Google Scholar Citations
  1. Low-cost and scalable projected light-sheet microscopy for the high-resolution imaging of cleared tissue and living samples.
    Chen Y, Chauhan S, Gong C, De La Cruz ED, Datta MS, Dayton H, Xu C, De La Cruz ED, Tsai Y, Datta MS, Rosoklija GB, Dwork AJ, Mann JJ, Boldrini M, Leong KW, Dietrich L, Tomer R
    Nature Biomedical Engg. Aug, 2024 [ Rdcu Link ] [ Link ] [ Nature Reviews Biongineering Highlight ] [ Supp. videos @ Youtube ] [ Github ]
  2. Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms.
    Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Janakiraman A, Min W, Tomer R., Price-Whelan A, Nirody JA, Dietrich LEP
    PLoS Biol 2024 [ Link ]
  3. ClearScope: a fully integrated light sheet theta microscope for sub-cellular resolution imaging without lateral size constraints.
    Fay MG, Lang PJ, Denu DS, O’Connor NJ, Haydock B, Blaisdell J, Roussel N, Wilson A, Aronson SM, Angstman PJ, Gong C, Butola T, Devinsky O, Basu J, Tomer R, Glaser JR
    bioRxiv Aug 2024. [ Link ] [ Original LSTM paper ]
  4. Capillary connections between sensory circumventricular organs and adjacent parenchyma enable local volume transmission.
    Yao Y, Chen Y, Tomer R, Silver R
    bioRxiv July 2024. [ Link ]
  5. Human vascular organoids with a mosaic AKT1 mutation recapitulate Proteus syndrome.
    He S, Zhu Y, Chauhan S, Tavakol DN, Lee JH, Berris RB, Xu C, Lee JH, Lee C, Cai S, McElroy S, Vunjak-Novakovic G, Tomer R, Azizi E, Xu B, Lao Y, Leong KW
    bioRxiv Jan 2024 [ Link ]
  6. Whole-brain mapping reveals the divergent impact of ketamine on the dopamine system.
    Datta MS*, Chen Y*, Chauhan C, Zhang J, De La Cruz ED, Gong C, Tomer R
    Cell Reports Dec 04, 2023 [ Link ] [ Columbia News ] [ PsyPost summary ] [ Supp. videos @ Youtube ]
  7. Aberrant pace of cortical neuron development in brain organoids from patients with 22q11. 2 deletion syndrome and schizophrenia.
    Rao SB, Brundu F, Chen Y, Sun Y, Zhu H, Shprintzen RJ, Tomer R, Rabadan R, Leong KW, Markx S, Xu B, Gogos JA
    bioRxiv Oct 05, 2023 [ Link ]
  8. Focused ultrasound-mediated brain genome editing.
    Lao Y, Ji R, Zhou JK, Snow KJ, Kwon N, Saville E, He S, Chauhan S, Chi C, Datta MS, Zhang H, Quek CH, Cai SS, Li M, Gaitan Y, Bechtel L, Wu S, Lutz CM, Tomer R, Murray SA, Chavez A, Konofagou EE, Leong KW
    PNAS Aug 2023 [ Link ]
  9. A Microfluidic Dual-Aptamer Sandwich Assay for Rapid and Cost-Effective Detection of Recombinant Proteins.
    Wen K, Chen Y, Meng X, Botros S, Dai W, Stojanovic MN*, Tomer R*, Lin Q*.
    Microchemical Journal (2023) [ Link ]
  10. An in vitro model of neuronal ensembles.
    Rabadan MA, De La Cruz ED, Rao SB, Chen Y, Gong C, Crabtree G, Xu B, Markx S, Gogos JA, Yuste R, Tomer R
    Nature Communications 13, 3340 (2022) [ Link ] [ rdcu.be ] [ Emulating Schizophrenia in a dish ]
  11. Mapping morphological malformation to genetic dysfunction in blood vessel organoids with 22q11. 2 Deletion Syndrome.
    He S, Xu C, Lao Y, Chauhan S, Xiao Y, Willner MJ, Jin Y, McElroy S, Rao SB, Gogos JA, Tomer R, Azizi E, Xu B, Leong KW
    bioRxiv Nov. 2021 [ Link ]
  12. Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder.
    Jong J, Llapashtica C, Genestine M, Strauss K, Provenzano F, Sun Y, Zhu H, Cortese GP, Brundu F, Brigatti KW, Corneo B, Migliori B, Tomer R, Kushner SA, Kellendonk C, Javitch JA, Xu B, Markx S
    Nature Communications 12, 4087 (2021) [ Link ]
  13. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution.
