De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis

[1]  Zhirong Bao,et al.  Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis , 2013, Development.

[2]  Philipp J. Keller,et al.  Imaging Morphogenesis: Technological Advances and Biological Insights , 2013, Science.

[3]  Daniel L. Mace,et al.  A High-Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns in Caenorhabditis elegans , 2013, G3: Genes, Genomes, Genetics.

[4]  Marc Garbey,et al.  Reconstructing regulatory networks from the dynamic plasticity of gene expression by mutual information , 2013, Nucleic acids research.

[5]  Claudiu A. Giurumescu,et al.  Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos , 2012, Development.

[6]  Wolfgang Busch,et al.  A microfluidic device and computational platform for high throughput live imaging of gene expression , 2012, Nature Methods.

[7]  Anthony A. Hyman,et al.  A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans , 2012, Cell.

[8]  R. Waterston,et al.  Multidimensional regulation of gene expression in the C. elegans embryo , 2012, Genome research.

[9]  F. Piano,et al.  A High-Resolution C. elegans Essential Gene Network Based on Phenotypic Profiling of a Complex Tissue , 2011, Cell.

[10]  Z. Bao,et al.  A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D , 2010, BMC Bioinformatics.

[11]  Jen-Yi Lee,et al.  Extracellular control of PAR protein localization during asymmetric cell division in the C. elegans embryo , 2010, Development.

[12]  Philipp J. Keller,et al.  Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy , 2010, Nature Methods.

[13]  Eugene W. Myers,et al.  Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans , 2009, Cell.

[14]  Jürgen Hench,et al.  Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps. , 2009, Developmental biology.

[15]  Thomas J. Nicholas,et al.  Automated analysis of embryonic gene expression with cellular resolution in C. elegans , 2008, Nature Methods.

[16]  Zhirong Bao,et al.  Control of cell cycle timing during C. elegans embryogenesis. , 2008, Developmental biology.

[17]  Charless C. Fowlkes,et al.  A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm , 2008, Cell.

[18]  Itai Yanai,et al.  Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression , 2008, Molecular systems biology.

[19]  Scott E. Fraser,et al.  Imaging in Systems Biology , 2007, Cell.

[20]  Scott J. Diede,et al.  EEL-1, a Hect E3 ubiquitin ligase, controls asymmetry and persistence of the SKN-1 transcription factor in the early C. elegans embryo , 2007, Development.

[21]  J. Collins,et al.  Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.

[22]  R. Waterston,et al.  Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. , 2006, Genes & development.

[23]  John Isaac Murray,et al.  The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree , 2006, Nature Protocols.

[24]  A. Fraser,et al.  Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways , 2006, Nature Genetics.

[25]  Zhirong Bao,et al.  AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis , 2006, BMC Bioinformatics.

[26]  R. Waterston,et al.  Automated cell lineage tracing in Caenorhabditis elegans. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[27]  C. Mello,et al.  The Conserved Kinases CDK-1, GSK-3, KIN-19, and MBK-2 Promote OMA-1 Destruction to Regulate the Oocyte-to-Embryo Transition in C. elegans , 2006, Current Biology.

[28]  Iva Greenwald,et al.  LIN-12/Notch trafficking and regulation of DSL ligand activity during vulval induction in Caenorhabditis elegans , 2005, Development.

[29]  Marc Vidal,et al.  Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis , 2005, Nature.

[30]  A. Coulson,et al.  Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans , 2005, Nature.

[31]  W. Wood,et al.  Multiple Wnt signaling pathways converge to orient the mitotic spindle in early C. elegans embryos. , 2004, Developmental cell.

[32]  David E Hill,et al.  Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. , 2004, Genome research.

[33]  J. Kimble,et al.  The C. elegans Hand gene controls embryogenesis and early gonadogenesis , 2003, Development.

[34]  R. Lin.  A gain-of-function mutation in oma-1, a C. elegans gene required for oocyte maturation, results in delayed degradation of maternal proteins and embryonic lethality. , 2003, Developmental biology.

[35]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[36]  C. Mello,et al.  SRC-1 and Wnt signaling act together to specify endoderm and to control cleavage orientation in early C. elegans embryos. , 2002, Developmental cell.

[37]  Morris F. Maduro,et al.  Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3beta homolog is mediated by MED-1 and -2 in C. elegans. , 2001, Molecular cell.

