{"id":70,"date":"2014-07-07T20:48:37","date_gmt":"2014-07-07T20:48:37","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/jgibbons\/?page_id=70"},"modified":"2018-07-30T10:51:33","modified_gmt":"2018-07-30T10:51:33","slug":"publications","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/jgibbons\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Google Scholar<\/a><\/p>\n

PubMed<\/a><\/p>\n

 <\/p>\n

\n

2018<\/strong><\/p>\n

\n

(24)<\/span><\/strong> Zhao, S., and J.G. Gibbons<\/strong>. A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus<\/em>. PLoS One<\/em> (in press<\/em>) <\/p>\n

\n

2017<\/strong><\/p>\n

\n

(23)<\/strong><\/span> Valsecchi, I., V. Dupres, E. Stephen-Victor, J.I. Guijarro, J.G. Gibbons<\/strong>, R. Beau, J. Bayry, J.-Y. Coppee, F. Lafont, J.-P. Latg\u00e9, and A. Beauvais. Role of Hydrophobins in Aspergillus fumigatus<\/em>. Journal of Fungi<\/em><\/strong>: 4:1.<\/p>\n

(22)<\/span><\/strong> Chacon-Vargas, K.<\/strong>, 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<\/strong>, and J.G. Gibbons<\/strong>. The Genome Sequence of Zymomonas mobilis<\/i> subsp. mobilis<\/i> NRRL B-1960. Genome Announcements<\/strong>: <\/em>5(30), pp.e00562- 17. PDF<\/a><\/strong><\/p>\n

Cl<\/a>ark University Research Matters Article<\/span><\/strong><\/span><\/p>\n

(21) <\/span><\/strong>Valsecchi, I., O. Sarikayabayram, J. Wong Sak Hoi, L. Muszkieta, J.G. Gibbons<\/strong>, 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. Latg\u00e9 (2017). MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus. Molecular Microbiology<\/strong><\/em>: 105: 880-900. PDF<\/a><\/strong><\/p>\n

(20)<\/span><\/strong> Wu, M., J.G. Gibbons<\/strong>, 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<\/strong>: <\/em>pp.ajplung-00075. PDF<\/a><\/strong><\/p>\n

\n

 2016<\/strong><\/p>\n

\n

(19)<\/span><\/strong> Steenwyk, J.L.<\/strong>, J.S. Soghigian, J.R. Perfect, and J.<\/strong>G. Gibbons <\/strong>(2016). <\/strong>Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii<\/em> from the North American Pacific Northwest. BMC Genomics<\/em><\/strong>: <\/em>17:700. <\/em>PDF<\/a><\/strong><\/span><\/p>\n

(18)<\/span> <\/strong>Staehlin, B. M., J. G. Gibbons<\/strong>, A. Rokas, T. V. O\u2019Halloran, & J. C. Slot (2016). Evolution of a heavy metal homeostasis\/resistance island reflects increasing copper stress in Enterobacteria. Genome Biology and Evolution<\/strong><\/em>: 8 (3), 811-826. PDF<\/a><\/span><\/strong><\/p>\n

\n

 2015<\/strong><\/p>\n

\n

(17)<\/span> Gibbons, J.G.<\/strong>, D.C. Rinker. (2015). The Genomics of Microbial Domestication in the Fermented Food Environment. Current Opinion in Genetics & Development: <\/em><\/strong>35: 1-8. PDF<\/a><\/strong><\/span><\/p>\n

(16)<\/span> Gibbons, J.G.*<\/strong>, 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<\/strong><\/em>: 8: 2485-2490. <\/em>(*Equal contributors) PDF<\/a><\/strong><\/span><\/p>\n

Commentary in PNAS<\/a><\/span><\/strong><\/p>\n

\n

 2014<\/strong><\/p>\n

\n

(15)<\/span> Gibbons, J.G.<\/strong>, 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<\/strong><\/em>: 5. PDF<\/a><\/span><\/strong><\/p>\n

\n

 2013<\/strong><\/p>\n

\n

(14)<\/strong><\/span> Muszkieta, L., A. Beauvais, V. P\u00e4htz, J. G. Gibbons<\/strong>, 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<\/em> biofilm formation by various \u201comics\u201d approaches. Frontiers in Microbiology<\/em><\/strong>: 4. PDF<\/a><\/strong><\/span><\/p>\n

(13)<\/strong><\/span> Ubaida Mohien, C., D. R. Colquhoun, D. K. Mathias, J. G. Gibbons<\/strong>, 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<\/em><\/strong>: 12: 120-131. PDF<\/a><\/strong><\/span><\/p>\n

