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PhD Thesis, Pre-prints on bioRxiv and Book Chapters

Engelken, J (2010) Evolution of the extended LHC protein superfamily in photosynthesis. (University of Konstanz)  PhD Thesis.

Engelken, J., Altmeyer, M., & Franklin, R. (2014). The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer. Pre-print at

Mills, I., Dall’Olio, G.M., Burke, D.F., Engelken, J., et al. Principles for the post-GWAS functional characterisation of risk loci.  Online article.

Engelken J, Funk C, Adamska I.  The extended light-harvesting complex (LHC) protein superfamily: Classification and evolutionary dynamics. In: Advances in Photosynthesis and Respiration, vol 33, Chapter 11, pp 265-284. (2012)  Book Chapter.

Heddad M, Engelken J, Adamska I.  Light stress proteins in viruses, cyanobacteria and photosynthetic eukaryotes. In: Advances in Photosynthesis and Respiration, vol 34, Chapter 14, pp 299-317. (2012)  Book Chapter.

Peer-reviewed journal articles

* equal contribution
** corresponding author

Marc Pybus, Pierre Luisi, Giovanni M Dall’Olio, Manu Uzkudun, Hafid Laayouni, Jaume Bertranpetit, Johannes Engelken. Hierarchical Boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. 2015. Bioinformatics Aug 26. pii: btv493.

Johannes Engelken*, Elena Carnero-Montoro*, Marc Pybus, Glen K. Andrews, Carles Lalueza-Fox, David Comas, Israel Sekler, Marco de la Rasilla, Antonio Rosas, Mark Stoneking, Miguel A. Valverde, Rubén Vicente, Elena Bosch. Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) are Explained by Positive Selection in Sub-Saharan Africa. PLOS genetics 10(2): e1004128

Marc Pybus, Giovanni M Dall’Olio, Pierre Luisi, Manu Uzkudun, Angel Carreño-Torres, Pavlos Pavlidis, Hafid Laayouni, Jaume Bertranpetit**Johannes Engelken** . 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in humans. Nucleic Acids Research.42 (D1): D903-D909

Sabine Sturm*, Johannes Engelken*, Ansgar Gruber*, Sascha Vugrinec, Iwona Adamska, Peter G. Kroth and Johann Lavaud. A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids. BMC Evolutionary Biology 2013, 13:159.

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics. 2013 May 31;14:363.

Carnero-Montoro E, Bonet L, Engelken J, Bielig T, Martínez-Florensa M, Lozano F, Bosch E. Evolutionary and functional evidence for positive selection at the human CD5 immune receptor gene. Mol Biol Evol. 2012 Feb;29(2):811-23.

Myles S, Lea RA, Ohashi J, Chambers GK, Weiss JG, Hardouin E, Engelken J, Macartney-Coxson DP, Eccles DA, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M. Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Med Genet. 2011 Jan 18;12:10.

Moreno-Estrada A, Aparicio-Prat E, Sikora M, Engelken J, Ramírez-Soriano A, Calafell F, Bosch E. African signatures of recent positive selection in human FOXI1. BMC Evol Biol. 2010 Sep 1;10:267.

Engelken J, Brinkmann H, Adamska I. Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily. BMC Evol Biol. 2010 Jul 30;10:233.

Myles S, Hradetzky E, Engelken J, Lao O, Nürnberg P, Trent RJ, Wang X, Kayser M, Stoneking M. Identification of a candidate genetic variant for the high prevalence of type II diabetes in Polynesians. Eur J Hum Genet. 2007 May;15(5):584-9.

Abila R, Barluenga M, Engelken J, Meyer A, Salzburger W. Population-structure and genetic diversity in a haplochromine cichlid fish [corrected] of a satellite lake of Lake Victoria. Mol Ecol. 2004 Sep;13(9):2589-602.

Articles in preparation or under review

Johannes Engelken*, Guadalupe Espadas*, Francesco Mancuso, Nuria Bonet, Anna-Lena Scherr, Victoria Jímenez-Álvarez, Marta Codina-Solà, Daniel Medina-Stacey, Nino Spataro, Mark Stoneking, Francesc Calafell, Eduard Sabidó, Elena Bosch. Identification of cis-regulatory variation and analysis of positive selection reveals signatures of adaptation on quantitative trait loci influencing trace element homeostasis in liver.    2nd round review