Jason E. Stajich, PhD - Publications

Affiliations: 
2001-2006 Molecular Genetics and Microbiology Duke University, Durham, NC 
 2006-2009 Plant and Microbial Biology University of California, Berkeley, Berkeley, CA 
 2009- Microbiology and Plant Pathology University of California, Riverside, Riverside, CA, United States 
Area:
Mycology, evolution, comparative genomics, bioinformatics
Website:
http://lab.stajich.org

136 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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 and in California. Plant Disease. PDIS01190201RE. PMID 31647694 DOI: 10.1094/PDIS-01-19-0201-RE  1
2019 Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between and Include Metabolite Exchange. Frontiers in Microbiology. 10: 2163. PMID 31632357 DOI: 10.3389/fmicb.2019.02163  1
2019 Kowalski CH, Kerkaert JD, Liu KW, Bond MC, Hartmann R, Nadell CD, Stajich JE, Cramer RA. Fungal biofilm morphology impacts hypoxia fitness and disease progression. Nature Microbiology. PMID 31548684 DOI: 10.1038/s41564-019-0558-7  1
2019 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 Genetics and Biology : Fg & B. 103269. PMID 31518652 DOI: 10.1016/j.fgb.2019.103269  1
2019 Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE. Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. Msystems. 4. PMID 31455637 DOI: 10.1128/mSystems.00247-19  1
2019 Coleine C, Stajich JE, Pombubpa N, Zucconi L, Onofri S, Canini F, Selbmann L. Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities. Environmental Microbiology Reports. PMID 31393667 DOI: 10.1111/1758-2229.12788  1
2019 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. 10: 1013. PMID 31156574 DOI: 10.3389/fmicb.2019.01013  1
2019 Murphy CL, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, Elshahed MS. Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage. Applied and Environmental Microbiology. PMID 31126947 DOI: 10.1128/AEM.00988-19  1
2019 Coleine C, Selbmann L, Masonjones S, Onofri S, Zucconi L, Stajich JE. Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus . Microbiology Resource Announcements. 8. PMID 31072892 DOI: 10.1128/MRA.00142-19  1
2019 Cissé OH, Stajich JE. FGMP: assessing fungal genome completeness. Bmc Bioinformatics. 20: 184. PMID 30987585 DOI: 10.1186/s12859-019-2782-9  1
2019 Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nature Ecology & Evolution. PMID 30778188 DOI: 10.1038/s41559-019-0810-9  1
2019 Chen J, Lu L, Benjamin J, Diaz S, Hancock CN, Stajich JE, Wessler SR. Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice. Nature Communications. 10: 641. PMID 30733435 DOI: 10.1038/s41467-019-08451-3  1
2019 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. Microbiology Resource Announcements. 8. PMID 30701257 DOI: 10.1128/MRA.01619-18  1
2019 Davis WJ, Amses KR, Benny GL, Carter-House D, Chang Y, Grigoriev I, Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). Molecular Phylogenetics and Evolution. PMID 30639767 DOI: 10.1016/j.ympev.2019.01.006  1
2018 Na F, Carrillo JD, Mayorquin JS, Ndinga-Muniania C, Stajich JE, Stouthamer R, Huang YT, Lin YT, Chen CY, Eskalen A. 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. 102: 1154-1164. PMID 30673440 DOI: 10.1094/PDIS-07-17-1042-RE  1
2018 Romsdahl J, 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 nidulans. Applied Microbiology and Biotechnology. PMID 30539259 DOI: 10.1007/s00253-018-9525-0  1
2018 Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. The New Phytologist. PMID 30485448 DOI: 10.1111/nph.15613  1
2018 Demers EG, Biermann AR, Masonjones S, Crocker AW, Ashare A, Stajich JE, Hogan DA. Evolution of drug resistance in an antifungal-naive chronic infection. Proceedings of the National Academy of Sciences of the United States of America. PMID 30389707 DOI: 10.1073/pnas.1807698115  1
2018 Arvidson R, Kaiser M, Lee SS, Urenda JP, Dail CJ, Mohammed H, Nolan C, Pan SQ, Stajich JE, Libersat F, Adams ME. Parasitoid Jewel Wasp Mounts Multi-Pronged Neurochemical Attack to Hijack a Host Brain. Molecular & Cellular Proteomics : McP. PMID 30293061 DOI: 10.1074/mcp.RA118.000908  0.44
2018 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. 3. PMID 30246146 DOI: 10.1128/mSystems.00112-18  1
2018 Arnesen JA, Malagocka J, Gryganskyi A, 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 (Bethesda, Md.). PMID 30111619 DOI: 10.1534/g3.118.200656  1
