Beatriz Díez, Johan A. A. Nylander, Karolina Ininbergs, Christopher L. Dupont, Andrew E. Allen, Shibu Yooseph, Douglas B. Rusch, Birgitta Bergman. 2016. Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community - Structure, Potential Function and Evolution. PLoS ONE 11.

John Larsson, Johan A. A. Nylander, Birgitta Bergman. 2011. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. BMC Evolutionary Biology 11: 187.

Sven Buerki, Felix Forest, Nadir Alvarez, Johan A. A. Nylander, Nils Arrigo, Isabel Sanmartin. 2011. An evaluation of new parsimony-based versus parametric inference methods in biogeography - a case study using the globally distributed plant family Sapindaceae. Journal of Biogeography 38: 531-550.

Liang Ran, John Larsson, Theoden Vigil-Stenman, Johan A. A. Nylander, Karolina Ininbergs, Wei-Wen Zheng, Alla Lapidus, Stephen Lowry, Robert Haselkorn, Birgitta Bergman. 2010. Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium. PLoS ONE 5.

Knud A. Jonsson, Rauri C. K. Bowie, Johan A. A. Nylander, Les Christidis, Janette A. Norman, Jon Fjeldsa. 2010. Biogeographical history of cuckoo-shrikes (Aves - Passeriformes): transoceanic colonization of Africa from Australo-Papua. Journal of Biogeography 37: 1767-1781.

Thomas R. Buckley, Dilini Attanayake, Johan A. A. Nylander, Sven Bradler. 2010. The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea). Systematic Entomology 35: 207-225.

A Antonelli, Johan Nylander, C Persson, I Sanmartín. 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution - evidence from the coffee family. Proceedings of the National Academy of Sciences of the United States of America 106: 9749-9754.

Magnus Lundberg, Mats Töpel, Bente Eriksen, Johan Nylander, Torsten Eriksson. 2009. Allopolyploidy in Fragariinae (Rosaceae) - Comparing four DNA sequence regions, with comments on classification. Molecular Phylogenetics and Evolution 51: 269-280.