2024

  • Ashlyn Kimura, Alwyn C Go, Therese Markow, José M Ranz. (2024) Evidence of Nonrandom Patterns of Functional Chromosome Organization in Danaus plexippusGenome Biology and Evolution, evae054, https://doi.org/10.1093/gbe/evae054
  • Greenspan, Z. S., Barter, T. T., Phillips, M. A., Ranz, J. M., Rose, M. R., & Mueller, L. D. (2024). Genomewide architecture of adaptation in experimentally evolved Drosophila characterized by widespread pleiotropy. Journal of genetics103, 08. https://doi.org/10.1007/s12041-023-01460-8

2023

  • Bryan D. Clifton, Imtiyaz Hariyani, Ashlyn Kimura, Fangning Luo, Alvin Nguyen, and José M. Ranz. (2023) Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages. Commun. Biol. https://doi.org/10.1038/s42003-023-05427-4
  • Ranz JM, Go AC, González PM, Clifton BD, Gomes S, Jaberyzadeh A, Woodbury A, Chan C, Gandasetiawan KA, Jayasekera S, Gaudreau C, Ma HC, Salceda VM, Abreu-Goodger C, Civetta A. (2023) Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids. Mol Ecol. doi: 10.1111/mec.16941. Epub ahead of print. PMID: 37000122

2022

  • Oropeza-Rodriguez E, Clifton BD, Ranz JM (2022) On the genetic basis of the effect of Spiroplasma on the male reproductive fitness of Glossina fuscipes fuscipes. PLoS Pathog 18(4): e1010442. https://doi.org/10.1371/journal.ppat.1010442
  • Ranz, J.M., P.M. Gonzalez, R.N. Su, S.J. Bedford, C. Abreu-Goodger, and T.A. Markow 2022 Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera. Proc. Royal Soc. B. doi.org/10.1098/rspb.2021.2183

2021

  • Ranz, J.M., P.M. Gonzalez, B.D. Clifton, N.O. Nazario-Yepiz, P.L. Hernandez-Cervantes, M.J. Palma-Martinez, D.I. Valvidia, A. Jimenez-Kaufman, M.M. Lu, T.A. Markow, C. Abrei-Goodger 2021 A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. Commun. Biol. 4, 791 doi: 10.1038/s42003-021-02335-3.
  • Patlar, B., V. Jayaswal, J.M. Ranz, A. Civetta 2021 Non-adaptive molecular evolution of seminal fluid proteins in Drosophila. Evolution doi: 10.1111/evo.14297.
  • Jayaswal, V., C. Ndo, H.C. Ma, B. Clifton, M. Pombi, K. Cabrera, A. Couhet, K. Mouline, A. Diabaté, R. Dabire, D. Ayala, J.M. Ranz 2021. Intraspecific transcriptome variation and sex-biased expression in Anopheles arabiensis. Genome Biol. Evol.  doi.org/10.1093/gbe/evab199.

2020

  • Clifton, B.D., Jimenez, J., Kimura, A., Chahine, Z., Librado, P., Sanchez-Gracia, A., Abbassi, M., Carranza, F., Chan, C., Marchetti, M., Zhang, W., Shi, M., Vu, C., Yeh, S., Fanti L., Xia, X., Rozas, J., & Ranz, J.M. 2020. Understanding the early evolutionary stages of a tandem D. melanogaster-specific gene family: a structural and functional population study. Mol. Biol. Evol. 37(9):2584–2600. doi:10.1093/molbev/msaa109

2019

  • Civetta A and Ranz JM (2019) Genetic Factors Influencing Sperm Competition. Front. Genet. 10:820. doi: 10.3389/fgene.2019.00820
  • Barter, T., Z.S. Greenspan, M.A. Phillips, L.D. Mueller, M.R. Rose, and J.M. Ranz  2019 Drosophila transcriptomics with and without ageing.  Biogerontology:1-12. doi: 10.1007/s10522-019-09823-4.
  • Ranz, J.M., & Clifton, B 2019 Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. Science China Life Sciences 62: 467-488.

2018

  • Jayaswal, V., J. Jimenez, R. Magie, K. Nguyen, B. Clifton, S. Yeh, & J.M. Ranz 2018 A species-specific multigene family mediates differential sperm displacement in Drosophila. Evolution 34: 51-65. doi: 10.1111/evo.13417.

