Neelima R. Sinha

image of Neelima R. Sinha



Plant Biology

Offices and Labs

2224 Life Sciences
(530) 754 8441
(530) 752-8692


1990 PhD Botany University of California, Berkeley

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.


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


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

CBS Grad Group Affiliations

Integrative Genetics and Genomics
Plant Biology

Specialties / Focus

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


Sinha Lab website

Teaching Interests

Genetic regulation of plant growth and development. Plant molecular biology. Introductory biology.


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


6/3/2015 9:19:17 PM
  • 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