2018 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 biosynthesis. Bmc Genomics. 19: 541. PMID 30016947 DOI: 10.1186/s12864-018-4904-6  1
2018 Coleine C, Stajich JE, Zucconi L, Onofri S, Pombubpa N, Egidi E, Franks A, Buzzini P, Selbmann L. Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes. Frontiers in Microbiology. 9: 1392. PMID 30008702 DOI: 10.3389/fmicb.2018.01392  1
2018 Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE, Selbmann L. Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities. Life (Basel, Switzerland). 8. PMID 29865244 DOI: 10.3390/life8020019  1
2018 Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. Mbio. 9. PMID 29764946 DOI: 10.1128/mBio.00636-18  1
2018 Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N. Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast. Bmc Genomics. 19: 364. PMID 29764372 DOI: 10.1186/s12864-018-4751-5  1
2018 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, et al. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen . Mbio. 9. PMID 29739910 DOI: 10.1128/mBio.00381-18  1
2018 Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Molecular Ecology. PMID 29675967 DOI: 10.1111/mec.14694  1
2018 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, ... ... Stajich JE, et al. Phylogenetic and Phylogenomic Definition of Species. G3 (Bethesda, Md.). PMID 29674435 DOI: 10.1534/g3.118.200235  1
2018 Kirkland TN, Muszewska A, Stajich JE. Analysis of Transposable Elements in Coccidioides Species. Journal of Fungi (Basel, Switzerland). 4. PMID 29371508 DOI: 10.3390/jof4010013  0.2
2018 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, et al. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biology. 8. PMID 29321239 DOI: 10.1098/rsob.170184  1
2017 Short DPG, O'Donnell K, Stajich JE, Hulcr J, Kijimoto T, Berger MC, Macias AM, Spahr EJ, Bateman CC, Eskalen A, Lynch SC, Cognato AI, Cooperband MF, 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. 101: 233-240. PMID 30682305 DOI: 10.1094/PDIS-07-16-1046-RE  1
2017 Beaudet D, Chen ECH, Mathieu S, Yildirir G, 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 : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 29211832 DOI: 10.1093/dnares/dsx051  0.48
2017 Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR. Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proceedings of the National Academy of Sciences of the United States of America. PMID 29158416 DOI: 10.1073/pnas.1716459114  1
2017 Park SY, Scranton MA, Stajich JE, Yee A, Walling LL. Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions. Plos One. 12: e0185492. PMID 29023459 DOI: 10.1371/journal.pone.0185492  0.16
2017 Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. Microbiology Spectrum. 5. PMID 28917057 DOI: 10.1128/microbiolspec.FUNK-0053-2016  1
2017 Aryal SK, Carter-House D, Stajich JE, Dillman AR. Microbial Associates of the Southern Mole Cricket (Scapteriscus borellii) are Highly Pathogenic. Journal of Invertebrate Pathology. PMID 28916147 DOI: 10.1016/j.jip.2017.09.008  1
2017 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. Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia. 1-16. PMID 28876195 DOI: 10.1080/00275514.2017.1364958  1
2017 Stajich JE. Fungal Genomes and Insights into the Evolution of the Kingdom. Microbiology Spectrum. 5. PMID 28820125 DOI: 10.1128/microbiolspec.FUNK-0055-2016  0.01
2017 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. 5. PMID 28684563 DOI: 10.1128/genomeA.00397-17  1
2017 Sinha S, Flibotte S, Niera M, Formby S, Plemenitaš A, Gunde Cimerman N, Lenassi M, Gostinčar C, Stajich JE, Nislow C. Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure. G3 (Bethesda, Md.). PMID 28500048 DOI: 10.1534/g3.117.040691  1
2017 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, ... ... Stajich JE, et al. Widespread adenine N6-methylation of active genes in fungi. Nature Genetics. PMID 28481340 DOI: 10.1038/ng.3859  1
2017 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. PMID 28462022 DOI: 10.7717/peerj.3206  0.2
2017 Nguyen TA, Cissé OH, Yun Wong J, Zheng P, Hewitt D, Nowrousian M, Stajich JE, Jedd G. Innovation and constraint leading to complex multicellularity in the Ascomycota. Nature Communications. 8: 14444. PMID 28176784 DOI: 10.1038/ncomms14444  1
2017 Chen J, Wrightsman TR, Wessler SR, Stajich JE. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. Peerj. 5: e2942. PMID 28149701 DOI: 10.7717/peerj.2942  1
