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John G. Gibbons, Ph.D. - Publications

Affiliations: 
Vanderbilt University, Nashville, TN 
Area:
Population genetics, evolution
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylogenomics reveals extensive misidentification of fungal strains from the genus . Microbiology Spectrum. e0398023. PMID 38445873 DOI: 10.1128/spectrum.03980-23  0.73
2023 Ghoshal M, Bechtel TD, Gibbons JG, McLandsborough L. Adaptive laboratory evolution of in acid stress. Frontiers in Microbiology. 14: 1285421. PMID 38033570 DOI: 10.3389/fmicb.2023.1285421  0.745
2023 Sierra-Patev S, Min B, Naranjo-Ortiz M, Looney B, Konkel Z, Slot JC, Sakamoto Y, Steenwyk JL, Rokas A, Carro J, Camarero S, Ferreira P, Molpeceres G, Ruiz-Dueñas FJ, Serrano A, ... ... Gibbons JG, et al. A global phylogenomic analysis of the shiitake genus . Proceedings of the National Academy of Sciences of the United States of America. 120: e2214076120. PMID 36848567 DOI: 10.1073/pnas.2214076120  0.808
2022 Gibbons JG, D'Avino P, Zhao S, Cox GW, Rinker DC, Fortwendel JR, Latge JP. Comparative Genomics Reveals a Single Nucleotide Deletion in That Results in White-Spore Phenotype in Natural Variants of . Frontiers in Fungal Biology. 3: 897954. PMID 37746219 DOI: 10.3389/ffunb.2022.897954  0.794
2022 Zhao S, Martin-Vicente A, Colabardini AC, Pereira Silva L, Rinker DC, Fortwendel JR, Goldman GH, Gibbons JG. Genomic and Molecular Identification of Genes Contributing to the Caspofungin Paradoxical Effect in . Microbiology Spectrum. e0051922. PMID 36094204 DOI: 10.1128/spectrum.00519-22  0.786
2022 Horta MAC, Steenwyk JL, Mead ME, Dos Santos LHB, Zhao S, Gibbons JG, Marcet-Houben M, Gabaldón T, Rokas A, Goldman GH. Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. Mbio. e0151922. PMID 35766381 DOI: 10.1128/mbio.01519-22  0.792
2022 Zhang J, Walker ME, Sanidad KZ, Zhang H, Liang Y, Zhao E, Chacon-Vargas K, Yeliseyev V, Parsonnet J, Haggerty TD, Wang G, Simpson JB, Jariwala PB, Beaty VV, Yang J, ... ... Gibbons JG, et al. Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. Nature Communications. 13: 136. PMID 35013263 DOI: 10.1038/s41467-021-27762-y  0.755
2021 Zhao S, Ge W, Watanabe A, Fortwendel JR, Gibbons JG. Genome-Wide Association for Itraconazole Sensitivity in Non-resistant Clinical Isolates of . Frontiers in Fungal Biology. 1: 617338. PMID 37743877 DOI: 10.3389/ffunb.2020.617338  0.617
2021 Yuan Z, Druzhinina IS, Gibbons JG, Zhong Z, Van de Peer Y, Rodriguez RJ, Liu Z, Wang X, Wei H, Wu Q, Wang J, Shi G, Cai F, Peng L, Martin FM. Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus. The Isme Journal. PMID 34408269 DOI: 10.1038/s41396-021-01083-w  0.412
2021 Chacón-Vargas K, McCarthy CO, Choi D, Wang L, Yu JH, Gibbons JG. Comparison of Two Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism. Frontiers in Microbiology. 12: 691296. PMID 34326825 DOI: 10.3389/fmicb.2021.691296  0.84
2021 Yuan Z, Druzhinina IS, Gibbons JG, Zhong Z, Van de Peer Y, Rodriguez RJ, Liu Z, Wang X, Wei H, Wu Q, Wang J, Shi G, Cai F, Peng L, Martin FM. Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus. The Isme Journal. PMID 34108667 DOI: 10.1038/s41396-021-01023-8  0.437