\n

 2012<\/strong><\/p>\n

\n

(12)<\/span> Gibbons, J. G.<\/strong>, and A. Rokas (2012). The function and evolution of the Aspergillus<\/em> genome. Trends in Microbiology<\/em><\/strong>: 21: 14-22. PDF<\/a><\/strong><\/span><\/p>\n

(11)<\/strong><\/span> Elmore, M.H.*, J.G. Gibbons<\/strong>*, and A. Rokas (2012). Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. G3<\/em><\/strong> 2:1643-1649. (*Equal contributors) PDF<\/a><\/strong><\/span><\/p>\n

(10)<\/strong><\/span> Rokas, A., J. G. Gibbons<\/strong>, X. Zhou, A. Beauvais, and J.-P. Latge (2012). The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus<\/em>. Annals of the New York Academy of Sciences<\/em><\/strong> 1273:25-34. PDF<\/a><\/strong><\/span><\/p>\n

(9)<\/span> Gibbons, J. G.<\/strong>, 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<\/em>. Current Biology<\/em><\/strong>: 22: 1-7. PDF<\/a><\/strong><\/span><\/p>\n

Scientific American podcast<\/span><\/a><\/strong><\/span>    ASM Small Things Considered blog<\/span><\/a><\/strong><\/span>   Science Daily article<\/span><\/a><\/strong><\/span><\/p>\n

(8)<\/span> <\/strong>Mart\u00ednez-Barnetche, J., R. E. G\u00f3mez-Barreto, M. Ovilla-Mu\u00f1oz, J. T\u00e9llez-Sosa, D. E. Garc\u00eda L\u00f3pez, R. R. Dinglasan, C. Ubaida-Mohien, R. M. MacCallum, S. N. Redmond, J. G. Gibbons<\/strong>, A.Rokas, C. A. Machado, F. Cazares-Raga, L. Gonz\u00e1lez-Cer\u00f3n, S. Hern\u00e1ndez-Mart\u00ednez, and M. H. Rodr\u00edguez L\u00f3pez (2012). Transcriptome of the adult female malaria mosquito vector Anopheles albimanus<\/em>. BMC Genomics<\/em><\/strong>. 13:207. PDF<\/a><\/strong><\/span><\/p>\n

(7)<\/strong><\/span> Klaassen,C. H. W.*, J. G. Gibbons<\/strong>*, 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<\/em>. Molecular Ecology<\/em><\/strong>. 21: 57-70. (*Equal contributors) PDF<\/a><\/strong><\/span><\/p>\n

(6)<\/span> Gibbons, J. G.<\/strong>, 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<\/em> fumigatus<\/em>. Eukaryotic Cell<\/em><\/strong>. 11: 68-78. PDF<\/a><\/strong><\/span><\/p>\n

\"EC_cover\"<\/a><\/p>\n

\n

 <\/span>2011<\/strong><\/p>\n

\n

(5)<\/strong><\/span> Kent, B. N., L. Salichos, J. G. Gibbons<\/strong>, A. Rokas, I. L. G. Newton, M. E. Clark, and S. R. Bordenstein (2011). Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia<\/em>) determined by targeted genome capture. Genome Biology and Evolution<\/em><\/strong>. 3: 209-218. PDF<\/a><\/strong><\/span><\/p>\n

\n

2010<\/strong><\/p>\n

\n

(4)<\/strong><\/span> An J.H., 102 additional co-authors including J.G. Gibbons<\/strong> (2010) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009. Molecular Ecology Resources<\/em><\/strong>. 10, 404-408. PDF<\/strong> <\/span>(summary article)<\/a> PDF<\/a><\/strong> (full article)<\/a><\/span><\/p>\n

\n

2009<\/strong><\/p>\n

\n

(3)<\/span> Gibbons, J. G.<\/strong>, 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<\/em><\/strong>. 26: 2731-2744. PDF<\/a><\/strong><\/span><\/p>\n

(2)<\/span> Gibbons, J. G.<\/strong> and A. Rokas (2009). Comparative and functional characterization of intragenic tandem repeats in ten Aspergillus<\/em> genomes. Molecular Biology and Evolution<\/em><\/strong>. 26: 591-602. PDF<\/a><\/strong><\/span><\/p>\n

\n

2007<\/strong><\/p>\n

\n

(1) <\/strong><\/span>Saxena, R., 65 additional co-authors including J.G. Gibbons<\/strong> (2007). Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science<\/em><\/strong> 316:1331-1336. PDF<\/a><\/strong><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Google Scholar PubMed   2018 (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)  2017 (23) […]<\/p>\n","protected":false},"author":421,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-70","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages\/70","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/users\/421"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/comments?post=70"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages\/70\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/media?parent=70"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}