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Variation in Disease Severity Caused by Phytophthora cinnamomi, P. plurivora, and Pythium cryptoirregulare on Two Rhododendron Cultivars.

Weiland JE, Scagel CF, Grünwald NJ, Davis EA, Beck BR, Fieland VJ.

Plant Dis. 2018 Oct 22:PDIS04180666RE. doi: 10.1094/PDIS-04-18-0666-RE. [Epub ahead of print]


Taxa: An R package implementing data standards and methods for taxonomic data.

Foster ZSL, Chamberlain S, Grünwald NJ.

Version 2. F1000Res. 2018 Mar 5 [revised 2018 Jan 1];7:272. doi: 10.12688/f1000research.14013.2. eCollection 2018.


Evolution of the U.S. Biological Select Agent Rathayibacter toxicus.

Davis EW 2nd, Tabima JF, Weisberg AJ, Lopes LD, Wiseman MS, Wiseman MS, Pupko T, Belcher MS, Sechler AJ, Tancos MA, Schroeder BK, Murray TD, Luster DG, Schneider WL, Rogers EE, Andreote FD, Grünwald NJ, Putnam ML, Chang JH.

MBio. 2018 Aug 28;9(4). pii: e01280-18. doi: 10.1128/mBio.01280-18.


Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.

Arsenault-Labrecque G, Sonah H, Lebreton A, Labbé C, Marchand G, Xue A, Belzile F, Knaus BJ, Grünwald NJ, Bélanger RR.

BMC Biol. 2018 Jul 26;16(1):80. doi: 10.1186/s12915-018-0549-9.


Response to comments on "Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management".

Chang JH, Putnam ML, Grünwald NJ, Savory EA, Fuller SL, Weisberg AJ.

Elife. 2018 May 8;7. pii: e35852. doi: 10.7554/eLife.35852.


Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.

Knaus BJ, Grünwald NJ.

Front Genet. 2018 Apr 13;9:123. doi: 10.3389/fgene.2018.00123. eCollection 2018.


Correction: Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH.

Elife. 2018 Mar 13;7. pii: e36350. doi: 10.7554/eLife.36350. No abstract available.


Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States.

Tabima JF, Coffey MD, Zazada IA, Grünwald NJ.

Mol Plant Microbe Interact. 2018 Jun;31(6):614-622. doi: 10.1094/MPMI-10-17-0258-R. Epub 2018 Apr 11.


Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH.

Elife. 2017 Dec 12;6. pii: e30925. doi: 10.7554/eLife.30925. Erratum in: Elife. 2018 Mar 13;7:.


Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae.

Tabima JF, Kronmiller BA, Press CM, Tyler BM, Zasada IA, Grünwald NJ.

Mol Plant Microbe Interact. 2017 Oct;30(10):767-769. doi: 10.1094/MPMI-04-17-0081-A. Epub 2017 Aug 22.


Best Practices for Population Genetic Analyses.

Grünwald NJ, Everhart SE, Knaus BJ, Kamvar ZN.

Phytopathology. 2017 Sep;107(9):1000-1010. doi: 10.1094/PHYTO-12-16-0425-RVW. Epub 2017 Jul 27.


Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

Foster ZS, Sharpton TJ, Grünwald NJ.

PLoS Comput Biol. 2017 Feb 21;13(2):e1005404. doi: 10.1371/journal.pcbi.1005404. eCollection 2017 Feb.


High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin.

Wang J, Fernández-Pavía SP, Larsen MM, Garay-Serrano E, Gregorio-Cipriano R, Rodríguez-Alvarado G, Grünwald NJ, Goss EM.

Mol Ecol. 2017 Feb;26(4):1091-1107. doi: 10.1111/mec.14000. Epub 2017 Feb 4.


Towards an integrated ecosystem of R packages for the analysis of population genetic data.

Paradis E, Gosselin T, Grünwald NJ, Jombart T, Manel S, Lapp H.

Mol Ecol Resour. 2017 Jan;17(1):1-4. doi: 10.1111/1755-0998.12636. No abstract available.


Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology.

Hansen ZR, Everts KL, Fry WE, Gevens AJ, Grünwald NJ, Gugino BK, Johnson DA, Johnson SB, Judelson HS, Knaus BJ, McGrath MT, Myers KL, Ristaino JB, Roberts PD, Secor GA, Smart CD.

