Progress on WormGUIDES:

1.     Kumar, A., Christensen, R., Chandris, P., Guo, M., Duncan, W., Wu, Y., Santella, A., Moyle, M., Winter, P.W., Colón-Ramos, D., Bao, Z., Shroff, H. (2016). Using stage- and slit-scanning to improve contrast and optical sectioning in dual-view inverted light-sheet microscopy (diSPIM). The Biological Bulletin, 231(1):26-39 PMID27638693

2.     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, e10070 PMC4764590

3.     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

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

5.     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

6.     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, 11, 1032-8 PMC4105320

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

Collaborations to Disseminate Technology and Results:

8.     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.

9.     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

10.  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

11.  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

12.  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  (* WormAtlas)

13.  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

14.  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

15.  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

16.  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