2016 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, ... ... Stajich JE, et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 108: 1028-1046. PMID 27738200 DOI: 10.3852/16-042  1
2016 Stajich JE. Fungal Evolution: Mucor and Phycomyces See Double. Current Biology : Cb. 26: R775-7. PMID 27554660 DOI: 10.1016/j.cub.2016.06.049  0.01
2016 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 Genetics. 12: e1006108. PMID 27294409 DOI: 10.1371/journal.pgen.1006108  1
2016 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, et al. Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation. Mbio. 7. PMID 27048799 DOI: 10.1128/mBio.00252-16  1
2016 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. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proceedings of the National Academy of Sciences of the United States of America. PMID 26976598 DOI: 10.1073/pnas.1518501113  1
2016 U'Ren JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Elizabeth Arnold A. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution. PMID 26903035 DOI: 10.1016/j.ympev.2016.02.010  1
2015 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 (Bethesda, Md.). 5: 2523-5. PMID 27034999  1
2015 Pieuchot L, Lai J, Loh RA, Leong FY, Chiam KH, Stajich J, Jedd G. Cellular Subcompartments through Cytoplasmic Streaming. Developmental Cell. 34: 410-20. PMID 26305593 DOI: 10.1016/j.devcel.2015.07.017  1
2015 Wang Y, Smith KM, Taylor JW, Freitag M, Stajich JE. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3 (Bethesda, Md.). PMID 26109355 DOI: 10.1534/g3.115.017921  1
2015 Liu P, Stajich JE. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genetics and Biology : Fg & B. 77: 31-9. PMID 25819009 DOI: 10.1016/j.fgb.2015.03.003  1
2015 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 (New York, N.Y.). 21: 997-1004. PMID 25805857 DOI: 10.1261/rna.047985.114  1
2015 Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA. Analysis of the Candida albicans Phosphoproteome. Eukaryotic Cell. 14: 474-85. PMID 25750214 DOI: 10.1128/EC.00011-15  1
2015 Kennedy P, Stajich J. Twenty-first century mycology: a diverse, collaborative, and highly relevant science. The New Phytologist. 205: 23-6. PMID 25427217 DOI: 10.1111/nph.13165  1
2015 Mélida H, Sain D, Stajich JE, Bulone V. Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches. Environmental Microbiology. 17: 1649-62. PMID 25143134 DOI: 10.1111/1462-2920.12601  1
2015 Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Chris Pires J, Stajich JE, Thomma BPHJ, Unruh S. Meeting report: Fungal genomics meets social media: Highlights of the 28th fungal genetics conference at asilomar G3: Genes, Genomes, Genetics. 5: 2523-2525. DOI: 10.1534/g3.115.024158  1
2015 Stajich JE. Phylogenomics enabling genome-based mycology The Mycota: a Comprehensive Treatise On Fungi as Experimental Systems For Basic and Applied Research: Vii Systematics and Evolution Part B 2nd Edition. 279-294. DOI: 10.1007/978-3-662-46011-5_11  1
2014 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, ... ... Stajich JE, et al. Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. Bmc Genomics. 15: 943. PMID 25351875 DOI: 10.1186/1471-2164-15-943  1
2014 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 Pathogens. 10: e1004464. PMID 25330340 DOI: 10.1371/journal.ppat.1004464  1
2014 Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL. Evolutionary histories of soil fungi are reflected in their large-scale biogeography. Ecology Letters. 17: 1086-93. PMID 24912000 DOI: 10.1111/ele.12311  1
2014 Inglis DO, Skrzypek MS, Liaw E, Moktali V, Sherlock G, Stajich JE. Literature-based gene curation and proposed genetic nomenclature for cryptococcus. Eukaryotic Cell. 13: 878-83. PMID 24813190 DOI: 10.1128/EC.00083-14  1
2014 Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, ... ... Stajich JE, et al. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. Plos Genetics. 10: e1004261. PMID 24743168 DOI: 10.1371/journal.pgen.1004261  1
2014 Sachs JL, Skophammer RG, Bansal N, Stajich JE. Evolutionary origins and diversification of proteobacterial mutualists. Proceedings. Biological Sciences / the Royal Society. 281: 20132146. PMID 24285193 DOI: 10.1098/rspb.2013.2146  1
2014 Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. The Isme Journal. 8: 1-3. PMID 24152717 DOI: 10.1038/ismej.2013.176  1
