About Us

Contributors and Contact:

The Digital Development database website was designed and programmed by members of the Bao lab including Anthony Santella, Zhuo Du and Ismar Kovacevich. The database was integrated with WORMATLAS by David Hall and Laura Herndon.

For questions, bug reports etc. contact: Anthony Santella, santella (at) mskcc.org.

The Bao Lab:


The Bao Lab at the Memorial Sloan Kettering Cancer Center is interested in developmental systems biology. In particular, we use C. elegans embryogenesis as a model to develop technologies for live imaging, automated cell tracking, and systematic single-cell analysis. We use these techniques to understand how complex tissues arise from networks of interacting genes and cells. From our efforts we have produced Starrynite, one of the leading software packages for automated cell tracking in 3D tissues. Besides the worm, Starrynite shows comparable accuracy, speed and robustness in other model organisms such as Drosophila, zebrafish and mouse.

Alumni site: Zhuo Du

Software:

Starrynite: automated cell tracking and lineaging
AceTree: image browsing and lineage editing 		Devscape: systematic single-cell phenotyping

References:

Quantitative Phenotypic Analysis of Embryogenesis at Single-Cell Resolution:
  1. Du Z, Santella A, He F, Tiongson M, Bao Z. De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. Cell. 2014. 156:359-72.
  2. Du, Z, He, F, Yu, Z, Bowerman, B, Bao, Z. E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. Developmental Biology. 2015. 398:267-79
  3. Du, Z, Santella, A, He, F, Shah, PK, Kamikawa, Y and Bao, Z. (2015). The regulatory landscape of lineage differentiation in a Metazoan embryo. Developmental Cell, 34(5):592-607.
  4. Moore JL, Du, Z, Bao Z. Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis. Development. 2013. 140:3266-74.
  5. Murray JI, Boyle TJ, Preston E, Vafeados D, Mericle B, Weisdepp P, Zhao Z, Bao Z, Boeck M, Waterston RH. Multidimensional regulation of gene expression in the C. elegans embryo. Genome Res. 2012. 22:1282-94.

Imaging and Image Analysis Algorithms:
  1. Santella A, Du Z, Bao Z. A semi-local neighborhood-based framework for probabilistic cell lineage tracing. BMC Bioinformatics. 2014. 15:217.
  2. Wu Y, Ghitani A, Christensen R, Santella A, Du Z, Rondeau G, Bao Z*, Colón-Ramos D*, Shroff H*. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. PNAS. 2011. 108:17708.
  3. Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z. A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics. 2010. 11:580.
  4. Murray JI*, Bao Z*, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods. 2008. 5:703-9.
  5. Bao Z, Murray JI, Boyle T, Ooi S-L, Sandel MJ, Waterston RH. Automated cell lineage tracing in Caenorhabditis elegans. PNAS. 2006. 103:2707-12.