Linnenbrink M*, Wang J*, Hardouin E, Künzel S, Metzler D, Baines JF, (2013).  The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Mol. Ecol. in press. *Equal author contribution


Franzenberg S, Altrock PM, Künzel S, Baines JF, Traulsen A, Fraune S, Bosch TC, (2013).  Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. The ISME J. in press.


Lachnit T, Fischer M, Künzel S, Baines JF, Harder T, (2013).  Compounds associated with algal surfaces mediate epiphytic colonisation of the marine macroalga Fucus vesiculosus. FEMS Microb Ecol. in press.




Franzenburg S, Fraune S, Künzel S, Baines JF, Domazet-Loso T, Bosch TC, (2012).  MyD88 deficient Hydra reveal ancient function of TLR-signaling in sensing bacterial colonizers. Proc Natl Acad Sci U S A. 109: 19374-19379.


Folseraas T, Melum E, Rausch P, Juran BD, Ellinghaus E, Shiryaev A, Laerdahl JK, Ellinghaus D, Schramm C, Weismüller TJ, Gotthardt DN, Hov JR, Clausen OP, Weersma RK, Janse M, Boberg KM, Björnsson E, Marschall HU, Cleynen I, Rosenstiel P, Holm K, Teufel A, Rust C, Gieger C, Wichmann HE, Bergquist A, Ryu E, Ponsioen CY, Runz H, Sterneck M, Vermeire S, Beuers U, Wijmenga C, Schrumpf E, Manns MP, Lazaridis KN, Schreiber S, Baines JF, Franke A, Karlsen TH, (2012). Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci. J Hepatol. 57: 366-375.


Staubach F, Künzel S, Baines AC, Yee A, McGee BM, Bäckhed F, Baines JF*, Johnsen JM*, (2012).  Expression of the blood group-related Glycosyltransferase B4galnt2 influences the intestinal microbiota in mice. The ISME J. 6: 1345-1355. *Equal author contribution




Rausch P, Rehman A, Künzel S, Häsler R, Ott S, Schreiber S, Rosenstiel P, Franke A, Baines JF (2011).  The mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc Natl Acad Sci U S A. 108: 19030-19035.


Linnenbrink, M, Johnsen JM, Montero I, Brzezinski CR, Harr B, Baines JF (2011). Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae). Mol. Biol. Evol. 28: 2999-3003.


Rehman A, Sina C, Gavrilova O, Häsler R, Ott S, Baines JF, Schreiber S, Rosenstiel P (2011).  Nod2 is essential for temporal development of intestinal microbial communities. Gut 60: 1354-1362.




Grath S, Baines JF, Parsch J (2009).  Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup. BMC Evol Biol. 9: 291.


Carpenter J, Hutter S, Baines JF, Roller J, Parsch J, Jiggins F (2009). The transcriptional response of Drosophila melanogaster to infection with the sigma virus (Rhabdoviridae). PLoS ONE. 4: e6838.


Johnsen J, Teschke M, Pavlidis P, McGee BM, Tautz D, Ginsburg D, Baines JF (2009).  Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand Factor levels in house mice. Mol. Biol. Evol. 26: 567-578.


Parsch J, Zhang Z, Baines JF (2009).  The influence of demography and weak selection on the McDonald-Kreitman test: an empirical study in Drosophila. Mol. Biol. Evol. 26: 691-698.




Baines J F, Sawyer SA, Hartl DL, Parsch J (2008).  Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Mol. Biol. Evol. 25: 1639-1650.


Schug MD, Baines JF, Killon-Atwood A, Mohanty S, Das A, Grath S, Smith S G, Zargham S, McEvey SF, Stephan W (2008).  Evolution of mating isolation between populations of Drosophila ananassae. Mol. Ecol. 17: 2706-2721.




Hense W, Baines JF, Parsch J (2007).  X chromosome inactivation during Drosophila spermatogenesis. PLoS Biol. 5: e273.


Baines JF, Harr B (2007).  Reduced X-linked diversity in derived populations of house mice. Genetics 175: 1911-1921.




Beye M, Gattermeier I, Hasselmann M, Gempe T, Schioett M, Baines J F, Schlipalius D, Mougel F, Emore C, Rueppell O, Sirvio A, Guzman-Novoa E, Hunt G, Solignac M, Page Jr RE (2006).  Exceptionally high levels of recombination across the honey bee genome. Genome Res. 16: 1339-1344.


Harr B, Voolstra C, Heinen TJAJ, Baines JF, Rottscheidt R, Ihle S, Müller W, Bonhomme F, Tautz D, (2006).  A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus. J. Evol. Biol. 19: 1486-1496.