Neelima R. Sinha

Neelima Sinha

Position Title

Department of Plant Biology, College of Biological Sciences

2224 Life Sciences

Research Interests

Evolution of developmental morphology and plant responses to stress

Genetic and molecular analysis of compound leaf development in tomato. Evolution of land plant form. Plasticity in cells and organs at the genomic level in response to developmental cues and environmental stresses. Deciphering the host-plant parasite interaction between tomato and Cuscuta using genomics.

Grad Group Affiliations

  • Integrative Genetics and Genomics
  • Plant Biology

Specialties / Focus

  • Cell and Developmental Biology
  • Developmental Genetics
  • Environmental and Integrative Biology
  • Model Plants
  • Molecular Biology, Biochemistry and Genomics
  • Systematics and Evolutionary Biology


  • PBI 220 Plant Development
  • PB! 227 Plant Molecular Biology
  • BIS 2C Introductory Biology

Honors and Awards

  • Katherine Esau Junior Faculty Fellow
  • Chancellor's award for excellence in Undergraduate Research Mentorship
  • Elected Fellow of the AAAS

    Professional Societies

    • American Society of Plant Biology
    • American Association for the Advancement of Science


    • 1990 PhD Botany University of California, Berkeley


    A Ranjan, BT Townsley, Y Ichihashi, NR Sinha, DH Chitwood. An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia PLoS genetics 11 (1), e1004900  DOI: 10.1371/journal.pgen.1004900

    Brad T. Townsley, Michael F. Covington, Yasunori Ichihashi†, Kristina Zumstein and Neelima R. Sinha* (2015) BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction  Front. Plant Sci., 22 May 2015 |

    Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JNM, Aradhya M, Prins B, Li L, Myles S, Sinha NR. (2014) A Modern Ampelography: A Genetic Basis for Leaf Shape and Venation Patterning in Grape Plant physiology 164 (1), 259-272

    Ichihashi Y, Aguilar-Martínez J, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JNM, and Sinha NR. (2014) Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape PNAS 111 (25) E2616-E2621

    Ranjan A, Ichihashi Y, Farhi M, Zumstein K, Townsley B, David-Schwartz R, Sinha NR. (2014) De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism. Plant Physiol.

    Koenig, D, Jiménez-Gómez, JM, Kimura, S, Fulop, D, Chitwood, DH, Headland, LR, Kumar, R, Covington, MF, Devisetty, UK, Tat, AV, Tohge, T, Bolger, A, Schneeberger, K, Ossowski, S, Lanz, C, Xiong, G, Taylor-Teeples, M, Brady, SM, Pauly, M, Weigel, D, Usadel, B, Fernie, AR, Peng, J, Sinha, NR, Maloof, JN (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci USA. 110: E2655-62.

    Chitwood, DH, Kumar, R, Headland, LR, Ranjan, A, Covington, MF, Ichihashi, Y, Fulop, D, Jimenez-Gomez, JM, Peng, J, Maloof, JN, Sinha, NR (2013) A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell 25: 2465-2481

    Chitwood, D., Headland, L., Ranjan, A., Braybrook, S., Koenig, D., Martinez, C., Kuhlemeier, C., Smith, R., and Sinha, N. (2012) – Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. Plant Cell. 24:2318-2327.

    Alakonya, A, Kumar, R, Koenig, D, Kimura, S, Townsley, B, Runo, S, Garces, HM, Kang, J, Yanez, A, David-Schwartz, R, Machuka, J, Sinha, N (2012) Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism. The Plant cell, 24(7): 3153-66.

    Koenig, D., Bayer, E., Kang, J., Kuhlemeier, C., and Neelima Sinha (2009). Auxin patterns Solanum lycopersicum leaf morphogenesis. Development 136:2997-06

    Kimura, S., Koenig, D., Kang, J., Yoong, F-Y., Sinha, N. (2008) Natural variation in leaf morphology results from mutation of a novel knox gene. Current Biology 18:672-677