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Scopus Author ID: 32668097800
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DOE Joint Genome Institute: Walnut Creek, CA, US

Lead Plant Functional Genomics group
Employment
Source: Self-asserted source
John Vogel

University of California Berkeley: Berkeley, CA, US

2023-06-01 | Adjunt Professor (Plant and Microbial Biology)
Employment
Source: Self-asserted source
John Vogel

Works (50 of 104)

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Page 1 of 3

Breeding of microbiomes conferring salt tolerance to plants

2025-01-16 | Preprint
DOI: 10.1101/2025.01.13.632835
Contributors: Caio Guilherme Pereira; Joseph A. Edwards; Albina Khasanova; Alexis L. Carlson; Vanessa Brisson; Estelle Schaefer; Tijana Glavina del Rio; Susannah Tringe; John P. Vogel; David L. Des Marais et al.
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Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei

Molecular Ecology
2024-10 | Journal article
DOI: 10.1111/mec.17513
Contributors: Miguel Campos; Ernesto Pérez‐Collazos; Antonio Díaz‐Pérez; Diana López‐Alvarez; Ali Oumouloud; Luis A. J. Mur; John P. Vogel; Pilar Catalán
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Degradation of organic matter by ecologically distinct microbiomes uniformly promotes plant growth

2024-10-27 | Preprint
DOI: 10.1101/2024.10.27.620506
Contributors: Bradie Lee; Devin Coleman-Derr; John P. Vogel
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Brachypodium: 20 years as a grass biology model system; the way forward?

Trends in Plant Science
2022-10 | Journal article
DOI: 10.1016/j.tplants.2022.04.008
Contributors: Robert Hasterok; Pilar Catalan; Samuel P. Hazen; Anne C. Roulin; John P. Vogel; Kai Wang; Luis A.J. Mur
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PHYTOCHROME C regulation ofPHOTOPERIOD1is mediated byEARLY FLOWERING 3inBrachypodium distachyon

2022-10-14 | Preprint
DOI: 10.1101/2022.10.11.511813
Contributors: Daniel P. Woods; Weiya Li; Richard Sibout; Mingqin Shao; Debbie Laudencia-Chingcuanco; John P. Vogel; Jorge Dubcovsky; Richard M. Amasino
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N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Journal of Experimental Botany
2022-09-03 | Journal article
DOI: 10.1093/jxb/erac184
Contributors: Weiqi Kuang; Stefan Sanow; Jana M Kelm; Mark Müller Linow; Peter Andeer; Dietrich Kohlheyer; Trent Northen; John P Vogel; Michelle Watt; Borjana Arsova et al.
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Regulation of hair cell and stomatal size by a hair-cell specific peroxidase in the grassBrachypodium distachyon

2022-07-03 | Preprint
DOI: 10.1101/2022.07.03.498611
Contributors: Tiago D. G. Nunes; Lea S. Berg; Magdalena W. Slawinska; Dan Zhang; Leonie Redt; Richard Sibout; John P. Vogel; Debbie Laudencia-Chingcuanco; Barbara Jesenofsky; Heike Lindner et al.
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Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

The Plant Journal
2022-03 | Journal article
DOI: 10.1111/tpj.15650
Contributors: Rubén Sancho; Luis A. Inda; Antonio Díaz‐Pérez; David L. Des Marais; Sean Gordon; John P. Vogel; Joanna Lusinska; Robert Hasterok; Bruno Contreras‐Moreira; Pilar Catalán
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The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

Science Advances
2022-02-11 | Journal article
DOI: 10.1126/sciadv.abj4633
Contributors: Kebede T. Muleta; Terry Felderhoff; Noah Winans; Rachel Walstead; Jean Rigaud Charles; J. Scott Armstrong; Sujan Mamidi; Chris Plott; John P. Vogel; Peggy G. Lemaux et al.
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Identification of candidate susceptibility genes to Puccinia graminis f. sp. tritici in wheat

