Publications
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. (2023)
Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.
Genome Res. 33:872-890.
Glaser-Schmitt A, Ramnarine TJS, Parsch J. (2023)
Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster.
Mol Ecol. 17024.
Glaser-Schmitt A., and J. Parsch J. (2023)
Dynamics and stage-specificity of between-population gene expression divergence in the Drosophila melanogaster larval fat body.
PLoS Genet. 19: e1010730.
Ramnarine TJS, S. Grath S, and J. Parsch (2022)
Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress.
G3 (Bethesda) 12: jkab366.
Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO (2021)
Drosophila evolution over space and time (DEST): a new population genomics resource.
Mol Biol Evol. 38: 5782-5805.
Glaser-Schmitt, A., M. J. Wittmann, T. J. S. Ramnarine, and J. Parsch (2021)
Sexual antagonism, temporally fluctuating selection, and variable dominance affect a regulatory polymorphism in Drosophila melanogaster.
Mol Biol Evol. 38: 4891-4907.
Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ (2021)
The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe.
Virus Evol. 7(1): veab031.
Belyi, A., E. Argyridou, and J. Parsch (2020)
The influence of chromosomal environment on X-linked gene expression in Drosophila melanogaster.
Genome Biol Evol. 12: 391-2402.
Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J (2020).
Genomic analysis of European Drosophila melanogaster populationsreveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses.
Mol. Biol. Evol. 37: 2661-2678.
Ramnarine, T. J. S., A. Glaser-Schmitt, A. Catalán, and J Parsch (2019)
Population genetic and functional analysis of a cis-regulatory polymorphism in the Drosophila melanogaster Metallothionein A gene.
Genes (Basel) 10: 147.
Glaser-Schmitt, A., A. Zečić, and J. Parsch (2018)
Gene regulatory variation in Drosophila melanogaster renal tissue.
Genetics 210: 287-301.
Argyridou E., and J. Parsch (2018)
Regulation of the X chromosome in the germline and soma of Drosophila melanogaster males.
Genes (Basel) 9: 242.
Glaser-Schmitt A., and J. Parsch (2018)
Functional characterization of adaptive variation within a cis-regulatory element influencing Drosophila melanogaster growth.
PLoS Biol 16: e2004538.
Argyridou E., A. K. Huylmans, A. Königer, and J. Parsch (2017)
X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
Heredity 119: 27-34.
Grath S., and J. Parsch (2016)
Sex-biased gene expression.
Annu. Rev. Genet. 50: 29-44.
Huylmans, A. K., A. López Ezquerra, J. Parsch, and M. Cordellier (2016)
De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata.
Genome Biol. Evol. 8: 3120-3139.
Catalán, A., A. Glaser-Schmitt, E. Argyridou, P. Duchen, and J. Parsch (2016)
An indel polymorphism in the MtnA 3' untranslated region is associated with gene expression variation and local adaptation in Drosophila melanogaster.
PLoS Genet. 12(4):e1005987.
Huylmans, A. K., and J. Parsch (2015)
Variation in the X:autosome distribution of male-biased genes among Drosophila melanogaster tissues and Its relationship with dosage compensation.
Genome Biol. Evol. 7: 1960-1971.
Huylmans, A. K., and J. Parsch (2014)
Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster.
G3 (Bethesda) 4: 2307-2315.
Kemkemer, C., A. Catalán, and J. Parsch (2014)
Escaping the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster.
Heredity 112: 149-155.
Glaser-Schmitt, A., A. Catalán, and J. Parsch (2013)
Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster
Phil. Trans. R. Soc. B 368: 20130024.
Parsch, J. and H. Ellegren (2013)
The evolutionary causes and consequences of sex-biased gene expression.
Nature Reviews Genetics 14: 83-87.
Catalán, A., S. Hutter, and J. Parsch (2012)
Population and sex differences in Drosophila melanogaster brain gene expression.
BMC Genomics 13: 654.
Grath, S., and J. Parsch (2012)
Rate of amino acid substitution is influenced by the degree and conservation of male-biased transcription over 50 million years of Drosophila evolution.
Genome Biol. Evol. 4: 346-359.
Ranz, J. M., and J. Parsch (2012)
Newly evolved genes: moving from comparative genomics to functional studies in model systems.
Bioessays 34: 477-483.
Saminadin-Peter, S. S., C. Kemkemer, P. Pavlidis, and J. Parsch (2012)
Selective sweep of a cis-regulatory sequence in a non-African population of Drosophila melanogaster.
Mol. Biol. Evol. 29: 1167-1174.
Müller, L., S. Grath, K. von Heckel, and J. Parsch (2012)
Inter- and intraspecific variation in Drosophila genes with sex-biased expression.
Int. J. Evol. Biol. 2012: 963976.
Stamboliyska, R., and J. Parsch (2011)
Dissecting gene expression in mosquito.
BMC Genomics 12: 297.
Parsch, J. (2011)
The cost of being male.
Science 332: 798-799.
Kemkemer, C., W. Hense, and J. Parsch (2011)
Fine-scale analysis of X chromosome inactivation in the male germline of Drosophila melanogaster.
Mol Biol Evol. 28: 1561-1563.
Müller, L., S. Hutter, R. Stamboliyska, S. S. Saminadin-Peter, W. Stephan, and J. Parsch (2011)
Population transcriptomics of Drosophila melanogaster females.
BMC Genomics 12: 81.
Parsch, J., S. Novozhilov, S. S. Saminadin-Peter, K. M. Wong, and P. Andolfatto (2010)
On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.
