Current citations also available at Google Scholar.
Lab members are indicated in bold.

Preprints

Fallon, TR, VV Shende, IH Wierzbicki, RP Auber, DJ Gonzalez, JH Wisecaver, & BS Moore. Giant polyketide synthase enzymes biosynthesize a giant marine polyether biotoxin. https://www.biorxiv.org/content/10.1101/2024.01.29.577497v1

Publications

2023

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

Wisecaver, JH, RP Auber, AL Pendleton, NF Watervoort, TR Fallon, OL Riedling, 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

Davidi, L, SD Gallaher, E Ben-David, SO Purvine, TL Filmore, CD Nicora, RJ Craig, S Schmollinger, S Roje, CE Blaby-Haas, RP Auber, JH Wisecaver, & 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

Driscoll, WW, JH Wisecaver, J Hackett, N Espinosa, J Padway, J Engers, & J Bower. Behavioral differences underlie toxicity and predation variation in blooms of Prymnesium parvum. Ecology Letters. 26: 677-691. | LINK

2022

Trujillo, JT, J Long, E Aboelnour, J Ogas & JH Wisecaver. 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

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

Franco, MEE, JH Wisecaver, AE Arnold, Y Ju, JC Slot, S Arhendt, LP Moore, KE Eastman, 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’Ren. 2022. Secondary metabolism drives ecological breadth in the Xylariaceae. New Phytologist. 233: 1317-1330. | LINK

2021

Kwon, MJ, C Steiniger, TC Cairns, JH Wisecaver, 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

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

Geng, Y, L Guo, H Han, X Liu, JA Banks, JH Wisecaver, & 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

2020

Smith, PM, E Gough, A Younts, B Werts, TJ Hacker, N Neumeister, & JH Wisecaver. 2020. The “Geddes” 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

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

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

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

2019

Verster, KI, JH Wisecaver, 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 | PDF

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

Colle, M and 24 other authors including JH Wisecaver. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience. 8:giz012 | LINK

Smith, SD, R Angelovici, K Heyduk, HA Maeda, GD Moghe, JC Pires, JR Widhalm, and JH Wisecaver. The Renaissance of comparative biochemistry. Am J Bot. 106: 1-11 | PDF

2018

Shen, X-X and 26 other authors including JH Wisecaver. The tempo and mode of genome evolution in the budding yeast subphylum. Cell. 175: 1533-1545. e20 | PDF

Eidem, HR, JL Steenwyk, JH Wisecaver, 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

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

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

Gonçalves, C, JH Wisecaver, M Salema-Oom, M José Leandro, X-X Shen, D Peris, CT Hittinger, A Rokas, P Gonçalves. Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage. eLife 7:e33034 | LINK

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, J Zhu & D Bhattacharya. Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. Scientific Reports 8: 5862 | LINK

2017

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 population. PLoS Biol 15: e2003583  | LINK

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. The Plant Cell 29: 944–959 | PDF 

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 2: e00176-17 | LINK

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

2016

Wisecaver, JH, 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 | Alien Index script

Alexander, WG, JH Wisecaver, A Rokas & CT Hittinger. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. PNAS 113: 4116–4121 | LINK | Alien Index script

Riley, R and 37 other authors including JH Wisecaver. Comparative genomics of biotechnologically important yeasts. PNAS 113: 9882–9887 | LINK

DeBlasio, DF & JH Wisecaver. SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees. PeerJ 4: e2359 | LINK | download SICLE

2015

Wisecaver, JH & A Rokas. Fungal metabolic gene clusters – caravans traveling across genomes and environments. Frontiers in Microbiology 6: 161 | LINK

Lasek-Nesselquist, E, JH Wisecaver, JD Hackett & MD Johnson. Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum. BMC Genomics 16: 805 | LINK

U’Ren, JM*, JH Wisecaver*, AL Paek, BL Dunn & BL Hurwitz. Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239. Genome Announcements 3:e00776-15 (*Equal contributors) | LINK

Lind, AL, JH Wisecaver, 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. PLOS Genetics 11: e1005096 | LINK

Elmore, MH, KL McGary, JH Wisecaver, JC Slot, DM Geiser, S Sink, KO’Donnell & A Rokas. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biol Evol 7: 789–800 | LINK

2014

Wisecaver, JH, JC Slot & A Rokas. The evolution of fungal metabolic pathways. PLOS Genetics 10: e1004816 | LINK

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

Wisecaver, JH & JD Hackett. The impact of automated sequence selection on genome-scale phylogenetic analysis. Mol Phylogenet Evol 71: 184–192 | PDF | pipeline .tar

2013

Wisecaver, JH, ML Brosnahan & JD Hackett. Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates. Genome Biol Evol 12: 2368–2381 | LINK | pipeline .tar

Hackett, JD, JH Wisecaver, 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: 70–78 | LINK

2012

Molnar, I, D Lopez, JH Wisecaver, 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 race B (Showa). BMC Genomics 13: 576 | LINK

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

2011 & earlier

Wisecaver, JH & JD Hackett. 2011. Dinoflagellate genome evolution. Annu Rev Microbiol 65: 369–387 | 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 | LINK

Sullivan, MB, B Krastins, JL Hughes, 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: 2935–2951 | LINK

Hughes, JL & ME Siddall. 2007. A new species of leech from the New York Metropolitan Area. American Museum Novitates 3578: 1–6 | PDF