2017

  • Clifton, B.D., P. Librado, S.D. Yeh, E. Solares, D. Real, S. Jayasekera, W. Zhang, M. Shi, R. Park, R. Magie, H.C. Ma, X.-Q. Xia, A. Marco, J. Rozas, & J.M. Ranz 2017 Rapid functional and sequence differentiation of a tandemly-repeated species-specific multigene family in DrosophilaMol. Biol. Evol. 34: 51-65.  doi: 10.1093/molbev/msw212.

2016

  • Mardiros, X.B., R. Park, B. Clifton, G. Grewal, A.K. Khizar, T.A. Markow, J.M. Ranz, & A. Civetta 2016 Postmating reproductive isolation between strains of Drosophila willistoni. Fly 8, 1-10.

2015

  • Chan, C., S. Jayasekera, B. Kao, M. Páramo, M. von Grotthuss, J.M. Ranz 2015 Remodeling of a homeobox gene cluster by multiple independent gene reunions in Drosophila. Nature Commun. 6, 6509. doi:10.1038/ncomms7509.

2014

  • Yeh, S.-D, M. von Grotthuss, K.A. Gandasetiawan, S. Jayasekera, X.-Q. Xia, C. Chan, V. Jayaswal, & J.M. Ranz 2014 Functional divergence of the miRNA transcriptome at the onset of Drosophila metamorphosis. Mol. Biol. Evol. 31(10): 2557-72. doi: 10.1093/molbev/msu195.

2013

  • Ranz, J.M., S.-D. Yeh, K.G. Nyberg, & C. Machado 2013 Transcriptome profiling of Drosophila interspecific hybrids: insights into mechanisms of regulatory divergence and hybrid dysfunction. Pp. 15-35, in Hybrid and Polyploid Genomics. Edited by Jeffrey Chen and Jim Birchler. John Wiley & Sons, Inc. NJ.
  • Yeh, S.-D., C. Chan, & J.M. Ranz 2013 Assessing differences in sperm competitive ability in Drosophila. J. Vis. Exp. (78), e50547, doi:10.3791/50547.

2012

  • Díaz-Castillo, C., X.-Q. Xia, & J.M. Ranz 2012 Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila. PLoS Genet. 8(2): e1002475. doi: 10.1371/journal.pgen.1002475.
  • Yeh, S.-D., T. Do, C. Chan, A. Cordova, F. Carranza, E.A. Yamamoto, M. Abbassi, K.A. Gandasetiawan, P. Librado, E. Damia, P. Dimitri, J. Rozas, D.L. Hartl, J. Roote & J.M. Ranz 2012 Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition. Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1121327109.
  • Ranz, J.M. & J. Parsch 2012 Newly evolved genes: Moving from comparative genomics to functional studies in model systems. BioEssays doi: 10.1002/bies.201100177.
  • Díaz-Castillo, C., & J.M. Ranz 2012 Nuclear chromosome dynamics in the Drosophila male germline contribute to the non-random genomic distribution of retrogenes. Mol. Biol. Evol. doi: 10.1093/molbev/mss096.
  • Díaz-Castillo, C., & J.M. Ranz 2012 Recent progress on the identity and characterization of factors that shape gene organization during eukaryotic evolution. Fly doi: 10.4161/fly.20861.
  • Yeh, S.-D., T. Do, M. Abbassi, & J.M. Ranz 2012 Functional relevance of the newly evolved sperm dynein intermediate chain multigene family in Drosophila melanogaster males. Communicative & Integrative Biology5:5, 462-5, doi: 10.4161/cib.21136.
  • Sahagun, V., & J.M. Ranz 2012 Characterization of genomic regulatory domains conserved across the genus Drosophila. Genome Biology and Evolution 4:10, 1054-60. doi: 10.1093/gbe/evs089.

2011

  • Ranz, J.M., C. Díaz-Castillo, & R. Petersen 2011 Conserved gene order at the nuclear periphery in Drosophila. Mol. Biol. Evol. doi: 10.1093/molbev/msr178.

2010

  • Von Grotthuss, M., Ashburner, M., & J.M. Ranz 2010 Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila. Genome Res. 20: 1084-1096 [Cover].