2021-01-25 | Other
DOI: 10.1101/2021.01.23.427871
Contributors: Eva C. Henningsen; Vahid Omidvar; Rafael Della Coletta; Jean-Michel Michno; Erin Gilbert; Feng Li; Marisa E. Miller; Chad L. Myers; Sean P. Gordon; John P. Vogel et al.
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Advances on genomics, biology, ecology and evolution of Brachypodium, a bridging model grass system for cereals and biofuel grasses

New Phytologist
2020 | Journal article
DOI: 10.1111/nph.16831
EID:

2-s2.0-85089515634

Part of ISSN: 14698137 0028646X
Contributors: Catalán, P.; Vogel, J.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance

Scientific Reports
2020 | Journal article
DOI: 10.1038/s41598-020-61081-4
EID:

2-s2.0-85081693406

Part of ISSN: 20452322
Contributors: Toubiana, D.; Sade, N.; Liu, L.; Rubio Wilhelmi, M.M.; Brotman, Y.; Luzarowska, U.; Vogel, J.P.; Blumwald, E.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics

Nature Communications
2020 | Journal article
DOI: 10.1038/s41467-019-13913-9
EID:

2-s2.0-85077505444

Part of ISSN: 20411723
Contributors: Gao, C.; Montoya, L.; Xu, L.; Madera, M.; Hollingsworth, J.; Purdom, E.; Singan, V.; Vogel, J.; Hutmacher, R.B.; Dahlberg, J.A. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Nature Communications
2020 | Journal article
DOI: 10.1038/s41467-020-17302-5
EID:

2-s2.0-85088698921

Part of ISSN: 20411723
Contributors: Gordon, S.P.; Contreras-Moreira, B.; Levy, J.J.; Djamei, A.; Czedik-Eysenberg, A.; Tartaglio, V.S.; Session, A.; Martin, J.; Cartwright, A.; Katz, A. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Integrated genome-scale analysis and northern blot detection of retrotransposon siRNAs across plant species

Methods in Molecular Biology
2020 | Book chapter
DOI: 10.1007/978-1-0716-0712-1_23
EID:

2-s2.0-85088679289

Part of ISSN: 19406029 10643745
Contributors: Böhrer, M.; Rymen, B.; Himber, C.; Gerbaud, A.; Pflieger, D.; Laudencia-Chingcuanco, D.; Cartwright, A.; Vogel, J.; Sibout, R.; Blevins, T.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon

New Phytologist
2020 | Journal article
DOI: 10.1111/nph.16546
EID:

2-s2.0-85083965555

Part of ISSN: 14698137 0028646X
Contributors: Woods, D.P.; Dong, Y.; Bouché, F.; Mayer, K.; Varner, L.; Ream, T.S.; Thrower, N.; Wilkerson, C.; Cartwright, A.; Sibout, R. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

The Plant Journal
2020-08 | Journal article
DOI: 10.1111/tpj.14869
Contributors: Natalia Borowska‐Zuchowska; Ales Kovarik; Ewa Robaszkiewicz; Metin Tuna; Gulsemin Savas Tuna; Sean Gordon; John P. Vogel; Robert Hasterok
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A new method to correct for habitat filtering in microbial correlation networks

Frontiers in Microbiology
2019 | Journal article
DOI: 10.3389/fmicb.2019.00585
EID:

2-s2.0-85066608526

Part of ISSN: 1664302X
Contributors: Brisson, V.; Schmidt, J.; Northen, T.R.; Vogel, J.P.; Gaudin, A.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Global diversity of the Brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate

Genetics
2019 | Journal article
DOI: 10.1534/genetics.118.301589
EID:

2-s2.0-85059797325

Part of ISSN: 19432631 00166731
Contributors: Wilson, P.B.; Streich, J.C.; Murray, K.D.; Eichten, S.R.; Cheng, R.; Aitken, N.C.; Spokas, K.; Warthmann, N.; Gordon, S.P.; Vogel, J.P. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

