Publications from the Jones Lab
Sorted by Publication Date
Sorted by Subject Area
Sorted by Publication Date
Baltrus DA, Romanchuk A, Nishmura M, Roach J, Jones CD, Dangl JD. Whole genome sequencing of a clade of Pseudomonads reveals complex interplay between effector repertoire and host utilization. PLoS Pathogens [accepted pending minor revision].
Sawyer JM, Glass S, Li T, Shemer G, White ND, Starostina NG, Kipreos ET, Jones CD, Goldstein B. Overcoming Redundancy: an RNAi Enhancer Screen for Morphogensis Genes in C. elegans. Genetics, 2011 [accepted].
Singh D, Orellana C, Hu Y, Jones CD, Liu Y, Chiang D, Liu J, Prins JF. FDM: A Graph-based Statistical Method to Analyze Differential Transcription using RNA-seq data. Bioinformatics [Accepted pending major revision].
2010
Anderson JA, Ping LH, Dibben O, Jabara CB, Arney L, Kincer L, Tang Y, Hobbs M, Hoffman I, Kazembe P, Jones CD, Borrow P, Fiscus S, Cohen MS, Swanstrom R; and the Center for HIV/AIDS Vaccine Immunology. HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog, 2010 Aug 19;6(8). pii: e1001053. PMC2924360
Temple, B. R. S, C D. Jones, and A. M. Jones. Evolution of a Signaling Nexus: How Constraints on Protein Interfaces and Conformational States Shaped the Evolution and Function of the Gα Subunit of the Heterotrimeric G Protein Complex. PLoS Comput Biol. 2010 Oct 14;6(10):e1000962. PMC2954821
2009
Earley, EJ, and B Wolford (2009) Mechanosensation diversity across and within Drosophila species. DIS 92: 119-122.
Friedman E.J., Temple B.R., Hicks S.N., Sondek J., Jones C.D., Jones A.M. 2009. Prediction of protein-protein interfaces on G-protein beta subunits reveals a novel phospholipase C beta2 binding domain. J Mol Biol. 392(4):1044-54.
Faddah D.A., Ganko E.W., McCoach C., Pickrell J,K,. Hanlon S.E., Mann F.G., Mieczkowska J.O., Jones C.D., Lieb J.D., Vision T.J. 2009. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet. 5(6):e1000502.
Dworkin I. and C. D. Jones. 2009. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics. 181(2):721-36.
Reinhardt J.A., Baltrus D.A., Nishimura M.T., Jeck W.R., Jones C.D., Dangl J.L. 2009. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19(2):294-305.
2008
Lawniczak M. K. N., A. K. Holloway, D. J. Begun and C. D. Jones. 2008. Linkage between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biology. 9:R125. PMC2575515.
Shih, H-J and C. D. Jones. 2008. Patterns of amino acid evolution in Drosophila ananassae chimeric gene, siren, parallel those of other Adh derived chimeras. Genetics. 2008 Oct;180(2):1261-3. Epub 2008 Sep 9.
Kopp A., O. Barmina, A.M. Hamilton, L. Higgins, L.M. McIntyre, and C. D. Jones. 2008. Evolution of Gene Expression in the Drosophila Olfactory System. Mol Biol Evol. 2008 Jun;25(6):1081-92. Epub 2008 Feb 23.
Mezey, J. G., S. V. Nuzhdin, F.F. Yu, and C. D. Jones. 2008 Co-expression domains: units of evolution in the Drosophila transcriptome. BMC Evol Biol. 2008; 8: 2. Published online 2008 January 7. doi: 10.1186/1471-2148-8-2.
2007
Begun, D.J., A. K. Holloway, K. Stevens, L W. Hillier, Y-P Poh, M. W. Hahn, P. M. Nista, C. D. Jones, A. D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langely. 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology. 5(11):e310.
Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-218.
Gabriel W N., R McNuff, S. K. Patel, T. R. Gregory, W. R. Jeck, C. D. Jones and B. Goldstein 2007. The Tardigrade Hypsibius dujardini, a New Model for Studies on the Evolution of Development. Developmental Biology. Dev Biol. 2007 Dec 15;312(2):545-59. Epub 2007 Oct 6.
Jeck, W. R. , J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones. 2007. Applications Note: Extending assembly of short DNA sequences to handle error through VCAKE. Bioinformatics. 23(21):2942-4.
