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(24) Zhao, S., and J.G. Gibbons. A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus. PLoS One (in press


(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. Role of Hydrophobins in Aspergillus fumigatus. Journal of Fungi: 4:1.

(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. The Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. Genome Announcements: 5(30), pp.e00562- 17. PDF

Clark University Research Matters Article

(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, vishu kumar; 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


(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


(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

Commentary in PNAS


(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


(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


(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



(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


(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)


(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


(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