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Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection.

Demers EG, Biermann AR, Masonjones S, Crocker AW, Ashare A, Stajich JE, Hogan DA.

Proc Natl Acad Sci U S A. 2018 Nov 2. pii: 201807698. doi: 10.1073/pnas.1807698115. [Epub ahead of print]


Parasitoid Jewel Wasp Mounts Multi-Pronged Neurochemical Attack to Hijack a Host Brain.

Arvidson R, Kaiser M, Lee SS, Urenda JP, Dail CJ, Mohammed H, Nolan C, Pan SQ, Stajich JE, Libersat F, Adams ME.

Mol Cell Proteomics. 2018 Oct 6. pii: mcp.RA118.000908. doi: 10.1074/mcp.RA118.000908. [Epub ahead of print]


Characterization of Aspergillus niger Isolated from the International Space Station.

Romsdahl J, Blachowicz A, Chiang AJ, Singh N, Stajich JE, Kalkum M, Venkateswaran K, Wang CCC.

mSystems. 2018 Sep 18;3(5). pii: e00112-18. doi: 10.1128/mSystems.00112-18. eCollection 2018 Sep-Oct.


Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases.

Arnesen JA, Małagocka J, Gryganskyi A, Grigoriev IV, Voigt K, Stajich JE, De Fine Licht HH.

G3 (Bethesda). 2018 Oct 3;8(10):3311-3319. doi: 10.1534/g3.118.200656.


Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.

Song Z, Stajich JE, Xie Y, Liu X, He Y, Chen J, Hicks GR, Wang G.

BMC Genomics. 2018 Jul 17;19(1):541. doi: 10.1186/s12864-018-4904-6.


Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes.

Coleine C, Stajich JE, Zucconi L, Onofri S, Pombubpa N, Egidi E, Franks A, Buzzini P, Selbmann L.

Front Microbiol. 2018 Jun 29;9:1392. doi: 10.3389/fmicb.2018.01392. eCollection 2018.


Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities.

Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE, Selbmann L.

Life (Basel). 2018 Jun 2;8(2). pii: E19. doi: 10.3390/life8020019.


Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.

Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM.

MBio. 2018 May 15;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18.


Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.

Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N.

BMC Genomics. 2018 May 15;19(1):364. doi: 10.1186/s12864-018-4751-5.


Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA.

MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18.


Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.

Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM.

Mol Ecol. 2018 May;27(10):2461-2476. doi: 10.1111/mec.14694. Epub 2018 May 10.


Phylogenetic and Phylogenomic Definition of Rhizopus Species.

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.

G3 (Bethesda). 2018 May 31;8(6):2007-2018. doi: 10.1534/g3.118.200235.


Analysis of Transposable Elements in Coccidioides Species.

Kirkland TN, Muszewska A, Stajich JE.

J Fungi (Basel). 2018 Jan 19;4(1). pii: E13. doi: 10.3390/jof4010013.


Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides.

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.

Open Biol. 2018 Jan;8(1). pii: 170184. doi: 10.1098/rsob.170184.


Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi.

Beaudet D, Chen ECH, Mathieu S, Yildirir G, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich JE, Corradi N.

DNA Res. 2018 Apr 1;25(2):217-227. doi: 10.1093/dnares/dsx051.


Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.

Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR.

Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):E10550-E10559. doi: 10.1073/pnas.1716459114. Epub 2017 Nov 20.


Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions.

Park SY, Scranton MA, Stajich JE, Yee A, Walling LL.

PLoS One. 2017 Oct 12;12(10):e0185492. doi: 10.1371/journal.pone.0185492. eCollection 2017.


The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.

Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M.

Microbiol Spectr. 2017 Sep;5(5). doi: 10.1128/microbiolspec.FUNK-0053-2016. Review.


Microbial associates of the southern mole cricket (Scapteriscus borellii) are highly pathogenic.

Aryal SK, Carter-House D, Stajich JE, Dillman AR.

J Invertebr Pathol. 2017 Nov;150:54-62. doi: 10.1016/j.jip.2017.09.008. Epub 2017 Sep 12.


Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

Torres-Cruz TJ, Billingsley Tobias TL, Almatruk M, Hesse CN, Kuske CR, Desirò A, Benucci GMN, Bonito G, Stajich JE, Dunlap C, Arnold AE, Porras-Alfaro A.

Mycologia. 2017 May-Jun;109(3):363-378. doi: 10.1080/00275514.2017.1364958. Epub 2017 Aug 8.


Fungal Genomes and Insights into the Evolution of the Kingdom.

Stajich JE.

Microbiol Spectr. 2017 Jul;5(4). doi: 10.1128/microbiolspec.FUNK-0055-2016.


Draft Genome Sequences of the Antarctic Endolithic Fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018.

Coleine C, Masonjones S, Selbmann L, Zucconi L, Onofri S, Pacelli C, Stajich JE.

Genome Announc. 2017 Jul 6;5(27). pii: e00397-17. doi: 10.1128/genomeA.00397-17.


Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure.

Sinha S, Flibotte S, Neira M, Formby S, Plemenitaš A, Cimerman NG, Lenassi M, Gostinčar C, Stajich JE, Nislow C.

G3 (Bethesda). 2017 Jul 5;7(7):2015-2022. doi: 10.1534/g3.117.040691.


Widespread adenine N6-methylation of active genes in fungi.

Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV.

Nat Genet. 2017 Jun;49(6):964-968. doi: 10.1038/ng.3859. Epub 2017 May 8.


Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling.

Ahrendt SR, Medina EM, Chang CA, Stajich JE.

PeerJ. 2017 Apr 27;5:e3206. doi: 10.7717/peerj.3206. eCollection 2017.


Innovation and constraint leading to complex multicellularity in the Ascomycota.

Nguyen TA, Cissé OH, Yun Wong J, Zheng P, Hewitt D, Nowrousian M, Stajich JE, Jedd G.

Nat Commun. 2017 Feb 8;8:14444. doi: 10.1038/ncomms14444.


RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.

Chen J, Wrightsman TR, Wessler SR, Stajich JE.

PeerJ. 2017 Jan 26;5:e2942. doi: 10.7717/peerj.2942. eCollection 2017.


A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.

Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE.

Mycologia. 2016 Sep;108(5):1028-1046.


Fungal Evolution: Mucor and Phycomyces See Double.

Stajich JE.

Curr Biol. 2016 Aug 22;26(16):R775-7. doi: 10.1016/j.cub.2016.06.049.


Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.

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.

PLoS Genet. 2016 Jun 13;12(6):e1006108. doi: 10.1371/journal.pgen.1006108. eCollection 2016 Jun.


Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation.

Lee MJ, Geller AM, Bamford NC, Liu H, Gravelat FN, Snarr BD, Le Mauff F, Chabot J, Ralph B, Ostapska H, Lehoux M, Cerone RP, Baptista SD, Vinogradov E, Stajich JE, Filler SG, Howell PL, Sheppard DC.

MBio. 2016 Apr 5;7(2):e00252-16. doi: 10.1128/mBio.00252-16.


Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.

Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma BP, Unruh S.

G3 (Bethesda). 2015 Dec;5(12):2523-5. No abstract available.


Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture.

de Man TJ, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3567-72. doi: 10.1073/pnas.1518501113. Epub 2016 Mar 14.


Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).

U'Ren JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Arnold AE.

Mol Phylogenet Evol. 2016 May;98:210-32. doi: 10.1016/j.ympev.2016.02.010. Epub 2016 Feb 20.


Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon.

Wang Y, Smith KM, Taylor JW, Freitag M, Stajich JE.

G3 (Bethesda). 2015 Jun 23;5(10):1949-60. doi: 10.1534/g3.115.017921.


Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis.

Liu P, Stajich JE.

Fungal Genet Biol. 2015 Apr;77:31-9. doi: 10.1016/j.fgb.2015.03.003. Epub 2015 Mar 25.


The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.

Collins RA, Stajich JE, Field DJ, Olive JE, DeAbreu DM.

RNA. 2015 May;21(5):997-1004. doi: 10.1261/rna.047985.114. Epub 2015 Mar 24.


Analysis of the Candida albicans Phosphoproteome.

Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA.

Eukaryot Cell. 2015 May;14(5):474-85. doi: 10.1128/EC.00011-15. Epub 2015 Mar 6.


Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.

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.

BMC Genomics. 2014 Oct 29;15:943. doi: 10.1186/1471-2164-15-943.


MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum.

Ouyang S, Park G, Atamian HS, Han CS, Stajich JE, Kaloshian I, Borkovich KA.

PLoS Pathog. 2014 Oct 16;10(10):e1004464. doi: 10.1371/journal.ppat.1004464. eCollection 2014 Oct.


Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches.

Mélida H, Sain D, Stajich JE, Bulone V.

Environ Microbiol. 2015 May;17(5):1649-62. doi: 10.1111/1462-2920.12601. Epub 2014 Sep 22.


Evolutionary histories of soil fungi are reflected in their large-scale biogeography.

Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL.

Ecol Lett. 2014 Sep;17(9):1086-93. doi: 10.1111/ele.12311. Epub 2014 Jun 9.


Literature-based gene curation and proposed genetic nomenclature for cryptococcus.

Inglis DO, Skrzypek MS, Liaw E, Moktali V, Sherlock G, Stajich JE.

Eukaryot Cell. 2014 Jul;13(7):878-83. doi: 10.1128/EC.00083-14. Epub 2014 May 9.


Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

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.

PLoS Genet. 2014 Apr 17;10(4):e1004261. doi: 10.1371/journal.pgen.1004261. eCollection 2014 Apr.


Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.

Gioti A, Stajich JE, Johannesson H.

Evolution. 2013 Dec;67(12):3600-16. doi: 10.1111/evo.12206. Epub 2013 Aug 5.


Evolutionary origins and diversification of proteobacterial mutualists.

Sachs JL, Skophammer RG, Bansal N, Stajich JE.

Proc Biol Sci. 2013 Nov 27;281(1775):20132146. doi: 10.1098/rspb.2013.2146. Print 2014 Jan 22.


The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M.

PLoS Genet. 2013;9(9):e1003820. doi: 10.1371/journal.pgen.1003820. Epub 2013 Sep 19.


Meeting report: fungal its workshop (october 2012).

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.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.


Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex.

Gryganskyi AP, Humber RA, Stajich JE, Mullens B, Anishchenko IM, Vilgalys R.

PLoS One. 2013 Aug 8;8(8):e71168. doi: 10.1371/journal.pone.0071168. eCollection 2013.


Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia.

James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE.

Curr Biol. 2013 Aug 19;23(16):1548-53. doi: 10.1016/j.cub.2013.06.057. Epub 2013 Aug 8.

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