Holloway, A.K., M.L. Lawniczak, D.J.Begun, J.G. Mezey, and C.D. Jones, 2007. Genome-wide comparison of structural and transcriptional divergence among Drosophila melanogaster, D. simulans, and D. yakuba. PLoS Genetics 3(10):2007-13. PMC2042001.
Begun D. J., A. D. Kern, H. A. Lindfors, & C. D. Jones. 2007. Rapid evolution and turnover of testis-expressed genes in the Drosophila yakuba/D. erecta lineage. Genetics. 176:1131-7 .
Jones C. D. 2007. Genetic ablation of antennae or basiconic sensillia reduces Drosophila melanogasters ability to perceive odors from the fruit of Morinda citrifolia. Drosophila Information Service. 90: .
VCAKE. 2007. W. R. Jeck, J. R. Reinhardt, and C. D. Jones , A utility program for estimating the number of QTLs. VCAKE-at sourceforge
2006
Masly, J. P., C. D. Jones, M. A.F. Noor, J. Locke & H. A. Orr. 2006. Gene transposition as a novel cause of hybrid sterility in Drosophila. Science. 313:1448-1450.
Levine, M. T., C. D. Jones, A. D. Kern, H. A. Lindfors, & D. J. Begun. 2006. Novel genes derived from non-coding DNA in Drosophila melanogaster are chromosome and sex biased. Proc Natl Acad Sci USA 103:9935-9.
2005
Jones C. D. and D. J. Begun. 2005. Parallel evolution of chimeric fusion genes. PNAS. 102:11373-8.
Jones C. D. A. W. Custer, and D. J. Begun. 2005. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, Drosophila madeirensis, and Drosophila guanche. Genetics 170: 207-19
Danzinger, R.S., and C. D. Jones. 2005. A time to reconsider our collaborations with the Dahl rat. Current Hypertension Reviews. 1(2):97-99
Jones, C. D. 2005. The genetics of adaptations in Drosophila sechellia. Genetica. 123:137-145. [also featured in The Georgia Genetics Review. Vol. 3. Kluwer Academic Publishing, New York.]
Jones, C. D. 2005. Drosophila sechellia: a system for studying the genetics of adaptation. The Georgia Genetics Review. Vol. 3. Kluwer Academic Publishing, New York
2004
Jones, C. D. 2004. The genetics of egg production in Drosophila sechellia. Heredity 92:235-41.
Kern, A.D., C. D. Jones, and D. J. Begun. 2004. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics. 167 (2): 715-35.
Dsim/Dyak Genome Project BLAST site. 2004. C. Jones and A. Kern. WWW.DPGP.ORG
Kern, A.D., C. D. Jones, and D. J. Begun. 2002 Genomic effects of nucleotide substitution. Genetics 162(4):1753-61
Jones, C. D. 2001. The genetic basis of larval resistance to a host plant toxin in Drosophila sechellia. Genetical Research. 78: 225-233
Jones, C. D. 2001. Extension of the Castle-Wright effective factor estimator to sex-linkage and haplodiploidy. Journal of Heredity. 92:274-276
Otto, S. P. and C. D. Jones. 2000. Detecting the undetected: estimating the number of loci underlying a trait in QTL studies. Genetics. 156:2093-2107.
Jones, C. D. 1998. The genetic basis of Drosophila sechellia's resistance to a host plant toxin. Genetics. 149:1899-1908. [see related: Science 284:2106-7]
Jones C. D. and H. A. Orr. 1998. Test of a Drosophila simulans balancer and a remapping of chromosome 3. Drosophila Information Service. 81:137-138.
Jones C. D. and H. A. Orr. 1996. An attempt to rescue hybrid fertility by germline mitotic recombination in Drosophila. Drosophila Information Service. 77:82-83.
Jones C. D. and J. D. Munnoch. 1994. Endangered plants of the Pacific Northwest. Mountaineers. April 1994:13-15.
PepCharge. © 1993 C. D. Jones. Version 1.01. A utility program for calculating peptide charges at various pH.
Electronic Blueprint Survey. © 1993-1994. Microsoft Corp. Programmed by C. D. Jones. Versions 1.00-1.04. A tool for conducting surveys electronically. Also included technical writing and help file programming.
CPTEST.DLL © 1994 Microsoft Corp. Programming by C. D. Jones. Version 1.0 A dynamic link library providing data access to a SQL server database.
KJBtest. 2002. C.D. Jones. Used for detecting nucleotide changes caused by natural selection.
