Corbin D Jones

Summary

Affiliation: University of North Carolina
Country: USA

Publications

  1. pmc Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates
    David A Baltrus
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Pathog 7:e1002132. 2011
  2. pmc Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans
    Mara K N Lawniczak
    Division of Cell and Molecular Biology, Imperial College London, London, SW7 2AZ, UK
    Genome Biol 9:R125. 2008
  3. pmc Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
    Jason G Mezey
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Evol Biol 8:2. 2008
  4. pmc Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche
    Corbin D Jones
    Center for Population Biology, University of California, Davis, 95616, USA
    Genetics 170:207-19. 2005
  5. ncbi request reprint The genetics of adaptation in Drosophila sechellia
    Corbin D Jones
    Department of Biology, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA
    Genetica 123:137-45. 2005
  6. pmc Parallel evolution of chimeric fusion genes
    Corbin D Jones
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 102:11373-8. 2005
  7. pmc De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    Josephine A Reinhardt
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genome Res 19:294-305. 2009
  8. pmc Genetic changes accompanying the evolution of host specialization in Drosophila sechellia
    Ian Dworkin
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genetics 181:721-36. 2009
  9. pmc Adaptive gene expression divergence inferred from population genomics
    Alisha K Holloway
    Section of Evolution and Ecology, University of California Davis, Davis, California, USA
    PLoS Genet 3:2007-13. 2007
  10. pmc Two rapidly evolving genes contribute to male fitness in Drosophila
    Josephine A Reinhardt
    Department of Biology, The University of North Carolina at Chapel Hill, CB 3280, Coker Hall, Chapel Hill, NC, 27599 3280, USA
    J Mol Evol 77:246-59. 2013

