{"id":31,"date":"2025-04-22T12:37:35","date_gmt":"2025-04-22T19:37:35","guid":{"rendered":"https:\/\/labs.wsu.edu\/wisecaver\/?page_id=31"},"modified":"2025-05-20T16:24:59","modified_gmt":"2025-05-20T23:24:59","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/wisecaver\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

Current citations also available at <\/em>Google <\/em><\/a>Scholar<\/a>.
Lab members are indicated in <\/em>bold<\/em><\/strong>.<\/em><\/p>\n\n\n\n

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Preprints<\/h2>\n\n\n\n

Nothing right now, but check back soon!<\/p>\n\n\n\n

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Publications<\/h2>\n\n\n\n

2025<\/h3>\n\n\n\n

Burow, KM<\/strong>, X Yang, Y Zhou, BP Dilkes, & JH Wisecaver<\/strong>. A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii<\/em>. The Plant Cell. 37: koaf058. | LINK<\/a><\/p>\n\n\n\n

2024<\/h3>\n\n\n\n

Fallon, TR, VV Shende, IH Wierzbicki, AL Pendelton<\/strong>, NF Watervoort<\/strong>, RP Auber<\/strong>, DJ Conzalez, JH Wisecaver<\/strong>, & BS Moore. Giant polyketise synthase enzymes in the biosynthesis of giant marine polyether toxins. Science. 385: 671-678.

Saha, D, JB Gregor, S Hoda, Eastman, KE<\/strong>, M Navarrete, JH Wisecaver<\/strong> & SD Briggs. Candida glabrata<\/em> maintains two Hap1 homologs, Zcf27 and Zcf4, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. mSphere. 9: e00524-24.<\/p>\n\n\n\n

2023<\/h3>\n\n\n\n

Eastman, KE<\/strong>, AL Pendleton<\/strong>, MA Shaikh, T Suttiyut, R Ogas<\/strong>, P Tomko<\/strong>, G Gavelis<\/strong>, JR Widhalm & JH Wisecaver<\/strong>. A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata<\/em> morphotype clarki. G3: Genes, Genomes, Genetics. 13: jkad234. | LINK<\/a><\/p>\n\n\n\n

Wisecaver, JH<\/strong>, RP Auber<\/strong>, AL Pendleton<\/strong>, NF Watervoort<\/strong>, TR Fallon, OL Riedling<\/strong>, SR Manning, BS Moore, & WW Driscoll. Extreme genome diversity and cryptic speciation in a harmful algal bloom forming eukaryote. Current Biology. 33: 2246-2259. | LINK<\/a><\/p>\n\n\n\n

Davidi, L, SD Gallaher, E Ben-David, SO Purvine, TL Filmore, CD Nicora, RJ Craig, S Schmollinger, S Roje, CE Blaby-Haas, RP Auber<\/strong>, JH Wisecaver<\/strong>, & SS Merchant. Pumping iron: A multi-omics analysis of two extremophilic algae reveals mechanisms of iron economy. Proceedings of the National Academy of Sciences U.S.A. 120: e2305495120. | LINK<\/a><\/p>\n\n\n\n

Driscoll, WW, JH Wisecaver<\/strong>, J Hackett, N Espinosa, J Padway, J Engers, & J Bower. Behavioral differences underlie toxicity and predation variation in blooms of Prymnesium parvum<\/em>. Ecology Letters. 26: 677-691. | LINK<\/a><\/p>\n\n\n\n

2022<\/h3>\n\n\n\n

Trujillo, JT<\/strong>, J Long, E Aboelnour, J Ogas & JH Wisecaver<\/strong>. 2022. Evolutionary history of chromodomain helicase DNA-binding chromatin remodelers reveals timing of diversification in land plants and animals. Genome Biology and Evolution.14: evac066. | LINK<\/a><\/p>\n\n\n\n

Suttiyut, T, R Auber<\/strong>, JW Crook, E Yakubova, JH Wisecaver<\/strong> & JR Widhalm. 2022. Global coexpression network analysis reveals the extraplastidal origin of the geranyl diphosphate precursor of shikonin. Horticulture Research. 9: uhab087. | LINK<\/a><\/p>\n\n\n\n

