Pujic, P. , Alloisio, N. , Fournier, P. , Roche, D. , Sghaier, H. , Miotello, G. , Armengaud, J. , Berry, A. M. and Normand, P. (2019), Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton. Environ Microbiol. doi:10.1111/1462-2920.14606

Gifford, I., Vance, S., Nguyen, G., Berry, A.M.  (2018).   Stable Genetic Transformation and Heterologous Expression in the Nitrogen-fixing Plant Endosymbiont Frankia alni ACN14a.  BioRxiv. doi: https://doi.org/10.1101/496703  

Battenberg, K., Potter, D., Tabuloc, C. A., Chiu, J. C., & Berry, A. M. (2018). Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicago truncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms. Frontiers in plant science, 9, 1256. doi:10.3389/fpls.2018.01256

Gifford, I., Battenberg, K., Vaniya, A., Wilson, A., Tian, L., Fiehn, O., & Berry, A. M. (2018). Distinctive Patterns of Flavonoid Biosynthesis in Roots and Nodules of Datisca glomerata and Medicago spp. Revealed by Metabolomic and Gene Expression Profiles. Frontiers in plant science, 9, 1463. doi:10.3389/fpls.2018.01463         

Griesmann Maximilian, Yue Chang, Xin Liu, Yue Song, Georg Haberer, Matthew B. Crook, Benjamin Billault-Penneteau, Dominique Lauressergues, Jean Keller, Leandro Imanishi, Yuda Purwana Roswanjaya, Wouter Kohlen, Petar Pujic, Kai Battenberg, Nicole Alloisio, Yuhu Liang, Henk Hilhorst, Marco G. Salgado, Valerie Hocher, Hassen Gherbi, Sergio Svistoonoff, Jeff J. Doyle, Shixu He, Yan Xu, Shanyun Xu, Jing Qu, Qiang Gao, Xiaodong Fang, Yuan Fu, Philippe Normand, Alison M. Berry, Luis G. Wall, Jean-Michel Ané, Katharina Pawlowski, Xun Xu, Huanming Yang, Manuel Spannagl, Klaus F. X. Mayer, Gane Ka-Shu Wong, Martin Parniske, Pierre-Marc Delaux, Shifeng Cheng.  (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science. 361. eaat1743. 10.1126/science.aat1743.

Salgado, M. G., van Velzen, R., Nguyen, T. V., Battenberg, K., Berry, A. M., Lundin, D., & Pawlowski, K. (2018). Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales). Frontiers in plant science, 9, 1629. doi:10.3389/fpls.2018.01629

Van Deynze, Allen & Zamora, Pablo & Delaux, Pierre-Marc & Heitmann, Cristobal & Jayaraman, Dhileepkumar & Rajasekar, Shanmugam & Graham, Danielle & Maeda, Junko & Gibson, Donald & D Schwartz, Kevin & M Berry, Alison & Bhatnagar, Srijak & Jospin, Guillaume & Darling, Aaron & Jeannotte, Richard & Lopez, Javier & C Weimer, Bart & Eisen, Jonathan & Shapiro, Howard-Yana & Bennett, Alan. (2018). Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biology. 16. e2006352.

McPherson EG, Berry AM, van Doorn NS.  2018. Performance testing to identify climate-ready trees.  Urban Forestry & Urban Greening 29:  28-39.

Harder LF, Ellsworth C, Hoss S, Waitman B, Lay M, Berry AM.  2018.  Assessment of Potential Tree Root Impacts on the 2017 Oroville Dam Spillway Incident.  Proceedings of the 2018 Annual Conference of the Association of State Dam Safety Officials, Seattle, WA, September 9 - 13, 2018.   Association of State Dam Safety Officials, Inc.

Battenberg K, Lee EK, Chiu JC, Berry AM, Potter D.  2017.  OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement.  BMC Bioinformatics. Jun 21;18(1):310. doi: 10.1186/s12859-017-1726-5.

Luke R. Thompson, Jon G. Sanders […] The Earth Microbiome Project Consortium.  2017.   A communal catalogue reveals Earth’s multiscale microbial diversity.     Nature 551, 457–463 (23 November 2017)

Normand P, Nguyen TV, Battenberg K, Berry AM, Heuvel BV, Fernandez MP, Pawlowski K.  2017.  Proposal of 'Candidatus Frankia californiensis', the uncultured symbiont in nitrogen-fixing root nodules of a phylogenetically broad group of hosts endemic to western North America.  Int J Syst Evol Microbiol. 67(10):3706-3715.

Nguyen T, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, and K Pawlowski.  2016.  An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH.  BMC Genomics. 2016; 17: 796.

Persson T, Nguyen T, Alloisio N, Pujic P, Berry AM, and P Normand. 2016. The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated? Symbiosis 70:1, 149-157.

Persson T, Battenberg K, Demina I, Vigil-Stenman T, VandenHeuvel B, Pujic P, Facciotti M, Wilbanks G, O’Brien A, Fournier P, Hernandez M, Mendoza A, Medigue C, Normand P, Pawlowski K, Berry AM.  2015.  Candidatus Frankia datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, expresses canonical nod genes in symbiosis with its host plant. PLOS ONE May 28, 2015 DOI: 10.1371/journal.pone.0127630

McPherson G and AM Berry. 2015.  Climate ready urban trees for Central Valley cities. Western Arborist, Spring 2015, 58-62.

Berry, AM, Gifford I, Pawlowski, K.  2015.  Functional analysis of nitrogen-fixing root nodule symbioses induced by Frankia: transport and metabolic interactions. IN:  F. DeBruin ed., Biological Nitrogen Fixation, Wiley/Blackwell. Ch. 48.

