Linda Kay Hanley-Bowdoin

A TIR ‐ NLR gene from Arabidopsis Pla‐1 confers resistance to geminivirus infection

Shen, W., Ruhel, R., Reyes, M. I., Wheeler, E., Deppong, D., Mickelson‐Young, L., … Ascencio‐Ibáñez, J. T. (2025, December 1). The Plant Journal.

A comparison of genomic methods to assess DNA replication timing

Wheeler, E., Mickelson-Young, L., Wear, E. E., Burroughs, M., Bass, H. W., Concia, L., … Hanley-Bowdoin, L. (2025, May 22). Scientific Reports, Vol. 15.

Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing

Wear, E. E., Mickelson‐Young, L., Bass, H. W., Hanley‐Bowdoin, L., Thompson, W. F., & Concia, L. (2025, August 1). The Plant Journal, Vol. 123.

Development of Modular Geminivirus‐Based Vectors for High Cargo Expression and Gene Targeting in Plants

Neubauer, M., Vollen, K., Zhao, C., Ascencio‐Ibáñez, J. T., Hanley‐Bowdoin, L., Stepanova, A. N., & Alonso, J. M. (2025, September 21). Plant Biotechnology Journal, Vol. 9.

Replication Timing Uncovers a Two-Compartment Nuclear Architecture of Interphase Euchromatin in Maize

Akram, H. S., Wear, E. E., Mickelson-Young, L., Turpin, Z. M., Hanley-Bowdoin, L., Thompson, W. F., … Bass, H. W. (2025, July 17). Biorxiv.

SEGS-1 episomes generated during cassava mosaic disease enhance disease severity

Chiunga, E., Aimone, C. D., Rajabu, C., Dallas, M. M., Ndunguru, J., Ascencio-Ibáñez, J. T., … Hanley-Bowdoin, L. (2025, January 10). Frontiers in Plant Science.

Cassava begomovirus species diversity changes during plant vegetative cycles

Frontiers in Microbiology, 14.

Genome segment ratios change during whitefly transmission of two bipartite cassava mosaic begomoviruses

Scientific Reports, 13(1).

SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana

Rajabu, C. A., Dallas, M. M., Chiunga, E., León, L. D., Ateka, E. M., Tairo, F., … Hanley-Bowdoin, L. (2023, October 17). Frontiers in Plant Science, Vol. 14.

Early detection of plant virus infection using multispectral imaging and spatial–spectral machine learning

Peng, Y., Dallas, M. M., Ascencio-Ibáñez, J. T., Hoyer, J. S., Legg, J., Hanley-Bowdoin, L., … Yin, H. (2022, February 24). Scientific Reports, Vol. 2.

Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts

McLaughlin, A. A., Hanley-Bowdoin, L., Kennedy, G. G., & Jacobson, A. L. (2022, November 27). Scientific Reports, Vol. 12.

A New Type of Satellite Associated with Cassava Mosaic Begomoviruses

Aimone, C. D., León, L. D., Dallas, M. M., Ndunguru, J., Ascencio-Ibáñez, J. T., & Hanley-Bowdoin, L. (2021, August 18). Journal of Virology, Vol. 11.

A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants

Wang, Y., Gong, Q., Wu, Y., Huang, F., Ismayil, A., Zhang, D., … Liu, Y. (2021, August 4). Cell Host & Microbe, Vol. 9.

A protocol for genome-wide analysis of DNA replication timing in intact root tips

Methods in Molecular Biology Series.

An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing

Aimone, C. D., Hoyer, J. S., Dye, A. E., Deppong, D. O., Duffy, S., Carbone, I., & Hanley-Bowdoin, L. (2021, December 9). Journal of Virological Methods, Vol. 2, p. 114405.

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

Journal of General Virology, 102(7).

Cotton leaf curl Multan virus βC1 Protein Induces Autophagy by Disrupting the Interaction of Autophagy-Related Protein 3 with Glyceraldehyde-3-Phosphate Dehydrogenases[OPEN]

Ismayil, A., Yang, M., Haxim, Y., Wang, Y., Li, J., Han, L., … Liu, Y. (2020, February 12). The Plant Cell, Vol. 32, pp. 1124–1135.

A plant DNA virus replicates in the salivary glands of its insect vector via recruitment of host DNA synthesis machinery

He, Y.-Z., Wang, Y.-M., Yin, T.-Y., Fiallo-Olivé, E., Liu, Y.-Q., Hanley-Bowdoin, L., & Wang, X.-W. (2020, July 7). Proceedings of the National Academy of Sciences, Vol. 117, pp. 16928–16937.

Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin

Wheeler, E., Brooks, A. M., Concia, L., Vera, D. L., Wear, E. E., LeBlanc, C., … Hanley-Bowdoin, L. (2020, March 23). PLANT PHYSIOLOGY, Vol. 183, pp. 206–220.

