2010. Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae. Nassonova E, Smirnov A, Fahrni J, Pawlowski J. Protist, 161 (1) :102-115.
2006. Tempo and mode of spliceosomal intron evolution in actin of foraminifera. Flakowski J, Bolivar I, Fahrni J, Pawlowski J. J. Mol. Evol., 63 (1) : 30-41.
2005. Actin phylogeny of foraminifera. Flakowski J, Bolivar I, Fahrni J, Pawlowski J. The Journal of Foraminiferal Research, 35 (2) : 93-102.
2004. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, Mylnikov AP, Aleshin VV, Petrov NB, Pawlowski J. Proc. Natl. Acad. Sci. U.S.A., 101 (21) : 8066-8071. Cover image: The heliozoan Actinosphaerium eichhornii. Photograph courtesy of José F. Fahrni.
2003. Phylogeny of lobose amoebae based on actin and small‐subunit ribosomal RNA genes.Fahrni JF, Bolivar I, Berney C, Nasson
2001. SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited. Bolivar I, Fahrni JF, Smirnov A, Pawlowski J. Molecular Biology and Evolution, 18 (12) : 2306-2314.
1999. Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer. Pawlowski J, Bolivar I, Fahrni JF, de Vargas C, Bowser SS. Journal of Eukaryotic Microbiology, 46 (6) : 612-617.
1999. Naked foraminiferans revealed. Pawlowski J, Bolivar I, Fahrni J, de Vargas C, Bowser SS. Nature, 399 : 27-27.
1995. Identification of actins in foraminifera: Phylogenetic perspectives. Fahrni JF, Pawlowski J. European Journal of Protistology, 31 (29) : 161-166.
1985. Morphogenesis in the heterotrich ciliate Climacostomum virens : II. Oral development during regeneration. Fahrni JF. J. Protozool., 32 : 460-473.
1977. Contribution à la connaissance de Spirochona gemmipara Stein (Cilié Chonotriche). Morphologie, ultrastructure, reproduction asexuée et cycle vital. Fahrni JF. Thèse de doctorat. Faculté des Sciences. Université de Lausanne. (PhD dissertation. Faculty of Sciences. Lausanne University)