2013 Gioti A, Stajich JE, Johannesson H. Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus. Evolution; International Journal of Organic Evolution. 67: 3600-16. PMID 24299411 DOI: 10.1111/evo.12206  1
2013 Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. Plos Genetics. 9: e1003820. PMID 24068976 DOI: 10.1371/journal.pgen.1003820  1
2013 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, ... ... Stajich JE, et al. Meeting report: fungal its workshop (october 2012). Standards in Genomic Sciences. 8: 118-23. PMID 23961317 DOI: 10.4056/sigs.3737409  1
2013 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. 8: e71168. PMID 23951101 DOI: 10.1371/journal.pone.0071168  1
2013 James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Current Biology : Cb. 23: 1548-53. PMID 23932404 DOI: 10.1016/j.cub.2013.06.057  1
2013 Hibbett DS, Stajich JE, Spatafora JW. Toward genome-enabled mycology. Mycologia. 105: 1339-49. PMID 23928422 DOI: 10.3852/13-196  1
2013 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, ... ... Stajich JE, et al. Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proceedings of the National Academy of Sciences of the United States of America. 110: 9385-90. PMID 23650365 DOI: 10.1073/pnas.1300130110  1
2013 Robb SM, Lu L, Valencia E, Burnette JM, Okumoto Y, Wessler SR, Stajich JE. The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3 (Bethesda, Md.). 3: 949-57. PMID 23576519 DOI: 10.1534/g3.112.005348  1
2013 Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. Regional control of histone H3 lysine 27 methylation in Neurospora. Proceedings of the National Academy of Sciences of the United States of America. 110: 6027-32. PMID 23530226 DOI: 10.1073/pnas.1303750110  1
2013 Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS. 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. Bmc Genomics. 14: 195. PMID 23514374 DOI: 10.1186/1471-2164-14-195  1
2013 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, et al. Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis. Mbio. 4: e00572-12. PMID 23341551 DOI: 10.1128/mBio.00572-12  1
2013 Fisher MC, Stajich JE, Farrer RA. Emergence of the Chytrid Fungus Batrachochytrium Dendrobatidis and Global Amphibian Declines Evolution of Virulence in Eukaryotic Microbes. 461-472. DOI: 10.1002/9781118308165.ch24  1
2012 Nygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, Karlsson M, Johannesson H. Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. Bmc Evolutionary Biology. 12: 229. PMID 23186325 DOI: 10.1186/1471-2148-12-229  1
2012 Abramyan J, Stajich JE. Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. Mbio. 3: e00150-12. PMID 22718849 DOI: 10.1128/mBio.00150-12  1
2012 Gioti A, Mushegian AA, Strandberg R, Stajich JE, Johannesson H. Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Molecular Biology and Evolution. 29: 3215-26. PMID 22593224 DOI: 10.1093/molbev/mss132  1
2012 Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ, Roos DS. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Research. 40: D675-81. PMID 22064857 DOI: 10.1093/nar/gkr918  1
2011 Joneson S, Stajich JE, Shiu SH, Rosenblum EB. Genomic transition to pathogenicity in chytrid fungi. Plos Pathogens. 7: e1002338. PMID 22072962 DOI: 10.1371/journal.ppat.1002338  1
2011 Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW. Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics. 189: 55-69. PMID 21750257 DOI: 10.1534/genetics.111.130690  1
2011 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, ... ... Stajich JE, et al. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. Mbio. 2: e00342-10. PMID 21304167 DOI: 10.1128/mBio.00342-10  1
2010 Rosenblum EB, Fisher MC, James TY, Stajich JE, Longcore JE, Gentry LR, Poorten TJ. A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis. Diseases of Aquatic Organisms. 92: 131-47. PMID 21268975 DOI: 10.3354/dao02179  1
2010 Burns C, Stajich JE, Rechtsteiner A, Casselton L, Hanlon SE, Wilke SK, Savytskyy OP, Gathman AC, Lilly WW, Lieb JD, Zolan ME, Pukkila PJ. Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution. Plos Genetics. 6: e1001135. PMID 20885784 DOI: 10.1371/journal.pgen.1001135  1
2010 McKay SJ, Vergara IA, Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 9.12. PMID 20836076 DOI: 10.1002/0471250953.bi0912s31  1
2010 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, et al. Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex. Eukaryotic Cell. 9: 1549-56. PMID 20675579 DOI: 10.1128/EC.00154-10  1
