Evolutionary Biology
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Publications

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.