OJest. 2000-2002. C. D. Jones and S. P. Otto, A utility program for estimating the number of QTLs.
Sorted by Subject Area
Dworkin I. and C. D. Jones. 2009. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics. 181(2):721-36.
Kopp A., O. Barmina, A.M. Hamilton, L. Higgins, L.M. McIntyre, and C. D. Jones. 2008. Evolution of Gene Expression in the Drosophila Olfactory System. Mol Biol Evol. 2008 Jun;25(6):1081-92. Epub 2008 Feb 23.
Jones C. D. 2007. Genetic ablation of antennae or basiconic sensillia reduces Drosophila melanogasters ability to perceive odors from the fruit of Morinda citrifolia. Drosophila Information Service. 90: .
Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-218.
Jones, C. D. 2005. The genetics of adaptations in Drosophila sechellia. Genetica. 123(1-2):137-45. [also featured in The Georgia Genetics Review. Vol. 3. Kluwer Academic Publishing, New York.]
Jones, C. D. 2005. Drosophila sechellia: a system for studying the genetics of adaptation. The Georgia Genetics Review. Vol. 3. Kluwer Academic Publishing, New York
Jones, C. D. 2004. The genetics of egg production in Drosophila sechellia. Heredity 92:235-41.
Jones, C. D. 2001. The genetic basis of larval resistance to a host plant toxin in Drosophila sechellia. Genetical Research. 78: 225-233
Jones, C. D. 1998. The genetic basis of Drosophila sechellia's resistance to a host plant toxin. Genetics. 149:1899-1908. [see related: Science 284:2106-7]
Sawyer JM, Glass S, Li T, Shemer G, White ND, Starostina NG, Kipreos ET, Jones CD, Goldstein B. Overcoming Redundancy: an RNAi Enhancer Screen for Morphogensis Genes in C. elegans. Genetics, 2011.
Friedman E.J., Temple B.R., Hicks S.N., Sondek J., Jones C.D., Jones A.M. 2009. Prediction of protein-protein interfaces on G-protein beta subunits reveals a novel phospholipase C beta2 binding domain. J Mol Biol. 392(4):1044-54.
Reinhardt J.A., Baltrus D.A., Nishimura M.T., Jeck W.R., Jones C.D., Dangl J.L. 2009. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19(2):294-305.
Shih, H-J and C. D. Jones. 2008. Patterns of amino acid evolution in Drosophila ananassae chimeric gene, siren, parallel those of other Adh derived chimeras. Genetics. 2008 Oct;180(2):1261-3. Epub 2008 Sep 9.
Begun D. J., A. D. Kern, H. A. Lindfors, & C. D. Jones. 2007. Rapid evolution and turnover of testis-expressed genes in the Drosophila yakuba/D. erecta lineage. Genetics. 176:1131-7.
Levine, M. T., C. D. Jones, A. D. Kern, H. A. Lindfors, & D. J. Begun. 2006. Novel genes derived from non-coding DNA in Drosophila melanogaster are chromosome and sex biased. Proc Natl Acad Sci USA 103:9935-9.
Jones C. D. A. W. Custer, and D. J. Begun. 2005. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, Drosophila madeirensis, and Drosophila guanche. Genetics 170: 207-19
Jones C. D. and D. J. Begun. 2005. Parallel evolution of chimeric fusion genes. Proc Natl Acad Sci USA. 102:11373-8
Baltrus DA, Romanchuk A, Nishmura M, Roach J, Jones CD, Dangl JD. Whole genome sequencing of a clade of Pseudomonads reveals complex interplay between effector repertoire and host utilization. PLoS Pathogens [accepted pending minor revision].
Singh D, Orellana C, Hu Y, Jones CD, Liu Y, Chiang D, Liu J, Prins JF. FDM: A Graph-based Statistical Method to Analyze Differential Transcription using RNA-seq data. Bioinformatics [Accepted pending major revision].
Temple, B. R. S, C D. Jones, and A. M. Jones. Evolution of a Signaling Nexus: How Constraints on Protein Interfaces and Conformational States Shaped the Evolution and Function of the Gα Subunit of the Heterotrimeric G Protein Complex. PLoS Comput Biol. 2010 Oct 14;6(10):e1000962. PMC2954821
Sawyer JM, Glass S, Li T, Shemer G, White ND, Starostina NG, Kipreos ET, Jones CD, Goldstein B. Overcoming Redundancy: an RNAi Enhancer Screen for Morphogensis Genes in C. elegans. Genetics, 2011.
