Publications

Legend:

Research Area(s)
(EDF) – Early Diverging Fungi
(A) – Ascomycete

(B)- Basidiomycetes
(BACT) – Bacteria
(F) – Fungi
(O) – Oomycetes and others
(P) – Plants
(M)- Bioinformatics Methods
[OA] – open access
Graduate student
Postdoctoral trainee
Undergraduate student
Visiting scholars
In prep / submitted
  • Cissé OH, Stajich JE* FGMP: assessing genome completion in fungal genomic data. (in revision). Preprint doi: 10.1101/049619 Code github: stajichlab/FGMP (M)
  • Medina EM, Ahrendt SR, Swafford A, Oakley TH, Stajich JE*. Coexistance and deep origin of Opisthokonta opsin-like GPCRs and Bacteriorhodopsins supports opsin convergent evolution. in prep (EDF)
  • Ahrendt SR, Jeong N, Liu P, Ear S, Swanson S, Stajich JE*. Investigation of the growth suppression properties of the chytridiomycete Homolaphlyctis polyrhiza JEL142. in prep (EDF)
  • Lu L§, Chen J§, Robb SM, Okumoto Y, Monden Y, Naito K, Stajich JE, Wessler SR. Massive amplification of TEs in nature occurs in the presence of normal genome surveillance. in prep (P)
2017
  1. Aryal SK, Carter-House D, Stajich JE, Dillman AR. Microbial Associates of the Southern Mole Cricket (Scapteriscus borellii) are Highly Pathogenic. Submitted (A) (BACT)
  2. Beaudet D, Chen E CH, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich, JE, Corradi N. Single-cell transcriptomics reveals hidden functional diversity and novel phylogenetic affiliations within arbuscular mycorrhizal fungi. Submitted github: zygolife/AMF_Phylogenomics (EDF)
  3. Park S, Scranton MA, Stajich JE,  Yee A, Holzer FM, Walling LW. Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions. Submitted (P) 
  4. Torres-Cruz  TJ, Billingsley Tobias TL, Almatruk M, Hesse C, Kuske CR, Desirò A, Benucci GN, Bonito G, Stajich JE, Dunlap C, Arnold AE, Porras-Alfaro A. Bifiguratus adelaidae gen. et sp. nov., a new lineage of Mucoromycotina with endophytic and soil-dwelling strains. Mycologia (in revision) Dataset: github.com/zygolife/Bifiguratus_Phylogenomics (EDF)
  5. Sinha S, Flibotte S, Neira M, Lenassi M, Gostinčar C,  Stajich JE*, Nislow CE*. Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure. G3 2017; doi: 10.1534/g3.117.040691  (A)
  6. Mondo SJ, Dannebaum RO, Kuo R, LaButti K, Haridas S, Kuo A, Salamov A, Arendt SR, Lipzen A, Sullivan W, Andreopoulos W, Clum A, Lindquist E, Daum C, Ramamoorthy G, Gryganskyi AP, Culley D, Magnuson JK, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. Pervasive Adenine N6-methylation of Active Genes in Fungi. Nature Genetics 2017; AOP doi: 10.1534/g3.117.040691(EDF)
  7. Ahrendt SR, Medina EM, Chang CA, Stajich JE*. Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PeerJ  5:e3206  doi: 10.7717/peerj.3206 and data repository (EDF)
  8. Nguyen T, Cissé OH, Wong J, Zheng P, Hewitt D, Nowrousian M, Stajich JE*, Jedd G*. Evolutionary innovation and constraint leading to complex multicellularity in the Ascomycota. Nature Communications 2017; 8:14444. doi: 10.1038/NCOMMS14444. (A)
  9. Chen J, Wrightsman T, Wessler SR, and Stajich JE*. RelocaTE2: a high resolution transposable element polymorphism mapping tool for population resequencing. PeerJ 2017; 5:e2942. doi: 10.7717/peerj.2942. Preprint doi:10.7287/peerj.preprints.2447. github code repository: stajichlab/RelocaTE2 (M) (P)
  10. Short DPG, O’Donnell K, Stajich JE, Hulcr J, Kijimoto T, Berger M, Macias AM, Spahr EJ, Bateman CC, Eskalen A, Lynch S, Cognato AI, Cooperband M, Kasson MT. PCR multiplexes discriminate Fusarium symbionts of invasive Euwallacea ambrosia beetles that inflict damage on numerous tree species throughout the United States. Plant Disease. 2017; 101(1):233-240. doi: 10.1094/PDIS-07-16-1046-RE (A)
2016
  1. Stajich JE. Fungal Evolution: Mucor and Phycomyces See Double. Current Biol. 2016; 26(16):R775-R777 doi: 10.1016/j.cub.2016.06.049(EDF)
  2. Spatafora JW, Chang Y, Benny GL, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O’Donnell K, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016; 108(5):1028-1046. doi: 10.3852/16-042Dataset doi: 10.5281/zenodo.46700 TreeBase: TB2:S18957. [PDF[OA] (EDF) 