2007

  • Ranz, J.M., D. Maurin, Y.S. Chan, M. von Grotthuss, L.D.W. Hillier, J. Roote, M. Ashburner, & C. Bergman 2007 Principles of genome evolution in the D. melanogaster species group. PLoS Biology 5(6): e152. doi:10.1371/journal.pbio.0050152.  [Featured in Heredity 99: 479-80 (2007)]
  • Landry, C.R., D.L. Hartl, & J.M. Ranz 2007 Genome clashes in hybrids: insights from gene expression. Heredity 99: 483-93.

2006

  • Ranz, J.M., & C. Machado 2006 Uncovering evolutionary patterns of gene expression using microarrays. Trends in Ecology and Evolution 21: 29-37.

2005

  • Landry, C.R., P.J. Wittkopp, C.H. Taubes, J.M. Ranz, A.G. Clark, & D.L. Hartl 2005 Compensatory cis-trans evolution and the misregulation of gene expression in interspecific hybrids. Genetics 171: 1813-22. [Featured by Faculty 1000]

2004

  • Ranz, J.M., K. Namgyal, G. Gibson, & D.L. Hartl 2004 Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res. 14: 373-9.
  • Kulathinal, R. J., S.A. Sawyer, C.D. Bustamante, D.I. Nurminsky, R. Ponce, J.M. Ranz, & D.L. Hartl 2004 Selective sweep in the evolution of a new sperm-specific gene in Drosophila.  Pp. 1-12, in Selective Sweeps, edited by D. I. Nurminsky. Kluwer Academic/Plenum Publishers, New York.

2003

  • Ranz, J.M., C.I. Castillo-Davis, C.D. Meiklejohn, & D.L. Hartl 2003 Sex-dependent gene expression and the evolution of the Drosophila transcriptome. Science 300: 1742-45. [Featured in Genome Biology –Research News- and in The Scientist]
  • Ranz, J.M., A.R. Ponce, D. Hartl, & D. Nurminsky 2003 Origin and evolution of a new gene expressed in the Drosophila sperm axoneme. Genetica 118: 233-44.
  • Ranz, J.M., J. González, F. Casals, & A. Ruiz 2003 Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution 57: 1325-35.
  • Negre, B., J.M. Ranz, F. Casals, M. Cáceres, & A. Ruiz 2003 A new split of the Hox gene complex in Drosophila: relocation and evolution of the gene labial. Mol. Biol. Evol. 20: 2042-54.
  • Hartl, D.L., C.D. Meiklejohn, C.I. Castillo-Davis, D. Cavalieri, J.M. Ranz, & J.P. Townsend 2003 Gene expression profiling in evolutionary genetics. Pp. 74-93, in The Evolution of Population Biology: Modern Synthesis. Eds. R. Singh & M. Uyenoyama. Cambridge University Press, Cambridge, UK.
  • Meiklejohn, C.D., J. Parsch, J.M. Ranz, & D.L. Hartl 2003 Rapid evolution of male-biased gene expression in Drosophila. Proc. Natl. Acad. Sci. USA 100: 9894-9. [Featured by Faculty 1000]

2002

  • González, J., J.M. Ranz, & A. Ruiz 2002 Chromosomal elements evolve at different rates in the Drosophila genome. Genetics 161: 1137-54.

2001

  • Ranz, J.M., F. Casals, & A. Ruiz 2001 How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res. 11: 230-9. [Featured in Nature Review Genetics 2:238-239 (2002)]

1999

  • Cáceres, M., J.M. Ranz, A. Barbadilla, M. Long, & A. Ruiz 1999 A transposon mediated the generation of a Drosophila widespread inversion. Science 285: 415-8.
  • Ranz, J.M., M. Cáceres, & A. Ruiz 1999 Comparative mapping of cosmids and gene clones from a 1.6 Mb chromosomal region of Drosophila melanogaster in three species of the distantly related subgenus Drosophila.Chromosoma 108: 32-43.

1997

  • Ranz, J.M., C. Segarra, & A. Ruiz 1997 Chromosomal homology and molecular organization of Muller´s elements D and E in the Drosophila repleta species group. Genetics 145: 281-95.
  • Ruiz, A., J.M. Ranz, M. Cáceres, C. Segarra, A. Navarro, & A. Barbadilla 1997 Chromosomal evolution and comparative gene mapping in the Drosophila repleta species group. Genetics and Mol. Biol. 20: 553-65.