Franco, MEE, JH Wisecaver<\/strong>, AE Arnold, Y Ju, JC Slot, S Arhendt, LP Moore, KE Eastman<\/strong>, K Scott, SJ Mondo, A Kuo, R Hayes, S Haridas, B Andreopoulos, R Riley, K LaButti, J Pangilinan, A Lipzen, V Ng, E Drula, B Henrissat, K Youens-Clark, F Lutzoni, J Miadlikowska, DC Eastwood, R Hamelin, IV Grigoriev, & JM U\u2019Ren. 2022. Secondary metabolism drives ecological breadth in the Xylariaceae. New Phytologist. 233: 1317-1330. | LINK<\/a><\/p>\n\n\n\n

2021<\/h3>\n\n\n\n

Kwon, MJ, C Steiniger, TC Cairns, JH Wisecaver<\/strong>, A Lind, C Pohl, C Regner, A Rokas & V Meyer. 2021. Beyond the biosynthetic gene cluster paradigm: Genome-wide co-expression networks connect clustered and unclustered transcription factors to secondary metabolic pathways. Microbiol. Spectrum. Sep 15: e0089821 | LINK<\/a><\/p>\n\n\n\n

Geng, Y, C Cai, SAM McAdam, JA Banks, JH Wisecaver <\/strong>& Y Zhou. 2021. A de novo <\/em>transcriptome assembly of Ceratopteris richardii <\/em>provides insights into the evolutionary dynamics of complex gene families in land plants. Genome Biology and Evolution. 13: evab042 | LINK<\/a>

Geng, Y, L Guo, H Han, X Liu, JA Banks, JH Wisecaver<\/strong>, & Y Zhou. 2021. Conservation and diversification of HAIRY MERISTEM gene family in land plants. The Plant Journal. https:\/\/doi.org\/10.1111\/tpj.15169 | LINK<\/a><\/p>\n\n\n\n

2020<\/h3>\n\n\n\n

Smith, PM, E Gough, A Younts, B Werts, TJ Hacker, N Neumeister, & JH Wisecaver<\/strong>. 2020. The \u201cGeddes\u201d Composable Platform-An Evolution of Community Clusters for a Composable World. IEEE\/ACM International Workshop on Interoperability of Supercomputing and Cloud Technologies (SuperCompCloud). 2020: 33-38 | LINK<\/a><\/p>\n\n\n\n

Thielen, PM, AL Pendleton<\/strong>, RA Player, KV Bowden, TJ. Lawton & JH Wisecaver<\/strong>. 2020. Reference genome for the highly transformable Setaria viridis<\/em> ME034V. G3: Genes, Genomes, Genetics. https:\/\/doi.org\/10.1534\/g3.120.401345 | LINK<\/a><\/p>\n\n\n\n

Auber, RP<\/strong>, T Suttiyut, RM McCoy, M Ghaste, JW Crook, AL Pendleton<\/strong>, JR Widhalm & JH Wisecaver<\/strong>. 2020. Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon<\/em>) reveals evolutionary insight into shikonin biosynthesis. Horticulture Research 7:1-15 <\/p>\n\n\n\n

DeMarco, AG, KL Milholland, AL Pendleton<\/strong>, JJ Whitney, P Zhu, DT Wesenberg, M Nambiar, A Pepe, S Paula, J Chmielewski, JH Wisecaver<\/strong>, WA Tao, & MC Hall. 2020. Conservation of Cdc14 phosphatase specificity in plant fungal pathogens: implications for antifungal development. Scientific Reports 10:12973 <\/p>\n\n\n\n

2019<\/h3>\n\n\n\n

Verster, KI, JH Wisecaver<\/strong>, RP Duncan, M Karageorgi, AD Gloss, E Armstrong, DK Price, AR Menon, ZM Ali, and NK Whiteman. Horizontal transfer of prokaryotic cytolethal distending toxin B genes to eukaryotes <\/p>\n\n\n\n

Gao, S, SE Gold, JH Wisecaver<\/strong>, Y Zhang, L Guo, L Ma, A Rokas, and AE Glenn. Genome-wide analysis of Fusarium verticillioides<\/em> reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism. Fungal Genetics and Biology. 128:60-73 <\/p>\n\n\n\n

Colle, M and 24 other authors including JH Wisecaver<\/strong>. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience. 8:giz012 | LINK<\/a><\/p>\n\n\n\n

Smith, SD, R Angelovici, K Heyduk, HA Maeda, GD Moghe, JC Pires, JR Widhalm, and JH Wisecaver<\/strong>. The Renaissance of comparative biochemistry. Am J Bot. 106: 1-11 <\/p>\n\n\n\n

