Progress on WormGUIDES

    Santella, A., Du, Z. & Bao Z. (2014). "A semi-local neighborhood-based framework for probabilistic cell lineage tracing", BMC Bioinformatics, 15, 217 PMC4085468. LINK

    Wu, Y., Christensen R., Colón-Ramos D., Shroff H. (2013). "Advanced optical imaging techniques for neurodevelopment", Curr Opin Neurobiol, 6, 1090-7 PMC3830703. LINK

    Kumar, A., Wu, Y., Christensen, R., Chandris, P., Gandler, W., McCreedy, E., Bokinsky, A., Colón-Ramos, D.A., Bao, Z., McAuliffe, M., Rondeau, G. & Shroff, H. (2014). "Dual-view plane illumination microscopy for rapid and spatially isotropic imaging", Nat Protoc, 9, 2555-73 PMC4386612. LINK

    Wu, Y., Wawrzusin, P., Senseney, J., Fischer, R.S., Christensen, R. Santella, A., York, A.G., Winter, P.W., Waterman, C.M., Bao, Z., Colón-Ramos, D.A., McAuliffe, M. & Shroff, H. (2013). "Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy", Nat Biotechnol, 231(1):26-39.31(11):1032-1038. LINK

    Christensen, R.P., Bokinsky, A., Santella, A., Wu, Y., Marquina-Solis, J., Guo, M, Kovacevic, I., Kumar, A., Winter, P.W., Tashakkori, N., McCreedy, E., Liu, H., McAuliffe, M., Mohler, W., Colón-Ramos, D.A., Bao, Z. & Shroff, H. (2015). "Untwisting the Caenorhabditis elegans embryo", eLife, 4. pii: e10070. doi: 10.7554/eLife.10070.. LINK

    Santella, A., Catena, R., Kovacevic, I., Shah, P., Yu, Z., Marquina-Solis, J., Kumar, A., Wu, Y., Schaff, J., Colón-Ramos, D., Shroff, H., Mohler, W.A.* & Bao, Z.* (2015). "WormGUIDES: an interactive single-cell developmental atlas and tool for collaborative multidimensional data exploration", BMC Bioinformatics, 16, 189 PMC4459063. LINK

Collaborations to Disseminate Technology and Results

    Vidal, B., Santella, A., Serrano-Saiz, E., Bao, Z., Chuang, C.F. & Hobert O. (2015). "C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types", Development, 142, 2464-77 PMC4510870. LINK

    Weicksel S.E., Mahadav A., Moyle M., Cipriani P.G., Kudron M., Pincus Z., Bahmanyar S., Abriola L., Merkel J., Gutwein M., Fernandez A.G., Piano F., Gunsalus K.C., Reinke V. (). "A Novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans.", Development, in press.. LINK

    Roy, D., Michaelson, D., Hochman, T., Santella, A., Bao, Z., Goldberg, J.D. & Hubbard, E.J. (2016). "Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially", Dev Bio, 409, 261-71 PMC4827254. LINK

    Roberts, S.E., Chang, S-S., Kumar, A., Occhipinti, P., Shroff, H., Roper, M., Gladfelter, A.S. (2016). "Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium.", Molecular Biology of the Cell, 27, 2000-7 PMC4927274. LINK

    Santella, A., Kovacevic, I., Herndon, L.A.*, Hall, D.H.*, Du, Z. & Bao, Z. (2016). "Digital Development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model", Nucleic Acids Res, 44(D1), D781-5 PMC4702815. LINK

    Vogel, J.L., Michaelson, D., Santella, A., Hubbard, E.J.* & Bao, Z. * (2014). "Irises: A practical tool for image-based analysis of cellular DNA content", Worm, 3, e29041 PMC4165541. LINK

    Murray, J.I., Boyle, T.J., Preston, E., Vafeados, D., Mericle, B.L., Weisdepp, P., Zhao, Z., Bao, Z., Boeck, M.E. & Waterston R.H. (2012). "Multidimensional regulation of gene expression in the C. elegans embryo", Genome Res., 22, 1282-94. PMC3396369. LINK

    Elewa, A., Shirayama, M., Kaymak, E., Harrison, P.F., Powell, D.R., Du, Z., Chute, C.D., Woolf, H., Yi, D., Ishidate, T., Srinivasan, J., Bao, Z., Beilharz, T.H., Ryder, S.P. & Mello, C.C. (2015). "POS-1 promotes endo-mesoderm development by inhibiting the cytoplasmic polyadenylation of neg-1 mRNA", Dev Cell, 34, 108-18 PMC4507413. LINK

    Wu, Y., Chandris, P., Winter, P.W., Kim, E.Y., Jaumouille, V., Kumar, A., Guo, M., Leung, J.M., Smith, C., Rey-Suarez, I., Liu, H., Waterman, C.M., Ramamurthi, K.S., LaRiviere, P., Shroff, H. (2016). "Simultaneous multi-view capture and fusion improves spatial resolution in wide-field and light-sheet microscopy.", Optica, 8, 897-910. LINK