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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » People & Locations » Barbara Baker
Barbara Baker
Plant Gene Expression Center
Research Plant Molecular Geneticist

Phone: (510) 559-5912
Fax: (510) 559-5678

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

Projects
Enhancing Crop Resilience to Biotic and Abiotic Stress Through Understanding the Microbiome and Immune Signaling Mechanisms
In-House Appropriated (D)
  Accession Number: 444646
Regulatory Mechanisms Controlling Plant Development, Biotic and Abiotic Stress Responses, and Microbiome Interactions
Non-Assistance Cooperative Agreement (S)
  Accession Number: 440675

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Clathrin light chains negatively regulate plant immunity by highjacking the autophagy pathway Reprint Icon - (Peer Reviewed Journal)
Lan, H., Ran, J., Wang, W., Zhang, L., Wu, N., Zhao, Y., Huang, M., Ni, M., Liu, F., Cheng, N., Nakata, P.A., Pan, J., Whitham, S.A., Baker, B.J., Liu, J. 2024. Clathrin light chains negatively regulate plant immunity by highjacking the autophagy pathway. Plant Communications. 5. Article 100937. https://doi.org/10.1016/j.xplc.2024.100937.
High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals Reprint Icon - (Peer Reviewed Journal)
Wang, J., Zhang, Q., Tung, J., Zhang, X., Liu, D., Deng, Y., Tian, Z., Chen, H., Wang, T., Yin, W., Li, B., Lai, Z., Dinesh-Kumar, S.P., Baker, B.J., Li, F. 2024. High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals. Molecular Plant. 17(3):423-437. https://doi.org/10.1016/j.molp.2024.01.008.
Conserved transcription factors NRZ1 and NRM1 regulate NLR receptor-mediated immunity Reprint Icon - (Peer Reviewed Journal)
Zhang, Q., Wang, J., Li, Y., Tung, J., Deng, Y., Baker, B.J., Dinesh-Kumar, S.P., Li, F. 2024. Conserved transcription factors NRZ1 and NRM1 regulate NLR receptor-mediated immunity. Plant Physiology. 195(1):832-849. https://doi.org/10.1093/plphys/kiae054.
LncRNA gets into the balancing act Reprint Icon - (Peer Reviewed Journal)
Li, F., Brunkard, J., Baker, B.J. 2022. LncRNA gets into the balancing act. Cell Host and Microbe. 30(8):1061-1063. https://doi.org/10.1016/j.chom.2022.07.004.
Polycistronic artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in cucumber Reprint Icon - (Peer Reviewed Journal)
Miao, S., Liang, C., Li, J., Baker, B.J., Luo, L. 2021. Polycistronic artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in cucumber. International Journal of Molecular Sciences. 22(22). Article 12237. https://doi.org/10.3390/ijms222212237.
Artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in Nicotiana benthamiana Reprint Icon - (Peer Reviewed Journal)
Liang, C., Hao, J., Li, J., Baker, B.J., Luo, L. 2019. Artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in Nicotiana benthamiana. Planta. 250:1591–1601. https://doi.org/10.1007/s00425-019-03252-w.
Artificial microRNA-mediated sresistance to cucumber green mottle mosiac virus in nicotiana benthamiana Reprint Icon - (Peer Reviewed Journal)
Liang, C., Hao, J., Li, J., Baker, B.J., Luo, L. 2019. Artificial microRNA-mediated sresistance to cucumber green mottle mosiac virus in nicotiana benthamiana. Frontiers in Plant Science. 250:1591–1601. https://doi.org/10.1007/s00425-019-03252-w.
A two-headed monster to avert disaster:HBS1/SK17 is alternatively spliced to build Eukaryotic RNA surveillance complexes Reprint Icon - (Peer Reviewed Journal)
Brunkard, J., Baker, B.J. 2018. A two-headed monster to avert disaster:HBS1/SK17 is alternatively spliced to build Eukaryotic RNA surveillance complexes. Frontiers in Plant Science. 9:1333. https://doi.org/10.3389/fpls.2018.01333.
A role for small RNA in regulation of innate immunity during plant growth Reprint Icon - (Peer Reviewed Journal)
Deng, Y., Wang, J., Tung, J., Liu, D., Zhou, Y., Shuang, H., Yunlian, D., Baker, B.J., Li, F. 2018. A role for small RNA in regulation of innate immunity during plant growth. Public Library of Science for Pathogens. 14(1):e1006756. https://doi.org/10.1371/journal.ppat.1006756.