    Chakraborty T, Driscoll MK, Jeffery E, Murphy MM, Roudot P, Chang B, Vora S, Wong WM, Nielson CD, Zhang H, Zhemkov V, Hiremath C, De La Cruz ED, Yi Y, Bezprozvanny I, Zhao H, Tomer R, Heintzmann R, Meeks JP, Marciano DK, Morrison SJ, Danuser G, Dean KM, Fiolka R
    Nature Methods 16, pages1109–1113(2019) [ Link ]
  14. A miniaturized multi-clamp CMOS amplifier for intracellular neural recording.
    Shekar S, Jayant K, Rabadan MA, Tomer R, Yuste R, Shepard KL
    Nature Electronics 2, pages343–350 (2019) [ Link ]
  15. Molecularly defined cortical astroglia subpopulation modulates neurons via secretion of Norrin.
    Miller SJ , Philips T , Kim N , Dastgheyb R , Chen Z , Hsieh YC , Daigle JG , Datta M , Chew J , Vidensky S , Pham JT , Hughes EG , Robinson MB , Sattler R , Tomer R, Suk JS , Bergles DE , Haughey N , Pletnikov M , Hanes J , Rothstein JD.
    Nature Neuroscience Apr 01, 2019 [ Link ]
  16. Uneven balance of power between hypothalamic peptidergic neurons in the control of feeding.
    Wei Q, Krolewski DM, Moore S, Kumar V, Li F, Martin B, Tomer R Murphy GG, Deisseroth K, Watson Jr. SJ, and Akil H.
    PNAS Sep 17, 2018 [ Link ]
  17. Light Sheet Theta Microscopy for High-resolution Quantitative Imaging of Large Biological Samples.
    Migliori B, Datta MS, Dupre C, Apak MC, Asano S, Gao R, Boyden ES, Hermanson O, Yuste R, Tomer R.
    BMC Biology 2018 16:57 [ Link ]
    preprint: bioRxiv 119289, Mar 22, 2017; doi: https://doi.org/10.1101/119289. [ bioRxiv link ]
    updated preprint: bioRxiv 119289, Aug 30, 2017; doi: https://doi.org/10.1101/119289. [ bioRxiv link ]
    High-res figures [ download ]
    High-res videos at [ figshare ]
  18. Quantitative validation of immunofluorescence and lectin staining using reduced CLARITY acrylamide formulations.
    Krolewski DM, Kumar V, Martin B, Tomer R, Deisseroth K, Myers RM, Schatzberg AF, Lee FS, Barchas JD, Bunney WE, Akil H, Watson Jr SJ.
    Brain Structure and Function. Dec 14, 2017. doi:https://doi.org/10.1007/s00429-017-1583-z. [ Link ]
  19. An interactive framework for whole-brain maps at cellular resolution.
    Fürth D, Vaissière T, Tzortzi O, Xuan Y, Märtin A, Lazaridis I, Spigolon G, Fisone G, Tomer R, Deisseroth K, Carlén M, Miller CA, Rumbaugh G, Meletis K
    Nature Neuroscience. Dec 04, 2017. doi:10.1038/s41593-017-0027-7. [ Link ]
  20. Whole-tissue biopsy phenotyping of three-dimensional tumours reveals patterns of cancer heterogeneity.
    Tanaka N, Kanatani S, Tomer R, Sahlgren C, Kronqvist P , Kaczynska D, Louhivuori L, Kis L,  Lindh C, Mitura P, Stepulak A , Corvigno S, Hartman J, Micke P, Mezheyeuski A, Strell C, Carlson JW , Fernández C, Dahlstrand H, Östman A, Matsumoto K, Wiklund P, Oya M, Miyakawa A, Deisseroth K, Uhlén P.
    Nature Biomedical Engg. Oct 02, 2017 AOP. doi:10.1038/s41551-017-0139-0. [ Link ]
  21. CLARITY reveals dynamics of ovarian follicular architecture and vasculature in three-dimensions.
    Feng Y, Cui P, Lu X, Hsueh B, Möller Billig F, Zarnescu Yanez L, Tomer R, Boerboom D, Carmeliet P, Deisseroth K, Hsueh AJ.
    Sci Rep. 2017 Mar 23;7:44810. doi:10.1038/srep44810. [ Link ]
  22. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.
    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.
    Nature Neuroscience, AOP (19 Dec 2016). doi:10.1038/nn.4462 [ Link ] [ Pdf ]

    Download High-res movie
  23. Advanced light microscopy enables rapid mapping of brain structure and function in high resolution.
    Migliori B, Datta MS, Tomer R.
    Laser Focus World, 52, 12, 47-52 (Dec. 2016). [Link] [Pdf] [High-res Fig01, Fig02, Fig03, Fig04, Fig05]
  24. SPED light sheet microscopy: fast mapping of biological system structure and function.
    Tomer R, Lovett-Barron M, Kauvar I, Andalman A, Burns VM, Sethuraman S, Grosenick L, Broxton M, Yang S, Deisseroth K.
