Raju Tomer, PhD

Departments And Divisions

  • Department of Biological Sciences (Columbia University)
  • Assistant Professor of Biological Sciences (Columbia University)

My research has been focused on development of enabling molecular, optical and computational methods that allow an integrated systems level understanding of the brain at multiple levels: evolution (Tomer et al. 2010, Cell; Pettit* & Tomer* et al. 2014, PLoS Comp. Bio.), development (Tomer et al. 2012, Nat. Methods), structure (Tomer et al. 2014, Nat. Protocols; Lerner et al. 2015, Cell; Tomer et al. 2015 Cell.) and function (Tomer et al., 2015 Cell).

Lab Locations

Research Interests

  • Brain Imaging
  • Cell specification and differentiation
  • Stem cell biology
  • Cognitive/Systems neuroscience


Romanov RA, Zeisel A, Bakker J, Girach F, Hellysaz A, Tomer R, Alpár A, Mulder J, Clotman F, Keimpema E, Hsueh B, Crow AK, Martens H, Schwindling C, Calvigioni D, Bains JS, Máté Z, Szabó G, Yanagawa Y, Zhang M, Rendeiro A, Farlik M, Uhlén M, Wulff P, Bock C, Broberger C, Deisseroth D, Hökfelt T, Linnarsson S, Horvath TL, Harkany T. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nature Neuroscience, AOP (19 Dec 2016). doi:10.1038/nn.4462.

Migliori B, Datta MS, Tomer R. Advanced light microscopy enables rapid mapping of brain structure and function in high resolution. Laser Focus World, 52, 12, 47-52 (Dec. 2016).

Tomer R, Lovett-Barron M, Kauvar I, Andalman A, Burns VM, Sethuraman S, Grosenick L, Broxton M, Yang S, Deisseroth K. (2015). SPED light sheet microscopy: fast mapping of biological system structure and function. Cell. Dec 17; 163(7):1796-1806.

Lerner TN, Shilyansky C, Davidson TJ, Evans KE, Beier KT, Zalocusky KA, Crow AK, Malenka R, Luo L, Tomer R, Deisseroth K. (2015). Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits. Cell. Jul 30; 162(3):635-647.

Pettit J, Tomer R, Achim K, Richardson S, Azizi L, Marioni J. (2014). Identifying cell types from spatially referenced single-cell expression datasets. PLoS Comp. Bio. Sep 25.

Lauri A, Brunet T, Handberg-Thorsager M, Fischer AHL, Simakov O, Steinmetz PRH, Tomer R, Keller PJ, and Arendt D. (2014). Development of the annelid axochord: insights into notochord evolution. Science. 12 Sep 2014: 345 (6202), 1365-1368.

Tomer R, Deisseroth K. (2015). Rapid High-resolution Brain Mapping with CLARITY Optimized Light Sheet Microscopy (COLM). Microscopy and Microanalysis, 21 (Suppl. 3), pp 717-718. doi:10.1017/S1431927615004389.

Tomer R, Ye L, Hseuh B, Lei A, Deisseroth K. Advanced CLARITY for rapid and highresolution imaging of large intact tissues. (2014). Nature Protocols. Jul;9(7):1682-97.

Zhang MD, Tortoriello G, Hsueh B, Tomer R, Ye L, Mitsios N, Borgius L, Grant G, Kiehn O, Watanabe M, Uhlén M, Mulder J, Deisseroth K, Harkany T, Hökfelt TG. (2014).

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury. Proc Natl Acad Sci USA. Mar 10.

Marlow H, Tosches MA, Tomer R, Steinmetz PR, Lauri A, Larsson T, Arendt D. (2014). Larval body patterning and apical organs are conserved in animal evolution. BMC Biol. Jan 29;12:7.

Tomer R, Khairy K, Amat F, Keller PJ. (2012). Quantitative High-Speed Imaging of Entire Developing Embryos with Simultaneous Multi-View Light Sheet Microscopy. Nature Methods. 9(7):755-63.

Kanodia JS, Kim Y, Tomer R, Khan Z, Chung K, Storey JD, Lu H, Keller PJ, Shvartsman SY. (2011). A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-74.

Tomer R*, Khairy K, Keller PJ*. (2011). Shedding light on the system: studying embryonic development with light sheet microscopy. Curr Opin Genet Dev. 21(5):558-65. *Cocorresponding authors.

Tomer R*, Denes AS, Tessmar-Raible K, Arendt D*. (2010). Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell. 142(5):800-9. *Co-corresponding authors.

Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D. (2010). Ancient animal microRNAs and the evolution of tissue identity. Nature. 463(7284):1084-8. Epub 2010 Jan 31.

Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J. (2007). A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome. Mol Microbiol. 66(5):1174-91. Epub 2007 Oct 29.

Dutta S*, Singhal P*, Agrawal P*, Tomer R*, Kritee K*, Khurana E, Jayaram B. (2006) A physicochemical model for analyzing DNA sequences. J Chem Inf Model. 46(1):78-85.

Laux H, Tomer R, Mader MT, Smida J, Budczies J, Kappler R, Hahn H, Blöchinger M, Schnitzbauer U, Eckardt-Schupp F, Höfler H, Becker KF. (2004) Tumor-associated Ecadherin mutations do not induce Wnt target gene expression, but affect E-cadherin repressors. Lab Invest. 84(10):1372-86.

Specht K, Haralambieva E, Bink K, Kremer M, Mandl-Weber S, Koch I, Tomer R, Hofler H, Schuuring E, Kluin PM, Fend F, Quintanilla-Martinez L. (2004) Different mechanisms of cyclin D1 overexpression in multiple myeloma revealed by fluorescence in situ hybridization and quantitative analysis of mRNA levels. Blood. 104(4):1120-6.