[38]  S. Hallam,et al.  The C. elegans NeuroD homolog cnd-1 functions in multiple aspects of motor neuron fate specification. , 2000, Development.

[39]  A. Sluder,et al.  nhr-25, the Caenorhabditis elegans ortholog of ftz-f1, is required for epidermal and somatic gonad development. , 2000, Developmental biology.

[40]  R. Lin,et al.  MEX-5 and MEX-6 function to establish soma/germline asymmetry in early C. elegans embryos. , 2000, Molecular cell.

[41]  M. Meneghini,et al.  Wnt pathway components orient a mitotic spindle in the early Caenorhabditis elegans embryo without requiring gene transcription in the responding cell. , 1999, Genes & development.

[42]  J. McGhee,et al.  The GATA-factor elt-2 is essential for formation of the Caenorhabditis elegans intestine. , 1998, Developmental biology.

[43]  R. Lin,et al.  POP-1 and Anterior–Posterior Fate Decisions in C. elegans Embryos , 1998, Cell.

[44]  C. Hunter,et al.  The maternal par genes and the segregation of cell fate specification activities in early Caenorhabditis elegans embryos. , 1997, Development.

[45]  C. Mello,et al.  Wnt Signaling and an APC-Related Gene Specify Endoderm in Early C. elegans Embryos , 1997, Cell.

[46]  Bruce Bowerman,et al.  Wnt Signaling Polarizes an Early C. elegans Blastomere to Distinguish Endoderm from Mesoderm , 1997, Cell.

[47]  H. Schnabel,et al.  Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: variability of development and regional specification. , 1997, Developmental biology.

[48]  J. Rothman,et al.  lin-12 and glp-1 are required zygotically for early embryonic cellular interactions and are regulated by maternal GLP-1 signaling in Caenorhabditis elegans. , 1996, Development.

[49]  C. Mello,et al.  MEX-3 Is a KH Domain Protein That Regulates Blastomere Identity in Early C. elegans Embryos , 1996, Cell.

[50]  K. Kemphues,et al.  par-6, a gene involved in the establishment of asymmetry in early C. elegans embryos, mediates the asymmetric localization of PAR-3. , 1996, Development.

[51]  B. Bowerman,et al.  Time-dependent responses to glp-1-mediated inductions in early C. elegans embryos. , 1996, Development.

[52]  R. Lin,et al.  pop-1 Encodes an HMG box protein required for the specification of a mesoderm precursor in Early C. elegans embryos , 1995, Cell.

[53]  R. Schnabel,et al.  Establishment of left-right asymmetry in the Caenorhabditis elegans embryo: a multistep process involving a series of inductive events. , 1995, Development.

[54]  J. Rothman,et al.  Combinatorial specification of blastomere identity by glp-1-dependent cellular interactions in the nematode Caenorhabditis elegans. , 1994, Development.

[55]  S. Mango,et al.  The pha-4 gene is required to generate the pharyngeal primordium of Caenorhabditis elegans. , 1994, Development.

[56]  S. Mango,et al.  Two maternal genes, apx-1 and pie-1, are required to distinguish the fates of equivalent blastomeres in the early Caenorhabditis elegans embryo. , 1994, Development.

[57]  R. Schnabel,et al.  glp-1 and inductions establishing embryonic axes in C. elegans. , 1994, Development.

[58]  B. Draper,et al.  The maternal genes apx-1 and glp-1 and establishment of dorsal-ventral polarity in the early C. elegans embryo , 1994, Cell.

[59]  Bruce Bowerman,et al.  The maternal gene skn-1 encodes a protein that is distributed unequally in early C. elegans embryos , 1993, Cell.

[60]  Harold Weintraub,et al.  The pie-1 and mex-1 genes and maternal control of blastomere identity in early C. elegans embryos , 1992, Cell.

[61]  Bruce Bowerman,et al.  skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo , 1992, Cell.

[62]  J. Sulston,et al.  The embryonic cell lineage of the nematode Caenorhabditis elegans. , 1983, Developmental biology.

[63]  L. Lum,et al.  Wnt Signaling , 2016, Methods in Molecular Biology.

[64]  Xing-Ming Zhao,et al.  Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information , 2012, Bioinform..

[65]  R. Schnabel,et al.  Specification of Cell Fates in the Early Embryo , 1997 .