2018<\/h3>\n\n\n\n

Shen, X-X and 26 other authors including JH Wisecaver<\/strong>. The tempo and mode of genome evolution in the budding yeast subphylum. Cell. 175: 1533-1545. e20 <\/p>\n\n\n\n

Eidem, HR, JL Steenwyk, JH Wisecaver<\/strong>, JA Capra, P Abbot, and A Rokas. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth. BMC Med Genomics. 11: 107 | LINK<\/a><\/p>\n\n\n\n

Rokas, A, JH Wisecaver<\/strong>, & AL Lind. The birth, evolution, and death of metabolic gene clusters in fungi. Nature Reviews Microbiology. 16: 10.1038\/s41579-018-0075-3 | LINK<\/a><\/p>\n\n\n\n

Lim, FY, TH Won, JA Baccile, JH Wisecaver<\/strong>, A Rokas, FC Schroeder, & NP Keller. Fungal isocyanide synthases: an unexplored resource in eukaryotic secondary metabolism. mBio 9: e00785-18 | LINK<\/a><\/p>\n\n\n\n

Gon\u00e7alves, C, JH Wisecaver<\/strong>, M Salema-Oom, M Jos\u00e9 Leandro, X-X Shen, D Peris, CT Hittinger, A Rokas, P Gon\u00e7alves. Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage. eLife 7:e33034 | LINK<\/a><\/p>\n\n\n\n

Zhang, N, G Cai, DC Price, JA Crouch, P Gladieux, B Hillman, CH Khang, M-H LeBrun, Y-H Lee, J Luo, H Qiu, D Veltri, JH Wisecaver<\/strong>, J Zhu & D Bhattacharya. Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. Scientific Reports 8: 5862 | LINK<\/a><\/p>\n\n\n\n

2017<\/h3>\n\n\n\n

Lind, AL, JH Wisecaver<\/strong>, 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 population. PLoS Biol 15: e2003583 <\/em> | LINK<\/a><\/p>\n\n\n\n

Wisecaver, JH, <\/strong>AT Borowsky, V Tzin, G Jander, D Kliebenstein & A Rokas. A global co-expression approach for connecting genes to specialized metabolic pathways in plants. The Plant Cell 29: 944\u2013959 <\/p>\n\n\n\n

Lojek, LJ, AJ Farrand, JH Wisecaver<\/strong>, CE Blaby-Haas, SS Merchant, A Rokas & EP Skaar. Chlamydomonas reinhardtii<\/em> cMO is an IsdG family heme oxygenase. mSphere 2: e00176-17 | LINK<\/a><\/p>\n\n\n\n

Ohkura M, RR Fitak, JH Wisecaver<\/strong>, D DeBlasio, F Niazi, M Egholm, SD Rounsley, CD Kodira & MJ Orbach. Genome sequence of Ophidiomyces ophiodiicola<\/em>, an emerging fungal pathogen of snakes. Genome Announcements 5: e00677-17 | LINK<\/a><\/p>\n\n\n\n

2016<\/h3>\n\n\n\n

Wisecaver, JH<\/strong>, WG Alexander, SB King, CT Hittinger & A Rokas. Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Mol Biol Evol 33: 1979-1987 | LINK<\/a> | Alien Index script<\/a><\/p>\n\n\n\n

Alexander, WG, JH Wisecaver<\/strong>, A Rokas & CT Hittinger. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. PNAS 113: 4116\u20134121 | LINK<\/a> | Alien Index script<\/a><\/p>\n\n\n\n

Riley, R and 37 other authors including JH Wisecaver<\/strong>. Comparative genomics of biotechnologically important yeasts. PNAS 113: 9882\u20139887 | LINK<\/a><\/p>\n\n\n\n

DeBlasio, DF & JH Wisecaver<\/strong>. SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees. PeerJ 4: e2359 | LINK<\/a> | download SICLE<\/a><\/p>\n\n\n\n

2015<\/h3>\n\n\n\n

Wisecaver, JH <\/strong>& A Rokas. Fungal metabolic gene clusters \u2013 caravans traveling across genomes and environments. Frontiers in Microbiology 6: 161 <\/em>| LINK<\/a><\/p>\n\n\n\n