2010 Lévesque 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, ... ... Stajich JE, et al. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology. 11: R73. PMID 20626842 DOI: 10.1186/gb-2010-11-7-r73  1
2010 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, et al. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology. 28: 957-63. PMID 20622885 DOI: 10.1038/nbt.1643  1
2010 Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genetics and Biology : Fg & B. 47: 869-78. PMID 20601044 DOI: 10.1016/j.fgb.2010.06.008  1
2010 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, et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America. 107: 11889-94. PMID 20547848 DOI: 10.1073/pnas.1003391107  1
2010 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, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20: 938-46. PMID 20516208 DOI: 10.1101/gr.103911.109  1
2010 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, et al. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. Plos Genetics. 6: e1000891. PMID 20386741 DOI: 10.1371/journal.pgen.1000891  1
2010 Rosenblum EB, Voyles J, Poorten TJ, Stajich JE. The deadly chytrid fungus: a story of an emerging pathogen. Plos Pathogens. 6: e1000550. PMID 20126439 DOI: 10.1371/journal.ppat.1000550  1
2009 Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW. The fungi. Current Biology : Cb. 19: R840-5. PMID 19788875 DOI: 10.1016/j.cub.2009.07.004  1
2009 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, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19: 1722-31. PMID 19717792 DOI: 10.1101/gr.087551.108  1
2009 Fisher MC, Bosch J, Yin Z, Stead DA, Walker J, Selway L, Brown AJ, Walker LA, Gow NA, Stajich JE, Garner TW. Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence. Molecular Ecology. 18: 415-29. PMID 19161465 DOI: 10.1111/j.1365-294X.2008.04041.x  1
2008 Regier JC, Shultz JW, Ganley AR, Hussey A, Shi D, Ball B, Zwick A, Stajich JE, Cummings MP, Martin JW, Cunningham CW. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Systematic Biology. 57: 920-38. PMID 19085333 DOI: 10.1080/10635150802570791  1
2008 Rosenblum EB, Stajich JE, Maddox N, Eisen MB. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proceedings of the National Academy of Sciences of the United States of America. 105: 17034-9. PMID 18852473 DOI: 10.1073/pnas.0804173105  1
2008 Bruns TD, Blackwell M, Edwards I, Taylor AFS, Horton T, Zhang N, Kõljalg U, May G, Kuyper TW, Bever JD, Gilbert G, Taylor JW, DeSantis TZ, Pringle A, Borneman J, ... ... Stajich J, et al. Preserving accuracy in GenBank Science. 319: 1616. PMID 18356505  1
2008 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, ... ... Stajich JE, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 452: 88-92. PMID 18322534 DOI: 10.1038/nature06556  1
2008 Lilly WW, Stajich JE, Pukkila PJ, Wilke SK, Inoguchi N, Gathman AC. An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea. Mycological Research. 112: 389-98. PMID 18313909 DOI: 10.1016/j.mycres.2007.11.013  1
2008 Hu G, Liu I, Sham A, Stajich JE, Dietrich FS, Kronstad JW. Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biology. 9: R41. PMID 18294377 DOI: 10.1186/gb-2008-9-2-r41  1
2007 Stajich JE. An Introduction to BioPerl. Methods in Molecular Biology (Clifton, N.J.). 406: 535-48. PMID 18287711  1
2007 Stajich JE, Dietrich FS, Roy SW. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biology. 8: R223. PMID 17949488 DOI: 10.1186/gb-2007-8-10-r223  1
2007 Fraser JA, Stajich JE, Tarcha EJ, Cole GT, Inglis DO, Sil A, Heitman J. Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. Eukaryotic Cell. 6: 622-9. PMID 17337636 DOI: 10.1128/EC.00018-07  1
2007 Harrison LB, Yu Z, Stajich JE, Dietrich FS, Harrison PM. Evolution of budding yeast prion-determinant sequences across diverse fungi. Journal of Molecular Biology. 368: 273-82. PMID 17320905 DOI: 10.1016/j.jmb.2007.01.070  1
2007 Erwin TA, Jewell EG, Love CG, Lim GA, Li X, Chapman R, Batley J, Stajich JE, Mongin E, Stupka E, Ross B, Spangenberg G, Edwards D. BASC: an integrated bioinformatics system for Brassica research. Nucleic Acids Research. 35: D870-3. PMID 17148473 DOI: 10.1093/nar/gkl998  1
2007 Edwards D, Hansen D, Stajich JE. DNA sequence databases Bioinformatics: Tools and Applications. 1-11. DOI: 10.1007/978-0-387-92738-1_1  1