2021 Zhao S, Koffi D, Latge JP, Sylla K, Gibbons JG. Genome Sequence of Aspergillus aculeatinus IC_8, Isolated from an Indoor Air Sample of an Urban Housing Complex in Abidjan, Ivory Coast. Microbiology Resource Announcements. 10. PMID 33707326 DOI: 10.1128/MRA.00096-21  0.624
2021 Bechtel TD, Gibbons JG. Population Genomic Analysis of From Food Reveals Substrate-Specific Genome Variation. Frontiers in Microbiology. 12: 620033. PMID 33633707 DOI: 10.3389/fmicb.2021.620033  0.773
2020 Chacón-Vargas K, Torres J, Giles-Gómez M, Escalante A, Gibbons JG. Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing. Scientific Reports. 10: 15115. PMID 32934253 DOI: 10.1038/s41598-020-71864-4  0.823
2019 Zhao S, Latgé JP, Gibbons JG. Genome Sequences of Two Strains of the Food Spoilage Mold Aspergillus fischeri. Microbiology Resource Announcements. 8. PMID 31831615 DOI: 10.1128/MRA.01328-19  0.649
2019 Rinker DC, Specian NK, Zhao S, Gibbons JG. Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. Proceedings of the National Academy of Sciences of the United States of America. 116: 13446-13451. PMID 31209046 DOI: 10.1073/Pnas.1901093116  0.73
2018 Rosienski MD, Lee MK, Yu JH, Kaspar CW, Gibbons JG. Genome Sequence of the Extremely Acidophilic Fungus Acidomyces richmondensis FRIK2901. Microbiology Resource Announcements. 7. PMID 30533739 DOI: 10.1128/MRA.01314-18  0.767
2018 Wu B, Xu Z, Knudson A, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, ... Gibbons J, et al. Genomics and development of Lentinus tigrinus, a white-rot wood-decaying mushroom with dimorphic fruiting bodies. Genome Biology and Evolution. PMID 30398645 DOI: 10.1093/Gbe/Evy246  0.515
2018 Zhao S, Gibbons JG. A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus. Plos One. 13: e0201611. PMID 30071059 DOI: 10.1371/Journal.Pone.0201611  0.717
2017 Chacon-Vargas K, Chirino AA, Davis MM, Debler SA, Haimer WR, Wilbur JJ, Mo X, Worthing BW, Wainblat EG, Zhao S, Gibbons JG. Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. Genome Announcements. 5. PMID 28751381 DOI: 10.1128/Genomea.00562-17  0.811
2017 Valsecchi I, Sarikaya Bayram Ö, Wong Sak Hoi J, Muszkieta L, Gibbons J, Prevost MC, Mallet A, Krijnse-Locker J, Ibrahim-Granet O, Mouyna I, Carr P, Bromley M, Aimanianda V, Yu YJ, Rokas A, et al. MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus. Molecular Microbiology. PMID 28677124 DOI: 10.1111/Mmi.13744  0.66
2016 Steenwyk JL, Soghigian JS, Perfect JR, Gibbons JG. Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. Bmc Genomics. 17: 700. PMID 27590805 DOI: 10.1186/S12864-016-3044-0  0.826
2016 Staehlin BM, Gibbons JG, Rokas A, O'Halloran TV, Slot JC. Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria. Genome Biology and Evolution. PMID 26893455 DOI: 10.1093/Gbe/Evw031  0.751
2015 Gibbons JG, Rinker DC. The genomics of microbial domestication in the fermented food environment. Current Opinion in Genetics & Development. 35: 1-8. PMID 26338497 DOI: 10.1016/J.Gde.2015.07.003  0.748
2015 Gibbons JG, Branco AT, Godinho SA, Yu S, Lemos B. Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes. Proceedings of the National Academy of Sciences of the United States of America. 112: 2485-90. PMID 25583482 DOI: 10.1073/Pnas.1416878112  0.489
2014 Gibbons JG, Branco AT, Yu S, Lemos B. Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nature Communications. 5: 4850. PMID 25209200 DOI: 10.1038/Ncomms5850  0.46