Frequent gain and loss of resistance against tobacco mosaic virus (TMV) in Nicotiana Species Reprint Icon - (Peer Reviewed Journal)
Yuan, X., Yan, C., Wu, Z., Ren, F., Zhan, H., Baker, B.J., Chen, J., Kuang, H. 2015. Frequent gain and loss of resistance against tobacco mosaic virus (TMV) in Nicotiana Species. Molecular Plant. 8(12):1813-1815. doi: 10.1016/j.molp.2015.09.001.
Identification of I-7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes Reprint Icon - (Peer Reviewed Journal)
Gonzales-Cendales, Y., Catanzariti, A., Baker, B.J., Mcgrath, D.J., Jones, D.A. 2015. Identification of I-7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes. Molecular Plant Pathology. doi: 10.1111/mpp.12294/epdf.
Loss of GSNOR1 function leads to compromised auxin signaling and polar auxin transport Reprint Icon - (Peer Reviewed Journal)
Wang, D., Shi, Y., Wang, C., Cohen, J., Hendrickson Culler, A., Baker, B.J., Liu, J. 2015. Loss of GSNOR1 function leads to compromised auxin signaling and polar auxin transport. Molecular Plant. 8(9):1350-1365.
S-nitrosylation mediates nitric oxide -auxin crosstalk in auxin signaling and polar auxin transport - (Peer Reviewed Journal)
Nb is a TIR-NLR innate immune receptor that requires EDS1 for induction of the hypersensitive response to the potato virus X movement protein - (Peer Reviewed Journal)
Preparation of cDNA Library for dRNA-seq Reprint Icon - (Other)
Li, F., Baker, B.J. 2012. Preparation of cDNA Library for dRNA-seq. Bio-protocol. Vol 70, Pages 891-901.
SoMART, a web server for miRNA, tasiRNA and target gene analysis in Solanaceae plants - (Peer Reviewed Journal)
Li, F., Orban, R., Baker, B.J. 2012. SoMART, a web server for miRNA, tasiRNA and target gene analysis in Solanaceae plants. Genome Research. 70:891-901.
miRNA regulation of plant innate receptors - (Peer Reviewed Journal)
Li, F., Pignatta, D., Bendix, C., Brunkard, J., Cohn, M., Tung, J., Sun, H., Kumar, P., Baker, B.J. 2012. miRNA regulation of plant innate receptors. Proceedings of the National Academy of Sciences. 5:1790-1795.
Inferred origin of several Native American potatoes from the Pacific Northwest using SSR markers - (Peer Reviewed Journal)
Zhang, L., Brown, C.R., Culley, D., Baker, B.J., Kunibe, E., Denny, H., Smith, C., Ward, N., Beavert, T., Coburn, J., Pavek, J.J., Dauenhauer, N., Dauenhauer, R. 2010. Inferred origin of several Native American potatoes from the Pacific Northwest using SSR markers. Euphytica. 174:15-29.
Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs - (Peer Reviewed Journal)
Kuang, H., Padmanabhan, C., Li, F., Kamei, A., Bhaskar, P.B., Ouyang, S., Jiang, J., Buell, C., Baker, B.J. 2008. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs. Genome Research. 19:42-56.
The Use of STS Markers in the Marker-assisted Selection of Columbia Root-knot Nematode Resistance Introgressed from Solanum bulbocastanum - (Peer Reviewed Journal)
Zhang, L., Mojtahedi, H., Kuang, H., Baker, B.J., Brown, C.R. 2007. The Use of STS Markers in the Marker-assisted Selection of Columbia Root-knot Nematode Resistance Introgressed from Solanum bulbocastanum. Crop Science. 47:2021-2026.
THE R1 RESISTANCE CLUSTER CONTAINS THREE GROUPS OF INDEPENDENTLY EVOLVING, TYPE I R1 HOMOLOGUES AND SHOWS SUBSTANTIAL STRUCTURAL VARIATION AMONG HAPLOTYPES OF SOLANUM DEMISSUM - (Peer Reviewed Journal)
Kuang, H., Wei, F., Marano, M., Wirtz, U., Wang, X., Liu, J., Shum, W., Zaborsky, J., Tallon, L.J., Rensink, W., Lobst, S., Zhang, P., Tornqvist, C., Tek, A., Bamberg, J., Helgeson, J.P., Fry, W., You, F., Luo, M., Jiang, J., Buell, C., Baker, B.J. 2005. The R1 resistance cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum. Plant Journal. 44(1):37-51.
