Thomas H. A. Haverkamp

Postdoctoral Fellow

Background

Postdoc with a background in microbial ecology. He is interested and specialized on the analysis of microbial diversity using amplicon or whole genome shot-gun sequencing, and is especially involved in the bioinformatic analysis of such data, He uses these techniques to understand bacterial species diversity in very different environments ranging from hydrothermal vents, desert soils and the gut communities of marine fish.

At CEES Thomas is involved in several projects:

- Metagenomics of anthrax carcass sites in semi-arid soils. (Collaboration with FFI)
- Genomics of Bacillus cereus strains. (Collaboration with the Department of Pharmacy, UIO)
- Genomics of Thermosiphio genomes.
- Mobile elements in Thermotogales.
- Genomics of Neisseria species (with Prof JM Koomey )
- Microbial diversity of Cod gut communities

Peer Review Publications:

Trucchi E., Frajman B., Haverkamp T.H.A., Schönswetter P., Paun O. Genomic and metagenomic analyses reveal parallel ecological divergence in Heliosperma pusillum(Caryophyllaceae). New Phytologist (2017), DOI: 10.1111/nph.14722.

Nesbø C.L., Swithers K.S., Dahle H., Haverkamp.T.H.A., Birkeland N.K., Sokolova T., Kublanov I. and Zhaxybayeva, O.  Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. The ISME Journal (2015) 9, 1532–1542.

Neumann R.S., Kumar S., Haverkamp, T.H.A., Shalchian-Tabrizi K. BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data. BMC Bioinformatics (2014), 15: 128.

Haverkamp, T.H.A., Hammer, Ø., Jakobsen, K.S. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure. Plos ONE (2014) 9(1): e85990.

Haverkamp, T.H.A., Star, B., Jentof, S., Jakobsen, K.S. Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BMC Microbiology (2013) 13: 248.

Håvelsrud, O.E., Haverkamp, T.H.A., Kristensen, T., Jakobsen, K.S,. Rike, A.G. Metagenomics in CO2 monitoring. Energy Procedia (2013) 37: 4215-4233.

Frisli, T., Haverkamp, T.H.A., Jakobsen, K.S., Stenseth, N.C., Rudi, K. Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next generation sequence data. Journal of Applied Microbiology. (2013) 114: 141-151.

Håvelsrud, OE; Haverkamp, THA; Kristensen, T; Jakobsen, KS and Rike, AG. Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea. BMC microbiology (2012) 12, 203.

Logares, R; Haverkamp, THA; Kumar, S; Lanzén, A; Nederbragt, AJ; Quince, C and Kauserud, H. Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches. Journal of Microbiological Methods (2012) 91, 106-113.

Kotlar, HK;  Lewin, A; Johansen, J; Throne-Holst, M; Haverkamp, T; Markussen, S; Winnberg, A; Ringrose, P; Aakvik, T; Ryeng, E; Jakobsen, K; Drabløs F and Svein V. High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface. Environmental Microbiology Reports (2011) 3, 674-681.

Havelsrud, OE; Haverkamp, THA; Kristensen, TJakobsen, KS and Rike, AG. A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments. BMC microbiology (2011) 11, 211.

Haverkamp, THA; Schouten, D; Doeleman, M; Wollenzien, U; Huisman, J and Stal, LJ. Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea. The ISME Journal (2009) 3, 397–408.

Acinas, SG; Haverkamp, THA; Huisman, J and Stal, LJ.Phenotypic and genetic diversification of Pseudanabaena spp. (cyanobacteria). The ISME Journal (2009) 3, 31–46.

Haverkamp, T; Acinas, SG; Doeleman, M; Stomp, M; Huisman, J; Stal, LJ. Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons. Environmental Microbiology (2008) 10, 174–188.

Stomp, M; Huisman, J; Vörös, L; Pick, FR; Laamanen, M; Haverkamp, T and Stal, LJ. Colourful coexistence of red and green picocyanobacteria in lakes and seas. Ecology Letters (2007) 10, 290–298.

Ketting, RF; Haverkamp, THA; van Luenen, HGAM and Plasterk, RHA. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell (1999) 99,133-141.

Genome Announcements:

Mercier, C; Lossouarn, J; Haverkamp, T; Bienvenu, N; Godfroy, A; Cueff-Gauchard, V; Geslin, C; Nesbo C. Draft genome sequences of two Marinitoga camini isolates producing bacterioviruses. Genome Announcements (2016) 4, e01261-16.

Valseth,K; Nesbø, CL; Easterday, WR; Turner, WC; Olsen, JS; Stenseth, NC and Haverkamp, THA. Draft genome sequences of two Bacillus anthracis strains from Etosha National Park, Namibia. Genome Announcements (2016) 4, e00861-16.

Haverkamp, THA; Tourasse, NJ; Nederbragt, AJ; Jakobsen, KS; Kolstø, AB and Økstad, OA. Draft genomes of clinical Bacillus cereus isolates AH725 and B06.009 closely related to reference strains ATCC 14579 and ATCC 10987.

Other Publications:

Herwijnen, R van; Janssen, PJCM; Haverkamp, THA and Poorter, LRM de. Handreiking voor de afleiding van indicatieve milieurisicogrenzen. [ Method for derivation of indicative environmental risk limits.] RIVM rapport 601782025 (2009)

Manuscripts in progress:

Valseth, K; Nesbø, CL; Easterday, WR; Turner, WC; Olsen, JS; Stenseth, NC, Haverkamp THA. Temporal dynamics in microbial soil communities at anthrax carcass sites. In revision.

Haverkamp, THA; Geslin, C; Lossouarn, J; Kublanov, I; Nesbø CL. Comparative genomics of Thermosipho lineages indicates genomic differences in habitat generalists and specialists. In revision.


Websites:
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The Microsized Mind

Tags: 454 sequencing, Microbiology, Microbial ecology, High-throughput sequencing, Genomics, Biogeochemistry, Bioinformatics, Comparative genomics, DNA sequence analysis, Environmental sampling, Microbial evolution, Molecular ecology, Pyrosequencing, Thermophiles, Marine sediments, Virus, Phage person:publications: Necessary property 'resource:username' is missing
Published May 26, 2011 9:57 PM - Last modified Aug. 28, 2017 2:49 PM