| Year |
Citation |
Score |
| 2022 |
Wang Z, Xu Y, Wang D, Yang J, Bao Z. Hierarchical deep reinforcement learning reveals novel mechanism of cell movement. Nature Machine Intelligence. 4: 73-83. PMID 35991585 DOI: 10.1038/s42256-021-00431-x |
0.33 |
|
| 2022 |
Shah P, Bao Z, Zaidel-Bar R. Visualizing and quantifying molecular and cellular processes in C. elegans using light microscopy. Genetics. PMID 35766819 DOI: 10.1093/genetics/iyac068 |
0.315 |
|
| 2022 |
Santella A, Kolotuev I, Kizilyaprak C, Bao Z. Cross-modality synthesis of EM time series and live fluorescence imaging. Elife. 11. PMID 35666127 DOI: 10.7554/eLife.77918 |
0.667 |
|
| 2021 |
Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler W, Shroff H, Colón-Ramos DA. Differential adhesion regulates neurite placement via a retrograde zippering mechanism. Elife. 10. PMID 34783657 DOI: 10.7554/eLife.71171 |
0.621 |
|
| 2021 |
Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, ... Bao Z, et al. Structural and developmental principles of neuropil assembly in C. elegans. Nature. PMID 33627875 DOI: 10.1038/s41586-020-03169-5 |
0.634 |
|
| 2020 |
Zhang T, Xu Y, Imai K, Fei T, Wang G, Dong B, Yu T, Satou Y, Shi W, Bao Z. A single-cell analysis of the molecular lineage of chordate embryogenesis. Science Advances. 6. PMID 33148647 DOI: 10.1126/sciadv.abc4773 |
0.327 |
|
| 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 |
0.618 |
|
| 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 |
0.676 |
|
| 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 |
0.668 |
|
| 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 |
0.325 |
|
| 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 |
0.729 |
|
| 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 |
0.337 |
|
| 2019 |
Fan L, Kovacevic I, Heiman MG, Bao Z. A multicellular rosette-mediated collective dendrite extension. Elife. 8. PMID 30767892 DOI: 10.7554/Elife.38065 |
0.323 |
|
| 2019 |
Christensen R, Bokinsky A, Santella A, Moyle M, Guo M, Lauziere A, Ardiel E, Vishwasrao HD, Harvey B, Levin M, Karaj N, Mohler W, Daniel Colón-Ramos D, Bao Z, Shroff H. Generating a 4D Atlas of Nuclear Positions in Embryonic Caenorhabditis elegans Biophysical Journal. 116: 558a. DOI: 10.1016/J.Bpj.2018.11.3001 |
0.616 |
|
| 2018 |
Wang D, Wang Z, Zhao X, Xu Y, Bao Z. An Observation Data Driven Simulation and Analysis Framework for Early Stage C. elegans Embryogenesis. Journal of Biomedical Science and Engineering. 11: 225-234. PMID 35574576 DOI: 10.4236/jbise.2018.118018 |
0.32 |
|
| 2018 |
Teuliere J, Kovacevic I, Bao Z, Garriga G. The Caenorhabditis elegans gene ham-1 regulates daughter cell size asymmetry primarily in divisions that produce a small anterior daughter cell. Plos One. 13: e0195855. PMID 29668718 DOI: 10.1371/Journal.Pone.0195855 |
0.385 |
|
| 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 |
0.634 |
|
| 2018 |
Ghose P, Rashid A, Insley P, Trivedi M, Shah P, Singhal A, Lu Y, Bao Z, Shaham S. EFF-1 fusogen promotes phagosome sealing during cell process clearance in Caenorhabditis elegans. Nature Cell Biology. PMID 29556089 DOI: 10.1038/S41556-018-0068-5 |
0.393 |
|
| 2018 |
Wang D, Wang Z, Zhao X, Xu Y, Bao Z. An Observation Data Driven Simulation and Analysis Framework for Early Stage <i>C. elegans</i> Embryogenesis Journal of Biomedical Science and Engineering. 11: 225-234. DOI: 10.4236/Jbise.2018.118018 |
0.317 |
|
| 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 |
0.687 |
|
| 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 |
0.354 |
|
| 2017 |
Wang E, Santella A, Wang Z, Wang D, Bao Z. Visualization of 3-Dimensional Vectors in a Dynamic Embryonic System—WormGUIDES Journal of Computer and Communications. 5: 70-79. DOI: 10.4236/Jcc.2017.512008 |
0.666 |
|
| 2016 |
Wang Z, Ramsey BJ, Wang D, Wong K, Li H, Wang E, Bao Z. An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis. Plos One. 11: e0166551. PMID 27851808 DOI: 10.1371/journal.pone.0166551 |
0.316 |
|
| 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 DOI: 10.1086/689589 |
0.668 |
|
| 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 |
0.705 |
|
| 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 |
0.669 |
|
| 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 |
0.706 |
|
| 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 |
0.688 |
|
| 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 |
0.675 |
|
| 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 |
0.346 |
|
| 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 |
0.683 |
|
| 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 |
0.402 |
|
| 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, Colón-Ramos DA, ... Bao Z, et al. Author response: Untwisting the Caenorhabditis elegans embryo Elife. DOI: 10.7554/Elife.10070.058 |
0.618 |
|
| 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 |
0.625 |
|
| 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 |
0.694 |
|
| 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 |
0.628 |
|
| 2014 |
Kumar A, Wu Y, Christensen R, Chandris P, Gandler W, McCreedy E, Bokinsky A, Colón-Ramos DA, Bao Z, McAuliffe M, Rondeau G, Shroff H. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nature Protocols. 9: 2555-73. PMID 25299154 DOI: 10.1038/Nprot.2014.172 |
0.369 |
|
| 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 |
0.624 |
|
| 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 |
0.675 |
|
| 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 |
0.714 |
|
| 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 |
0.667 |
|
| 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 |
0.652 |
|
| 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 |
0.722 |
|
| 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 |
0.435 |
|
| 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 |
0.392 |
|
| 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 |
0.698 |
|
| 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 |
0.471 |
|
| 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 |
0.407 |
|
| 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 |
0.676 |
|
| 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 |
0.395 |
|
| 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 |
0.674 |
|
| 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 |
0.406 |
|
| 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 |
0.435 |
|
| 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 |
0.415 |
|
| 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 |
0.427 |
|
| 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 |
0.424 |
|
| 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 |
0.506 |
|
| 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 |
0.523 |
|
| 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 |
0.301 |
|
| 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 |
0.515 |
|
| 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 |
0.496 |
|
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