Publications
2024
(47) Steenwyk, JL, Charu Balamurugan, Huzefa A Raja, Carla Gonçalves, Ningxiao Li, Frank Martin, Judith Berman, Nicholas H Oberlies, John G Gibbons, Gustavo H Goldman, David M Geiser, Jos Houbraken, David S Hibbett and Antonis Rokas (2024). Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiology Spectrum, pp.e03980-23.
(46) Ghoshal, M., Bechtel, T.D., Gibbons, J.G. and McLandsborough, L., (2024). Transcriptomic analysis using RNA sequencing and phenotypic analysis of Salmonella enterica after acid exposure for different time durations using adaptive laboratory evolution. Frontiers in Microbiology, 15, p.1348063.
2023
(45) Ghoshal, M., Bechtel, T.D., Gibbons, J.G. and McLandsborough, L., (2023). Adaptive laboratory evolution of Salmonella enterica in acid stress. Frontiers in Microbiology, 14, p.1285421.
(44) Sierra-Patev, S, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C Slot, Yuichi Sakamoto, Jacob L Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco J Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W Hughes, Juan L Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, Kerrie Barry, Angel T Martínez, Yang Xiao, John G Gibbons, Kazuhisa Terashima, Igor V Grigoriev, David Hibbett (2023). A global phylogenomic analysis of the shiitake genus Lentinula. Proceedings of the National Academy of Sciences, 120(10), p.e2214076120.
2022
(43) Zhao, S., Martin-Vicente, A., Colabardini, A.C., Pereira Silva, L., Rinker, D.C., Fortwendel, J.R., Goldman, G.H. and Gibbons, J.G., (2022). Genomic and Molecular Identification of Genes Contributing to the Caspofungin Paradoxical Effect in Aspergillus fumigatus. Microbiology spectrum, 10(5), pp.e00519-22.
(42) Horta, M.A.C., Steenwyk, J.L., Mead, M.E., Dos Santos, L.H.B., Zhao, S., Gibbons, J.G., Marcet-Houben, M., Gabaldón, T., Rokas, A. and Goldman, G.H., (2022). Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus. Mbio, pp.e01519-22.
(41) Gibbons, J.G., D'Avino, P., Zhao, S., Cox, G.W., Rinker, D.C., Fortwendel, J.R. and Latgé, J.P. (2022) Comparative genomics reveals a single nucleotide deletion in pksP that results in white-spore phenotype in natural variants of Aspergillus fumigatus. Frontiers in Fungal Biology, p.25.
(40) Ajmal M., Alshannaq A.F., Moon H., Choi D., Akram A., Nayyar B.G., Gibbons J.G., Yu J.-H. Characterization of 260 Isolates of Aspergillus Section Flavi Obtained from Sesame Seeds in Punjab, Pakistan (2022). Toxins. 14(2):117. Article link
(39) Zhang, J., Walker, M.E., Sanidad, K.Z., Zhang, H., Liang, Y., Zhao, E., Chacon-Vargas, K., Yeliseyev, V., Parsonnet, J., Haggerty, T.D. and Wang, G., Simpson, J.S., Jariwala, P.B., Beaty, V.V., Yang, J., Yang, H., Panigrahy, A., Minter, L.M., Kim, D., Gibbons, J.G., Liu, L., Li, Z., Xiao, H., Borlandelli, V., Overkleeft, H.S., Cloer, E.W., Major, M.B., Goldfarb, D., Cai, Z., Redinbo, M.R. and Zhang, G. (2022). Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. Nature Communications, 13(1), pp.1-14.
2021
(38) Chacon-Vargas, K., C.O. McCarthy, D. Choi, L. Wang, J.H. Yu and J.G. Gibbons (2021). Comparison of two Aspergillus oryzae 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, p.1958.