PLoS One. 2016 Nov 3;11(11):e0165690. doi: 10.1371/journal.pone.0165690. eCollection 2016.


Microbe-ID: an open source toolbox for microbial genotyping and species identification.

Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Grünwald NJ.

PeerJ. 2016 Aug 18;4:e2279. doi: 10.7717/peerj.2279. eCollection 2016.


Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria.

Davis Ii EW, Weisberg AJ, Tabima JF, Grunwald NJ, Chang JH.

PeerJ. 2016 Jul 19;4:e2222. doi: 10.7717/peerj.2222. eCollection 2016.


vcfr: a package to manipulate and visualize variant call format data in R.

Knaus BJ, Grünwald NJ.

Mol Ecol Resour. 2017 Jan;17(1):44-53. doi: 10.1111/1755-0998.12549. Epub 2016 Jul 12.


Developing educational resources for population genetics in R: an open and collaborative approach.

Kamvar ZN, López-Uribe MM, Coughlan S, Grünwald NJ, Lapp H, Manel S.

Mol Ecol Resour. 2017 Jan;17(1):120-128. doi: 10.1111/1755-0998.12558. Epub 2016 Jul 12.


Population Genomics of Fungal and Oomycete Pathogens.

Grünwald NJ, McDonald BA, Milgroom MG.

Annu Rev Phytopathol. 2016 Aug 4;54:323-46. doi: 10.1146/annurev-phyto-080614-115913. Epub 2016 Jan 8. Review.


Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum.

Kasuga T, Bui M, Bernhardt E, Swiecki T, Aram K, Cano LM, Webber J, Brasier C, Press C, Grünwald NJ, Rizzo DM, Garbelotto M.

BMC Genomics. 2016 May 20;17:385. doi: 10.1186/s12864-016-2717-z.


Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers.

Biasi A, Martin FN, Cacciola SO, di San Lio GM, Grünwald NJ, Schena L.

Phytopathology. 2016 Sep;106(9):1006-14. doi: 10.1094/PHYTO-11-15-0299-R. Epub 2016 Jun 23.


Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora.

Bollmann SR, Fang Y, Press CM, Tyler BM, Grünwald NJ.

Front Plant Sci. 2016 Mar 15;7:284. doi: 10.3389/fpls.2016.00284. eCollection 2016.


Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans.

Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grünwald NJ, Smart CD.

J Appl Microbiol. 2016 Apr;120(4):1010-20. doi: 10.1111/jam.13079. Epub 2016 Mar 7.


Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

Kamvar ZN, Brooks JC, Grünwald NJ.

Front Genet. 2015 Jun 10;6:208. doi: 10.3389/fgene.2015.00208. eCollection 2015.


Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests.

Kamvar ZN, Larsen MM, Kanaskie AM, Hansen EM, Grünwald NJ.

Phytopathology. 2015 Jul;105(7):982-9. doi: 10.1094/PHYTO-12-14-0350-FI. Epub 2015 Jun 12.


Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen.

Fry WE, Birch PR, Judelson HS, Grünwald NJ, Danies G, Everts KL, Gevens AJ, Gugino BK, Johnson DA, Johnson SB, McGrath MT, Myers KL, Ristaino JB, Roberts PD, Secor G, Smart CD.

Phytopathology. 2015 Jul;105(7):966-81. doi: 10.1094/PHYTO-01-15-0005-FI. Epub 2015 Jun 26. Review.


Population Structure of Pythium irregulare, P. ultimum, and P. sylvaticum in Forest Nursery Soils of Oregon and Washington.

Weiland JE, Garrido P, Kamvar ZN, Espíndola AS, Marek SM, Grünwald NJ, Garzón CD.

Phytopathology. 2015 May;105(5):684-94. doi: 10.1094/PHYTO-05-14-0147-R.


An ephemeral sexual population of Phytophthora infestans in the Northeastern United States and Canada.

Danies G, Myers K, Mideros MF, Restrepo S, Martin FN, Cooke DE, Smart CD, Ristaino JB, Seaman AJ, Gugino BK, Grünwald NJ, Fry WE.

PLoS One. 2014 Dec 31;9(12):e116354. doi: 10.1371/journal.pone.0116354. eCollection 2014.


The Top 10 oomycete pathogens in molecular plant pathology.