New Phytologist
2019 | Journal article
DOI: 10.1111/nph.15662
EID:

2-s2.0-85060633058

Part of ISSN: 14698137 0028646X
Contributors: Sasse, J.; Kant, J.; Cole, B.J.; Klein, A.P.; Arsova, B.; Schlaepfer, P.; Gao, J.; Lewald, K.; Zhalnina, K.; Kosina, S. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses

Proceedings of the National Academy of Sciences of the United States of America
2019 | Journal article
DOI: 10.1073/pnas.1907500116
EID:

2-s2.0-85077248062

Part of ISSN: 10916490 00278424
Contributors: Varoquaux, N.; Cole, B.; Gao, C.; Pierroz, G.; Baker, C.R.; Patel, D.; Madera, M.; Jeffers, T.; Hollingsworth, J.; Sievert, J. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens

The Plant Journal
2019-12 | Journal article
DOI: 10.1111/tpj.14497
Contributors: Dawn Chiniquy; William Underwood; Jason Corwin; Andrew Ryan; Heidi Szemenyei; Candice C. Lim; Solomon H. Stonebloom; Devon S. Birdseye; John Vogel; Daniel Kliebenstein et al.
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PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

BMC Genomics
2019-12 | Journal article
DOI: 10.1186/s12864-019-5828-5
Contributors: Sean P. Gordon; Joshua J. Levy; John P. Vogel
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Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Scientific Reports
2019-10-30 | Journal article
DOI: 10.1038/s41598-019-52148-y
Contributors: Vanessa L. Brisson; Jennifer E. Schmidt; Trent R. Northen; John P. Vogel; Amélie C. M. Gaudin
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Metabotyping as a Stopover in Genome-to-Phenome Mapping

Scientific Reports
2019-02-12 | Journal article
DOI: 10.1038/s41598-019-38483-0
Contributors: Pubudu P. Handakumbura; Bryan Stanfill; Albert Rivas-Ubach; Dan Fortin; John P. Vogel; Christer Jansson
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Analysis of Brachypodium genomes with genome-wide optical maps

Genome
2018 | Journal article
DOI: 10.1139/gen-2018-0013
EID:

2-s2.0-85051164302

Part of ISSN: 08312796
Contributors: Zhu, T.; Hu, Z.; Rodriguez, J.C.; Deal, K.R.; Dvorak, J.; Vogel, J.P.; Liu, Z.; Luo, M.-C.; Belzile, F.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Broad spectrum developmental role of Brachypodium AUX1

New Phytologist
2018 | Journal article
DOI: 10.1111/nph.15332
EID:

2-s2.0-85051119869

Part of ISSN: 14698137 0028646X
Contributors: van der Schuren, A.; Voiniciuc, C.; Bragg, J.; Ljung, K.; Vogel, J.; Pauly, M.; Hardtke, C.S.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Climate-smart crops with enhanced photosynthesis

Journal of Experimental Botany
2018 | Journal article
DOI: 10.1093/jxb/ery213
EID:

2-s2.0-85050884089

Part of ISSN: 14602431 00220957
Contributors: Jansson, C.; Vogel, J.; Hazen, S.; Brutnell, T.; Mockler, T.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes

New Phytologist
2018 | Journal article
DOI: 10.1111/nph.14926
EID:

2-s2.0-85037671080

Part of ISSN: 14698137 0028646X
Contributors: Sancho, R.; Cantalapiedra, C.P.; López-Alvarez, D.; Gordon, S.P.; Vogel, J.P.; Catalán, P.; Contreras-Moreira, B.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Ecosystem fabrication (EcoFAB) protocols for the construction of laboratory ecosystems designed to study plant-microbe interactions

Journal of Visualized Experiments
2018 | Journal article
DOI: 10.3791/57170
EID:

2-s2.0-85045508063

Part of ISSN: 1940087X
Contributors: Gao, J.; Sasse, J.; Lewald, K.M.; Zhalnina, K.; Cornmesser, L.T.; Duncombe, T.A.; Yoshikuni, Y.; Vogel, J.P.; Firestone, M.K.; Northen, T.R.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of themediterranean grass brachypodium distachyon

Genome Biology and Evolution
2018 | Journal article
DOI: 10.1093/gbe/evx276
EID:

2-s2.0-85045181324

Part of ISSN: 17596653
Contributors: Stritt, C.; Gordon, S.P.; Wicker, T.; Vogel, J.P.; Roulin, A.C.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Salt tolerance of two perennial grass Brachypodium sylvaticum accessions

Plant Molecular Biology
2018 | Journal article
DOI: 10.1007/s11103-017-0696-3
EID:

2-s2.0-85040352967

Part of ISSN: 15735028 01674412
Contributors: Sade, N.; del Mar Rubio Wilhelmi, M.; Ke, X.; Brotman, Y.; Wright, M.; Khan, I.; De Souza, W.; Bassil, E.; Tobias, C.M.; Thilmony, R. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae

Plant Journal
2018 | Journal article
DOI: 10.1111/tpj.14047
EID:

2-s2.0-85053419748

Part of ISSN: 1365313X 09607412
Contributors: Handakumbura, P.P.; Brow, K.; Whitney, I.P.; Zhao, K.; Sanguinet, K.A.; Lee, S.J.; Olins, J.; Romero-Gamboa, S.P.; Harrington, M.J.; Bascom, C.J. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

BMC Genomics
2018-12 | Journal article
DOI: 10.1186/s12864-018-5055-5
Contributors: Jennifer E. Spindel; Jeffery Dahlberg; Matthew Colgan; Joy Hollingsworth; Julie Sievert; Scott H. Staggenborg; Robert Hutmacher; Christer Jansson; John P. Vogel
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Expanding the breeder’s toolbox for perennial grasses

2018-11-26 | Report
DOI: 10.2172/1483299
Contributors: Eduardo Blumwald; John Vogel; Roger Thilmony; Christian Tobias
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Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

The Plant Journal
2018-10 | Journal article
DOI: 10.1111/tpj.14042
Contributors: Yann Bourgeois; Christoph Stritt; Jean‐Claude Walser; Sean P. Gordon; John P. Vogel; Anne C. Roulin
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Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species

Frontiers in Plant Science
2017 | Journal article
DOI: 10.3389/fpls.2017.00184
EID:

2-s2.0-85013127786

Part of ISSN: 1664462X
Contributors: Contreras-Moreira, B.; Cantalapiedra, C.P.; García-Pereira, M.J.; Gordon, S.P.; Vogel, J.P.; Igartua, E.; Casas, A.M.; Vinuesa, P.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

Nature Communications
2017 | Journal article
DOI: 10.1038/s41467-017-02292-8
EID:

2-s2.0-85038638355

Part of ISSN: 20411723
Contributors: Gordon, S.P.; Contreras-Moreira, B.; Woods, D.P.; Des Marais, D.L.; Burgess, D.; Shu, S.; Stritt, C.; Roulin, A.C.; Schackwitz, W.; Tyler, L. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Mobile MUTE specifies subsidiary cells to build physiologically improved grass stomata

Science
2017 | Journal article
DOI: 10.1126/science.aal3254
EID:

2-s2.0-85015262802

Part of ISSN: 10959203 00368075
Contributors: Raissig, M.T.; Matos, J.L.; Gil, M.X.A.; Kornfeld, A.; Bettadapur, A.; Abrash, E.; Allison, H.R.; Badgley, G.; Vogel, J.P.; Berry, J.A. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat

Scientific Reports
2017 | Journal article
DOI: 10.1038/s41598-017-17454-3
EID:

2-s2.0-85037639845

Part of ISSN: 20452322
Contributors: Powell, J.J.; Carere, J.; Sablok, G.; Fitzgerald, T.L.; Stiller, J.; Colgrave, M.L.; Gardiner, D.M.; Manners, J.M.; Vogel, J.P.; Henry, R.J. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Cross-species functional diversity within the PIN auxin efflux protein family

eLife
2017-10-24 | Journal article
DOI: 10.7554/eLife.31804
Contributors: Devin Lee O'Connor; Samuel Elton; Fabrizio Ticchiarelli; Mon Mandy Hsia; John P Vogel; Ottoline Leyser
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Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

The Plant Journal
2017-08 | Journal article
DOI: 10.1111/tpj.13582
Contributors: Mon Mandy Hsia; Ronan O'Malley; Amy Cartwright; Rita Nieu; Sean P. Gordon; Sandra Kelly; Tina G. Williams; Delilah F. Wood; Yunjun Zhao; Jennifer Bragg et al.
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Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

Plant Physiology
2017-01 | Journal article
DOI: 10.1104/pp.16.01178
Contributors: Daniel P. Woods; Ryland Bednarek; Frédéric Bouché; Sean P. Gordon; John P. Vogel; David F. Garvin; Richard M. Amasino
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A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

eLife
2016 | Journal article
DOI: 10.7554/eLife.20522
EID:

2-s2.0-84995532860

Part of ISSN: 2050084X
Contributors: Rabe, F.; Bosch, J.; Stirnberg, A.; Guse, T.; Bauer, L.; Seitner, D.; Rabanal, F.A.; Czedik-Eysenberg, A.; Uhse, S.; Bindics, J. et al.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

A Xyloglucan Backbone 6-O-Acetyltransferase from Brachypodium distachyon Modulates Xyloglucan Xylosylation

Molecular Plant
2016 | Journal article
DOI: 10.1016/j.molp.2015.11.004
EID:

2-s2.0-84951814810
Contributors: Liu, L.; Hsia, M.M.; Dama, M.; Vogel, J.; Pauly, M.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

Frontiers in Plant Science
2016 | Journal article
DOI: 10.3389/fpls.2016.00055
EID:

2-s2.0-84958525315
Contributors: Petrik, D.L.; Cass, C.L.; Padmakshan, D.; Foster, C.E.; Vogel, J.P.; Karlen, S.D.; Ralph, J.; Sedbrook, J.C.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8

Functional Plant Biology
2016 | Journal article
DOI: 10.1071/FP15244
EID:

2-s2.0-84955151761
Contributors: Schneebeli, K.; Mathesius, U.; Zwart, A.B.; Bragg, J.N.; Vogel, J.P.; Watt, M.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Recreating stable Brachypodium hybridum allotetraploids by uniting the divergent genomes of B. distachyon and B. stacei

PLoS ONE
2016 | Journal article
DOI: 10.1371/journal.pone.0167171
EID:

2-s2.0-85006076427

Part of ISSN: 19326203
Contributors: Thi, V.H.D.; Coriton, O.; Le Clainche, I.; Arnaud, D.; Gordon, S.P.; Linc, G.; Catalan, P.; Hasterok, R.; Vogel, J.P.; Jahier, J. et al.
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John Vogel via Scopus - Elsevier

Use of agrobacterium rhizogenes strain 18r12v and paromomycin selection for transformation of brachypodium distachyon and brachypodium sylvaticum

Frontiers in Plant Science
2016 | Journal article
DOI: 10.3389/fpls.2016.00716
EID:

2-s2.0-84971273020

Part of ISSN: 1664462X
Contributors: Collier, R.; Bragg, J.; Hernandez, B.T.; Vogel, J.P.; Thilmony, R.
Source: Self-asserted source
John Vogel via Scopus - Elsevier

Cross-species functional diversity within the PIN auxin efflux protein family

2016-12-15 | Preprint
DOI: 10.1101/089854
Contributors: Devin Lee O’Connor; Samuel Elton; Fabrizio Ticchiarelli; Mon Mandy Hsia; John Vogel; Ottoline Leyser
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Review activity for Nature plants. (1)
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