(37) Yuan, Z., Druzhinina, I.S., Gibbons, J.G., Zhong, Z., Van de Peer, Y., Rodriguez, R.J., Liu, Z., Wang, X., Wei, H., Wu, Q. and Wang, J., (2021). Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus. The ISME Journal, pp.1-12. Article link
(36) Zhao, S., D. Koffi, J.-P. Latge, K. Sylla and J.G. Gibbons (2021). 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:e00096-21. Article link
(35) Bechtel, T.D. and J.G. Gibbons (2021). Population genomic analysis of Listeria monocytogenes from food reveals substrate-specific genome variation. Frontiers in Microbiology, 12. Article link
(34) Ahnan-Winarno, A.D., L. Cordeiro, F.L. Winarno, J.G. Gibbons, and H. Xiao. Tempeh: A semi-centennial review on its health benefits, fermentation, safety, processing, sustainability, and affordability. Comprehensive Reviews in Food Science and Food Safety. Article Link
(33) Zhao, S., W. Ge, A. Watanabe, J.R. Fortwendel and J.G. Gibbons. Genome-Wide Association for Itraconazole Sensitivity in Non-Resistant Clinical Isolates of Aspergillus fumigatus. Frontiers in Fungal Biology, 1:617338. Article Link
2020
(32) Chacon-Vargas, K., J. Torres, M. Giles-Gómez, A. Escalante, and J.G. Gibbons (2020). Genomic Profiling of Bacterial and Fungal communities and their Predictive Functionality during Pulque Fermentation by Whole-Genome Shotgun Sequencing. Scientific Reports , 10(1), pp.1-13. Article Link
(31) Farrington, S.J., R.W. King, J.A. Baker, and J.G. Gibbons (2020). Population genetics of freshwater pearl mussel (Margaritifera margaritifera) in central Massachusetts and implications for conservation. Aquatic Conservation: Marine and Freshwater Ecosystems, 30(10), pp.1945-1958. Article Link
2019
(30) Gibbons, J.G. (2019). How to Train your Fungus. mBio: 6:e03031-19. PDF
(29) Zhao, S., J.-P. Latge and J.G. Gibbons (2019). Genome Sequences of Two Strains of the Food Spoilage Mold Aspergillus fischeri . Microbiology Resource Announcements: 8:e01328-19. PDF
(28) Rinker, D.C.*, N.K. Specian*, S. Zhao and J.G. Gibbons (2019). Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. PNAS, p.201901093 (*Equal contributors) Article Link
2018
(27) Alshannaq, A. F., J.G. Gibbons, M.K. Lee, K.H. Han, S.B. Hong, and J.H. Yu (2018). Controlling aflatoxin contamination and propagation of Aspergillus flavus by a soy-fermenting Aspergillus oryzae strain. Scientific Reports, 8(1), 16871. PDF
(26) Wu, B., Z. Xu, A. Knudson, A. Carlson, N. Chen, S. Kovaka, K. LaButti, A. Lipzen, C. Pennachio, R. Riley, W. Schakwitz, K. Umezawa, R.A. Ohm, I.V. Grigoriev, L.G. Nagy, J.G. Gibbons, D. Hibbett (2018). Genomics and development of Lentinus tigrinus, a white-rot wood-decaying mushroom with dimorphic fruiting bodies. Genome Biology and Evolution.
(25) Rosienski, M.D., M.-K. Lee, J.-H. Yu, C.W. Kaspar and J.G. Gibbons (2018). Genome Sequence of the Extremely Acidophilic Fungus Acidomyces richmondensis FRIK2901. Microbiology Resource Announcements: 7:e01314-18. PDF
(24) Zhao, S., and J.G. Gibbons (2018). A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus. PLoS One: 13(8): e0201611. PDF
(23) Valsecchi, I., V. Dupres, E. Stephen-Victor, J.I. Guijarro, J.G. Gibbons, R. Beau, J. Bayry, J.-Y. Coppee, F. Lafont, J.-P. Latgé, and A. Beauvais (2017). Role of Hydrophobins in Aspergillus fumigatus. Journal of Fungi: 4:1. PDF
2017
(22) Chacon-Vargas, K., A.A. Chirino, M.M. Davis, S.A. Debler, W.R. Haimer, J.J. Wilbur, X. Mo, B.W. Worthing, E.G. Wainblat, S. Zhao, and J.G. Gibbons (2017). The Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. Genome Announcements: 5(30), pp.e00562- 17. PDF
(21) Valsecchi, I., O. Sarikayabayram, J. Wong Sak Hoi, L. Muszkieta, J.G. Gibbons, M.-C. Prevost, A. Mallet, J. Krijnse-Locker, O. Granet, I. Mouyna, P. Carr, M. Bromley, V. K. Aimanianda, J.-H. Yu, A. Rokas, G. Braus, C. Saveanu, O. Bayram, & J.-P. Latgé (2017). MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus. Molecular Microbiology: 105: 880-900. PDF
(20) Wu, M., J.G. Gibbons, G. Deloid, A. Bedugnis, R. Thimmulappa, S. Biswal, and L. Kobzik (2017). Immunomodulators Targeting MARCO Expression Improve Resistance to Post-influenza Bacterial Pneumonia. American Journal of Physiology-Lung Cellular and Molecular Physiology: pp.ajplung-00075. PDF