Sen A, Daubin A, Gifford I, Berry AM, Normand P.  2014.  Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov.,

Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Intl J of Systematic & Evolutionary Microbiology, v. 64: 3821-3832. 

Berry, AM, Barabote RD, Normand P.  2014.  Family Acidothermaceae.  IN:  E Rosenberg, EF DeLong, F Thompson, S Lory, E Stackebrandt, Eds, The Prokaryotes (PK4), Prokaryotic Biology and Symbiotic Associations, Springer.

Berry, AM, Mendoza-Herrera A, Guo Y-Y, Hayashi J, Persson T, Barabote R, Demchenko K, Zhang S, and Pawlowski K.  2011.  New perspectives on nodule nitrogen assimilation in actinorhizal symbioses.  Functional Plant Biology 38:  645-652.

Pawlowski K, Bogusz D, Ribeiro A, and Berry AM.  2011.  Progress in research on actinorhizal plants.  Functional Plant Biology 38:  633-638.

Rezaei F, Joh LD, Berry AM, VanderGheynst JS.  2011.  Xylanase and cellulase production by Acidothermus cellulolyticus grown on switchgrass in solid-state fermentation.  Biofuels 2 (1): 21-32.

Barabote R, Parales J, Parales R, and AM Berry.  2010.  Characterization of a thermostable family 10 endo-xylanase (Xyl-1) from Acidothermus cellulolyticus 11B.  Appl. & Env. Microbiology.

Joh LD, Rezaei F, Barabote RD, Parales JV, Parales RE, Berry AM, VanderGheynst JS.  2010. Effects of Phenolic Monomers on Growth of Acidothermus cellulolyticus .  Biotechnology Progress.

VanderGheynst J, Rezaei F, Dooley TM and AM Berry.  2010.  Switchgrass leaching requirements for solid-state fermentation by Acidothermus cellulolyticus.  Biotechnology Progress,26 (3): 622-626.

Holmes, K.A., K.E. Veblen, A.M. Berry & T.P. Young.  2010. Effects of prescribed fires on planted valley oak saplings at a research restoration site in the Sacramento Valley.  Restoration Ecology.

Li T, Shilling F, Thorne J, Li F, Schott H, Boynton R, Berry AM.  2010.  Fragmentation of China’s landscape by roads and urban areas.  Landscape Ecology.

Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Medigue C, Adney WS, Xu XC, Lapidus A, Detter JC, Pujic P, Parales R, Bruce D, Lavire C,  Challacombe JF, Brettin TS, and AM Berry.  2009.  Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.  Genome Research 19(6):  1033-1043.

Adney WS, van der Lelie N, Berry A, and ME Himmel.  2008.  Understanding the biomass decay community:  Biomass recalcitrance.  IN: M. Himmel, ed., Deconstructing the Plant Cell Wall for Bioenergy. Oxford, UK: Blackwell Publishing pp. 454-479.

Girvetz EH, Thorne JH, Berry AM, and JAG Jaeger.  2008.  Integration of landscape fragmentation analysis into regional planning: A statewide multi-scale case study from California, USA.  Landscape & Urban Planning 86: 205-218

Solomeshch A.I., S.N. Long, M.G. Barbour, and A.M. Berry. 2009.  Floristic Composition of Roadside Grasslands, Yolo County, California.  IN:  IN:  Espinosa-García F, Hubbard T, Van Devender TR, Harper-Lore B, editors. Invasive Plants on the Move. Controlling them in North America. Proceedings, Weeds Across Borders 2006, Hermosillo, Mexico.  Arizona-Sonora Desert Museum Press, Tucson, AZ.

Normand P. , Lapierre P.,  Tisa L.S.,  J.P., Alloisio N., Bassi C.A., Berry A.M.,   Bickhart D.M.,  Choisne N.,  Couloux A., Cournoyer B, Cruveiller S., Daubin V., Demange N., Pilar Francino M., Goltsman E., Huang Y., Kopp O., Labarre L., Lapidus A., Lavire C., Marechal J., Martinez M., E. Mastronunzio J.E., Mullin B., Niemann J., Pujic P., Rawnsley T., Rouy Z., Schenowitz C., Sellstedt A., Tavares F., Tomkins J.P., Vallenet D., Valverde C., Wall L., Wang Y., Medigue C. & Benson D.R..  2007.  Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.  Genome Research 17(1): 7-15.  

Pawlowski K., K.R. Jacobsen, N. Alloisio, R.F. Denison, M. Klein, J.D. Tjepkema, T. Winzer, A. Sirrenberg, C. Guan, A.M. Berry. 2007.   Truncated hemoglobins in actinorhizal nodules of Datisca glomerata.  Plant Biol. 9, 776-785.

Alloisio N, Maréchal J,  Brian Vanden Heuvel B, Normand P,  Berry AM.   Characterization of a gene locus containing squalene-hopene cyclase (shc) in Frankia ACN14a and an shc homolog in Acidothermus cellulolyticus .  2005.  Symbiosis 39:  83-90.

King AP and AM Berry.  2005.  Vineyard 15N, nitrogen and water status in perennial clover and bunch grass cover crop systems of California’s Central Valley.  Agriculture Ecosystems & Environment 109 (3-4):  262-272.

Berry AM, Murphy TM, Okubara PA, Jacobsen KR, Swensen SM, and K Pawlowski.    2004.  Novel expression pattern of cytosolic glutamine synthetase in nitrogen-fixing root nodules of the actinorhizal host, Datisca glomerata  Plant Physiology 135: 1849-1862.