Faddah D.A., Ganko E.W., McCoach C., Pickrell J,K,. Hanlon S.E., Mann F.G., Mieczkowska J.O., Jones C.D., Lieb J.D., Vision T.J. 2009. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet. 5(6):e1000502.
Friedman E.J., Temple B.R., Hicks S.N., Sondek J., Jones C.D., Jones A.M. 2009. Prediction of protein-protein interfaces on G-protein beta subunits reveals a novel phospholipase C beta2 binding domain. J Mol Biol. 392(4):1044-54.
Dworkin I. and C. D. Jones. 2009. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics. 181(2):721-36.
Shih, H-J and C. D. Jones. 2008. Patterns of amino acid evolution in Drosophila ananassae chimeric gene, siren, parallel those of other Adh derived chimeras. Genetics. 2008 Oct;180(2):1261-3. Epub 2008 Sep 9.
Kopp A., O. Barmina, A.M. Hamilton, L. Higgins, L.M. McIntyre, and C. D. Jones. 2008. Evolution of Gene Expression in the Drosophila Olfactory System. Mol Biol Evol. 2008 Jun;25(6):1081-92. Epub 2008 Feb 23.
Mezey, J. G., S. V. Nuzhdin, F.F. Yu, and C. D. Jones. 2008 Co-expression domains: units of evolution in the Drosophila transcriptome. BMC Evol Biol. 2008; 8: 2. Published online 2008 January 7. doi: 10.1186/1471-2148-8-2.
Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-218.
Gabriel W N., R McNuff, S. K. Patel, T. R. Gregory, W. R. Jeck, C. D. Jones and B. Goldstein 2007. The Tardigrade Hypsibius dujardini, a New Model for Studies on the Evolution of Development. Developmental Biology. Dev Biol. 2007 Dec 15;312(2):545-59. Epub 2007 Oct 6.
Begun D. J., A. D. Kern, H. A. Lindfors, & C. D. Jones. 2007. Rapid evolution and turnover of testis-expressed genes in the Drosophila yakuba/D. erecta lineage. Genetics. 176:1131-7.
Jeck, W. R. , J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones. 2007. Applications Note: Extending assembly of short DNA sequences to handle error through VCAKE. Bioinformatics. 23(21):2942-4.
Begun, D.J., A. K. Holloway, K. Stevens, L W. Hillier, Y-P Poh, M. W. Hahn, P. M. Nista, C. D. Jones, A. D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langely. 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology. 5(11):e310.
Holloway, A.K., M.L. Lawniczak, D. J. Begun, J. G. Mezey, and C. D. Jones. 2007. Genome-wide comparison of structural and transcriptional divergence among Drosophila melanogaster, D. simulans, and D. yakuba. PLoS Genetics 3(10):2007-13.
Masly, J. P., C. D. Jones, M. A.F. Noor, J. Locke & H. A. Orr. 2006. Gene transposition as a novel cause of hybrid sterility in Drosophila. Science. 313:1448-1450.
Jones C. D. and D. J. Begun. 2005. Parallel evolution of chimeric fusion genes. PNAS. 102:11373-8.
Jones C. D. A. W. Custer, and D. J. Begun. 2005. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, Drosophila madeirensis, and Drosophila guanche. Genetics 170: 207-19
Jones, C. D. 2005. The genetics of adaptations in Drosophila sechellia. Genetica. 123(1-2):137-45. [also featured in The Georgia Genetics Review. Vol. 3. Kluwer Academic Publishing, New York.]
Jones, C. D. 2004. The genetics of egg production in Drosophila sechellia. Heredity 92:235-41.
Population and Quantitative Genetics
Baltrus DA, Romanchuk A, Nishmura M, Roach J, Jones CD, Dangl JD. Whole genome sequencing of a clade of Pseudomonads reveals complex interplay between effector repertoire and host utilization. PLoS Pathogens [accepted pending minor revision].
Lawniczak M. K. N., A. K. Holloway, D. J. Begun and C. D. Jones. 2008. Linkage between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biology. 9:R125. PMC2575515.
Begun, D.J., A. K. Holloway, K. Stevens, L W. Hillier, Y-P Poh, M. W. Hahn, P.M. Nista, C. D. Jones, A. D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langely. 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology. 5(11):e310.
