Zhirong Bao - Publications

Weill Cornell Medical College, New York, NY, United States 
Human Development, Computer Science, Anatomy Biology

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Barnes KM, Fan L, Moyle MW, Brittin CA, Xu Y, Colón-Ramos DA, Santella A, Bao Z. Cadherin preserves cohesion across involuting tissues during neurulation. Elife. 9. PMID 33030428 DOI: 10.7554/eLife.58626  0.68
2020 Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, ... ... Bao Z, et al. Rapid image deconvolution and multiview fusion for optical microscopy. Nature Biotechnology. PMID 32601431 DOI: 10.1038/s41587-020-0560-x  0.68
2019 Wang D, Lu Z, Xu Y, Wang ZI, Santella A, Bao Z. Cellular structure image classification with small targeted training samples. Ieee Access : Practical Innovations, Open Solutions. 7: 148967-148974. PMID 32832309 DOI: 10.1109/access.2019.2940161  0.68
2019 Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. Elife. 8. PMID 31386623 DOI: 10.7554/eLife.46703  0.36
2019 Duncan LH, Moyle MW, Shao L, Sengupta T, Ikegami R, Kumar A, Guo M, Christensen R, Santella A, Bao Z, Shroff H, Mohler W, Colón-Ramos DA. Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution. Journal of Visualized Experiments : Jove. PMID 31233035 DOI: 10.3791/59533  0.68
2019 Brandt JP, Rossillo M, Zhuo D, Ichikawa D, Barnes K, Chen A, Noyes M, Bao Z, Ringstad N. Lineage context switches the function of a Pax6 homolog in determining a neuronal fate. Development (Cambridge, England). PMID 30890567 DOI: 10.1242/dev.168153  0.36
2018 Katzman B, Tang D, Santella A, Bao Z. AceTree: a major update and case study in the long term maintenance of open-source scientific software. Bmc Bioinformatics. 19: 121. PMID 29618316 DOI: 10.1186/s12859-018-2127-0  0.68
2017 Shah PK, Santella A, Jacobo A, Siletti K, Hudspeth AJ, Bao Z. An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues. Developmental Cell. 43: 530-540.e4. PMID 29161596 DOI: 10.1016/j.devcel.2017.10.021  0.68
2017 Shah PK, Tanner MR, Kovacevic I, Rankin A, Marshall TE, Noblett N, Tran NN, Roenspies T, Hung J, Chen Z, Slatculescu C, Perkins TJ, Bao Z, Colavita A. PCP and SAX-3/Robo Pathways Cooperate to Regulate Convergent Extension-Based Nerve Cord Assembly in C. elegans. Developmental Cell. 41: 195-203.e3. PMID 28441532 DOI: 10.1016/j.devcel.2017.03.024  0.36
2016 Kumar A, Christensen R, Guo M, Chandris P, Duncan W, Wu Y, Santella A, Moyle M, Winter PW, Colón-Ramos D, Bao Z, Shroff H. Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM). The Biological Bulletin. 231: 26-39. PMID 27638693  0.68
2016 Vanloo G, Wong K, Ng C, Ramsey B, Bao Z, Osborne K, Wang D. Using high performance computing to model cellular embryogenesis Acm International Conference Proceeding Series. 17. DOI: 10.1145/2949550.2949576  0.68
2015 Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colon-Ramos DA, ... Bao Z, et al. Untwisting the Caenorhabditis elegans embryo. Elife. 4. PMID 26633880 DOI: 10.7554/eLife.10070  0.68
2015 Roy D, Michaelson D, Hochman T, Santella A, Bao Z, Goldberg JD, Hubbard EJ. Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially. Developmental Biology. PMID 26577869 DOI: 10.1016/j.ydbio.2015.10.031  0.68
2015 Santella A, Kovacevic I, Herndon LA, Hall DH, Du Z, Bao Z. Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. Nucleic Acids Research. PMID 26503254 DOI: 10.1093/nar/gkv1119  0.68
2015 Du Z, Santella A, He F, Shah PK, Kamikawa Y, Bao Z. The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo. Developmental Cell. 34: 592-607. PMID 26321128 DOI: 10.1016/j.devcel.2015.07.014  0.68
2015 Vidal B, Santella A, Serrano-Saiz E, Bao Z, Chuang CF, Hobert O. C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types. Development (Cambridge, England). 142: 2464-77. PMID 26153233 DOI: 10.1242/dev.125740  0.68
2015 Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Developmental Cell. 34: 108-18. PMID 26096734 DOI: 10.1016/j.devcel.2015.05.024  0.52
2015 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 WA, Bao Z. WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. Bmc Bioinformatics. 16: 189. PMID 26051157 DOI: 10.1186/s12859-015-0627-8  0.68
2015 Du Z, He F, Yu Z, Bowerman B, Bao Z. E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. Developmental Biology. 398: 267-79. PMID 25523393 DOI: 10.1016/j.ydbio.2014.12.009  0.4
2015 Vidal B, Santella A, Serrano-Sai E, Bao Z, Chuang CF, Hobert O. C. Elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types Development (Cambridge). 142: 2464-2477. DOI: 10.1242/dev.125740  0.68
2015 Christensen R, Bokinsky A, Santella A, Wu Y, Marquina J, Kovacevic I, Kumar A, Winter P, McCreedy E, Mohler W, Bao Z, Colón-Ramos D, Shroff H. An imaging and analysis toolset for the study of Caenorhabditis elegans neurodevelopment Progress in Biomedical Optics and Imaging - Proceedings of Spie. 9334. DOI: 10.1117/12.2082394  0.68
