| Year |
Citation |
Score |
| 2024 |
Luecke D, Luo Y, Krzystek H, Jones C, Kopp A. Highly Contiguous Genome Assembly of - a Model for Evolution of Sexual Dimorphism and Male-specific Innovations. Biorxiv : the Preprint Server For Biology. PMID 38352395 DOI: 10.1101/2024.01.29.577853 |
0.385 |
|
| 2023 |
Burch CL, Romanchuk A, Kelly M, Wu Y, Jones CD. Empirical evidence that complexity limits horizontal gene transfer. Genome Biology and Evolution. PMID 37232518 DOI: 10.1093/gbe/evad089 |
0.322 |
|
| 2021 |
Kim BY, Wang J, Miller DE, Barmina O, Delaney EK, Thompson A, Comeault AA, Peede D, D'Agostino ER, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong E, Zych M, ... ... Jones CD, et al. Highly contiguous assemblies of 101 drosophilid genomes. Elife. 10. PMID 34279216 DOI: 10.7554/eLife.66405 |
0.321 |
|
| 2020 |
Liu Y, Jones CD, Day LB, Summers K, Burmeister SS. Cognitive phenotype and differential gene expression in a hippocampal homologue in two species of frog. Integrative and Comparative Biology. PMID 32413121 DOI: 10.1093/icb/icaa032 |
0.317 |
|
| 2020 |
Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. Virus expression detection reveals RNA-sequencing contamination in TCGA. Bmc Genomics. 21: 79. PMID 31992194 DOI: 10.1186/S12864-020-6483-6 |
0.345 |
|
| 2020 |
Li W, Hannig J, Jones CD. A note on optimal sampling strategy for structural variant detection using optical mapping Communications in Statistics-Theory and Methods. 1-15. DOI: 10.1080/03610926.2020.1723638 |
0.331 |
|
| 2019 |
Matute DR, Comeault AA, Earley E, Serrato-Capuchina A, Peede D, Monroy-Eklund A, Huang W, Jones CD, Mackay TFC, Coyne JA. Rapid and Predictable Evolution of Admixed Populations Between Two Species Pairs. Genetics. PMID 31767631 DOI: 10.1534/Genetics.119.302685 |
0.766 |
|
| 2019 |
Seidl F, Levis NA, Jones CD, Monroy-Eklund A, Ehrenreich IM, Pfennig KS. Variation in hybrid gene expression: implications for the evolution of genetic incompatibilities in interbreeding species. Molecular Ecology. PMID 31541560 DOI: 10.1111/Mec.15246 |
0.403 |
|
| 2018 |
Melvin RG, Lamichane N, Havula E, Kokki K, Soeder C, Jones CD, Hietakangas V. Natural variation in sugar tolerance associates with changes in signaling and mitochondrial ribosome biogenesis. Elife. 7. PMID 30480548 DOI: 10.7554/Elife.40841 |
0.41 |
|
| 2018 |
Wang JR, Holt J, McMillan L, Jones CD. FMLRC: Hybrid long read error correction using an FM-index. Bmc Bioinformatics. 19: 50. PMID 29426289 DOI: 10.1186/S12859-018-2051-3 |
0.368 |
|
| 2017 |
Wern Pan J, Li Q, Barish S, Okuwa S, Zhao S, Soeder C, Kanke M, Jones CD, Volkan PC. Patterns of transcriptional parallelism and variation in the developing olfactory system of Drosophila species. Scientific Reports. 7: 8804. PMID 28821769 DOI: 10.1038/s41598-017-08563-0 |
0.342 |
|
| 2017 |
O'Keeffe KR, Carbone I, Jones CD, Mitchell CE. Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants. Current Opinion in Plant Biology. 38: 78-83. PMID 28505582 DOI: 10.1016/J.Pbi.2017.04.014 |
0.303 |
|
| 2017 |
Wang J, Paredes S, Yourstone S, Furey T, Sheikh S, Dangl J, Jones C. P-310 YI Characterizing Gut Metagenome Variation with Host Contamination Using Nanopore Sequencing Inflammatory Bowel Diseases. 23. DOI: 10.1097/01.Mib.0000512851.06959.15 |
0.352 |
|
| 2016 |
Welch JD, Williams LA, DiSalvo M, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD. Selective single cell isolation for genomics using microraft arrays. Nucleic Acids Research. PMID 27530426 DOI: 10.1093/Nar/Gkw700 |
0.339 |
|
| 2016 |
Li Q, Barish S, Okuwa S, Maciejewski A, Brandt AT, Reinhold D, Jones CD, Volkan PC. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. Plos Genetics. 12: e1005780. PMID 26765103 DOI: 10.1371/Journal.Pgen.1005780 |