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

Wear, E. E., Song, J., Zynda, G. J., Mickelson-Young, L., LeBlanc, C., Lee, T.-J., … Thompson, W. F. (2020, October 14). PLoS Genetics, Vol. 16.

Deeply Sequenced Infectious Clones of Key Cassava Begomovirus Isolates from Cameroon

Hoyer, J. S., Fondong, V. N., Dallas, M. M., Aimone, C. D., Deppong, D. O., Duffy, S., & Hanley-Bowdoin, L. (2020, November 11). Microbiology Resource Announcements, Vol. 9.

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Borges, F., Donoghue, M. T. A., LeBlanc, C., Wear, E. E., Tanurdžić, M., Berube, B., … Martienssen, R. A. (2020, December 3). Current Biology, Vol. 31, pp. 591-+.

SnRK1: a versatile plant protein kinase that limits geminivirus infection

Shen, W., & Hanley-Bowdoin, L. (2020, December 25). Current Opinion in Virology, Vol. 47, pp. 18–24.

Geminiviral V2 Protein Suppresses Transcriptional Gene Silencing through Interaction with AGO4

Wang, Y., Wu, Y., Gong, Q., Ismayil, A., Yuan, Y., Lian, B., … Liu, Y. (2019, January 7). Journal of Virology, Vol. 93.

Cassava viruses – host jumps, virus recombination, spread in plant material

In A. Records & J. Ristaino (Eds.), Emerging Plant Diseases and Global Food Security. St. Paul, MN: APS Press.

Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)

Turpin, Z. M., Vera, D. L., Savadel, S. D., Lung, P.-Y., Wear, E. E., Mickelson-Young, L., … Bass, H. W. (2018, August 9). Data in Brief, Vol. 20, pp. 358–363.

Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase

PLOS Pathogens, 14(8), e1007282.

Diacylglycerol acyltransferase 1 is activated by phosphatidate and inhibited by SnRK1‐catalyzed phosphorylation

Caldo, K. M. P., Shen, W., Xu, Y., Hanley‐Bowdoin, L., Chen, G., Weselake, R. J., & Lemieux, M. J. (2018, July 13). The Plant Journal, Vol. 96, pp. 287–299.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

Concia, L., Brooks, A. M., Wheeler, E., Zynda, G. J., Wear, E. E., LeBlanc, C., … Hanley-Bowdoin, L. (2018, January 4). PLANT PHYSIOLOGY.

Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses

Rajabu, C. A., Kennedy, G. G., Ndunguru, J., Ateka, E. M., Tairo, F., Hanley-Bowdoin, L., & Ascencio-Ibáñez, J. T. (2018, March 9). Journal of Virological Methods, Vol. 256, pp. 89–99.

Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection

Shen, W., Bobay, B. G., Greeley, L. A., Reyes, M. I., Rajabu, C. A., Blackburn, R. K., … Hanley-Bowdoin, L. (2018, July 13). PLANT PHYSIOLOGY, Vol. 178, pp. 372–389.

AVIGSscreen identifies immunity in the Arabidopsis Pla‐1 accession to viruses in two different genera of the Geminiviridae

Reyes, M. I., Flores‐Vergara, M. A., Guerra‐Peraza, O., Rajabu, C., Desai, J., Hiromoto‐Ruiz, Y. H., … Robertson, D. (2017, September 13). The Plant Journal, Vol. 92, pp. 796–807.

Foundational and Translational Research Opportunities to Improve Plant Health

Molecular Plant-Microbe Interactions, 30(7), 515–516.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear, E. E., Song, J., Zynda, G. J., LeBlanc, C., Lee, T.-J., Mickelson-Young, L., … Thompson, W. F. (2017, August 25). The Plant Cell, Vol. 29, pp. 2126–2149.

Repliscan: a tool for classifying replication timing regions

Zynda, G. J., Song, J., Concia, L., Wear, E. E., Hanley-Bowdoin, L., Thompson, W. F., & Vaughn, M. W. (2017, August 7). BMC Bioinformatics, Vol. 18, pp. 1–14.

A flow cytometric method for estimating S-phase duration in plants

Mickelson-Young, L., Wear, E., Mulvaney, P., Lee, T.-J., Szymanski, E. S., Allen, G., … Thompson, W. (2016, October 3). Journal of Experimental Botany, Vol. 11, pp. 6077–6087.

Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease

Ndunguru, J., León, L. D., Doyle, C. D., Sseruwagi, P., Plata, G., Legg, J. P., … Hanley-Bowdoin, L. (2016, February 11). Journal of Virology, Vol. 90, pp. 4160–4173.

Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei

Bass, H. W., Hoffman, G. G., Lee, T.-J., Wear, E. E., Joseph, S. R., Allen, G. C., … Thompson, W. F. (2015, September 22). Plant Molecular Biology, Vol. 89, pp. 339–351.

Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry

In Methods in Molecular Biology (pp. 69–86).

A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development

Bass, H. W., Wear, E. E., Lee, T.-J., Hoffman, G. G., Gumber, H. K., Allen, G. C., … Hanley-Bowdoin, L. (2014, January 21). Journal of Experimental Botany, Vol. 65, pp. 2747–2756.

In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts

Pascuzzi, P. E., Flores-Vergara, M. A., Lee, T.-J., Sosinski, B., Vaughn, M. W., Hanley-Bowdoin, L., … Allen, G. C. (2014, January 1). The Plant Cell, Vol. 26, pp. 102–120.

SnRK1 Phosphorylation of AL2 Delays Cabbage Leaf Curl Virus Infection in Arabidopsis

Shen, W., Dallas, M. B., Goshe, M. B., & Hanley-Bowdoin, L. (2014, July 3). Journal of Virology, Vol. 88, pp. 10598–10612.

Geminiviruses: masters at redirecting and reprogramming plant processes

Hanley-Bowdoin, L., Bejarano, E. R., Robertson, D., & Mansoor, S. (2013, October 8). Nature Reviews Microbiology, Vol. 11, pp. 777–788.

Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato

Reyes, M. I., Nash, T. E., Dallas, M. M., Ascencio-Ibáñez, J. T., & Hanley-Bowdoin, L. (2013, July 4). Journal of Virology, Vol. 87, pp. 9691–9706.

Interaction between Geminivirus Replication Protein and the SUMO-Conjugating Enzyme Is Required for Viral Infection

Sánchez-Durán, M. A., Dallas, M. B., Ascencio-Ibañez, J. T., Reyes, M. I., Arroyo-Mateos, M., Ruiz-Albert, J., … Bejarano, E. R. (2011, July 21). Journal of Virology, Vol. 85, pp. 9789–9800.

Tomato SlSnRK1 Protein Interacts with and Phosphorylates βC1, a Pathogenesis Protein Encoded by a Geminivirus β-Satellite      

Shen, Q., Liu, Z., Song, F., Xie, Q., Hanley-Bowdoin, L., & Zhou, X. (2011, September 1). PLANT PHYSIOLOGY, Vol. 157, pp. 1394–1406.

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State

PLoS Genetics, 6(6), e1000982.

Functional Analysis of a Novel Motif Conserved across Geminivirus Rep Proteins

Nash, T. E., Dallas, M. B., Reyes, M. I., Buhrman, G. K., Ascencio-Ibañez J. Trinidad, & Hanley-Bowdoin, L. (2010, November 18). Journal of Virology, Vol. 85, pp. 1182–1192.

Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop    

Shen, W., Reyes, M. I., & Hanley-Bowdoin, L. (2009, April 1). PLANT PHYSIOLOGY, Vol. 150, pp. 996–1005.

Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants    

Shultz, R. W., Lee, T.-J., Allen, G. C., Thompson, W. F., & Hanley-Bowdoin, L. (2009, April 8). PLANT PHYSIOLOGY, Vol. 150, pp. 658–669.

Isolation of Peptide Aptamers to Target Protein Function

In Methods in Molecular Biology (pp. 333–360).

The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis

Plant Molecular Biology, 72(4-5), 381–395.

Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection

[Review of ]. Plant Physiology, 148(1), 436–454.

Geminivirus-induced gene silencing of the tobacco retinoblastoma-related gene results in cell death and altered development

Jordan, C. V., Shen, W., Hanley-Bowdoin, L. K., & Robertson, D. (2007, July 17). Plant Molecular Biology, Vol. 65, pp. 163–175.

Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])

[Review of ]. Plant Physiology, 144(4), 1697–1714.

High-Frequency Reversion of Geminivirus Replication Protein Mutants during Infection

Arguello-Astorga, G., Ascencio-Ibáñez J. Trinidad, Dallas, M. B., Orozco, B. M., & Hanley-Bowdoin, L. (2007, August 2). Journal of Virology, Vol. 81, pp. 11005–11015.

Geminivirus Infection Up-Regulates the Expression of Two Arabidopsis Protein Kinases Related to Yeast SNF1- and Mammalian AMPK-Activating Kinases

Shen, W., & Hanley-Bowdoin, L. (2006, October 13). PLANT PHYSIOLOGY, Vol. 142, pp. 1642–1655.

Peptide Aptamers That Bind to a Geminivirus Replication Protein Interfere with Viral Replication in Plant Cells

Lopez-Ochoa, L., Ramirez-Prado, J., & Hanley-Bowdoin, L. (2006, May 26). Journal of Virology, Vol. 80, pp. 5841–5853.