  3. Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, Pérez G, Pisabarro AG, Grigoriev IV, Stajich JE*, Ramírez L*. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet. 2016;12(6):e1006108. doi: 10.1371/journal.pgen.1006108 [PDF]
    Code github: stajichlab/localizaTE & release info [OA] (B)
  4. Lee MJ, Geller AM,  Bamford NC, Liu H, Gravelat FN, Snarr BD, Cerone RP, Baptista SD, Vinogradov E, Stajich JE, Filler SG, Howell P, Sheppard DC. Deacetylation of fungal exopolysaccharide mediates adhesion and biofilm formation: lessons learned from pathogenic bacteria. mBio 2016; 5;7(2). pii: e00252-16. doi: 10.1128/mBio.00252-16. [PDF] [OA] (A)
  5. de Man TJB, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Suen G, Currie CR, Gerardo NM. The small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. PNAS 2016; 113(13):3567-72. doi: 10.1073/pnas.1518501113. [PDF(A)
  6. U’Ren JM, Miadlikowska J, Zimmerman N, Lutzoni F, Stajich JE, Arnold AE. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 2016; 98:210-32. doi: 10.1016/j.ympev.2016.02.010. [PDF(A) 
2015
  1. Wang Y, Smith KM, Taylor JW, Freitag M, Stajich JE*. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3. 2015; pii: g3.115.017921. doi: 10.1534/g3.115.017921. [PDF[OA] (A)
  2. Liu P, Stajich JE*. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genet Biol. 2015;77:31-9. doi: 10.1016/j.fgb.2015.03.003. [PDF(EDF)
  3. Pieuchot L, Lai J, Loh RA, Leong FY, Chiam KH, Stajich J, Jedd G. Cellular Subcompartments through Cytoplasmic Streaming. Dev Cell. 2015;34(4):410-20. doi: 10.1016/j.devcel.2015.07.017. [PDF(A)
  4. Collins RA, Stajich JE, Field DJ, Olive JE, DeAbreu DM. The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin. RNA. 2015;21(5):997-1004. doi: 10.1261/rna.047985.114. [PDF] [OA] (A)
  5. Mélida H, Sain D, Stajich JE, Bulone V. Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches. Environ Microbiol. 2015;17(5):1649-62. doi: 10.1111/1462-2920.12601. [PDF(EDF)
  6. Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA. Analysis of the Candida albicans Phosphoproteome. Eukaryot Cell. 2015; 14(5):474-85. doi: 10.1128/EC.00011-15. [PDF[OA] (A)
2014
  1. Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA. MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum. PLoS Pathog. 2014;10(10):e1004464. doi: 10.1371/journal.ppat.1004464. [PDF[OA] (A)
  2. Teixeira MM, de Almeida LG, Kubitschek-Barreira P, Alves FL, Kioshima ES, Abadio AK, Fernandes L, Derengowski LS, Ferreira KS, Souza RC, Ruiz JC, de Andrade NC, Paes HC, Nicola AM, Albuquerque P, Gerber AL, Martins VP, Peconick LD, Neto AV, Chaucanez CB, Silva PA, Cunha OL, de Oliveira FF, dos Santos TC, Barros AL, Soares MA, de Oliveira LM, Marini MM, Villalobos-Duno H, Cunha MM, de Hoog S, da Silveira JF, Henrissat B, Niño-Vega GA, Cisalpino PS, Mora-Montes HM, Almeida SR, Stajich JE, Lopes-Bezerra LM, Vasconcelos AT, Felipe MS. Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. BMC Genomics. 2014;15:943. doi: 10.1186/1471-2164-15-943. [PDF[OA] (A)
  3. Inglis DO, Skrzypek MS, Liaw E, Moktali V, Sherlock G, Stajich JE. Literature-based gene curation and proposed genetic nomenclature for Cryptococcus. Eukaryot Cell. 2014; 13(7):878-83. doi: 10.1128/EC.00083-14. [PDF[OA] (B) (M)
  4. Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL. Evolutionary histories of soil fungi are reflected in their large-scale biogeography. Ecol Lett. 2014;17(9):1086-93. doi: 10.1111/ele.12311. [PDF(F)
  5. Janbon G, Ormerod KL, Paulet D, Byrnes EJ 3rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014;10(4):e1004261. doi: 10.1371/journal.pgen.1004261. [PDF[OA] (B)
2013
  1. Rosenblum EB, James TY, Zamudio KR, Poorten TJ, Ilut D, Rodriguez D, Eastman JM, Richards-Hrdlicka K, Joneson S, Jenkinson TS, Longcore JE, Parra Olea G, Toledo LF, Arellano ML, Medina EM, Restrepo S, Flechas SV, Berger L, Briggs CJ, Stajich JE. (2013) Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. PNAS. 110(23):9385-90. doi: 10.1073/pnas.1300130110.[PDF[OA] (EDF)
  2. Gioti A, Stajich JE, Johannesson H. (2013) Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus. Evolution. 67(12):3600-16 doi: 10.1111/evo.12206. [PDF(A)
  3. James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. Shared signatures of parasitism and phylogenomics unite Cryptomycota and Microsporidia. Curr Biol. 2013; 23(16):1548-53. doi: 10.1016/j.cub.2013.06.057. [PDF(EDF)
  4. Robb SM, Lu L, Valencia E, Burnette JM 3rd, Okumoto Y, Wessler SR, Stajich JE. (2013) The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice. G3  3(6):949-57.  doi: 10.1534/g3.112.005348. [PDF[OA] (P) (M)
  5. Gioti A, Nystedt B, Li W, Xu J, Andersson A, Averette AF, Münch K, Wang X, Kappauf C, Kingsbury JM, Kraak B, Walker LA, Johansson HJ, Holm T, Lehtiö J, Stajich JE, Mieczkowski P, Kahmann R, Kennell JC, Cardenas ME, Lundeberg J, Saunders CW, Boekhout T, Dawson TL, Munro CA, de Groot PW, Butler G, Heitman J, Scheynius A. Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis. mBio. 2013;4(1):e00572-12. doi: 10.1128/mBio.00572-12. [PDF[OA] (B)
  6. Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M. (2013) The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genetics 9(9):e1003820. DOI: 10.1371/journal.pgen.1003820 [PDF[OA] (A)
  7. Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. (2013) Regional control of histone H3 lysine 27 methylation in Neurospora. PNAS 110(15):6027-32. DOI: 10.1073/pnas.1303750110. [PDF[OA] (A)
  8. Evolutionary origins and diversification of proteobacterial mutualists.
    Sachs JL, Skophammer RG, Bansal N, Stajich JE. Proc Biol Sci. 2013; 281(1775):20132146. doi: 10.1098/rspb.2013.2146. [PDF]
  9. Gryganskyi AP, Humber RA, Stajich JE, Mullens B, Anishchenko IM, Vilgalys R. Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex. PLoS One. 2013; 8(8):e71168. doi: 10.1371/journal.pone.0071168. [PDF[OA] (EDF)
  10. Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS. (2013) 5′-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics 14:195. doi: 10.1186/1471-2164-14-195. [PDF] [OA] (B)
  11. Hibbett DS, Stajich JE, Spatafora JW. (2013). Towards genome-enabled mycology. Mycologia  105(6):1339-1349. doi: 10.3852/13-196. [PDF[OA] (F)
2012-earlier
  1. Abramyan J and Stajich JE Species-specific Chitin Binding Module 18 (CBM18) expansion in the Amphibian Pathogen Batrachochytrium dendrobatidis. mBio. 2012; 3(3):e00150-12. doi: 10.1128/mBio.00150-12. [PDF[OA] (EDF)
  2. Gioti A, Mushegian AA, Strandberg R, Stajich JE, Johannesson H. Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Mol Biol Evol. 2012; 29 (10):3215-3226. doi: 10.1093/molbev/mss132. [PDF[OA] (A)
  3. Fisher MC, Stajich JE, and Farrer RA. 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 (EDF)
  4. Joneson S, Stajich JE, Shin-Han S, Rosenblum EB. Genomic Transition to Pathogenicity in Chytrid Fungi. PLoS Pathogens. 2011; 7(11): e1002338. doi: 10.1371/journal.ppat.1002338. [OA] (EDF)
  5. 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. Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts. mBio 2011;  2(1): e00342-10. doi: 10.1128/mBio.00342-10 [OA] (B)
  6. 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] (B)
  7. 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. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotech 2010; 28(9):957-63. doi: 10.1038/nbt.1643 (B)
  8. 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. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). PNAS 2010; 107(26):11889-94. doi: 10.1073/pnas.1003391107 Cover article & photo of C. cinerea on the cover. [OA] (B)
  9. Rosenblum EB, Voyles J, Poorten TJ, and Stajich, JE. The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens 2010; 6(1): e1000550. doi: 10.1371/journal.ppat.1000550 [OA] (EDF)
  10. Rosenblum EB, Fisher MC, James TY, Stajich JE, Longcore JE, Gentry LR, and Porten TJ. A molecular perspective on the biology of the emerging pathogen Batrachochytrium dendrobatidis. Diseases of Aquatic Organisms. 2010; 92(2-3):131-47. doi: 10.3354/dao02179 (EDF)