0.303 |
|
| 2015 |
Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Osborne Nishimura E, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America. PMID 26598659 DOI: 10.1073/Pnas.1510461112 |
0.486 |
|
| 2015 |
Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina Del Rio T, Jones CD, Tringe SG, Dangl JL. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science (New York, N.Y.). PMID 26184915 DOI: 10.1126/Science.Aaa8764 |
0.688 |
|
| 2015 |
Zhou S, Jones C, Mieczkowski P, Swanstrom R. Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations. Journal of Virology. 89: 8540-55. PMID 26041299 DOI: 10.1128/Jvi.00522-15 |
0.404 |
|
| 2015 |
Dworkin I, Jones CD. Evolutionary genetics: you are what you evolve to eat. Current Biology : Cb. 25: R341-4. PMID 25898107 DOI: 10.1016/j.cub.2015.01.044 |
0.651 |
|
| 2014 |
Yourstone SM, Lundberg DS, Dangl JL, Jones CD. MT-Toolbox: improved amplicon sequencing using molecule tags. Bmc Bioinformatics. 15: 284. PMID 25149069 DOI: 10.1186/1471-2105-15-284 |
0.727 |
|
| 2014 |
Jabara CB, Hu F, Mollan KR, Williford SE, Menezes P, Yang Y, Eron JJ, Fried MW, Hudgens MG, Jones CD, Swanstrom R, Lemon SM. Hepatitis C Virus (HCV) NS3 sequence diversity and antiviral resistance-associated variant frequency in HCV/HIV coinfection. Antimicrobial Agents and Chemotherapy. 58: 6079-92. PMID 25092699 DOI: 10.1128/Aac.03466-14 |
0.764 |
|
| 2014 |
Romanchuk A, Jones CD, Karkare K, Moore A, Smith BA, Jones C, Dougherty K, Baltrus DA. Bigger is not always better: transmission and fitness burden of ∼1MB Pseudomonas syringae megaplasmid pMPPla107. Plasmid. 73: 16-25. PMID 24792221 DOI: 10.1016/J.Plasmid.2014.04.002 |
0.405 |
|
| 2014 |
Bartoli C, Berge O, Monteil CL, Guilbaud C, Balestra GM, Varvaro L, Jones C, Dangl JL, Baltrus DA, Sands DC, Morris CE. The Pseudomonas viridiflava phylogroups in the P. syringae species complex are characterized by genetic variability and phenotypic plasticity of pathogenicity-related traits. Environmental Microbiology. 16: 2301-15. PMID 24612372 DOI: 10.1111/1462-2920.12433 |
0.387 |
|
| 2014 |
Reinhardt JA, Kolaczkowski B, Jones CD, Begun DJ, Kern AD. Parallel geographic variation in Drosophila melanogaster. Genetics. 197: 361-73. PMID 24610860 DOI: 10.1534/Genetics.114.161463 |
0.781 |
|
| 2014 |
Baltrus DA, Yourstone S, Lind A, Guilbaud C, Sands DC, Jones CD, Morris CE, Dangl JL. Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations. Genome Announcements. 2. PMID 24459267 DOI: 10.1128/Genomea.01195-13 |
0.423 |
|
| 2014 |
Zhao L, Saelao P, Jones CD, Begun DJ. Origin and spread of de novo genes in Drosophila melanogaster populations. Science (New York, N.Y.). 343: 769-72. PMID 24457212 DOI: 10.1126/Science.1248286 |
0.712 |
|
| 2014 |
Mucyn TS, Yourstone S, Lind AL, Biswas S, Nishimura MT, Baltrus DA, Cumbie JS, Chang JH, Jones CD, Dangl JL, Grant SR. Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny. Plos Pathogens. 10: e1003807. PMID 24391493 DOI: 10.1371/Journal.Ppat.1003807 |
0.457 |
|
| 2014 |
Guo X, Zheng S, Dang H, Pace RG, Stonebraker JR, Jones CD, Boellmann F, Yuan G, Haridass P, Fedrigo O, Corcoran DL, Seibold MA, Ranade SS, Knowles MR, O'Neal WK, et al. Genome reference and sequence variation in the large repetitive central exon of human MUC5AC. American Journal of Respiratory Cell and Molecular Biology. 50: 223-32. PMID 24010879 DOI: 10.1165/Rcmb.2013-0235Oc |
0.489 |
|
| 2013 |
Reinhardt JA, Jones CD. Two rapidly evolving genes contribute to male fitness in Drosophila. Journal of Molecular Evolution. 77: 246-59. PMID 24221639 DOI: 10.1007/S00239-013-9594-8 |
0.799 |
|
| 2013 |
Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. Plos Genetics. 9: e1003860. PMID 24146629 DOI: 10.1371/Journal.Pgen.1003860 |
