Santella, A., Du, Z., Nowotschin, S., Hadjantonakis, A.-K. & Bao, Z. (2010). A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics, 11, 580.

Pohl, C. & Bao, Z. (2010). Chiral forces organize left-right patterning in C. elegans by uncoupling midline and anteroposterior axis. Dev Cell, 19, 402-12.

Keller, P.J., Schmidt, A.D., Santella, A., Khairy, K., Bao, Z., Wittbrodt, J.& Stelzer, E.H.K. (2010). Fast high-contrast imaging of animal development with scanned light sheet-based structured illumination microscopy. Nat Methods, 7, 637-42.

Bao, Z., Murray, J.I., Boyle, T., Ooi, S.-L., Sandel, M.J. & Waterston R.H. Automated cell lineage tracing in Caenorhabditis elegans, PNAS, 103, 2707-12, 2006.

Bao, Z. & Murray, J.I. (2010). Live imaging of Caenorhabditis elegans embryogenesis, in Imaging in Developmental Biology: A Laboratory Manual, eds Sharpe J. & Wong R., Chapter 1, Cold Spring Harbor Laboratory Press, New York.

Murray, J.I. & Bao, Z. (2010). Automated lineage and expression profiling in live Caenorhabditis elegans embryos, in Imaging in Developmental Biology: A Laboratory Manual, eds Sharpe, J. & Wong, R., Chapter 56, Cold Spring Harbor Laboratory Press, New York.

Murray, J.I., Bao, Z., Boyle, T.J., Boeck, M.E., Mericle, B.L., Nicholas, T.J., Zhao, Z., Sandel, M.J. & Waterston R.H. (2008). Automated analysis of embryonic gene expression with cellular resolution in C. elegans, Nat Methods, 5, 703-9.

Bao, Z., Zhao, Z., Boyle, T.J., Murray, J.I. & Waterston R.H. (2008). Control of cell cycle timing during Caenorhabditis elegans embryogenesis, Dev Biol, 318, 65-72.

Jiang, N.*, Bao, Z.*, Zhang, X., Eddy, S.R., McCouch, S.R., Hirochika, H. & Wessler S.R. An active DNA transposon family in rice. Nature, 421, 163-7, 2003. (* co-first authors)

Stein, L.D., Bao, Z. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology, 1, 166-92, 2003.

Jiang, N.*, Bao, Z.*, Zhang, X., Eddy, S.R. & Wessler S.R. Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431, 569-72, 2004. (* co-first authors)

Bao, Z. & Eddy S.R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res, 12, 1269-76, 2002.