2003

• Helgen, K.M. 2003. Major mammalian clades: A review under consideration of molecular and palaeontological evidence. Mammalian Biology 68(1): 1–15. DOI: 10.1078/1616-5047-1610057 Reference page. 

• Helgen, K.M. 2003. A review of the rodent fauna of Seram, Moluccas, with the description of a new subspecies of mosaic-tailed rat, Melomys rufescens paveli. Journal of Zoology 261(2): 165–172. DOI: 10.1017/S0952836903004035 Reference page. 

• Helgen, K.M. & Flannery, T.F. 2003. Taxonomy and historical distribution of the wallaby genus Lagostrophus. Australian Journal of Zoology 51(3): 199–212. DOI: 10.1071/ZO02078 Full article (PDF) via ResearchGate Reference page. 

• Helgen, K.M. & Wilson, D.E. 2003. Taxonomic status and conservation relevance of the raccoons (Procyon spp.) of the West Indies. Journal of Zoology 259(1): 69–76. DOI: 10.1017/S0952836902002972 Reference page. 

2004

• Helgen, K.M. & Flannery, T.F. 2004. A new species of bandicoot, Microperoryctes aplini, from western New Guinea Journal of Zoology 264(2): 117–124. DOI: 10.1017/S0952836904005667 Reference page. 

• Helgen, K.M. & Flannery, T.F. 2004. Notes on the phalangerid marsupial genus Spilocuscus, with description of a new species from Papua. Journal of Mammalogy 85(5): 825–833. DOI: 10.1644/BER-110 Reference page. 

2005

• Helgen, K.M. 2005. A new species of murid rodent (genus Mayermys) from south-eastern New Guinea. Mammalian Biology 70(1): 61–67. DOI: 10.1078/1616-5047-00176 Reference page. 

• Helgen, K.M. 2005. The amphibious murines of New Guinea (Rodentia, Muridae): The generic status of Baiyankamys and description of a new species of Hydromys. Zootaxa 913: 1–20. Abstract & excerpt. Reference page. 

• Helgen, K.M. 2005. Systematics of the Pacific monkey-faced bats (Chiroptera: Pteropodidae), with a new species of Pteralopex and a new Fijian genus. Systematics and Biodiversity 3(4): 433–453. DOI: 10.1017/S1477200005001702 Reference page. 

2007

• Helgen, K.M. 2007. A taxonomic and geographic overview of the mammal fauna of Papua. pp. 689–749 in Marshall, A.J. & Beehler, B.M. (eds.). The ecology of Papua. Ecology of Indonesia. Part One. Periplus Editions: Singapore. 784 pp. ISBN 9781462906796 Reference page. 

2008

• Helgen, K.M., Lim, N.T-L. & Helgen, L.E. 2008. The hog-badger is not an edentate: systematics and evolution of the genus Arctonyx (Mammalia: Mustelidae). Zoological journal of the Linnean Society 154(2): 353–385. DOI: 10.1111/j.1096-3642.2008.00416.x Full article (PDF) Reference page. 

• Musser, G.G., Helgen, K.M. & Lunde, D.P. 2008. Systematic review of New Guinea Leptomys (Muridae: Murinae) with descriptions of two new species. American Museum Novitates 3624: 1–60. DOI: 10.1206/587.1 handle Reference page. 

• Helgen, K.M., Maldonado, J.E., Wilson, D.E. & Buckner, S.D. 2008. Molecular confirmation of the origin and invasive status of West Indian raccoons. Journal of Mammalogy 89(2): 282–291. DOI: 10.1644/07-MAMM-A-155R.1 Reference page. 

2009

• Helgen, K.M. & Helgen, L.E. 2009. Chapter 8. Biodiversity and biogeography of the moss-mice of New Guinea: a taxonomic revision of Pseudohydromys (Muridae: Murinae). Pp. 230–313 in Voss, R.S. & Carleton, M.D. (eds.). Systematic mammalogy: contributions in honor of Guy G. Musser. Bulletin of the American Museum of Natural History 331: 450 pp. DOI: 10.1206/582-8.1 handle. Reference page. 