2015 Du Z, Santella A, He F, Shah PK, Kamikawa Y, Bao Z. The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo Developmental Cell. DOI: 10.1016/j.devcel.2015.07.014  0.68
2014 Vogel JL, Michaelson D, Santella A, Hubbard EJ, Bao Z. Irises: A practical tool for image-based analysis of cellular DNA content. Worm. 3: e29041. PMID 25254149 DOI: 10.4161/worm.29041  0.68
2014 Santella A, Du Z, Bao Z. A semi-local neighborhood-based framework for probabilistic cell lineage tracing. Bmc Bioinformatics. 15: 217. PMID 24964866 DOI: 10.1186/1471-2105-15-217  0.68
2014 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. 156: 359-72. PMID 24439388 DOI: 10.1016/j.cell.2013.11.046  0.68
2013 Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colón-Ramos DA, McAuliffe M, Shroff H. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nature Biotechnology. 31: 1032-8. PMID 24108093 DOI: 10.1038/nbt.2713  0.68
2013 Moore JL, Du Z, Bao Z. Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis. Development (Cambridge, England). 140: 3266-74. PMID 23861063 DOI: 10.1242/dev.096040  0.68
2012 Pohl C, Tiongson M, Moore JL, Santella A, Bao Z. Actomyosin-based self-organization of cell internalization during C. elegans gastrulation. Bmc Biology. 10: 94. PMID 23198792 DOI: 10.1186/1741-7007-10-94  0.68
2012 Murray JI, Bao Z. Automated lineage and expression profiling in live Caenorhabditis elegans embryos. Cold Spring Harbor Protocols. 2012. PMID 22854571 DOI: 10.1101/pdb.prot070615  0.68
2012 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 Research. 22: 1282-94. PMID 22508763 DOI: 10.1101/gr.131920.111  0.68
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 17708-13. PMID 22006307 DOI: 10.1073/pnas.1108494108  0.68
2011 Bao Z, Murray JI. Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis. Cold Spring Harbor Protocols. 2011. PMID 21880814 DOI: 10.1101/pdb.prot065599  0.68
2011 Boeck ME, Boyle T, Bao Z, Murray J, Mericle B, Waterston R. Specific roles for the GATA transcription factors end-1 and end-3 during C. elegans E-lineage development Developmental Biology. 358: 345-355. PMID 21854766 DOI: 10.1016/j.ydbio.2011.08.002  0.68
2010 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. 11: 580. PMID 21114815 DOI: 10.1186/1471-2105-11-580  0.68
2010 Pohl C, Bao Z. Chiral forces organize left-right patterning in C. elegans by uncoupling midline and anteroposterior axis. Developmental Cell. 19: 402-12. PMID 20833362 DOI: 10.1016/j.devcel.2010.08.014  0.68
2010 Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EH. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nature Methods. 7: 637-42. PMID 20601950 DOI: 10.1038/nmeth.1476  0.68
2008 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. Nature Methods. 5: 703-9. PMID 18587405 DOI: 10.1038/nmeth.1228  0.68
2008 Bao Z, Zhao Z, Boyle TJ, Murray JI, Waterston RH. Control of cell cycle timing during C. elegans embryogenesis. Developmental Biology. 318: 65-72. PMID 18430415 DOI: 10.1016/j.ydbio.2008.02.054  0.68
2008 Zhao Z, Boyle TJ, Bao Z, Murray JI, Mericle B, Waterston RH. Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans. Developmental Biology. 314: 93-9. PMID 18164284 DOI: 10.1016/j.ydbio.2007.11.015  0.68
2006 Murray JI, Bao Z, Boyle TJ, Waterston RH. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nature Protocols. 1: 1468-76. PMID 17406437 DOI: 10.1038/nprot.2006.222  0.68
2006 Boyle TJ, Bao Z, Murray JI, Araya CL, Waterston RH. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. Bmc Bioinformatics. 7: 275. PMID 16740163 DOI: 10.1186/1471-2105-7-275  0.68
2006 Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH. Automated cell lineage tracing in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America. 103: 2707-12. PMID 16477039 DOI: 10.1073/pnas.0511111103  0.68
2005 Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE, Waterston RH. Genomics in C. elegans: so many genes, such a little worm. Genome Research. 15: 1651-60. PMID 16339362 DOI: 10.1101/gr.3729105  0.68
2004 Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR. Pack-MULE transposable elements mediate gene evolution in plants. Nature. 431: 569-73. PMID 15457261 DOI: 10.1038/nature02953  0.68
2003 Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. Plos Biology. 1: E45. PMID 14624247 DOI: 10.1371/journal.pbio.0000045  0.68
2003 Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR. An active DNA transposon family in rice. Nature. 421: 163-7. PMID 12520302 DOI: 10.1038/nature01214  0.68
2002 Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research. 12: 1269-76. PMID 12176934 DOI: 10.1101/gr.88502  0.68
2002 Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics. 161: 1293-305. PMID 12136031  0.68
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