EDS1 IN TOMATO IS REQUIRED FOR RESISTANCE MEDIATED BY TIR-CLASS R GENES AND THE RECEPTOR-LIKE R GENE VE - (Peer Reviewed Journal)
Hu, G., Dehart, A.K., Li, Y., Ustach, C., Handley, V., Navarre, R., Hwang, C.F., Aegerter, B.J., Williamson, V., Baker, B.J. 2005. EDS1 in tomato is required for resistance mediated by TIR-class R genes and the receptor-like R gene Ve. Plant Journal. 42(3):376-91.
COMPARATIVE GENOMICS ENABLED THE ISOLATION OF THE R3A LATE BLIGHT RESISTANCE GENE IN POTATO - (Peer Reviewed Journal)
Huang, S., Van Der Vossen, E.A., Kuang, H., Vleeshouwers, V.G., Zhang, N., Borm, T.J., Van Eck, H.J., Baker, B.J., Jacobsen, E., Visser, R.G. 2005. Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. Plant Journal. 42(2):251-61.
VPEY EXHIBITS A CASPASE-LIKE ACTIVITY THAT CONTRIBUTES TO DEFENSE AGAINST PATHOGENS - (Peer Reviewed Journal)
Rojo, E., Martin, R., Carter, C., Zouhar, J., Pan, S., Plotnikova, J., Jin, H., Paneque, M., Sanchez-Serrano, J., Baker, B.J., Ausubel, F.M., Raikhel, N.V. 2004. VPEy Exhibits a Caspase-like Activity that Contributes to Defense against Pathogens. Current Biology, 14:1897-1906.
VIRUS-INDUCED GENE SILENCING IN SOLANUM SPECIES - (Peer Reviewed Journal)
Gianinna, B., Martin-Hermandez, A.M., Jin, H., Chen, J., Baulcombe, D.C., Baker, B.J., Jones, J.G. 2004. Virus-induced gene silencing in Solanum species. Plant Journal 39(2)264-271.
VIRUS-INDUCED GENE SILENCING IN SOLANUM SPECIES - (Peer Reviewed Journal)
Brigneti, G., Martin-Hernandezx, A.M., Jin, H., Chen, J., Baulcombe, D.C., Baker, B.J., Jones, J.G. 2004. Virus-induced gene silencing in solanum species. Plant Journal, 39(2): 264.
THE TOMATO RESISTANCE PROTEIN BS4 IS A PREDICTED NON-NUCLEAR TIR-NB-LRR PROTEIN THAT MEDIATES DEFENSE RESPONSES TO SEVERELY TRUNCATED DERIVATIVES OF AVRBS4 AND OVEREXPRESSED AVRBS3 - (Peer Reviewed Journal)
Schornack, S., Ballvora, A., Gurlebeck, D., Peart, J., Ganal, M., Baker, B.J., Bonas, U., Lahaye, T. 2003. The tomato resistance protein Bs4 is a predicted non-nuclear TIR-NB-LRR protein that mediates defense responses to severely truncated derivatives of AvrBs4 and overexpressed AvrBs3. Plant Journal 37(1) 46-60.
BIOTIC INTERACTIONS - SIGNALS FROM THE ENVIRONMENT: THE GOOD, THE BAD AND THE UGLY! - (Peer Reviewed Journal)
BAKER, B.J., PARKER, J. BIOTIC INTERACTIONS - SIGNALS FROM THE ENVIRONMENT: THE GOOD, THE BAD AND THE UGLY! CURRENT OPINION IN PLANT BIOLOGY. 2003. 6(4):297-299.
FUNCTION OF A MITOGREN-ACTIVATED PROTEIN KINASE PATHWAY IN N GENE-MEDIATED RESISTANCE IN TOBACCO - (Peer Reviewed Journal)
JIN, H., LIU, Y., YANG, K., KIM, C., BAKER, B.J., ZHANG, S. FUNCTION OF A MITOGREN-ACTIVATED PROTEIN KINASE PATHWAY IN N GENE-MEDIATED RESISTANCE IN TOBACCO. PLANT JOURNAL. 2003. 33(4):719-731.
