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October 2012
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Publications

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 [OA]
  • 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 [OA]
  • 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

Batrachochytrium and Chytrids

  • Abramyan J and Stajich JE (2012) Species-specific Chitin Binding Module 18 (CBM18) expansion in the Amphibian Pathogen Batrachochytrium dendrobatidis. mBio 3(3):e00150-12. DOI: 10.1128/mBio.00150-12. [OA]
  • Joneson S, Stajich JE, Shin-Han S, Rosenblum EB (2011) Genomic Transition to Pathogenicity in Chytrid Fungi. PLoS Pathogens, 7(11): e1002338. DOI: 10.1371/journal.ppat.1002338. [OA]
  • Fisher MC, Stajich JE, and Farrer RA. 2012. Emergence of the chytrid fungus Batrachochytrium dendrobatidis and global amphibian declines. In D. Sibley, B. Howlett, and J. Heitman, editors, Evolution of Virulence in Eukaryotic Microbes. Wiley Blackwell. 2012
  • Rosenblum EB, Voyles J, Poorten TJ, and Stajich, JE. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6(1): e1000550. DOI: 10.1371/journal.ppat.1000550 [OA]
  • Rosenblum EB, Fisher MC, James TY, Stajich JE, Longcore JE, Gentry LR, and Porten TJ. (2010). A molecular perspective on the biology of the emerging pathogen Batrachochytrium dendrobatidis. Diseases of Aquatic Organisms. 92(2-3):131-47. DOI: 10.3354/dao02179
  • 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 [OA]

Fungal Pathogens of Animals and Plants

  • D’Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. (2011) Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts. MBio. 2(1): e00342-10. DOI: 10.1128/mBio.00342-10 [OA]
  • Levesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. (2010). Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biol, 11(7):R73. DOI: 10.1186/gb-2010-11-7-r73 [OA]
  • Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. (2010). Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res, 20(7):938-46. DOI: 10.1101/gr.103911.109 [OA]
  • 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 [OA]
  • 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 [OA]
  • 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

Neurospora and Ascomycete genomics

  • Gioti A, Mushegian AA, Strandberg R, Stajich JE, Johannesson H. (2012) Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Mol Biol Evol. (advance access) DOI: 10.1093/molbev/mss132
  • Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW. (2011) Massive Changes in Genome Architecture Accompany the Transition to Self-fertility in the Filamentous Fungus Neurospora tetrasperma. Genetics (in press). DOI: 10.1534/genetics.111.130690. [OA]
  • Smith KM, Sancar G, Dekhang R, Sullivan CM, Li S, Tag AG, Sancar C, Bredeweg EL, Priest HD, McCormick RF, Thomas TL, Carrington JC, Stajich JE, Bell-Pedersen D, Brunner M, Freitag M. (2010) Transcription Factors in Light and Circadian Clock Signaling Networks Revealed by Genomewide Mapping of Direct Targets for Neurospora White Collar Complex. Euk Cell 9(10):1549-1556. DOI: 10.1128/EC.00154-10 [OA]
  • Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. (2010) Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genetics & Biology 47(10):869-78. DOI: 10.1016/j.fgb.2010.06.008
  • Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M. (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6(4):e1000891. DOI: 10.1371/journal.pgen.1000891 [OA]
  • 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

Basidiomycete genomics

  • Burns C, Stajich JE, Rechtsteiner A, Casselton L, Hanlon S, Wilke SK, Savytskyy O, Gathman A, Lilly W, Lieb J, Zolan ME, Pukkila PJ. (2010) Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program Over Half a Billion Years of Evolution. PLoS Genetics 6(9): e1001135. DOI: 10.1371/journal.pgen.1001135 [OA]
  • Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, Vankuyk PA, Horton JS, Grigoriev IV, Wösten HA. (2010) Genome sequence of the model mushroom Schizophyllum commune. Nature Biotech 28(9):957-63. DOI: 10.1038/nbt.1643
  • Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ. (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). PNAS 107(26):11889-94. DOI: 10.1073/pnas.1003391107 Cover article & photo of C. cinerea on the cover. [OA]
  • 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 [OA]

Evolutionary, Population Genomics, and Bioinformatics 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 [OA]
  • 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 [OA]
  • 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 [OA]
  • 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 [OA]
  • 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 [OA]

Other Genomes

  • 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 [OA]

Full list of publications on PubMed