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Zhi-Rong Bao · SciRah

Researcher profile · Semantic Scholar

Zhi-Rong Bao

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Zhi-Rong Bao — researcher profile on SciRah

h-index: 36
Works: 92
Citations: 10K

Most-cited papers

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
L. Hillier, W. Miller, E. Birney, W. Warren +171 more
2004Nature2,815 citations Open access
Semantic Scholar
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
L. Stein, Zhi-Rong Bao, Darin Blasiar, T. Blumenthal +32 more
2003PLoS Biology1,022 citations Open access
Semantic Scholar
Automated de novo identification of repeat sequence families in sequenced genomes.
Zhi-Rong Bao, S. Eddy
2002Genome Research942 citations Open access
Semantic Scholar
Pack-MULE transposable elements mediate gene evolution in plants
Ning Jiang, Zhi-Rong Bao, Xiaoyu Zhang, S. Eddy +1 more
2004Nature553 citations
Semantic Scholar
Fast high-contrast imaging of animal development with scanned light sheet-based structured illumination microscopy
P. Keller, Annette D. Schmidt, A. Santella, K. Khairy +3 more
2010Nature Methods509 citations Open access
Semantic Scholar
An active DNA transposon family in rice
Ning Jiang, Zhi-Rong Bao, Xiaoyu Zhang, H. Hirochika +3 more
2003Nature458 citations
Semantic Scholar
Automated cell lineage tracing in Caenorhabditis elegans.
Zhi-Rong Bao, J. I. Murray, Thomas J. Boyle, S. Ooi +2 more
2006Proceedings of the National Academy of Sciences of the United States of America378 citations Open access
Semantic Scholar
Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy
Yi-Cong Wu, Peter J Wawrzusin, Justin Senseney, Robert S. Fischer +9 more
2013Nature Biotechnology305 citations Open access
Semantic Scholar
Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans
Yi-Cong Wu, A. Ghitani, Ryan Christensen, A. Santella +5 more
2011Proceedings of the National Academy of Sciences of the United States of America293 citations Open access
Semantic Scholar
Automated analysis of embryonic gene expression with cellular resolution in C. elegans
J. I. Murray, Zhi-Rong Bao, Thomas J. Boyle, Max E. Boeck +5 more
2008Nature Methods200 citations Open access
Semantic Scholar
Genomics in C. elegans: so many genes, such a little worm.
L. Hillier, A. Coulson, J. I. Murray, Zhi-Rong Bao +2 more
2005Genome Research197 citations Open access
Semantic Scholar
Dual-view plane illumination microscopy for rapid and spatially isotropic imaging
Abhishek Kumar, Yi-Cong Wu, Ryan Christensen, P. Chandris +8 more
2014Nature Protocols189 citations Open access
Semantic Scholar
Multidimensional regulation of gene expression in the C. elegans embryo
J. I. Murray, Thomas J. Boyle, E. Preston, D. Vafeados +6 more
2012Genome Research164 citations Open access
Semantic Scholar
Rapid image deconvolution and multiview fusion for optical microscopy
Min Guo, Yue Li, Yijun Su, Talley J. Lambert +25 more
2020Nature Biotechnology162 citations Open access
Semantic Scholar
The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree
J. I. Murray, Zhi-Rong Bao, Thomas J. Boyle, R. Waterston
2006Nature Protocols121 citations
Semantic Scholar
A single-cell transcriptome atlas profiles early organogenesis in human embryos
Yi-Chi Xu, Teng-Jiao Zhang, Qin Zhou, Mengzhu Hu +6 more
2023Nature Cell Biology120 citations Open access
Semantic Scholar
Chiral forces organize left-right patterning in C. elegans by uncoupling midline and anteroposterior axis
C. Pohl, Zhi-Rong Bao
2010Developmental Cell119 citations Open access
Semantic Scholar
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
Thomas J. Boyle, Zhi-Rong Bao, J. I. Murray, C. L. Araya +1 more
2006BMC Bioinformatics113 citations Open access
Semantic Scholar
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D
A. Santella, Z. Du, Sonja Nowotschin, A. Hadjantonakis +1 more
2010BMC Bioinformatics110 citations Open access
Semantic Scholar
Control of cell cycle timing during C. elegans embryogenesis.
Zhi-Rong Bao, Zhong-Ying Zhao, Thomas J. Boyle, J. I. Murray +1 more
2008Developmental Biology92 citations Open access
Semantic Scholar
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
Zhi-Rong Bao, Sean R. Eddy
200289 citations
Semantic Scholar
Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice.
Ning Jiang, Zhi-Rong Bao, S. Temnykh, Zhu-Kuan Cheng +4 more
2002Genetics89 citations
Semantic Scholar
Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans.
Zhong-Ying Zhao, Thomas J. Boyle, Zhi-Rong Bao, J. I. Murray +2 more
2008Developmental Biology84 citations Open access
Semantic Scholar
De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis
Z. Du, A. Santella, Fei He, Michael Tiongson +1 more
2014Cell76 citations Open access
Semantic Scholar
The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo
Z. Du, A. Santella, Fei He, Pavak K. Shah +2 more
2015Developmental Cell64 citations Open access
Semantic Scholar
Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis
Julia L. Moore, Z. Du, Zhi-Rong Bao
2013Development63 citations Open access
Semantic Scholar
A semi-local neighborhood-based framework for probabilistic cell lineage tracing
A. Santella, Z. Du, Zhi-Rong Bao
2014BMC Bioinformatics59 citations Open access
Semantic Scholar
Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis.
Zhi-Rong Bao, J. I. Murray
2011Cold Spring Harbor Protocols52 citations
Semantic Scholar
Specific roles for the GATA transcription factors end-1 and end-3 during C. elegans E-lineage development
Max E. Boeck, Thomas J. Boyle, Zhi-Rong Bao, J. I. Murray +2 more
2011Developmental Biology49 citations Open access
Semantic Scholar
C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types
Berta Vidal, A. Santella, Esther Serrano-Saiz, Zhi-Rong Bao +2 more
2015Development47 citations Open access
Semantic Scholar
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration
A. Santella, R. Catena, Ismar Kovacevic, Pavak K. Shah +9 more
2015BMC Bioinformatics47 citations Open access
Semantic Scholar
Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially
D. Roy, David Michaelson, T. Hochman, A. Santella +3 more
2015Developmental Biology44 citations Open access
Semantic Scholar
Untwisting the Caenorhabditis elegans embryo
R. Christensen, Alexandra Bokinsky, A. Santella, Yi-Cong Wu +13 more
2015eLife43 citations Open access
Semantic Scholar
Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification
Molly B. Reilly, Tessa Tekieli, Cyril C Cros, G. Aguilar +15 more
2022bioRxiv40 citations Open access
Semantic Scholar
Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis
Z. Wang, Da-Li Wang, Chengcheng Li, Yi-Chi Xu +2 more
2018Bioinform.39 citations Open access
Semantic Scholar
PCP and SAX-3/Robo pathways cooperate to regulate convergent-extension-based nerve cord assembly in C. elegans
Pavak K. Shah, M. Tanner, Ismar Kovacevic, Aysha Rankin +10 more
2017Developmental Cell38 citations Open access
Semantic Scholar
AceTree: a major update and case study in the long term maintenance of open-source scientific software
Braden Katzman, Doris Tang, A. Santella, Zhi-Rong Bao
2018BMC Bioinformatics36 citations Open access
Semantic Scholar
Actomyosin-based Self-organization of cell internalization during C. elegans gastrulation
C. Pohl, Michael Tiongson, Julia L. Moore, A. Santella +1 more
2012BMC Biology36 citations Open access
Semantic Scholar
Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM)
Abhishek Kumar, Ryan Christensen, Min Guo, Panos Chandris +8 more
2016The Biological Bulletin35 citations Open access
Semantic Scholar
A multicellular rosette-mediated collective dendrite extension
Li Fan, Ismar Kovacevic, Maxwell G. Heiman, Zhi-Rong Bao
2018bioRxiv33 citations Open access
Semantic Scholar
Hierarchical deep reinforcement learning reveals novel mechanism of cell movement
Zi Wang, Yi-Chi Xu, Da-Li Wang, Jia-Wei Yang +1 more
2022Nature Machine Intelligence30 citations Open access
Semantic Scholar
Single-cell topographical profiling of the immune synapse reveals a biomechanical signature of cytotoxicity
Miguel M. de Jesus, Alexander H. Settle, D. Vorselen, Thomas K. Gaetjens +16 more
2024Science immunology28 citations
Semantic Scholar
E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis
Z. Du, Fei He, Zidong Yu, B. Bowerman +1 more
2014Developmental Biology27 citations Open access
Semantic Scholar
A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes
Joo Lee, Caitlin A. Taylor, Kristopher M. Barnes, Ao Shen +5 more
2019eLife26 citations Open access
Semantic Scholar
POS-1 promotes endo-mesoderm development by inhibiting the cytoplasmic polyadenylation of neg-1 mRNA
Ahmed Elewa, M. Shirayama, Ebru Kaymak, P. Harrison +11 more
2015Developmental Cell24 citations Open access
Semantic Scholar
A single-cell analysis of the molecular lineage of chordate embryogenesis
Teng-Jiao Zhang, Yi-Chi Xu, K. Imai, T. Fei +6 more
2020Science Advances23 citations Open access
Semantic Scholar
An in toto approach to dissecting cellular interactions in complex tissues
Pavak K. Shah, A. Santella, A. Jacobo, K. Siletti +2 more
2017Developmental Cell23 citations Open access
Semantic Scholar
Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution
Leighton H. Duncan, Mark W. Moyle, Lin Shao, T. Sengupta +9 more
2019Journal of Visualized Experiments22 citations Open access
Semantic Scholar
EFF-1 fusogen promotes phagosome sealing during cell process clearance in C. elegans
Piya Ghose, Alina Rashid, P. Insley, Meera Trivedi +5 more
2018Nature Cell Biology20 citations Open access
Semantic Scholar
Cellular structure image classification with small targeted training samples
Da-Li Wang, Zheng Lu, Yi-Chi Xu, Z. Wang +3 more
2019bioRxiv18 citations Open access
Semantic Scholar

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A. Santella×19
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