Mezey, J. G., S. V. Nuzhdin, F.F. Yu, and C. D. Jones. 2007 Co-expression domains: units of evolution in the Drosophila transcriptome. BMC Evolutionary Biology. In press.
Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-218.
Holloway, A.K., M.L. Lawniczak, D.J.Begun, J.G. Mezey, and C.D. Jones, 2007. Genome-wide comparison of structural and transcriptional divergence among Drosophila melanogaster, D. simulans, and D. yakuba. PLoS Genetics 3(10):2007-13. PMC2042001.
Masly, J. P., C. D. Jones, M. A.F. Noor, J. Locke & H. A. Orr. 2006. Gene transposition as a novel cause of hybrid sterility in Drosophila. Science. 313:1448-1450.
Danzinger, R.S., and C. D. Jones. 2005. A time to reconsider our collaborations with the Dahl rat. Current Hypertension Reviews. 1(2):97-99
Kern, A.D., C. D. Jones, and D. J. Begun. 2004. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics. 167 (2): 715-35.
Kern, A.D., C. D. Jones, and D. J. Begun. 2002 Genomic effects of nucleotide substitution. Genetics 162(4):1753-61
Jones, C. D. 2001. Extension of the Castle-Wright effective factor estimator to sex-linkage and haplodiploidy. Journal of Heredity. 92:274-276
Otto, S. P. and C. D. Jones. 2000. Detecting the undetected: estimating the number of loci underlying a trait in QTL studies. Genetics. 156:2093-2107.
Reinhardt J.A., Baltrus D.A., Nishimura M.T., Jeck W.R., Jones C.D., Dangl J.L. 2009. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19(2):294-305.
Faddah D.A., Ganko E.W., McCoach C., Pickrell J,K,. Hanlon S.E., Mann F.G., Mieczkowska J.O., Jones C.D., Lieb J.D., Vision T.J. 2009. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet. 5(6):e1000502.
Jeck, W. R. , J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones. 2007. Applications Note: Extending assembly of short DNA sequences to handle error through VCAKE. Bioinformatics. 23(21):2942-4.
Begun, D.J., A. K. Holloway, K. Stevens, L W. Hillier, Y-P Poh, M. W. Hahn, P. M. Nista, C. D. Jones, A. D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langely. 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology. 5(11):e310.
Software and Technical Writing
PepCharge. © 1993 C. D. Jones. Version 1.01. A utility program for calculating peptide charges at various pH.
Electronic Blueprint Survey. © 1993-1994. Microsoft Corp. Programmed by C. D. Jones. Versions 1.00-1.04. A tool for conducting surveys electronically. Also included technical writing and help file programming.
CPTEST.DLL © 1994 Microsoft Corp. Programming by C. D. Jones. Version 1.0 A dynamic link library providing data access to a SQL server database.
KJBtest. 2002. C.D. Jones. Used for detecting nucleotide changes caused by natural selection.
OJest. 2000-2002. C. D. Jones and S. P. Otto, A utility program for estimating the number of QTLs.
Dsim/Dyak Genome Project BLAST site. 2004. C. Jones and A. Kern. www.DPGP.org
VCAKE. 2007. W. R. Jeck, J. R. Reinhardt, and C. D. Jones , A utility program for estimating the number of QTLs. VCAKE-at sourceforge
Jones C. D. and J. D. Munnoch. 1994. Endangered plants of the Pacific Northwest. Mountaineers. April 1994:13-15.
Jones C. D. and H. A. Orr. 1996. An attempt to rescue hybrid fertility by germline mitotic recombination in Drosophila. Drosophila Information Service. 77:82-83.
Jones C. D. and H. A. Orr. 1998. Test of a Drosophila simulans balancer and a remapping of chromosome 3. Drosophila Information Service. 81:137-138.
Jones, C. D. 2004. Drosophila sechellia: a system for studying the genetics of adaptation. Vol. 3. Kluwer Academic Publishing, New York. pp 137-146
Jones C. D. 2007. Genetic ablation of antennae or basiconic sensillia reduces Drosophila melanogasters ability to perceive odors from the fruit of Morinda citrifolia. Drosophila Information Service. 90: 45-49.
Jeck, W.R, H-J Shih and C.D. Jones. 2008 Rapidly Evolving Genes Show Well Resolved but Conflicting Phylogenies: Evidence from Drosophila simulans Complex. Drosophila Information Service. 91: