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

(B)- Basidiomycetes
(BACT) – Bacteria
(F) – Fungi
(E) Eukaryotes and Oomycetes
(P) – Plants
(PA) – Pathogen study
(M)- Bioinformatics Methods
(MB) – Micro/Mycobiome
[OA] – open access

Graduate student
Postdoctoral trainee
Undergraduate student
Visiting scholars

In prep / submitted

  • Lofgren LA, Vilgalys R, Nguyen NH, Ruytinx J, Liao H, Branco S, Kuo A, LaButti K, Lipzen A, Andreoploulos W, Pangilinan J, Riley R, Hundley H, Na H, Barry K, Grigoriev IV, Stajich JE, Kennedy PG. Comparative Genomics Reveals Dynamic Signatures of Host Specificity in Mutualist Fungi. Submitted.
  • Chang Y, Rochon D, Sekimoto S, Wang Y, Chovatia M, Sandor L, Grigoriev IV, Berbee M, Stajich JE, Spatafora JW. Phylogenomic analyses of Olpidium reveal hard polytomies of the backbone of Kingdom Fungi.  In Prep. (EDF)
  • Albanese D, Coleine C, Rota-Stabelli O, Onofri S, Tringe SG, Stajich JE*, Selbmann L,* Donati C. Antarctic cryptoendolithic bacterial lineages of pre-Cambrian origin as proxy for Mars colonization. Submitted. Preprint doi: 10.1101/2020.02.27.967604.
  • Carrillo AJ, Cabrera IE, Spasojevic M, Schacht P, Stajich JE, Borkovich KA. Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa. In Revision. (A)
  • Unruh SA, Pires CA, Zettler LW, Erba L, Grigoriev IV, Barry KW, Daum C,  Lipzen AV, Stajich JE*. Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids. Preprint doi: 10.1101/862763
  • Schwartze VU, Klassert TE, Riege K, Marcet-Houben M, Nowrousian M, Binder U, Grigoriev IV, Grøtli M, Gryganskyi A, Fleischauer M, Gräler MH, Horn F, Linde J, Lipzen A, Park H, Salamov A, Sieber P, Stajich JE, Tamás MJ, Tritt A, Winter S, Böcker S, Gabaldón T, Schuster S, Marz M, Lass-Flörl C, Slevogt H, Voigt K. To the limit and beyond: Comparative ‘Omics’-approaches provide insights into stress adaptation and pathogenicity of basal fungal pathogens (Lichtheimia spp.). Resubmission. (EDF) (PA)
  • Alvarado P, Teixeira M, Pérez-Rojas Y, Barker B, Stajich JE, Zambrano E, Gonzatti MI. Genomic characterization and biochemical identification of secreted antigens and peptidases in a Venezuelan clinical isolate of Histoplasma suramericanum. In Prep. (A) (PA)
  • 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 SRJeong N, Liu P, Ear S, Swanson S, Stajich JE*. Investigation of the growth suppression properties of the chytridiomycete Homolaphlyctis polyrhiza JEL142. In prep (EDF)


  1. Lee Y, Vidal-Diez de Ulzurrun G, Schwarz EM, Stajich JE, Hsueh Y-P. Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9. G3. In Press. preprint  doi: 10.1101/2020.09.03.281683
  2. J Chen, L Lu, SMC Robb, M Collin, Y Okumoto, JE Stajich, SR Wessler. Genomic diversity generated by a transposable element burst in a rice recombinant inbred population. 2020. Proc Natl Acad Sciences. In Press. Preprint 10.1101/2020.08.24.265538
  3. Myers JM, Bonds  AE, Clemons RA, Thapa NA, Simmons DR, Longcore JE, Bonito G, Carter-House D, Ortanez J, Liu P, Stajich JE, Spatafora JW, Chang Y, Corrochano L, Gryganskyi A,  Grigoriev I, James TY. Survey of early-diverging lineages of fungi reveals abundant and diverse mycoviruses. 2020. mBio  11 (5) e02027-20; DOI: 10.1128/mBio.02027-20 (EDF)
  4. Coleine C*, Stajich JE*, de los Ríos A, Selbmann L. Beyond the extremes: rocks as ultimate refuge for fungi in drylands. Mycologia. In Press. (A)
  5. James TY, Stajich JE, Hittinger CT, Rokas A. Toward a Fully Resolved Fungal Tree of Life 
    Annual Review of Microbiology 2020 74:1291-313 doi: 10.1146/annurev-micro-022020-051835 (F)
  6. Collins CG, Spasojevic MJ, Alados CL, Aronson EL, Benavides JC, Cannone N, Caviezel C, Grau O,  Guo H,  Kudo G, Kuhn NJ, Müllerová J, Phillips ML, Pombubpa N, Reverchon F, Shulman HB, Stajich JE, Stokes A, Weber SE, Diez JM. Global Impacts of Alpine Woody Encroachment on Soil Microbial Communities. Global Change Biology. 10.1111/gcb.15340 (MB)
  7. Tabima JF, Trautman IA, Chang Y, Wang Y, Grigoriev IV, Stajich JE, Spatafora JW. Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus. G3: Genomes | Genes | Genetics 10(9):3417-3433. doi: 10.1534/g3.120.401516   Preprint doi: 10.1101/2020.04.08.030916. (EDF)
  8. Vandepol N, Liber J, Desirò A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller AN, O’Donnell K, Stajich JE, and Bonito G. 2020. Resolving the Mortierellaceae phylogeny through synthesis of Multi-Locus Sequence Typing (MLST) and phylogenomics. Fungal Diversity. doi: 10.1007/s13225-020-00455-5  (EDF)
  9. Pombubpa N, Pietrasiak N, De Ley P, Stajich JE*. Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA. FEMS Microbiol Ecol. 2020; AOP: fiaa125. doi: 10.1093/femsec/fiaa125. Preprint doi: 10.1101/810002. (MB)
  10. Pombubpa N, Kurbessoian T, Stajich JE, La Doux T, Pietrasiak N. Exploring the Microbial Diversity in Biological Soil Crusts at Joshua Tree National Park.
  11. Coleine C, Pombubpa N, Zucconi L, Onofri S, Turchetti B, Buzzini P, Stajich JE, Selbmann L. Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land. Microorganisms. 2020;8(6):E942. doi:10.3390/microorganisms8060942 (MB)
  12. Lovett B, Macias A, Stajich JE, Cooley J, Eilenberg J, de Fine Licht HH, Kasson MT. Behavioral betrayal: how select fungal parasites enlist living insects to do their bidding. PLoS Pathogens. 2020; 16(6):e1008598. doi: 10.1371/journal.ppat.1008598 (EDF)
  13. Fisher MC, Gurr S, Cuomo CA, Blehert D, Jin H, Stukenbrock E, Stajich JE, Kahmann R, Boone C, Denning D, Gow N, Klein B, Kronstad J, Sheppard D, Taylor JW, Wright G, Heitman J, Casadevall A, Cowen L. Threats posed by the Fungal Kingdom to humans, wildlife, and agriculture. mBio. 2020; 11(3):e00449-20. doi: 10.1128/mBio.00449-20. (F)
  14. James TY, Stajich JE, Hittinger CT, Rokas A. Toward a Fully Resolved Fungal Tree of Life. Annual Reviews of Microbiology. In Press. (F)
  15. Coleine C, Masonjones S, Onofri S, Selbmann L, Stajich JE*. Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica. Microbiol Resour Announc. 2020; 9(14). pii: e00020-20. doi: 10.1128/MRA.00020-20. (B)
  16. Macias AM, Geiser DM, Stajich JE, Lukasik P, Veloso C, Bublitz DC, Berger MC, Boyce GR, Hodge K, Kasson MT. Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas. Mycologia. 2020; 1-15. doi: 10.1080/00275514.2020.1742033.  Preprint doi: 10.1101/811836. (EDF)
  17. Yang C-T , Vidal-Diez de Ulzurrun G, Gonçalves Pedro, Lin H-C, Chang C-W, Huang T-Y, Chen S-A, Lai C-K, Tsai IJ, Schroeder FC, Stajich JE, Hsueh Y-P. Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi. Proc National Academy of Sciences 2020. 117 (12), 6762-6770. doi: 10.1073/pnas.1919726117. Preprint doi: 10.1101/843698 (A) (PA) 
  18. Coleine C, Albanese D, Onofri S, Zucconi L, Tringe SG, Pennacchio C, Donati C*, Stajich JE*, Selbmann L. Metagenomes in the borderline ecosystems of the Antarctic cryptoendolithic communities. Microbial Resource Announcements. 2020; (Longer form in Preprint) doi: 10.1101/725200 (MB)
  19. Coleine C, Pombubpa N, Zucconi L, Onofri S, Stajich JE*, Selbmann L. Endolithic fungal species markers for harshest conditions in the McMurdo Dry Valleys, Antarctica. Life. 2020; 10(2):E13.  doi: 10.3390/life10020013 (A) (MB)
  20. Coleine C, Stajich JE*, Zucconi L, Onofri S, Selbmann L. Sun exposure drives Antarctic cryptoendolithic community structure and composition. Polar Biology. 2020. doi: 10.1007/s00300-020-02650-1. Preprint 10.1101/676692 (MB)
  21. Coleine C, Stajich JEPombubpa N, Zucconi L, Onofri S, Selbmann L. Sampling strategies to assess microbial diversity of Antarctic cryptoendolithic communities. Polar Biology. 2020; 43:225–235. doi: 10.1007/s00300-020-02625-2. Preprint doi: 10.1101/676775 (MB)
  22. Coleine C, Masonjones S, Sterflinger K, Onofri S, Selbmann L*, Stajich JE*. Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus. Fungal Biology. 2020. In press. doi: 10.1016/j.funbio.2020.01.005 (A)
  23. Knudsen K*, Adams J. N., Kocourková J, Wang Y, Ortañez J, Stajich JE. The monophyletic Sarcogyne canadensis–wheeleri clade, a newly recognized group sister to the European Acarospora glaucocarpa group. The Bryologist. 2020. 123(1):11-30. doi: 10.1639/0007-2745-123.1.011 (A) 
  24. Odebode A, Adekunle A, Stajich J, Adeonipekun P. Airborne Fungi Spores Distribution in Various Locations in Lagos, Nigeria. Environ Monit Assess 2020; 192(2): 87. doi: 10.1007/s10661-019-8038-3.  (A) [OA]
  25. Carrillo JD, Mayorquin JS, Stajich JE, Eskalen A. Probe-Based Multiplex Real-Time PCR as a Diagnostic Tool to Distinguish Distinct Fungal Symbionts Associated With Euwallacea kuroshio and Euwallacea whitfordiodendrus in California. Plant Dis. 2020; 104 (1), 227-238. doi: 10.1094/PDIS-01-19-0201-RE (A) [OA]


  1. Carrillo JD, Rugman-Jones PF, Husein D, Stajich JE, Kasson MT, Carrillo D, Stouthamer R, Eskalen A. Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan. Fungal Genet Biol. 2019; 133:103269. doi: 10.1016/j.fgb.2019.103269. (A) 
  2. Kowalski C, Kerkaert JD, Liu K, Bond MC, Hartmann R, Nadell CD, Stajich JE, and Cramer RA.  Fungal biofilm morphology impacts hypoxia fitness and disease progression. Nature Microbiology. 2019; 4:2430–2441. doi: 10.1038/s41564-019-0558-7. (A) (PA)
  3. Uehling JK, Entler M, Meredith H, Millet L, Timm C, Aufrecht J, Bonito G, Engle N, Labbé JL, Doktycz MJ, Retterer S, Spatafora J, Stajich JE, Tschaplinski T, Vilgalys R. Microfluidics and metabolomics reveal symbiotic bacterial-fungal interactions between Mortierella elongata and Burkholderia include metabolite exchange. Frontiers in Microbiology. 2019; 10:2163. doi: 10.3389/fmicb.2019.02163. (EDF) [OA]
  4. Warren SD, St. Clair LL, Stark LR, Lewis LA, Stajich JE, Pombubpa N, Kurbessoian T, Aanderud ZT. Reproduction and Dispersal of Biological Soil Crust Organisms. Review, Front. Ecol. Evol. – Biogeography and Macroecology. 2019; 7:344. doi: 10.3389/fevo.2019.00344. (MB) [OA]
  5. Coleine C, Stajich JE*, Pombubpa N, Zucconi L, Onofri S, Canini F, Selbmann L. (2019) Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities. Environ Microbiology Reports.  doi: 10.1111/1758-2229.12788 (MB)
  6. Wang Y, Youssef N, Couger MB, Hanafy R, Elshahed MS, & Stajich JE*. Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. mSphere. 2019; 4(4). pii: e00247-19 doi: 10.1128/mSystems.00247-19 (EDF) [OA]
  7. Teixeira M, Barker BM, Stajich JE*An improved reference genome of Coccidioides immitis, Washington population. Microbial Resource Announcements. 2019; 8(33). pii: e00149-1. doi: 10.1128/MRA.00149-19 BioProject PRJNA169242  (A) (PA) [OA]
  8. Macias AM, Marek PE, Morrissey EM, Brewer MS, Short DPG, Stauder CM, Wickert KL, Berger MC, Metheny AM, Stajich JE, Boyce G, Rio RVM, Panaccione DG, Wong V, Jones TH, Kasson  MT.  Diversity and function of fungi associated with the fungivorous millipede, Brachycybe lecontii. Fungal Ecology. 2019; 41:187-197. doi: 10.1016/j.funeco.2019.06.006. Preprint DOI: 10.1101/515304 (MB) (EDF)
  9. Boyce G, Gluck-Thaler E,  Slot JC, Stajich JE,  Davis WJ, James TY, Cooley JR, Panaccione DG, Eilenberg J, De Fine Licht H, Macias AM, Berger MC, Wickert KL, Stauder CM,  Spahr EJ, Maust MD, Metheny AM, Simon C, Kritsky G,  Hodge KT, Humber RA, Gullion T, Short DPG, Kijimoto T, Mozgai D, Arguedas N,  Kasson MT. Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens. Fungal Ecology. 2019;  41:147-164. doi: 10.1016/j.funeco.2019.06.002

    . Preprint doi: 10.1101/375105. (EDF) [OA]

  10. Murphy CM, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Dagar SS, Griffith GW, Farag IF, Callagan TM, Elshahed MS. Horizontal gene transfer as an indispensible driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage.  Appl Env Microbiology. 2019; 85(15). pii: e00988-19 doi: 10.1128/AEM.00988-19 preprint doi: 10.1101/487215  (EDF) 
  11. Coleine C, Selbmann L*, Masonjones S, Onofri S, Zucconi L, Stajich JE*. Draft genome of an Antarctic isolate of the black yeast fungus Exophiala mesophila. Microbial Resource Announcements. 2019; 8 (19) e00142-19; DOI: 10.1128/MRA.00142-19 (A) [OA]
  12. Blachowicz A, Chiang AJ, Elsaesser A, Kalkum M, Ehrenfreund P, Stajich JE, Torok T, Wang CCC, Venkateswaran K. Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions. Frontiers in Microbiology. 2019; 10:1013. doi: 10.3389/fmicb.2019.01013 (A) [OA]
  13. Cissé OH, Stajich JEFGMP: assessing genome completion in fungal genomic data. BMC Bioinformatics. 2019; 20(1):184. doi: 10.1186/s12859-019-2782-9. Preprint doi: 10.1101/049619. Code github: stajichlab/FGMP (M) [OA]
  14. Bewick AJ, Hofmeister BT, Powers R, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nature Ecology and Evolution. 2019; 3(3):479-490. doi: 10.1038/s41559-019-0810-9 (F)
  15. Chen J, Lu L, Benjamin, J Diaz S, Hancock N, Stajich JE*, Wessler SR*. Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice. Nature Comm. 2019; 10:641.  doi: 10.1038/s41467-019-08451-3 Preprint doi: 10.1101/405290. ReadCube (P) [OA]
  16. Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE. Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. Microbiol Resource Announcements. 2019;8(36). pii: e00954-19. doi: 10.1128/MRA.00954-19. [OA] 
  17. Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich JE, Varga-Muñiz J, Walker AK, Yarden O, Gladfelter AS. Fungi in the marine environment: open questions and unsolved problems. mBio. 2019; 10(2). pii: e01189-18. doi: 10.1128/mBio.01189-18 (F) [OA]
  18. Valent B, Farman M, Tosa Y, Begerow D, Fournier E, Gladieux P, Islam MT, Kamoun S, Kemler M, Kohn LM, Lebrun MH, Stajich JE, Talbot NJ, Terauchi R, Tharreau D, Zhang N. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Mol Plant Pathol. 2019;20(2):173-179. doi: 10.1111/mpp.12778 [OA] 
  19. Davis W, Amses K, Benny G, Carter-House D, Chang Y, Grigoriev I,  Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics analyses reveals a monophyletic Zoopagales (Zoopagomycota, Fungi) with predacious taxa evolving from mycoparasite ancestors. Molecular Phylogenetics and Evolution.  2019; 133:152-163. doi: 10.1016/j.ympev.2019.01.006 (EDF)
  20. Kasson MT, Kasson LR, Wickert KL, Davis DD, Stajich JE. Genome Sequence of a Lethal Vascular Wilt Fungus, Verticillium nonalfalfae, a Biological Control Used Against the Invasive Ailanthus altissima. Microbial Resource Announcements. 2019; doi10.1128/MRA.01619-18 (A) (PA) [OA] BioProject: PRJNA531016
  21. Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev I, Martin F, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizae within Mucoromycota. New Phytologist. 2019; 222: 511-525. doi: 10.1111/nph.15613 (EDF)
  22. Arvidson R, Kaiser M, Lee SS, Urenda J, Dail C, Mohammed H, Nolan C, Pan S-Q, Stajich JE, Libersat F, and Adams M. Parasitoid Jewel Wasp Mounts Multi-Pronged Neurochemical Attack to Hijack a Host Brain. Mol Cell Proteomics. 2019;18(1):99-114. doi: 10.1074/mcp.RA118.000908


  1. Blachowicz A, Chiang AJ, Chiang YM, Masonjones S, Yaegashi J, Countryman S, Karouia F, Kalkum M, Stajich JE, Venkateswaran K, Wang CCC. International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulansAppl Microbiol Biotechnol. 2018 . doi: 10.1007/s00253-018-9525-0 (A)
  2. Demers E, Biermann AR, Masonjones S, Crocker AW, Ashare A, Stajich JE, Hogan DA. Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection. Proc National Acad Sciences. 2018;  115(47):12040-12045. doi: 10.1073/pnas.1807698115 (A) [OA]
  3. Arnesen JA, Malagocka J, Gryganskyi AP,  Grigoriev IV, Voigt K, Stajich JE, De Fine Licht HH. Early diverging insect-pathogenic fungi of the order Entomophthorales possess diverse and unique subtilisin-like serine proteases. G3.  2018; 8(10):3311-3319. doi: 10.1534/g3.118.200656 Preprint doi: 10.1101/247858(EDF) [OA]
  4. Romsdahl J, Blachowicz A, Chiang AJ, Singh N, Stajich JE, Kalkum M, Venkateswaran K, Wang CCC. Characterization of Aspergillus niger Isolated from the International Space Station. mSystems. 2018; 3(5):e00112-18. doi: 10.1128/mSystems.00112-18 (A) [OA]
  5. Song Z, Stajich JE, Xie Y, Liu X, He Y, Chen J, Hicks GR, Wang G. Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesisBMC Genomics. 2018;19(1):541. doi: 10.1186/s12864-018-4904-6. (E) [OA]
  6. Coleine C, Stajich JE*, Zucconi L, Onofri S, Pombubpa N, Egidi E, Franks A, Buzzini P, and Selbmann L. 2017. Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes. Frontiers in Microbiology. 2018; 9:1392 doi: 10.3389/fmicb.2018.01392 (MB) [OA]
  7. Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE*, Selbmann L*. Sun exposure shapes functional grouping of fungi in cryptoendolithic Antarctic communities. Life. 2018; 8(2): 19. doi: 10.3390/life8020019 (MB) [OA]
  8. Gostinčara C, Stajich JE,  Zupančiča J, Zalara P, Gunde-Cimermana N. Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast. BMC Genomics2018;19(1):364. doi: 10.1186/s12864-018-4751-5(A) [OA]
  9. Wang Y, Stata M, Wang W, Stajich JE, White MM, and Moncalvo J-M. Comparative genomics reveals the core gene toolbox for the fungus-insect symbiosis. mBio. 2018;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18. (EDF) [OA]
  10. Cissé OH, Ma L, Huang DW, Khil P, Dekker J, Kutty G, Bishop L, Liu Y, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, and Kovacs JA.  Population bottlenecks shaped the evolution of the fungal pathogen Pneumocystis in mammals. mBio. 2018;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18(A) [OA]
  11. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and Phylogenomic Definition of Rhizopus Species. G3. 2018; 8(6):2007-2018 doi: 10.1534/g3.118.200235. (EDF) [OA]
  12. Collins C, Stajich JE, Weber S, Pombubpa N, and Diez J. 2017. Shrub range expansion alters diversity and distribution of soil fungal communities in a high elevation alpine ecosystem. Molecular Ecology. 2018; 27(10): 2461-2476. doi: 10.1111/mec.14694 (MB)
  13. Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoidesOpen Biol. 2018; 8:170184; doi: 10.1098/rsob.170184 (E) [OA]
  14. Kirkland TN, Muszewska A, Stajich JE. Analysis of transposable elements in Coccidioides species and their potential impact on gene expression. Journal of Fungi 2018; 4(1): 13. doi: 10.3390/jof4010013 (A) [OA]
  15. Beaudet D, Chen E CH, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich JE, Corradi N. Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. DNA Research 2018; 2(1):217-227. doi: 10.1093/dnares/dsx051
    github: zygolife/AMF_Phylogenomics (EDF) [OA]
  16. Na F, Carrillo JD, Mayorquin JS, Ndinga-Muniania C, Stajich JE, Stouthamer R, Huang Y-T, Lin Y-T, Chen C-Y, and Eskalen A. 2017. Two novel fungal symbionts Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. of kuroshio shot hole borer (Euwallacea sp. nr. fornicatus) cause Fusarium dieback on woody host species in California. Plant Disease 2018; 102(6): 1154-1164. doi: 10.1094/PDIS-07-17-1042-RE (A)


  1. Lu L§, Chen J§, Robb SM, Okumoto Y, Monden Y, Naito K, Stajich JE, Wessler SR.  Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. PNAS. 2017; 14 (49) E10550-E10559. doi: 10.1073/pnas.1716459114 (P) [OA]
  2. Stajich JE.  Fungal Genomes and Insights into the Evolution of the Kingdom. The Fungal Kingom. Available in Microbiology Spectrum 2017; 5(4). doi: 10.1128/microbiolspec.FUNK-0055-2016 (F) 
  3. Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. The Fungal Kingom available in Microbiology Spectrum 2017; 5(5). doi: 10.1128/microbiolspec.FUNK-0053-2016 (F)
  4. Aryal SK, Carter-House D, Stajich JE, Dillman AR. Microbial Associates of the Southern Mole Cricket (Scapteriscus borellii) are Highly Pathogenic. J Invertebrate Pathology 2017; 150:54-62. doi:  10.1016/j.jip.2017.09.008 (A) (BACT)
  5. Park S, Scranton MA, Stajich JE,  Yee A, Holzer FM, Walling LW. Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions. PLoS One. 2017; 2(10):e0185492. doi: 10.1371/journal.pone.0185492 (P)  [OA]
  6. Coleine C, Masonjones S, Selbmann L, Zucconi L, Onofri S, Pacelli C, Stajich JE*Draft Genome Sequences of the Antarctic Endolithic Fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018. Genome announcements. 2017; 5(27). doi: 10.1128/genomeA.00397-17 (A) [OA]
  7. 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 109(3):363-378. doi: 10.1080/00275514.2017.1364958
    Dataset: (EDF) 
  8. 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; 7(7):2015-2022. doi: 10.1534/g3.117.040691  (A) [OA]
  9. 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; 49(6):964-968. doi: 10.1038/ng.3859 (EDF) [OA]
  10. 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)
  11. 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)
  12. 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) [OA]
  13. 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)


  1. Stajich JEFungal 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. 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) 


  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)


  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)


  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)
  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] (E)
  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
    , 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