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2012
Vos RA, Balhoff JP, Caravas J, Holder MT, Lapp H, Maddison WP, Midford P, Priyam A, Sukumaran J, Xia X et al..  2012.  NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61(4):675-689.
2011
Sukumaran J, Holder MT.  2011.  Ginkgo: spatially-explicit simulator of complex phylogeographic histories. Molecular Ecology Resources. 11(2):364-369.
2010
Sukumaran J, Holder MT.  2010.  DendroPy: A Python library for phylogenetic computing. Bioinformatics. 26:1569-1571.
Matsui M, Tominaga A, Liu W, Khonsue W, Grismer LL, Diesmos AC, Das I, Sudin A, Yambun P, Yong H et al..  2010.  Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution. 54:561-570.
Holder MT, Sukumaran J, Brown RM.  2010.  Recent Developments in Bayesian Phylogenetics. Bayesian Modeling in Bioinformatics. :inpress.
2009
Wiens J, Sukumaran J, Pyron A, Brown RM.  2009.  Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae). Evolution. 63:1217–1231.
Sukumaran J, Linkem CW.  2009.  Choice of topology estimators in Bayesian phylogenetic analysis. Molecular Biology and Evolution. 26:1–3.
2008
Holder MT, Sukumaran J, Lewis PO.  2008.  A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology. 57:814-821.
2007
Das I, Yaakob N, Sukumaran J.  2007.  A new species of Microhyla (Anura: Microhylidae) from the Malay Peninsula. Hamadryad. 31:304–314.
2006
Sukumaran J, Yaakob N, Yong D.  2006.  The herpetofauna of the Southeast Pahang peat-swamp forests. Hamadryad. 30:75–91.
Yaakob N, Sukumaran J.  2006.  An inventory of the amphibians of Pasoh Forest Reserve, Negeri Sembilan, Peninsular Malaysia. Hamadryad. 30:102–107.
Brown RM, Richards S, Sukumaran J, Fougopoulos J.  2006.  A new morphologically cryptic species of forest frog (genus Platymantis) from New Britain Island, Bismarck Archipelago. Zootaxa. 1334:45–68.
Sukumaran J, Das I, Haas A.  2006.  A synopsis of bioacoustic studies of Anuran amphibians of Borneo. Herpetological Review. 37:288–293.
2005
Grismer L, Sukumaran J, Grismer J, Youmans T, Wood P, Johnson R.  2005.  Report on the herpetofauna from the Temengor Forest Reserve, Perak, West Malaysia. Hamadryad. 29:15–35.
2002
Sukumaran J.  2002.  The amphibian fauna of a forested area in Temengor, Northern Peninsular Malaysia. Hamadryad. 27:1–10.