Kamoun S, Furzer O, Jones JD, Judelson HS, Ali GS, Dalio RJ, Roy SG, Schena L, Zambounis A, Panabières F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grünwald NJ, Mukhtar MS, Tomé DF, Tör M, Van Den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJ, Petre B, Ristaino J, Yoshida K, Birch PR, Govers F.

Mol Plant Pathol. 2015 May;16(4):413-34. doi: 10.1111/mpp.12190. Epub 2014 Dec 11. Review.


Speciation in fungal and oomycete plant pathogens.

Restrepo S, Tabima JF, Mideros MF, Grünwald NJ, Matute DR.

Annu Rev Phytopathol. 2014;52:289-316. doi: 10.1146/annurev-phyto-102313-050056. Epub 2014 May 30. Review.


The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes.

Goss EM, Tabima JF, Cooke DE, Restrepo S, Fry WE, Forbes GA, Fieland VJ, Cardenas M, Grünwald NJ.

Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8791-6. doi: 10.1073/pnas.1401884111. Epub 2014 Jun 2.


Fungal Planet description sheets: 154-213.

Crous PW, Wingfield MJ, Guarro J, Cheewangkoon R, van der Bank M, Swart WJ, Stchigel AM, Cano-Lira JF, Roux J, Madrid H, Damm U, Wood AR, Shuttleworth LA, Hodges CS, Munster M, de Jesús Yáñez-Morales M, Zúñiga-Estrada L, Cruywagen EM, de Hoog GS, Silvera C, Najafzadeh J, Davison EM, Davison PJ, Barrett MD, Barrett RL, Manamgoda DS, Minnis AM, Kleczewski NM, Flory SL, Castlebury LA, Clay K, Hyde KD, Maússe-Sitoe SN, Chen S, Lechat C, Hairaud M, Lesage-Meessen L, Pawłowska J, Wilk M, Sliwińska-Wyrzychowska A, Mętrak M, Wrzosek M, Pavlic-Zupanc D, Maleme HM, Slippers B, Mac Cormack WP, Archuby DI, Grünwald NJ, Tellería MT, Dueñas M, Martín MP, Marincowitz S, de Beer ZW, Perez CA, Gené J, Marin-Felix Y, Groenewald JZ.

Persoonia. 2013 Dec;31:188-296. doi: 10.3767/003158513X675925. Epub 2013 Nov 26.


Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management.

Parke JL, Knaus BJ, Fieland VJ, Lewis C, Grünwald NJ.

Phytopathology. 2014 Oct;104(10):1052-62. doi: 10.1094/PHYTO-01-14-0014-R.


Evolution of an Experimental Population of Phytophthora capsici in the Field.

Dunn AR, Bruening SR, Grünwald NJ, Smart CD.

Phytopathology. 2014 Oct;104(10):1107-17. doi: 10.1094/PHYTO-12-13-0346-R.


Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.

Kamvar ZN, Tabima JF, Grünwald NJ.

PeerJ. 2014 Mar 4;2:e281. doi: 10.7717/peerj.281. eCollection 2014.


Population history and pathways of spread of the plant pathogen Phytophthora plurivora.

Schoebel CN, Stewart J, Grünwald NJ, Rigling D, Prospero S.

PLoS One. 2014 Jan 10;9(1):e85368. doi: 10.1371/journal.pone.0085368. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e105259. Gruenwald, Niklaus J [corrected to Grünwald, Niklaus J].


Evolution of RXLR-class effectors in the oomycete plant pathogen Phytophthora ramorum.

Goss EM, Press CM, Grünwald NJ.

PLoS One. 2013 Nov 7;8(11):e79347. doi: 10.1371/journal.pone.0079347. eCollection 2013.


Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC.

PLoS One. 2013 Oct 21;8(10):e77181. doi: 10.1371/journal.pone.0077181. eCollection 2013.


Phytophthora database 2.0: update and future direction.

Park B, Martin F, Geiser DM, Kim HS, Mansfield MA, Nikolaeva E, Park SY, Coffey MD, Russo J, Kim SH, Balci Y, Abad G, Burgess T, Grünwald NJ, Cheong K, Choi J, Lee YH, Kang S.

Phytopathology. 2013 Dec;103(12):1204-8. doi: 10.1094/PHYTO-01-13-0023-R.