    Cell. Dec 17, 2015. [ Link ] [ Pdf ]
  25. Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits.
    Lerner TN, Shilyansky C, Davidson TJ, Evans KE, Beier KT, Zalocusky KA, Crow AK, Malenka R, Luo L, Tomer R, Deisseroth K.
    Cell. Jul 30, 2015. [ Link ] [ Pdf ]
  26. Rapid High-resolution Brain Mapping with CLARITY Optimized Light Sheet Microscopy (COLM).
    Tomer R, Deisseroth K.
    Microscopy and Microanalysis. 21(Suppl. 3), pp717-718, 2015. [ Link ] [ Pdf ]
  27. Identifying cell types from spatially referenced single-cell expression datasets.
    Pettit J*, Tomer R*, Achim K, Richardson S, Azizi L, Marioni J.
    PLoS Comp. Bio. Sep 25, 2014. * equal contributions [ Link ] [ Pdf ]
  28. Development of the annelid axochord: insights into notochord evolution.
    Lauri A, Brunet T, Handberg-Thorsager M, Fischer AHL, Simakov O, Steinmetz PRH, Tomer R, Keller PJ, and Arendt D.
    Science. Sep 12, 2014. [ Link ] [ Pdf ]
  29. Advanced CLARITY Methods for Rapid and High-Resolution Imaging of Intact Tissues.
    Tomer R, Deisseroth K.
    SfN 2014. [ Pdf ]
  30. Advanced CLARITY for rapid and high-resolution imaging of large intact tissues.
    Tomer R, Ye L, Hseuh B, Lei A, Deisseroth K.
    Nature Protocols. Jul, 2014. [ Link ] [ Pdf ]
  31. Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury.
    Zhang MD, Tortoriello G, Hsueh B, Tomer R, Ye L, Mitsios N, Borgius L, Grant G, Kiehn O, Watanabe M, Uhlen M, Mulder J, Deisseroth K, Harkany T, Hoekfelt TG.
    Proc Natl Acad Sci USA. Mar 10, 2014. [ Link ] [ Pdf ]
  32. Larval body patterning and apical organs are conserved in animal evolution.
    Marlow H, Tosches MA, Tomer R, Steinmetz PR, Lauri A, Larsson T, Arendt D.
    BMC Biology. Jan 29, 2014. [ Link ] [ Pdf ]
  33. Quantitative High-Speed Imaging of Entire Developing Embryos with Simultaneous Multi-View Light Sheet Microscopy.
    Tomer R, Khairy K, Amat F, Keller PJ.
    Nature Methods. July, 2012. [ Link ] [ Pdf ]
  34. A computational statistics approach for estimating the spatial range of morphogen gradients.
    Kanodia JS, Kim Y, Tomer R, Khan Z, Chung K, Storey JD, Lu H, Keller PJ, Shvartsman SY.
    Development. Nov, 2011. [ Link ] [ Pdf ]
  35. Shedding light on the system: studying embryonic development with light sheet microscopy.
    Tomer R*, Khairy K, Keller PJ*.
    Curr Opin Genet Dev. Oct, 2011. *Co-Corresponding authors. [ Link ] [ Pdf ]
  36. Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium.
    Tomer R*, Denes AS, Tessmar-Raible K, Arendt D*.
    Cell. Sep 3, 2010. *Co-Corresponding authors. [ Link ] [ Pdf ]
  37. Ancient animal microRNAs and the evolution of tissue identity.
    Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D.
    Nature. Feb 25, 2010. [ Link ] [ Pdf ]
    38. Pre-PhD work
  38. A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome.
    Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J.
    Mol Microbiol. Oct 29, 2007. [ Pdf ]
  39. A physicochemical model for analyzing DNA sequences.
    Dutta S*, Singhal P*, Agrawal P*, Tomer R*, Kritee K*, Khurana E, Jayaram B.
    J Chem Inf Model. 2006. * equal contributions [ Pdf ]
  40. Tumor-associated E-cadherin mutations do not induce Wnt target gene expression, but affect E-cadherin repressors.
    Laux H, Tomer R, Mader MT, Smida J, Budczies J, Kappler R, Hahn H, Bloechinger M, Schnitzbauer U, Eckardt-Schupp F, Hoefler H, Becker KF.
    Lab Invest. Aug 16, 2004. [ Pdf ]
  41. Different mechanisms of cyclin D1 overexpression in multiple myeloma revealed by fluorescence in situ hybridization and quantitative analysis of mRNA levels.
    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.
    Blood. Aug 15, 2004. [ Pdf ]
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