A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue

Shultz, R. W., Settlage, S. B., Hanley-Bowdoin, L., & Thompson, W. F. (2005, December 1). Plant Molecular Biology Reporter, Vol. 23, pp. 405–409.

Geminivirus C3 Protein: Replication Enhancement and Protein Interactions

Settlage, S. B., See, R. G., & Hanley-Bowdoin, L. (2005, July 13). Journal of Virology, Vol. 79, pp. 9885–9895.

A Novel Motif in Geminivirus Replication Proteins Interacts with the Plant Retinoblastoma-Related Protein

Arguello-Astorga, G., Lopez-Ochoa, L., Kong, L.-J., Orozco, B. M., Settlage, S. B., & Hanley-Bowdoin, L. (2004, April 12). Journal of Virology, Vol. 78, pp. 4817–4826.

Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis

Lee, T.-J., Shultz, R. W., Hanley-Bowdoin, L., & Thompson, W. F. (2004, September 1). Plant Molecular Biology Reporter, Vol. 22, pp. 259–267.

Geminivirus resistant transgenic plants

Washington, DC: U.S. Patent and Trademark Office.

Geminivirus resistant transgenic plants expressing a mutant geminivirus AL3/C3 coding sequence

Washington, DC: U.S. Patent and Trademark Office.

Interaction between a Geminivirus Replication Protein and the Plant Sumoylation System

Castillo, A. G., Kong, L. J., Hanley-Bowdoin, L., & Bejarano, E. R. (2004, February 27). Journal of Virology.

Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication

Hanley‐Bowdoin, L., Settlage, S. B., & Robertson, D. (2004, February 25). Molecular Plant Pathology, Vol. 5, pp. 149–156.

A Geminivirus Replication Protein Interacts with a Protein Kinase and a Motor Protein That Display Different Expression Patterns during Plant Development and Infection

Kong, L.-J., & Hanley-Bowdoin, L. (2002, July 25). The Plant Cell, Vol. 14, pp. 1817–1832.

Host DNA Replication Is Induced by Geminivirus Infection of Differentiated Plant Cells

Nagar, S., Hanley-Bowdoin, L., & Robertson, D. (2002, November 20). The Plant Cell, Vol. 14, pp. 2995–3007.

Two E2F Elements Regulate the Proliferating Cell Nuclear Antigen Promoter Differently during Leaf Development

Egelkrout, E. M., Mariconti, L., Settlage, S. B., Cella, R., Robertson, D., & Hanley-Bowdoin, L. (2002, November 26). The Plant Cell, Vol. 14, pp. 3225–3236.

Dual Interaction of a Geminivirus Replication Accessory Factor with a Viral Replication Protein and a Plant Cell Cycle Regulator

Settlage, S. B., Miller, A. B., Gruissem, W., & Hanley-Bowdoin, L. (2001, January 1). Virology, Vol. 279, pp. 570–576.

Proliferating Cell Nuclear Antigen Transcription Is Repressed through an E2F Consensus Element and Activated by Geminivirus Infection in Mature Leaves

Egelkrout, E. M., Robertson, D., & Hanley-Bowdoin, L. (2001, June 1). The Plant Cell, Vol. 13, pp. 1437–1452.

Silencing of a meristematic gene using geminivirus‐derived vectors

Peele, C., Jordan, C. V., Muangsan, N., Turnage, M., Egelkrout, E., Eagle, P., … Robertson, D. (2001, August 1). The Plant Journal, Vol. 27, pp. 357–366.

A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants

Kong, L. J., Orozco, B. M., Roe, J. L., Nagar, S., Ou, S., Feiler, H. S., … Hanley-Bowdoin, L. (2000, July 3). The EMBO Journal, Vol. 19, pp. 3485–3495.

Chromosome condensation induced by geminivirus infection of mature plant cells

Journal of Cell Science, 113(7), 1149–1160.

Geminiviruses - Models for plant DNA replication, transcription and cell cycle regulation ([correction to] vol 35, pg 105, 2000)

Critical Reviews in Biochemistry and Molecular Biology, 35(4), U4.

Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation

Critical Reviews in Biochemistry and Molecular Biology, 35(2), 105–140.

The Multifunctional Character of a Geminivirus Replication Protein Is Reflected by Its Complex Oligomerization Properties

Orozco, B. M., Kong, L.-J., Batts, L. A., Elledge, S., & Hanley-Bowdoin, L. (2000, March 1). Journal of Biological Chemistry, Vol. 275, pp. 6114–6122.

Geminiviruses: Models for Plant DNA Replication, Transcription, and Cell Cycle Regulation

Hanley-Bowdoin, L., Settlage, S. B., Orozco, B. M., Nagar, S., & Robertson, D. (1999, January 1). Critical Reviews in Plant Sciences, Vol. 18, pp. 71–106.