2012	Stubbins A, Niggemann J, Dittmar T (2012) Photo-lability of deep ocean dissolved black carbon. Biogeosciences 9: 1661-1670
2009	Lomstein BAa, Niggemann J, Jørgensen BB, Langerhuus AT (2009) Accumulation of prokaryotic remains during organic matter diagenesis in surface sediments off Peru. Limnology and Oceanography 54(4): 1139-1151
2007	Niggemann J, Ferdelman TG, Lomstein BAa, Kallmeyer J, Schubert CJ (2007) How depositional conditions control input, composition, and degradation of organic matter in sediments from the Chilean coastal upwelling region. Geochimica Cosmochimica Acta, 71(6): 1513-1527
2006	Niggemann J and Schubert CJ (2006) Fatty acid biogeochemistry in sediments from the Chilean coastal upwelling region: sources and diagenetic changes. Organic Geochemistry 37(5): 626-647
	Niggemann J and Schubert CJ (2006) Sources and fate of amino sugars in coastal Peruvian sediments. Geochimica Cosmochimica Acta 70(9): 2229-2237
	Lomstein BAa, Jørgensen BB, Schubert CJ, Niggemann J (2006) Amino acid biogeo- and stereochemistry in coastal Chilean sediments. Geochimica et Cosmochimica Acta 70(12): 2970-2989
2005	Niggemann J (2005) Composition and degradation of organic matter in sediments from the Peru-Chile upwelling region. PhD-thesis, University of Bremen, Germany. urn:nbn:de:gbv:46-diss000102428 (available online)
	Schubert CJ, Niggemann J, Klockgether G, Ferdelman TG (2005) Chlorin Index: A new parameter for organic matter freshness in sediments. Geochemistry, Geophysics, Geosystems 6: Q03005, doi:10.1029/2004GC000837
	Treude T, Niggemann J, Kallmeyer J, Wintersteller P, Schubert CJ, Boetius A, Jørgensen BB (2005) Anaerobic oxidation of methane and sulfate reduction along the Chilean continental margin. Geochimica et Cosmochimica Acta 69(11): 2767-2779