Fungal Evolution

• Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW. 2009. The fungi. Current Biol 19(18):R840-5. DOI:10.1016/j.cub.2009.07.004
• Stajich JE, Dietrich FS, Roy SW. 2007. Comparative genomic analysis of fungal genomes reveals intron rich ancestors. Genome Biology 8:R223. DOI:10.1186/gb-2007-8-10-r223
• Fitzpatrick DA, Logue ME, Stajich JE, and Butler G. 2006. A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology 6:99. DOI: 10.1186/1471-2148-6-99
• James TY, Kauff F, Schoch C, Matheny PB,Hofstetter V, Cox CJ, Celio G, Gueidan D, Fraker E, Miadlikowska J,Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O’Rourke B, Crockett M, Binder M, CurtisJH, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, and Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443(7113):818-822. DOI: 10.1038/nature05110

Fungal Pathogens

• Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, and Taylor JW. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19(10): 1722-1731. DOI:10.1101/gr.087551.108
• Fisher MC, Bosch J, Yin Z, Stead DA, Walker J, Selway L, Brown AJP, Walker LA, Gow NAR, Stajich JE, Garner TWJ. 2009. Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence. Mol Ecol. 18:415-429. DOI:10.1111/j.1365-294X.2008.04041.x
• Rosenblum EB, Stajich JE, Maddox N, Eisen MB. 2008. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci. 105(44):17034-17039. DOI:10.1073/pnas.0804173105
• Fraser JA,Stajich JE, Tarcha EJ, Cole GT, Inglis DO, Sil A, Heitman J. 2007. Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. Euk Cell. 2007 6(4):622-9. DOI:10.1128/EC.00018-07
• Cramer RA Jr, Stajich JE, Yamanaka Y, Dietrich FS, Steinbach WJ, Perfect JR. 2006. Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus. Gene 383:24-32. DOI: 10.1016/j.gene.2006.07.008
• Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Wright JR, Diezmann S, Allen A, Stajich JE, Dietrich FS, Perfect JR, Heitman J. 2005. Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 437(7063):1360-1364. DOI:10.1038/nature04220

Basidiomycete genomics

• Martin F, Aerts A, Ahrén D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buée M, Brokstein P, Canbäk B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbé J, Lin YC, Legué V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kües U, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouzé P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV. 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183):88-92. DOI:10.1038/nature06556
• Lilly WW, Stajich JE, Pukkila PJ, Wilke SK, Inoguchi N, Gathman AC. 2008. An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea. Mycol Res. 389-98. DOI:10.1016/j.mycres.2007.11.013
• Kamper J, Kahmann R, Bolker M, Ma L-J, Saville BJ, Banuett F, Kronstad JW, Gold SE, Brefort T, Muller O, Perlin MH, Wosten HAB, deVries R, Ruiz-Herrera J, Reynaga-Pena CG, Snetselaar K, McCann M, Perez-Martin J, Feldbrugge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, Gonzaalez-Prietro JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Scherer M, Vranes M, Ladendorf O, Fuchs U, Sandrock B, Meng S, Ho ECH, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Hauser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schluter T, Platt D, Swimmer C, Gnirke A, Chen A, Vysotskaia V, Mannhaupt G, Guldener U, Munsterkotter M, Haase D, Mewes H, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DD, Calvo S, Nusbaum C, Galagan J, and Birren BW. 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115):97-101. DOI:10.1038/nature05248
• Stajich JE and Dietrich FS. 2006. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryot Cell 5(5):789-93. DOI: 10.1128/EC.5.5.789-793.2006

Evolutionary, Population Genomics, and Bioinformatic Methods

• Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15(8):1153-60. DOI:10.1101/gr.3567505
• Stajich JE and Hahn MW. 2005. Disentangling the effects of demography and selection in human history. Mol Biol Evol 22(1):63-73. DOI: 10.1093/molbev/msh252
• Hahn MW, Stajich JE, Wray GA. 2003. The effects of selection against spurious transcription factor binding sites. Mol Biol Evol 20(6):901-906. DOI: 10.1093/molbev/msg096
• Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. 2002.The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12(10):1611-1618. DOI:10.1101/gr.361602
• Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. 2002. The generic genome browser: a building block for a model organism system database. Genome Res 12(10):1599-1610. DOI: 10.1101/gr.403602

Other genomics related

• Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. 2004. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1(2):E45. DOI:10.1371/journal.pbio.0000045

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