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preprint articles

Lind, AL, JH Wisecaver, C Lameiras, P Wiemann, JM Palmer, NP Keller, F Rodrigues, GH Goldman, & A Rokas. Drivers of genetic diversity in secondary metabolic gene clusters in a fungal populationPreprint on BioRxiv server

research articles

Wisecaver, JH, AT Borowsky, V Tzin, G Jander, D Kliebenstein & A Rokas. A global co-expression approach for connecting genes to specialized metabolic pathways in plants. Plant Cell. Advance Publication April 13, 2017; doi:10.1105/tpc.17.00009.

Lojek, LJ, AJ Farrand, JH Wisecaver, CE Blaby-Haas, SS Merchant, A Rokas, & EP Skaar. Chlamydomonas reinhardtii cMO is an IsdG family heme oxygenase. mSphere. In press.

Ohkura M, RR Fitak, JH Wisecaver, D DeBlasio, F Niazi, M Egholm, SD Rounsley, CD Kodira, and MJ Orbach. Genome sequence of Ophidiomyces ophiodiicola, an emerging fungal pathogen of snakes. Genome Announcements. In press.

Wisecaver, J H, W G Alexander, S B King, C T Hittinger, & A Rokas. 2016. Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Molecular Biology and Evolution. 33: 1979-1987. doi: 10.1093/molbev/msw073 | reprint .pdf | Alien Index perl script

Alexander, W G, J H Wisecaver, A Rokas, & C T Hittinger. 2016. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. PNAS. 113: 4116–4121. doi: 10.1073/pnas.1517242113 | reprint .pdf | Alien Index perl script

Riley, R and 37 other authors including J H Wisecaver. 2016. Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1603941113 | reprint .pdf

DeBlasio, D F, & J H Wisecaver. 2016. SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees. PeerJ. 4: e2359. |reprint .pdf | download SICLE

Wisecaver, J H & A Rokas. 2015. Fungal metabolic gene clusters – caravans traveling across genomes and environments. Frontiers in Microbiology. 6: 161. | reprint .pdf

Lasek-Nesselquist, E, J H Wisecaver, J D Hackett, & M D Johnson. 2015. Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum. BMC Genomics. 16: 805. doi: 10.1186/s12864-015-2052-9. | reprint .pdf

U’Ren, J M*, J H Wisecaver*, A L Paek, B L Dunn, & B L Hurwitz. 2015. Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239. Genome Announcements. 3:e00776-15. doi:10.1128/genomeA.00776–15. (*Equal contributors) | reprint .pdf

Lind, A L, J H Wisecaver, T D Smith, X Feng, A M Calvo, & A Rokas. 2015. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genetics. 11: e1005096. | reprint .pdf

Elmore, M H*, K L McGary*, J H Wisecaver, J C Slot, D M Geiser, S Sink, K O’Donnell, & A Rokas. 2015. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biology and Evolution. 7: 789–800. (*Equal contributors) | reprint .pdf

Wisecaver, J H, J C Slot, & A Rokas. 2014. The Evolution of Fungal Metabolic Pathways. PLoS Genetics. 10: e1004816. doi:10.1371/journal.pgen.1004816 | reprint .pdf

Gusev, O. and 27 other authors including J H Wisecaver. 2014. Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nature Communications 5: 4784. doi:10.1038/ncomms5784

Wisecaver, J H & J D Hackett. 2014. The impact of automated sequence selection on genome-scale phylogenetic analysis. Molecular Phylogenetics and Evolution 71: 184–192. | reprint .pdf | pipeline .tar

Wisecaver, J H, M L Brosnahan, & J D Hackett. 2013. Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates. Genome Biology and Evolution 12: 2368–2381. | reprint .pdf | pipeline .tar

Hackett, J D, J H Wisecaver, M L Brosnahan, D M Kulis, D M Anderson, et al. 2013. Independent evolution of saxitoxin synthesis in cyanbacteria and dinoflagellates. Molecular Biology and Evolution 30: 70–78.

Molnar, I, D Lopez, J H Wisecaver, M Pellegrini, & J D Hackett. 2012. Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). BMC Genomics 13: 576.

Chan, C X, M Soares, M Bonaldo, J H Wisecaver, J D Hackett, D M Anderson, D Erdner, & D Bhattacharya. 2012. Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology 48: 1130–1142.

Wisecaver, J H & J D Hackett. 2011. Dinoflagellate genome evolution. Annual Reviews of Microbiology 65: 369–387 | reprint .pdf

Wisecaver, J H & J D Hackett. 2010. Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata, BMC Genomics 11:366 | reprint .pdf

Sullivan, M B, B Krastins, J L Hughes, L Kelly, M Chase, D Sarracino, & S W Chisholm. 2009. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'. Environmental Microbiology 11: 2935–2951.

Hughes, J L & M E Siddall. 2007. A new species of leech from the New York Metropolitan Area. American Museum Novitates 3578: 1–6 | reprint .pdf