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

Preprints

Eidem, HR, JL Steenwyk, JH Wisecaver, JA Capra, P Abbot, & A Rokas. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth | LINK

Publications

2018

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 | LINKAlien 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 | LINKAlien 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 | LINKdownload 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 | PDFpipeline .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