0.805 |
|
| 2013 |
Hungate EA, Earley EJ, Boussy IA, Turissini DA, Ting CT, Moran JR, Wu ML, Wu CI, Jones CD. A locus in Drosophila sechellia affecting tolerance of a host plant toxin. Genetics. 195: 1063-75. PMID 24037270 DOI: 10.1534/Genetics.113.154773 |
0.7 |
|
| 2013 |
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. Practical innovations for high-throughput amplicon sequencing. Nature Methods. 10: 999-1002. PMID 23995388 DOI: 10.1038/Nmeth.2634 |
0.744 |
|
| 2013 |
Sarris PF, Trantas EA, Baltrus DA, Bull CT, Wechter WP, Yan S, Ververidis F, Almeida NF, Jones CD, Dangl JL, Panopoulos NJ, Vinatzer BA, Goumas DE. Comparative genomics of multiple strains of Pseudomonas cannabina pv. alisalensis, a potential model pathogen of both monocots and dicots. Plos One. 8: e59366. PMID 23555661 DOI: 10.1371/Journal.Pone.0059366 |
0.436 |
|
| 2013 |
Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J. A robust method for transcript quantification with RNA-seq data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 167-87. PMID 23461570 DOI: 10.1089/Cmb.2012.0230 |
0.321 |
|
| 2013 |
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, et al. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Research. 41: e39. PMID 23155066 DOI: 10.1093/nar/gks1026 |
0.35 |
|
| 2012 |
Pfennig KS, Allenby A, Martin RA, Monroy A, Jones CD. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.). Molecular Ecology Resources. 12: 909-17. PMID 22564443 DOI: 10.1111/J.1755-0998.2012.03150.X |
0.357 |
|
| 2012 |
Leichty AR, Pfennig DW, Jones CD, Pfennig KS. Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity. Integrative and Comparative Biology. 52: 16-30. PMID 22526866 DOI: 10.1093/Icb/Ics049 |
0.472 |
|
| 2011 |
Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proceedings of the National Academy of Sciences of the United States of America. 108: 20166-71. PMID 22135472 DOI: 10.1073/Pnas.1110064108 |
0.803 |
|
| 2011 |
Earley EJ, Jones CD. Next-generation mapping of complex traits with phenotype-based selection and introgression. Genetics. 189: 1203-9. PMID 21940681 DOI: 10.1534/Genetics.111.129445 |
0.723 |
|
| 2011 |
Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics (Oxford, England). 27: 2633-40. PMID 21824971 DOI: 10.1093/Bioinformatics/Btr458 |
0.344 |
|
| 2011 |
Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, Cherkis K, Roach J, Grant SR, Jones CD, Dangl JL. Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. Plos Pathogens. 7: e1002132. PMID 21799664 DOI: 10.1371/Journal.Ppat.1002132 |
0.447 |
|
| 2011 |
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 morphogenesis genes in Caenorhabditis elegans. Genetics. 188: 549-64. PMID 21527776 DOI: 10.1534/Genetics.111.129486 |
0.425 |
|
| 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, et al. HIV-1 Populations in Semen Arise through Multiple Mechanisms. Plos Pathogens. 6: e1001053. PMID 20808902 DOI: 10.1371/Journal.Ppat.1001053 |
0.747 |
|
| 2010 |
Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, et al. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. Journal of Immunology (Baltimore, Md. : 1950). 184: 6986-92. PMID 20495067 DOI: 10.4049/Jimmunol.1000445 |
0.354 |
|
| 2009 |
Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. Plos Genetics. 5: e1000502. PMID 19503594 DOI: 10.1371/Journal.Pgen.1000502 |
0.441 |
|
| 2009 |
Dworkin I, Jones CD. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics. 181: 721-36. PMID 19033155 DOI: 10.1534/genetics.108.093419 |
0.693 |
|
| 2009 |
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research. 19: 294-305. PMID 19015323 DOI: 10.1101/Gr.083311.108 |
0.776 |
|
| 2008 |