Detail Information

Publications38

  1. pmc Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates
    David A Baltrus
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Pathog 7:e1002132. 2011
    ..This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species...
  2. pmc Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans
    Mara K N Lawniczak
    Division of Cell and Molecular Biology, Imperial College London, London, SW7 2AZ, UK
    Genome Biol 9:R125. 2008
    ..Addressing this question requires linking population genomic data with gene expression variation...
  3. pmc Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
    Jason G Mezey
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Evol Biol 8:2. 2008
    ..Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution...
  4. pmc Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche
    Corbin D Jones
    Center for Population Biology, University of California, Davis, 95616, USA
    Genetics 170:207-19. 2005
    ..We present a model for the origin of this new gene and discuss genetic and evolutionary factors affecting the evolution of new genes and functions...
  5. ncbi request reprint The genetics of adaptation in Drosophila sechellia
    Corbin D Jones
    Department of Biology, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA
    Genetica 123:137-45. 2005
    ..The data from D. sechellia suggest that adaptations are not as genetically complex as historically thought, although almost all of the adaptations of D. sechellia involve several genes...
  6. pmc Parallel evolution of chimeric fusion genes
    Corbin D Jones
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 102:11373-8. 2005
    ..Our data indicate that shifting away from ancestral functions may be a critical step early in the evolution of chimeric fusion genes. We suggest that the patterns we observed are both general and predictive...
  7. pmc De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    Josephine A Reinhardt
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genome Res 19:294-305. 2009
    ..syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species...
  8. pmc Genetic changes accompanying the evolution of host specialization in Drosophila sechellia
    Ian Dworkin
    Department of Biology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genetics 181:721-36. 2009
    ..sechellia to its host. Our results suggest that a subset of genes reduce or lose function as a consequence of host specialization, which may explain why, in general, specialist insects tend to shift to chemically similar hosts...
  9. pmc Adaptive gene expression divergence inferred from population genomics
    Alisha K Holloway
    Section of Evolution and Ecology, University of California Davis, Davis, California, USA
    PLoS Genet 3:2007-13. 2007
    ..Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution...
  10. pmc Two rapidly evolving genes contribute to male fitness in Drosophila
    Josephine A Reinhardt
    Department of Biology, The University of North Carolina at Chapel Hill, CB 3280, Coker Hall, Chapel Hill, NC, 27599 3280, USA
    J Mol Evol 77:246-59. 2013
    ..Together these data provide a clear case where a lack of sequence conservation does not imply a lack of conservation of expression or function. ..
  11. ncbi request reprint Origin and Spread of de Novo Genes in Drosophila melanogaster Populations
    Li Zhao
    Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Science 343:769-72. 2014
    ..These results reveal a heretofore unappreciated dynamism of gene content. ..
  12. pmc De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences
    Josephine A Reinhardt
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America Department of Biology, University of Maryland at College Park, College Park, Maryland, United States of America
    PLoS Genet 9:e1003860. 2013
    ..This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. ..
  13. pmc Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade
    David J Begun
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Genetics 176:1131-7. 2007
    ..melanogaster, support the idea that many de novo Drosophila genes function in male reproduction and that a small region of the X chromosome in the melanogaster subgroup may be a hotspot for the evolution of novel testis-biased genes...
  14. pmc Overcoming redundancy: an RNAi enhancer screen for morphogenesis genes in Caenorhabditis elegans
    Jacob M Sawyer
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genetics 188:549-64. 2011
    ..Our results implicate new genes in C. elegans gastrulation, and they show that an RNAi-based enhancer screen in C. elegans can be used as an efficient means to identify important but redundant or partially redundant developmental genes...
  15. pmc Evolution of gene expression in the Drosophila olfactory system
    Artyom Kopp
    Section of Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 25:1081-92. 2008
    ..citrifolia, and several genes that are yet to be characterized in detail. Increased expression of these genes in D. sechellia may have contributed to the evolution of its unique chemotactic behavior...
  16. pmc Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny
    Tatiana S Mucyn
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Pathog 10:e1003807. 2014
    ....
  17. pmc Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity
    Aaron R Leichty
    Department of Biology, University of North Carolina, Chapel Hill, NC 27599 3280, USA
    Integr Comp Biol 52:16-30. 2012
    ..Thus, relaxed genetic constraint may be a cause--not a consequence--of the evolution of phenotypic plasticity, and thereby contribute to the evolution of novel traits...
  18. pmc Patterns of amino acid evolution in the Drosophila ananassae chimeric gene, siren, parallel those of other Adh-derived chimeras
    Hung Jui Shih
    Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genetics 180:1261-3. 2008
    ..D. ananassae, however, harbors a single homolog of these genes. Like other Adh-derived chimeric genes, siren evolved adaptively shortly after it was formed. These changes likely shifted the catalytic activity of siren...
  19. pmc Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex
    Andrew D Kern
    Center for Population Biology, University of California, Davis, 95616, USA
    Genetics 167:725-35. 2004
    ....
  20. pmc Evolution of a signaling nexus constrained by protein interfaces and conformational States
    Brenda R S Temple
    R L Juliano Structural Bioinformatics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Comput Biol 6:e1000962. 2010
    ..These Gα class-distinctive residues are rational targets for future structural and functional studies...
  21. ncbi request reprint Extending assembly of short DNA sequences to handle error
    William R Jeck
    Department of Biology, University of Carolina Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 23:2942-4. 2007
    ..Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error...
  22. pmc Next-generation mapping of complex traits with phenotype-based selection and introgression
    Eric J Earley
    Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 3280, USA
    Genetics 189:1203-9. 2011
    ..Finally, in contrast to more widely used mapping techniques like F(2) bulk-segregant analysis, our method produces near-isogenic lines that can be kept and reused indefinitely...
  23. ncbi request reprint Gene transposition as a cause of hybrid sterility in Drosophila
    John P Masly
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 313:1448-50. 2006
    ..simulans lineage. Because of this transposition, a fraction of hybrids completely lack JYAlpha and are sterile, representing reproductive isolation without sequence evolution...
  24. ncbi request reprint The tardigrade Hypsibius dujardini, a new model for studying the evolution of development
    Willow N Gabriel
    Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Dev Biol 312:545-59. 2007
    ..We present a cell lineage of the early embryo and an embryonic staging series. We expect that these data can serve as a platform for using H. dujardini as a model for studying the evolution of developmental mechanisms...
  25. pmc Suppressor analysis reveals a role for SecY in the SecA2-dependent protein export pathway of Mycobacteria
    Lauren S Ligon
    Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
    J Bacteriol 195:4456-65. 2013
    ..Our findings reveal a detrimental effect of SecA2 K129R on SecY, arguing for an integrated system in which SecA2 works with SecY and the canonical Sec translocase to export proteins. ..
  26. pmc Evolution of an MCM complex in flies that promotes meiotic crossovers by blocking BLM helicase
    Kathryn P Kohl
    Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
    Science 338:1363-5. 2012
    ..Thus, MCMs were co-opted into a novel complex that replaced the meiotic pro-crossover function of Msh4-Msh5 in flies...
  27. pmc Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
    Cassandra B Jabara
    Department of Biology, Lineberger Comprehensive Cancer Center, University of North Carolina Center for AIDS Research, Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 108:20166-71. 2011
    ..These results provide an unprecedented view of a complex viral population in the absence of PCR resampling...
  28. pmc Genomic effects of nucleotide substitutions in Drosophila simulans
    Andrew D Kern
    Center for Population Biology, University of California, Davis, California 95616, USA
    Genetics 162:1753-61. 2002
    ..We show evidence of pervasive small-scale hitchhiking effects in this lineage. Furthermore, our results reveal that different types of fixations are associated with different levels of linked variation...
  29. pmc Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae
    Dina A Faddah
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    PLoS Genet 5:e1000502. 2009
    ..Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism...
  30. pmc FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
    Darshan Singh
    Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    Bioinformatics 27:2633-40. 2011
    ..To understand these processes, there is a great need for methods to detect differential transcription between samples. Our focus is on samples observed using short-read RNA sequencing (RNA-seq)...
  31. pmc Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression
    Mia T Levine
    Center for Population Biology, University of California Davis, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 103:9935-9. 2006
    ..These data support the idea that these novel genes are derived from ancestral noncoding sequence and that new, favored genes are likely to invade populations under selective pressures relating to male reproduction...
  32. pmc Prediction of protein-protein interfaces on G-protein beta subunits reveals a novel phospholipase C beta2 binding domain
    Erin J Friedman
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    J Mol Biol 392:1044-54. 2009
    ..Finally, this comparative evolutionary approach is suitable for application to any protein involved in a significant number of protein-protein interactions...
  33. pmc Parallel geographic variation in Drosophila melanogaster
    Josie A Reinhardt
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
    Genetics 197:361-73. 2014
    ....
  34. pmc Phylogeny of Toll-like receptor signaling: adapting the innate response
    Jeffrey M Roach
    Research Computing Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS ONE 8:e54156. 2013
    ..Our results further support the hypothesis that phylogeny of specific domains involved in signaling pathway can shed light on key processes that link innate to adaptive immune response...
  35. doi request reprint A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.)
    Karin S Pfennig
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Mol Ecol Resour 12:909-17. 2012
    ..Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow...
  36. doi request reprint Practical innovations for high-throughput amplicon sequencing
    Derek S Lundberg
    1 Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA 2 Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, USA 3
    Nat Methods 10:999-1002. 2013
    ..PCR clamps block amplification of contaminating sequences from a eukaryotic host, thereby substantially enriching microbial sequences without introducing bias. ..
  37. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  38. pmc Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
    David J Begun
    Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
    PLoS Biol 5:e310. 2007
    ..simulans...