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.

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.

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.

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.

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.