enabled comparative genomics. Presented at: BioSystematics 2011. Berlin.
2010 Hankeln W, Buttigieg PL, Kostadinov I, Kottmann R, Yilmaz P, Duhaime MB, Glöckner FO (2010) Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function. In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (pp. 478–80). Niagara Falls.
  Buttigieg PL (2010) Mobilising genomic data: ontology-enabled comparative genomics. Presented at: Locating Biology: The Development and Application of an Environment Ontology. Dagstuhl, Germany.
2009 Buttigieg PL, Kottmann R, Pommier T, Glöckner FO (2009). Investigating environmental signatures in genomic data: the value of structured habitat descriptors in comparative analysis. In ISMB/ECCB SIG: Metagenomics, Metadata & Meta-analysis. Stockholm.
2007 Zhurina D, Srivastava A, Weingart H, Buttigieg PL, Ullrich M (2007). Regulation of the levansucrase genes from Pseudomonas syringae pv. glycinea at the level of transcription. In Association for General and Applied Microbiology (VAAM) annual conference. Osnabrück.


Conference papers / extended abstracts


Buttigieg PL, Walls RL, Jensen M, Mungall CJ. Environmental semantics for sustainable development in an interconnected biosphere. Seventh International Conference on Biomedical Ontology (ICBO). Corvallis, Oregon, USA: 1-4, August.


Devare M, Aubert C, Laporte MA, Valette L, Arnaud E, Buttigieg PL. Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics. Seventh International Conference on Biomedical Ontology (ICBO). Corvallis, Oregon, USA: 1-4, August.


Griffiths E, Dooley D, Buttigieg PL, Hoehndorf R, Brinkman F, Hsiao W. FoodON: A Global Farm-to-Fork Food Ontology. Seventh International Conference on Biomedical Ontology (ICBO). Corvallis, Oregon, USA: 1-4, August.


Other publications


Buttigieg PLA brief encounter with ontology in the context of environmental monitoring. Environment Under Review: United Nations Environment Programme Document Repository.


UNEP with contributions from the SDG Interface Ontology task group. A Common Approach for developing SDG integrated indicators. In collaboration with United Nations Environment Programme.


UNEP with contributions from the SDG Interface Ontology task group. Clarifying terms in the SDGs: representing the meaning behind the terminology. In collaboration with United Nations Environment Programme. Circulated at the 2nd Meeting of the Inter-Agency Expert Group on Sustainable Development Goal Indicators, working on behalf of the United Nations Statistical Department.


UNEP et al. Design and development of integrated indicators for the Sustainable Development Goals Report. Report on the Senior Expert Meeting, Gland, Switzerland: December 3-5, 2014. In collaboration with United Nations Environment Programme.


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