Bao Y, Aggarwal P, Robbins II NE, Sturrock CJ, Thompson, MC, Tan HQ, Tham C, Rodriguez PL, Vernoux T, Mooney SJ, Bennett MJ, Dinneny JR (2014) Plant roots employ a patterning mechanism to position lateral root branches towards available water. Proc. Natl. Acad. Sci. June 9 online

Sebastian J, Wong MK, Tang E, Dinneny JR (2014) Methods to Promote Germination of Dormant Setaria viridis seeds. PLoS One 18;9(4):e95109.

Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. (2014) Circular RNA is expressed across the eukaryotic tree of life. PLoS One. 7;9(3):e90859

 Emami, S, Yee MC, Dinneny JR (2013) A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front. Plant Sci. 2;4:339

Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PMY, Tham C, Duan L, Dinneny JR (2013) A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis.  The Plant Cell doi:10.1105/tpc.113.112896

Duan L, Dietrich D, Ng CH, Chan PMY, Bhalerao R, Bennett MJ, Dinneny JR (2013) Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis thaliana seedlings. The Plant Cell PMID: 23341337

Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN (2009) Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods in Molecular Biology 553:57-77
Dinneny JR, Long TA, Wang JY, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein, JS, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science May 16;320(5878):942-5
Filiault D, Wessinger C, Dinneny JR, Lutes J, Borevitz J, Weigel D, Chory J, and Maloof JN (2008) Amino acid polymorphisms in Arabidopsis Phytochrome B causes differential response to light. Proc. Natl. Acad. Sci. Feb 26;105(8):3157-62
Brady SM, Orlando D, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science Nov 2;318(5851):801-6
Dinneny JR, Weigel D, Yanofsky MF (2006) NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development 133, 1645-1655
Dinneny JR, Weigel D, Yanofsky MF (2005) A genetic framework for fruit patterning in Arabidopsis. Development 132, 4687-4696
Dinneny JR, Yadegari R, Fischer RL, Yanofsky MF, Weigel D (2004) The role of JAGGED in shaping lateral organs. Development 131, 1101-1110
(‘Previews’ in Developmental Cell 6(3), 318-319)
Wu X, Dinneny JR, Crawford KM, Rhee Y, Citovsky V, Zambryski PC, Weigel D (2003) Modes of intercellular transcription factor movement in the Arabidopsis apex. Development 130, 3735-3745.
Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, Wells D, Katz A, Margossian L, Harada J, Goldberg R, Fischer RL (1999) Control of fertilization-independent-endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc. Natl. Acad. Sci. 96, 4186-4191.

Reviews and Book Chapters
Sebastian, J, Duan, L, Dinneny JR, (in press) Salt-stress regulation of root system growth and architecture in Arabidopsis seedlings. Plant Cell Expansion: Methods and Protocols. Springer Publishing
Dinneny JR, (2014) A gateway with a guard: how the endodermis regulates growth through hormone signaling. Plant Sci. 214, 14-19
Dinneny JR (2012) Cell-type resolution analysis of root development and environmental responses. Roots and their soil interactions: What we can learn from genomics. Wiley Publishing
Wee CW and Dinneny JR (2010) Tools for high-spatial and temporal-resolution analysis of environmental responses in plants. Biotechnology Letters PMID: 20502944
Dinneny JR (2010) Analysis of the salt-stress response at cell-type resolution. Plant Cell & Environment 1;33(4):543-51
Dinneny JR, Benfey PN (2009) Studying root development using a genomic approach. Annual Plant Reviews, Volume 37, Root Development Chapter 12: 325-351 Blackwell Publishing
Dinneny JR and Benfey PN (2008) Plant stem cell niches: standing the test of time. Cell Feb 22;132(4):553-7
Dinneny JR and Benfey PN, (2005) Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell 123, 1180-1182
Dinneny JR and Yanofsky MF (2005) Drawing lines and borders: how the dehiscent fruit of Arabidopsis is patterned. Bioessays 27, 42-49
Dinneny JR and Yanofsky MF (2004) Floral Development: An ABC Gene Chips in Downstream. Curr. Biol. 14, R840-R841
Dinneny JR and Yanofsky MF (2004) Vascular Patterning: Xylem or Phloem? Curr. Biol. 14, R112-R114