Mol. Biol. Evol. 27: 1226-1234.
Hense, W., N. Anderson, S. Hutter, W. Stephan, J. Parsch, and D. B. Carlini (2010)
Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity.
Genetics 184: 547-555.
Grath, S., J. F. Baines, and J. Parsch (2009)
Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup.
BMC Evol. Biol. 9: 291.
Parsch, J. (2009)
X chromosome: expression and escape.
PLoS Genetics 5: e1000724.
Carpenter, J., S. Hutter, J. F. Baines, J. Roller, S. S. Saminadin-Peter, J. Parsch, and F. M. Jiggins (2009)
The transcriptional response of Drosophila melanogaster to infection with the sigma virus (Rhabdoviridae).
PLoS ONE 4: e6838.
Parsch, J., Z. Zhang, and J. F. Baines (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., S. A. Sawyer, D. L. Hartl, and J. Parsch (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.
Hutter, S., S. S. Saminadin-Peter, W. Stephan, and J. Parsch (2008)
Gene expression variation in African and European populations of Drosophila melanogaster.
Genome Biology 9: R12.
Röhlk, C, M. Rohlfs, S. Leier, M. Schliwa, X. Liu, J. Parsch, and G. Woehlke (2008)
Properties of the Kinesin-1 motor DdKif3 from Dictyostelium discoideum.
Eur. J. Cell Biol. 87: 237-249.
Hense, W., J. F. Baines, and J. Parsch (2007)
X chromosome inactivation during Drosophila spermatogenesis.
PLoS Biology 5: e273.
Ellegren, H., and J. Parsch (2007)
The evolution of sex-biased genes and sex-biased gene expression.
Nature Reviews Genetics 8: 689-698.
Sawyer, S. A., J. Parsch, Z. Zhang, and D. L. Hartl (2007)
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila.
Proc. Natl. Acad. Sci. USA 104: 6504-6510.
Pröschel, M., Z. Zhang, and J. Parsch (2006)
Widespread adaptive evolution of Drosophila genes with sex-biased expression.
Genetics 174: 893-900.
Gnad, F., and J. Parsch (2006)
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.
Bioinformatics 22: 2577-2579.
Zhang, Z., and J. Parsch (2005)
Positive correlation between evolutionary rate and recombination rate in Drosophila genes with male-biased expression.
Mol. Biol. Evol. 22: 1945-1947.
Hambuch, T. M., and J. Parsch (2005)
Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression.
Genetics 170: 1691-1700.
Parsch, J., C. D. Meiklejohn, and D. L. Hartl (2005)
Inferring evolutionary history through inter- and intraspecific DNA sequence comparison: the Drosophila janus and ocnus genes.
Book Chapter in Selective Sweep. D. Nurminksy, Ed. Landes Bioscience: Georgetown, TX, USA.
Zhang, Z., T. M. Hambuch, and J. Parsch (2004)
Molecular evolution of sex-biased genes in Drosophila.
Mol. Biol. Evol. 21: 2130-2139.
Parsch, J. (2004)
Functional analysis of Drosophila melanogaster gene regulatory sequences by transgene coplacement.
Genetics 168: 559-561.
Meiklejohn, C. D., Y. Kim, D. L. Hartl, and J. Parsch (2004)
Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite likelihood estimation.
Genetics 168: 265-279.
Baines, J. F., J. Parsch, and W. Stephan (2004)
Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene.
Genetics 66: 237-242.
Parsch, J. (2003)
Selective constraints on intron evolution in Drosophila.
Genetics 165: 1843-1851.
Meiklejohn, C. M., J. Parsch, J. M. Ranz, and D. L. Hartl (2003)
Rapid evolution of male-biased gene expression in Drosophila.
Proc. Natl. Acad. Sci. USA 100: 9894-9899.
Parsch, J., C. D. Meiklejohn, and D. L. Hartl (2001)
Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of Drosophila simulans.
Genetics 159: 647-657.
Parsch, J., C. D. Meiklejohn, E. Hauschteck-Jungen, P. Hunziker, and D. L. Hartl (2001)
Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup.
Mol. Biol. Evol. 18: 801-811.
Parsch, J., J. A. Russell, I. Beerman, D. L. Hartl, and W. Stephan (2000)
Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased alcohol dehydrogenase activity but also delays development.
Genetics 156: 219-227.
Parsch, J., J. M. Braverman, and W. Stephan (2000)
Comparative sequence analysis and patterns of covariation in RNA secondary structures.
Genetics 154: 909-921.
Chen, Y., D. B. Carlini, J. F. Baines, J. Parsch, J. M. Braverman, S. Tanda, and W. Stephan (1999)
RNA secondary structure and compensatory evolution.
Genes Genet. Syst. 74: 271-286.
Parsch J., W. Stephan, and S. Tanda (1999)
A highly conserved sequence in the 3' untranslated region of the Drosophila Adh gene plays a functional role in Adh expression.
Genetics 151: 667-674.
Parsch J., W. Stephan, and S. Tanda (1998)
Long-range base pairing in Drosophila and human mRNA sequences.
Mol. Biol. Evol. 15: 820-826.
Parsch J., S. Tanda, and W. Stephan (1997)
Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster.
Proc. Natl. Acad. Sci. USA 94: 928-933.
Stephan W., V. S. Rodriguez, B. Zhou, and J. Parsch (1994)
Molecular evolution of the metallothionein gene Mtn in the melanogaster species group: results from Drosophila ananassae.
Genetics 138: 135-143.