2010

• Helgen, K.M., Leary, T. & Aplin, K.P. 2010. A review of Microhydromys (Rodentia: Murinae), with description of a new species from Southern New Guinea. American Museum Novitates 3676: 1–22. DOI: 10.1206/632.1 handle. Reference page. 

2013

• Helgen, K.M., Pinto, C.M., Kays, R., Helgen, L.E., Tsuchiya, M.T.N., Quinn, A., Wilson, D.E. & Maldonado, J.E. 2013. Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito. ZooKeys 324: 1–83. DOI: 10.3897/zookeys.324.5827 Reference page. 

• Fabre, P.-H., Pagès, M., Musser, G.G., Fitriana, Y.S., Fjeldså, J., Jennings, A., Jønsson, K., Kennedy, J., Michaux, J., Semiadi, G., Supriatna, N., Helgen, K.M. 2013. A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics. Zoological Journal of the Linnean Society 169(2): 408–447. DOI: 10.1111/zoj.12061 Reference page. 

2014

• Scheel, D.-M., Slater, G.J., Kolokotronis, S.-O., Potter, C.W., Rotstein, D.S., Tsangaras, K., Greenwood, A.D. & Helgen, K.M. 2014. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409: 1–33. DOI: 10.3897/zookeys.409.6244 . Reference page. 

2015

• Gutiérrez, E., Maldonado, J., Radosavljevic, A. & Molinari, J., Patterson, B., Martínez-C, J., Rutter, A., Hawkins, M. & Garcia, F. & Helgen, K. 2015. The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela. PLoS ONE 10(6): e0129113. DOI: 10.1371/journal.pone.0129113 Reference page. 

2016

• Hawkins, M.T.R., Helgen, K.M., Maldonado, J.E., Rockwood, L.L., Tsuchiya, M.T.N. & Leonard, J.A. 2016. Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae). Molecular Phylogenetics and Evolution 94(part B): 752–764. DOI: 10.1016/j.ympev.2015.10.023 Reference page. 

• Hawkins, M.T.R., Leonard, J.A., Helgen, K.M., McDonough, M.M., Rockwood, L.L. & Maldonado, J.E. 2016. Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. BMC Evolutionary Biology 16: 80. DOI: 10.1186/s12862-016-0650-z Reference page. 

2017

• Moratelli, R., Wilson, D.E., Novaes, R.L.M., Helgen, K.M. & Gutiérrez, E.E. 2017. Caribbean Myotis (Chiroptera, Vespertilionidae), with description of a new species from Trinidad and Tobago. Journal of Mammalogy 98(4): 994–1008. DOI: 10.1093/jmammal/gyx062 Reference page. 

• Gutiérrez, E.E., Helgen, K.M., McDonough, M.M., Bauer, F., Hawkins, M.T.R., Escobedo-Morales, L.A., Patterson, B.D. & Maldonado, J.E. 2017. A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87–131. DOI: 10.3897/zookeys.697.15124 Reference page. 

• Jackson, S.M., Groves, C.P., Fleming, P.J.S., Aplin, K.P., Eldridge, M.D.B., Gonzalez, A. & Helgen, K.M. 2017. The Wayward Dog: Is the Australian native dog or Dingo a distinct species? Zootaxa 4317(2): 201–224. DOI: 10.11646/zootaxa.4317.2.1 . Full article (PDF) Reference page. 

2018

• Fabre, P.-H., Reeve, A.H., Fitriana, Y.S., Aplin, K.P. & Helgen, K.M. 2018. A new species of Halmaheramys (Rodentia: Muridae) from Bisa and Obi Islands (North Maluku Province, Indonesia). Journal of Mammalogy 99(1): 187–208. DOI: 10.1093/jmammal/gyx160 Reference page.