2007 Edwards D, Stajich J, Hansen D. Bioinformatics: Tools and applications Bioinformatics: Tools and Applications. 1-451. DOI: 10.1007/978-0-387-92738-1  1
2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Pond SLK, Poon AFY, ... ... Stajich JE, et al. The 2006 NESCent phyloinformatics hackathon: A field report Evolutionary Bioinformatics. 3: 287-296.  1
2006 Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. The evolution of mammalian gene families. Plos One. 1: e85. PMID 17183716 DOI: 10.1371/journal.pone.0000085  1
2006 Fitzpatrick DA, Logue ME, Stajich JE, Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. Bmc Evolutionary Biology. 6: 99. PMID 17121679 DOI: 10.1186/1471-2148-6-99  1
2006 Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HA, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, ... ... Stajich JE, et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature. 444: 97-101. PMID 17080091 DOI: 10.1038/nature05248  1
2006 James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, ... Stajich JE, et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature. 443: 818-22. PMID 17051209 DOI: 10.1038/nature05110  1
2006 Coghlan A, Stajich JE, Harris TW. Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species. Methods in Molecular Biology (Clifton, N.J.). 351: 13-29. PMID 16988423 DOI: 10.1385/1-59745-151-7:13  1
2006 Giles SS, Stajich JE, Nichols C, Gerrald QD, Alspaugh JA, Dietrich F, Perfect JR. The Cryptococcus neoformans catalase gene family and its role in antioxidant defense. Eukaryotic Cell. 5: 1447-59. PMID 16963629 DOI: 10.1128/EC.00098-06  1
2006 Cramer RA, Stajich JE, Yamanaka Y, Dietrich FS, Steinbach WJ, Perfect JR. Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus. Gene. 383: 24-32. PMID 16962256 DOI: 10.1016/j.gene.2006.07.008  1
2006 Stajich JE, Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we? Briefings in Bioinformatics. 7: 287-96. PMID 16899494 DOI: 10.1093/bib/bbl026  1
2006 Stajich JE, Dietrich FS. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryotic Cell. 5: 789-93. PMID 16682456 DOI: 10.1128/EC.5.5.789-793.2006  1
2006 Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S. Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biology. 7: R30. PMID 16606443 DOI: 10.1186/gb-2006-7-4-r30  1
2005 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. 437: 1360-4. PMID 16222245 DOI: 10.1038/nature04220  1
2005 Leman SC, Chen Y, Stajich JE, Noor MA, Uyenoyama MK. Likelihoods from summary statistics: recent divergence between species. Genetics. 171: 1419-36. PMID 16143628 DOI: 10.1534/genetics.104.040402  1
2005 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 Research. 15: 1153-60. PMID 16077014 DOI: 10.1101/gr.3567505  1
2005 Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin W, Clifton SW, Waterston RH, Wilson RK. Investigating hookworm genomes by comparative analysis of two Ancylostoma species. Bmc Genomics. 6: 58. PMID 15854223 DOI: 10.1186/1471-2164-6-58  1
2005 Stajich JE, Hahn MW. Disentangling the effects of demography and selection in human history. Molecular Biology and Evolution. 22: 63-73. PMID 15356276 DOI: 10.1093/molbev/msh252  1
2004 Kraus PR, Boily MJ, Giles SS, Stajich JE, Allen A, Cox GM, Dietrich FS, Perfect JR, Heitman J. Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray. Eukaryotic Cell. 3: 1249-60. PMID 15470254 DOI: 10.1128/EC.3.5.1249-1260.2004  1
2003 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, ... ... Stajich JE, et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. Plos Biology. 1: E45. PMID 14624247 DOI: 10.1371/journal.pbio.0000045  1
2003 Hahn MW, Stajich JE, Wray GA. The effects of selection against spurious transcription factor binding sites. Molecular Biology and Evolution. 20: 901-6. PMID 12716998 DOI: 10.1093/molbev/msg096  1
2002 Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Research. 12: 1611-8. PMID 12368254 DOI: 10.1101/gr.361602  1
2002 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 Research. 12: 1599-610. PMID 12368253 DOI: 10.1101/gr.403602  1
2002 Baxter RV, Ben Othmane K, Rochelle JM, Stajich JE, Hulette C, Dew-Knight S, Hentati F, Ben Hamida M, Bel S, Stenger JE, Gilbert JR, Pericak-Vance MA, Vance JM. Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21. Nature Genetics. 30: 21-2. PMID 11743579 DOI: 10.1038/ng796  1
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