Lasek-Nesselquist, E, JH Wisecaver, <\/strong>JD Hackett & MD Johnson. Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum<\/em>. BMC Genomics 16: 805 | LINK<\/a><\/p>\n\n\n\n

U\u2019Ren, JM*, JH Wisecaver*<\/strong>, AL Paek, BL Dunn & BL Hurwitz. Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae<\/em> strain GSY2239. Genome Announcements 3:e00776-15 (*Equal contributors) | LINK<\/a><\/p>\n\n\n\n

Lind, AL, JH Wisecaver<\/strong>, TD Smith, X Feng, AM Calvo & A Rokas. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus<\/em>. PLOS Genetics 11: e1005096 | LINK<\/a><\/p>\n\n\n\n

Elmore, MH, KL McGary, JH Wisecaver<\/strong>, JC Slot, DM Geiser, S Sink, KO\u2019Donnell & A Rokas. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biol Evol 7: 789\u2013800 | LINK<\/a><\/p>\n\n\n\n

2014<\/h3>\n\n\n\n

Wisecaver, JH<\/strong>, JC Slot & A Rokas. The evolution of fungal metabolic pathways. PLOS Genetics 10: e1004816 | LINK<\/a><\/p>\n\n\n\n

Gusev, O. and 27 other authors including JH Wisecaver<\/strong>. Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nature Communications 5: 4784 | LINK<\/a><\/p>\n\n\n\n

Wisecaver, JH<\/strong> & JD Hackett. The impact of automated sequence selection on genome-scale phylogenetic analysis. Mol Phylogenet Evol 71: 184\u2013192 <\/p>\n\n\n\n

2013<\/h3>\n\n\n\n

Wisecaver, JH<\/strong>, ML Brosnahan & JD Hackett. Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates. Genome Biol Evol 12: 2368\u20132381 <\/p>\n\n\n\n

Hackett, JD, JH Wisecaver<\/strong>, ML Brosnahan, DM Kulis, DM Anderson, D Bhattacharya, FG Plumley & DL Erdner. Independent evolution of saxitoxin synthesis in cyanbacteria and dinoflagellates. Mol Biol Evol 30: 70\u201378 | LINK<\/a><\/p>\n\n\n\n

2012<\/h3>\n\n\n\n

Molnar, I, D Lopez, JH Wisecaver<\/strong>, M Pellegrini & JD Hackett. Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii <\/em>race B (Showa). BMC Genomics 13: 576 | LINK<\/a><\/p>\n\n\n\n

Chan, CX, M Soares, M Bonaldo, JH<\/strong> Wisecaver, <\/strong>JD Hackett, DM Anderson, D Erdner & D Bhattacharya. Analysis of Alexandrium tamarense<\/em> (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. J Phycology 48: 1130\u20131142<\/p>\n\n\n\n

2011 & EARLIER<\/h3>\n\n\n\n

Wisecaver, JH <\/strong>& JD Hackett. 2011. Dinoflagellate genome evolution. Annu Rev Microbiol 65: 369\u2013387<\/p>\n\n\n\n

Wisecaver, J H <\/strong>& J D Hackett. 2010. Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata<\/em>. BMC Genomics 11: 366 | LINK<\/a><\/p>\n\n\n\n

Sullivan, MB, B Krastins, JL Hughes<\/strong>, L Kelly, M Chase, D Sarracino & SW Chisholm. 2009. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’. Environ Microbiol 11: 2935\u20132951 | LINK<\/a><\/p>\n\n\n\n

Hughes, JL <\/strong>& ME Siddall. 2007. A new species of leech from the New York Metropolitan Area. American Museum Novitates 3578: 1\u20136 <\/p>\n","protected":false},"excerpt":{"rendered":"

Current citations also available at Google Scholar.Lab members are indicated in bold. Preprints Nothing right now, but check back soon! Publications 2025 Burow, KM, X Yang, Y Zhou, BP Dilkes, & JH Wisecaver. A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii. The Plant Cell. 37: koaf058. | LINK […]<\/p>\n","protected":false},"author":44135,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"categories":[],"tags":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/31"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/users\/44135"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/comments?post=31"}],"version-history":[{"count":21,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/31\/revisions"}],"predecessor-version":[{"id":208,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/31\/revisions\/208"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/media?parent=31"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/categories?post=31"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/tags?post=31"},{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/wsuwp_university_location?post=31"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/wsuwp_university_org?post=31"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}