Shih HJ, Jones CD. Patterns of amino acid evolution in the Drosophila ananassae chimeric gene, siren, parallel those of other Adh-derived chimeras. Genetics. 180: 1261-3. PMID 18780749 DOI: 10.1534/genetics.108.090068 |
0.417 |
|
| 2008 |
Lawniczak MK, Holloway AK, Begun DJ, Jones CD. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biology. 9: R125. PMID 18700012 DOI: 10.1186/Gb-2008-9-8-R125 |
0.809 |
|
| 2008 |
Kopp A, Barmina O, Hamilton AM, Higgins L, McIntyre LM, Jones CD. Evolution of gene expression in the Drosophila olfactory system. Molecular Biology and Evolution. 25: 1081-92. PMID 18296696 DOI: 10.1093/Molbev/Msn055 |
0.434 |
|
| 2008 |
Mezey JG, Nuzhdin SV, Ye F, Jones CD. Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. Bmc Evolutionary Biology. 8: 2. PMID 18179715 DOI: 10.1186/1471-2148-8-2 |
0.422 |
|
| 2007 |
Gabriel WN, McNuff R, Patel SK, Gregory TR, Jeck WR, Jones CD, Goldstein B. The tardigrade Hypsibius dujardini, a new model for studying the evolution of development. Developmental Biology. 312: 545-59. PMID 17996863 DOI: 10.1016/J.Ydbio.2007.09.055 |
0.335 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Jones CD, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.805 |
|
| 2007 |
Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Plos Biology. 5: e310. PMID 17988176 DOI: 10.1371/Journal.Pbio.0050310 |
0.814 |
|
| 2007 |
Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD. Adaptive gene expression divergence inferred from population genomics. Plos Genetics. 3: 2007-13. PMID 17967066 DOI: 10.1371/Journal.Pgen.0030187 |
0.823 |
|
| 2007 |
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error. Bioinformatics (Oxford, England). 23: 2942-4. PMID 17893086 DOI: 10.1093/Bioinformatics/Btm451 |
0.75 |
|
| 2007 |
Begun DJ, Lindfors HA, Kern AD, Jones CD. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics. 176: 1131-7. PMID 17435230 DOI: 10.1534/genetics.106.069245 |
0.778 |
|
| 2006 |
Masly JP, Jones CD, Noor MA, Locke J, Orr HA. Gene transposition as a cause of hybrid sterility in Drosophila. Science (New York, N.Y.). 313: 1448-50. PMID 16960009 DOI: 10.1126/Science.1128721 |
0.78 |
|
| 2006 |
Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proceedings of the National Academy of Sciences of the United States of America. 103: 9935-9. PMID 16777968 DOI: 10.1073/Pnas.0509809103 |
0.814 |
|
| 2005 |
Jones CD, Begun DJ. Parallel evolution of chimeric fusion genes. Proceedings of the National Academy of Sciences of the United States of America. 102: 11373-8. PMID 16076957 DOI: 10.1073/pnas.0503528102 |
0.636 |
|
| 2005 |
Jones CD. The genetics of adaptation in Drosophila sechellia. Genetica. 123: 137-45. PMID 15881686 DOI: 10.1007/s10709-004-2728-6 |
0.396 |
|
| 2005 |
Jones CD, Custer AW, Begun DJ. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics. 170: 207-19. PMID 15781692 DOI: 10.1534/Genetics.104.037283 |
0.696 |
|
| 2004 |
Kern AD, Jones CD, Begun DJ. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics. 167: 725-35. PMID 15238524 DOI: 10.1534/genetics.103.020883 |
0.768 |
|
| 2004 |
Jones CD. Genetics of egg production in Drosophila sechellia Heredity. 92: 235-241. PMID 14710171 DOI: 10.1038/sj.hdy.6800401 |
0.352 |
|
| 2002 |
Kern AD, Jones CD, Begun DJ. Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics. 162: 1753-61. PMID 12524346 |
0.724 |
|
| 2001 |
Jones CD. The genetic basis of larval resistance to a host plant toxin in Drosophila sechellia Genetical Research. 78: 225-233. PMID 11865712 DOI: 10.1017/S0016672301005298 |
0.32 |
|
| 2001 |
Jones CD. Extension of the castle - Wright effective factor estimator to sex linkage and haplodiploidy Journal of Heredity. 92: 274-276. PMID 11447245 DOI: 10.1093/Jhered/92.3.274 |
0.307 |
|
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