Evidence for multiple introductions and clonality in Spanish populations of Fusarium circinatum.

Berbegal M, Pérez-Sierra A, Armengol J, Grünwald NJ.

Phytopathology. 2013 Aug;103(8):851-61. doi: 10.1094/PHYTO-11-12-0281-R.


Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

Cooke DE, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, Grünwald NJ, Hein I, MacLean D, McNicol JW, Randall E, Oliva RF, Pel MA, Shaw DS, Squires JN, Taylor MC, Vleeshouwers VG, Birch PR, Lees AK, Kamoun S.

PLoS Pathog. 2012;8(10):e1002940. doi: 10.1371/journal.ppat.1002940. Epub 2012 Oct 4.


Novel insights into the emergence of pathogens: the case of chestnut blight.

Grünwald NJ.

Mol Ecol. 2012 Aug;21(16):3896-7. doi: 10.1111/j.1365-294X.2012.05597.x.


Emergence of the sudden oak death pathogen Phytophthora ramorum.

Grünwald NJ, Garbelotto M, Goss EM, Heungens K, Prospero S.

Trends Microbiol. 2012 Mar;20(3):131-8. doi: 10.1016/j.tim.2011.12.006. Epub 2012 Feb 9. Review.


The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans.

Goss EM, Cardenas ME, Myers K, Forbes GA, Fry WE, Restrepo S, Grünwald NJ.

PLoS One. 2011;6(9):e24543. doi: 10.1371/journal.pone.0024543. Epub 2011 Sep 16.


Identification of new polymorphic microsatellite markers in the NA1 and NA2 lineages of Phytophthora ramorum.

Vercauteren A, Larsen M, Goss E, Grünwald NJ, Maes M, Heungens K.

Mycologia. 2011 Nov-Dec;103(6):1245-9. doi: 10.3852/10-420. Epub 2011 Jun 3.


Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010.

Molecular Ecology Resources Primer Development Consortium, Anderson CM, Aparicio GJ, Atangana AR, Beaulieu J, Bruford MW, Cain F, Campos T, Cariani A, Carvalho MA, Chen N, Chen PP, Clamens AL, Clark AM, Coeur D'Acier A, Connolly P, Cordero-Rivera A, Coughlan JP, Cross TS, David B, DE Bruyn C, DE Meyer M, DE Ridder C, Delatte H, Dettori MT, Downer SJ, Dubreuil C, Evans KJ, Fan B, Ferrara G, Gagné A, Gaillard M, Gigliarelli L, Giovinazzi J, Gomez DR, Grünwald NJ, Hansson B, Huotari T, Jank L, Jousselin E, Jungmann L, Kaczmarek ME, Khasa DP, Kneebone J, Korpelainen H, Kostamo K, Lanfaloni L, Lin H, Liu X, Lucentini L, Maes GE, Mahaffee WF, Meng Z, Micali S, Milano I, Mok HF, Morin L, Neill TM, Newton CH, Gigi Ostrow D, Palomba A, Panara F, Puletti ME, Quarta R, Quilici S, Ramos AK, Rigaud T, Risterucci AM, Salomon MP, Sánchez-Guillén RA, Sarver SK, Sequeira AS, Sforça DA, Simiand C, Smith B, Sousa AC, Souza AP, Stepien CC, Stuckert AJ, Sulikowski J, Tayeh A, Tinti F, Tsang PC, VAN Houdt JK, Vendramin E, Verde I, Virgilio M, Wang HL, Wang LE, Wattier RA, Wellenreuther M, Xie CX, Zane L, Zhang XJ, Zhang Y, Zhuang Z, Zucchi MI.

Mol Ecol Resour. 2010 May;10(3):576-9. doi: 10.1111/j.1755-0998.2010.02851.x. Epub 2010 Mar 23.


Genetic and pathogenic relatedness of Pseudoperonospora cubensis and P. humuli.

Mitchell MN, Ocamb CM, Grünwald NJ, Mancino LE, Gent DH.

Phytopathology. 2011 Jul;101(7):805-18. doi: 10.1094/PHYTO-10-10-0270.


Evolution and population genetics of exotic and re-emerging pathogens: novel tools and approaches.

Grünwald NJ, Goss EM.

Annu Rev Phytopathol. 2011;49:249-67. doi: 10.1146/annurev-phyto-072910-095246. Review.


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