2016
(19) Steenwyk, J.L., J.S. Soghigian, J.R. Perfect, and J.G. Gibbons (2016). Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics: 17:700. PDF
(18) Staehlin, B. M., J. G. Gibbons, A. Rokas, T. V. O’Halloran, & J. C. Slot (2016). Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria. Genome Biology and Evolution: 8 (3), 811-826. PDF
2015
(17) Gibbons, J.G., D.C. Rinker. (2015). The Genomics of Microbial Domestication in the Fermented Food Environment. Current Opinion in Genetics & Development: 35: 1-8. PDF
(16) Gibbons, J.G.*, A. Branco*, S.A. Godinho, S. Yu, and B. Lemos (2015). Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes. PNAS: 8: 2485-2490. (*Equal contributors) PDF
2014
(15) Gibbons, J.G., A. Branco, S. Yu, and B. Lemos (2014). Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nature Communications: 5. PDF
2013
(14) Muszkieta, L., A. Beauvais, V. Pähtz, J. G. Gibbons, V. A. Leberre, R. Beau, K. Shibuya, A. Rokas, J. M. Francois, O. Kniemeyyer, A. A. Brakhage, and J.-P. Latge (2013). Investigation of Aspergillus fumigatus biofilm formation by various “omics” approaches. Frontiers in Microbiology: 4. PDF
(13) Ubaida Mohien, C., D. R. Colquhoun, D. K. Mathias, J. G. Gibbons, J. S. Armistead, M. del Carmen-Rodriguez, M. H. Rodriguez, N. J. Edwards, J. Hartler, G. G. Thallinger, D. R. Graham, J. Martinez-Barnetche, A. Rokas, and R. R. Dinglasan (2013). A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Molecular & Cellular Proteomics: 12: 120-131. PDF
2012
(12) Gibbons, J. G., and A. Rokas (2012). The function and evolution of the Aspergillus genome. Trends in Microbiology: 21: 14-22. PDF
(11) Elmore, M.H.*, J.G. Gibbons*, and A. Rokas (2012). Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. G3 2:1643-1649. (*Equal contributors) PDF
(10) Rokas, A., J. G. Gibbons, X. Zhou, A. Beauvais, and J.-P. Latge (2012). The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Annals of the New York Academy of Sciences 1273:25-34. PDF
(9) Gibbons, J. G., L. Salichos, J. C. Slot, D. C. Rinker, K. L. McGary, J. G. King, M. A. Klich, D. L. Tabb, W. H. McDonald, and A. Rokas (2012). The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Current Biology: 22: 1-7. PDF
Scientific American podcast ASM Small Things Considered blog Science Daily article
(8) Martínez-Barnetche, J., R. E. Gómez-Barreto, M. Ovilla-Muñoz, J. Téllez-Sosa, D. E. García López, R. R. Dinglasan, C. Ubaida-Mohien, R. M. MacCallum, S. N. Redmond, J. G. Gibbons, A.Rokas, C. A. Machado, F. Cazares-Raga, L. González-Cerón, S. Hernández-Martínez, and M. H. Rodríguez López (2012). Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics. 13:207. PDF
(7) Klaassen,C. H. W.*, J. G. Gibbons*, N. D. Fedorova, J. F. Meis, and A. Rokas (2012). Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Molecular Ecology. 21: 57-70. (*Equal contributors) PDF
(6) Gibbons, J. G., A. Beauvais, R. Beau, K. L. McGary, J.-P. Latge, and A. Rokas (2012). Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryotic Cell. 11: 68-78. PDF
2011
(5) Kent, B. N., L. Salichos, J. G. Gibbons, A. Rokas, I. L. G. Newton, M. E. Clark, and S. R. Bordenstein (2011). Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biology and Evolution. 3: 209-218. PDF
2010
(4) An J.H., 102 additional co-authors including J.G. Gibbons (2010) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009. Molecular Ecology Resources. 10, 404-408. PDF (summary article) PDF (full article)
2009
(3) Gibbons, J. G., E. Janson, C. T. Hittinger, M. Johnston, P. Abbot and A. Rokas (2009). Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution. 26: 2731-2744. PDF
(2) Gibbons, J. G. and A. Rokas (2009). Comparative and functional characterization of intragenic tandem repeats in ten Aspergillus genomes. Molecular Biology and Evolution. 26: 591-602. PDF
2007
(1) Saxena, R., 65 additional co-authors including J.G. Gibbons (2007). Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316:1331-1336. PDF