2013 Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP. Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches. Frontiers in Microbiology. 4: 13. PMID 23407341 DOI: 10.3389/Fmicb.2013.00013  0.659
2013 Gibbons JG, Rokas A. The function and evolution of the Aspergillus genome. Trends in Microbiology. 21: 14-22. PMID 23084572 DOI: 10.1016/J.Tim.2012.09.005  0.776
2013 Ubaida Mohien C, Colquhoun DR, Mathias DK, Gibbons JG, Armistead JS, Rodriguez MC, Rodriguez MH, Edwards NJ, Hartler J, Thallinger GG, Graham DR, Martinez-Barnetche J, Rokas A, Dinglasan RR. A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Molecular & Cellular Proteomics : McP. 12: 120-31. PMID 23082028 DOI: 10.1074/Mcp.M112.019596  0.664
2012 Elmore MH, Gibbons JG, Rokas A. Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. G3 (Bethesda, Md.). 2: 1643-9. PMID 23275886 DOI: 10.1534/G3.112.004663  0.741
2012 Rokas A, Gibbons JG, Zhou X, Beauvais A, Latgé JP. The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Annals of the New York Academy of Sciences. 1273: 25-34. PMID 23230834 DOI: 10.1111/J.1749-6632.2012.06755.X  0.774
2012 Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Current Biology : Cb. 22: 1403-9. PMID 22795693 DOI: 10.1016/J.Cub.2012.05.033  0.77
2012 Martínez-Barnetche J, Gómez-Barreto RE, Ovilla-Muñoz M, Téllez-Sosa J, García López DE, Dinglasan RR, Ubaida Mohien C, MacCallum RM, Redmond SN, Gibbons JG, Rokas A, Machado CA, Cazares-Raga FE, González-Cerón L, Hernández-Martínez S, et al. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. Bmc Genomics. 13: 207. PMID 22646700 DOI: 10.1186/1471-2164-13-207  0.705
2012 Klaassen CH, Gibbons JG, Fedorova ND, Meis JF, Rokas A. Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Molecular Ecology. 21: 57-70. PMID 22106836 DOI: 10.1111/J.1365-294X.2011.05364.X  0.674
2012 Gibbons JG, Beauvais A, Beau R, McGary KL, Latgé JP, Rokas A. Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryotic Cell. 11: 68-78. PMID 21724936 DOI: 10.1128/Ec.05102-11  0.815
2011 Kent BN, Salichos L, Gibbons JG, Rokas A, Newton IL, Clark ME, Bordenstein SR. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biology and Evolution. 3: 209-18. PMID 21292630 DOI: 10.1093/Gbe/Evr007  0.832
2010 An J, Bechet A, Berggren A, Brown SK, Bruford MW, Cai Q, Cassel-Lundhagen A, Cezilly F, Chen SL, Cheng W, Choi SK, Ding XY, Fan Y, Feldheim KA, ... ... Gibbons JG, et al. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009. Molecular Ecology Resources. 10: 404-8. PMID 21565039 DOI: 10.1111/J.1755-0998.2009.02827.X  0.65
2009 Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution. 26: 2731-44. PMID 19706727 DOI: 10.1093/Molbev/Msp188  0.744
2009 Gibbons JG, Rokas A. Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes. Molecular Biology and Evolution. 26: 591-602. PMID 19056904 DOI: 10.1093/Molbev/Msn277  0.727
2007 Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn JN, Daly MJ, Hughes TE, Groop L, Altshuler D, Almgren P, ... ... Gibbons J, et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science (New York, N.Y.). 316: 1331-6. PMID 17463246 DOI: 10.1126/Science.1142358  0.401
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