  11. 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. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 2010; 11(7):R73. doi: 10.1186/gb-2010-11-7-r73 [OA] (O)
  12. 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. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010; 20(7):938-46. doi: 10.1101/gr.103911.109 [OA] (A)
  13. Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW. The fungi. Current Biol. 2009; 19(18):R840-5. doi:10.1016/j.cub.2009.07.004 (F)
  14. 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. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 2009; 19(10): 1722-1731. doi: 10.1101/gr.087551.108 [OA] (A)
  15. Fisher MC, Bosch J, Yin Z, Stead DA, Walker J, Selway L, Brown AJP, Walker LA, Gow NAR, Stajich JE, Garner TWJ. Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence. Mol Ecol. 2009; 18:415-429. doi: 10.1111/j.1365-294X.2008.04041.x
  16. Rosenblum EB, Stajich JE, Maddox N, Eisen MB. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci. 2008; 105(44):17034-17039. doi: 10.1073/pnas.0804173105 [OA] (EDF)
  17. 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. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008; 452(7183):88-92. doi: 10.1038/nature06556 (B)
  18. Lilly WW, Stajich JE, Pukkila PJ, Wilke SK, Inoguchi N, Gathman AC. An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea. Mycol Res. 2008; 389-98. doi: 10.1016/j.mycres.2007.11.013 (B)
  19. Stajich JE, Dietrich FS, Roy SW. Comparative genomic analysis of fungal genomes reveals intron rich ancestors. Genome Biology 2007; 8:R223. doi: 10.1186/gb-2007-8-10-r223 [OA] (F)
  20. Fitzpatrick DA, Logue ME, Stajich JE, and Butler G. A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology 2007; 6:99. doi: 10.1186/1471-2148-6-99 [OA] (F)
  21. 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] (A)
  22. 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, Curtis JH, 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 2006; 443(7113):818-822. doi: 10.1038/nature05110 (F)
  23. 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. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006; 444(7115):97-101. doi: 10.1038/nature05248 (B)
  24. Stajich JE and Dietrich FS. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryot Cell 2006; 5(5):789-93. doi: 10.1128/EC.5.5.789-793.2006 [OA] (B)
  25. Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Wright JR, Diezmann S, Allen A, Stajich JE, Dietrich FS, Perfect JR, Heitman J. Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 2005; 437(7063):1360-1364. doi: 10.1038/nature04220 [OA] (B)
  26. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 2005; 15(8):1153-60. doi: 10.1101/gr.3567505 [OA] (M)
  27. Stajich JE and Hahn MW. Disentangling the effects of demography and selection in human history. Mol Biol Evol 2005; 22(1):63-73. doi: 10.1093/molbev/msh252[OA] (M)
  28. 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. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 2004; 1(2):E45. doi: 10.1371/journal.pbio.0000045[OA]
  29. Hahn MW, Stajich JE, Wray GA. The effects of selection against spurious transcription factor binding sites. Mol Biol Evol 2003; 20(6):901-906. doi: 10.1093/molbev/msg096. [OA] (M)
  30. 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. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002;
    12(10):1611-1618. doi: 10.1101/gr.361602[OA] (M)
  31. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002; 12(10):1599-1610. doi: 10.1101/gr.403602[OA] (M)

Reviews and Meeting reports

  1. Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma BP, Unruh S. Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.  G3. 2015;5(12):2523-5. doi: 10.1534/g3.115.024158
  2. Kennedy P, Stajich JE Twenty-first century mycology: a diverse, collaborative, and highly relevant science. New Phytol. 2015; 205(1):23-6. doi: 10.1111/nph.13165.
  3. Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE. Meeting report: fungal ITS workshop (October 2012). Stand Genomic Sci. 2013; 15;8(1):118-23. doi: 10.4056/sigs.3737409.

Full list of publications on PubMed