COMPARATIVE ANALYSES OF POTATO EXPRESSED SEQUENCE TAG LIBRARIES - (Peer Reviewed Journal)
RONNING, C.M., STEGALKINA, S.S., ASCENZI, R.A., BOUGRI, O., HART, A.L., UTTERBACH, T.R., VANAKEN, S.E., RIEDMULLER, S.B., WHITE, J.A., CHO, J., PERTEA, G.M., LEE, Y., KARAMYCHEVA, S., SULTANA, R., TSAI, J., QUACKENBUSH, J., GRIFFITHS, H.M., RESTREPO, S., SMART, C.D., FRY, W.E., VAN DER HOEVEN, R., TANKSLEY, S., ZHANG, P., JIN, H., YAMAMOTO, M.L., BAKER, B.J., BUELL, C. COMPARATIVE ANALYSES OF POTATO EXPRESSED SEQUENCE TAG LIBRARIES. PLANT PHYSIOLOGY. 2003. 131:419-429.
INTERACTION BETWEEN TWO MITOGEN-ACTIVATED PROTEIN KINASES DURING TOBACCO DEFENSE SIGNALING - (Peer Reviewed Journal)
BAKER, B.J. INTERACTION BETWEEN TWO MITOGEN-ACTIVATED PROTEIN KINASES DURING TOABCCOM DEFENSE SIGNALING. PLANT JOURNAL. 2003. 34:149-160.
STRUCTURE-FUNCTION ANALYSIS OF THE TOBACCO MOSAIC VIRUS RESISTANCE GENE N - (Peer Reviewed Journal)
Dinehsh-Kumar, S., Baker, B.J. 2000. Structure-function analysis of the tobacco mosaic virus resistance gene N. Proceedings of the National Academy of Sciences 97(26):14789-14794.
ALTERNATIVELY SPLICED N RESISTANCE GENE TRANSCRIPTS: THEIR POSSIBLE ROLE INTOBACCO MOSAIC VIRUS RESISTANCE - (Peer Reviewed Journal)
Baker, B.J., Dinesh-Kumar, S.P. 2000. Alternatively spliced N resistance gene transcripts: Their possible role in tobacco mosaic virus resistance. Proceedings of the National Academy of Sciences 97(4):1908-1913.
THE HELICASE DOMAIN OF THE TMV REPLICASE PROTEINS INDUCES THE N-MEDIATED DEFENCE RESPONSE IN TOBACCO - (Peer Reviewed Journal)
Erickson, F., Holzberg, S., Calderon-Urrea, A., Handley, V., Axtell, M., Corr, C., Baker, B.J. 1999. The helicase domain of the TMV replicase proteins induces the N-mediated defence response in tobacco. Plant Journal 18(1) 67-75.
INTERACTIONS BETWEEN TOBACCO MOSAIC VIRUS AND THE TOBACCO N GENE - (Peer Reviewed Journal)
Baker, B.J., Erickson, F.L., Dinesh-Kumar, S.P., Holzberg, S., Ustach, C., Dutton, M., Handley, V., Corr, C. 1999. Interactions between tobacco mosaic virus and the tobacco N gene. Proceedings of the Royal Society of London B., 354(1383):653-658.
SIGNALING IN PLANT-MICROBE INTERACTIONS - (Peer Reviewed Journal)
Baker, B.J., Zambryski, P., Staskawicz, B., Dinesh-Kumar, S.P. 1997. Signaling in plant-microbe interactions. Science 276(5313):726-733.
DS EXCISION FROM EXTRACHROMOSOMAL GEMINIVIRUS VECTOR DNA IS COUPLED TO VECTOR DNA REPLICATION IN MAIZE - (Peer Reviewed Journal)
Wirtz, U., Obsorne, B., Baker, B.J. 1997. Ds excision from extrachromosomal geminivirus vector DNA is coupled to vector DNA replicaiton in maize. Plant Journal 11(1):125.
MOVERS AND SHAKERS: MAIZE TRANSPOSONS AS TOOLS FOR ANALYZING OTHER PLANT GENOMES - (Review Article)
Osborne, B.I., Baker, B.J. 1995. Movers and shakers: maize transposons as tools for analyzing other plant genomes. Current Opinion in Cell Biology, 7(3), 407-413.
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