A single-embryo, single-cell time-resolved model for mouse gastrulation

[1]  S. Orkin,et al.  An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells , 2020, Cell.

[2]  Zachary D. Smith,et al.  Epigenetic regulator function through mouse gastrulation , 2020, Nature.

[3]  P. Tam,et al.  Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes , 2020, Development.

[4]  G. Sanguinetti,et al.  Multi-omics profiling of mouse gastrulation at single cell resolution , 2019, Nature.

[5]  A. Tanay,et al.  MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions , 2019, Genome Biology.

[6]  J. Han,et al.  Molecular architecture of lineage allocation and tissue organization in early mouse embryo , 2019, Nature.

[7]  A. del Sol,et al.  Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects , 2019, Nature.

[8]  Fabian J. Theis,et al.  Concepts and limitations for learning developmental trajectories from single cell genomics , 2019, Development.

[9]  Amos Tanay,et al.  MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing , 2019, Nature Protocols.

[10]  Deanna M. Church,et al.  The emergent landscape of the mouse gut endoderm at single-cell resolution , 2019, Nature.

[11]  Fabian J Theis,et al.  Inferring population dynamics from single-cell RNA-sequencing time series data , 2019, Nature Biotechnology.

[12]  B. Reinius,et al.  Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. , 2019, Cell reports.

[13]  J. Marioni,et al.  A single-cell molecular map of mouse gastrulation and early organogenesis , 2019, Nature.

[14]  P. Rigollet,et al.  Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming , 2019, Cell.

[15]  Andrew J. Hill,et al.  The single cell transcriptional landscape of mammalian organogenesis , 2019, Nature.

[16]  R. Lovell-Badge,et al.  Nervous System Regionalization Entails Axial Allocation before Neural Differentiation , 2018, Cell.

[17]  George M. Church,et al.  Developmental barcoding of whole mouse via homing CRISPR , 2018, Science.

[18]  Thomas M. Norman,et al.  Molecular recording of mammalian embryogenesis , 2018, bioRxiv.

[19]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[20]  Zhisong He,et al.  Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells , 2018, Stem cell reports.

[21]  James Briscoe,et al.  What does time mean in development? , 2018, Development.

[22]  J. Junker,et al.  Simultaneous lineage tracing and cell-type identification using CRISPR/Cas9-induced genetic scars , 2018, Nature Biotechnology.

[23]  B. Göttgens,et al.  Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq , 2018, Science.

[24]  S. Orkin,et al.  Mapping the Mouse Cell Atlas by Microwell-Seq , 2018, Cell.

[25]  David J. Jörg,et al.  Defining murine organogenesis at single cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation , 2018, Nature Cell Biology.

[26]  James A. Gagnon,et al.  Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT , 2017, bioRxiv.

[27]  J. Marioni,et al.  Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation , 2017, Cell reports.

[28]  A. Regev,et al.  Scaling single-cell genomics from phenomenology to mechanism , 2017, Nature.

[29]  Nicola K. Wilson,et al.  Resolving Early Mesoderm Diversification through Single Cell Expression Profiling , 2016, Nature.

[30]  T. Kume,et al.  Foxc1 and Foxc2 deletion causes abnormal lymphangiogenesis and correlates with ERK hyperactivation. , 2016, The Journal of clinical investigation.

[31]  A. Hadjantonakis,et al.  Notochord morphogenesis in mice: Current understanding & open questions , 2016, Developmental Dynamics.

[32]  A. Hadjantonakis,et al.  Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development , 2015, Genes & development.

[33]  J. L. Mateo,et al.  CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool , 2015, PloS one.

[34]  M. Zernicka-Goetz,et al.  Developmental plasticity, cell fate specification and morphogenesis in the early mouse embryo , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[35]  I. Amit,et al.  Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types , 2014, Science.

[36]  Erdahl T. Teber,et al.  The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. , 2014, Cell stem cell.

[37]  Wei Tang,et al.  Correction of a genetic disease in mouse via use of CRISPR-Cas9. , 2013, Cell stem cell.

[38]  Julie Moss,et al.  EMAGE mouse embryo spatial gene expression database: 2014 update , 2013, Nucleic Acids Res..

[39]  J. Rossant,et al.  Location of transient ectodermal progenitor potential in mouse development , 2013, Development.

[40]  P. Tam,et al.  Initiating head development in mouse embryos: integrating signalling and transcriptional activity , 2012, Open Biology.

[41]  A. Camus,et al.  Clonal and molecular analysis of the prospective anterior neural boundary in the mouse embryo , 2012, Development.

[42]  P. Rathjen,et al.  Response to BMP4 signalling during ES cell differentiation defines intermediates of the ectoderm lineage , 2010, Journal of Cell Science.

[43]  Janet Rossant,et al.  Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse , 2009, Development.

[44]  Elizabeth J. Robertson,et al.  Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo , 2009, Nature Reviews Molecular Cell Biology.

[45]  A. Hadjantonakis,et al.  The endoderm of the mouse embryo arises by dynamic widespread intercalation of embryonic and extraembryonic lineages. , 2008, Developmental cell.

[46]  A. Regev,et al.  An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors , 2008, Nature Genetics.

[47]  C. Viebahn,et al.  The mouse homeobox gene Noto regulates node morphogenesis, notochordal ciliogenesis, and left–right patterning , 2007, Proceedings of the National Academy of Sciences.

[48]  M. Trotter,et al.  Derivation of pluripotent epiblast stem cells from mammalian embryos , 2007, Nature.

[49]  R. McKay,et al.  New cell lines from mouse epiblast share defining features with human embryonic stem cells , 2007, Nature.

[50]  F. Spagnoli,et al.  Guiding embryonic stem cells towards differentiation: lessons from molecular embryology. , 2006, Current opinion in genetics & development.

[51]  N. Hirokawa,et al.  Nodal Flow and the Generation of Left-Right Asymmetry , 2006, Cell.

[52]  Jacqueline Deschamps,et al.  Head-tail patterning of the vertebrate embryo: one, two or many unresolved problems? , 2006, The International journal of developmental biology.

[53]  V. Kouskoff,et al.  Haemangioblast commitment is initiated in the primitive streak of the mouse embryo , 2004, Nature.

[54]  R. Behringer,et al.  Nodal antagonists in the anterior visceral endoderm prevent the formation of multiple primitive streaks. , 2002, Developmental cell.

[55]  K. Rajewsky,et al.  Ability of the hydrophobic FGF and basic TAT peptides to promote cellular uptake of recombinant Cre recombinase: A tool for efficient genetic engineering of mammalian genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Palis,et al.  Development of erythroid and myeloid progenitors in the yolk sac and embryo proper of the mouse. , 1999, Development.

[57]  J. Chen,et al.  Mutation of the mouse hepatocyte nuclear factor/forkhead homologue 4 gene results in an absence of cilia and random left-right asymmetry. , 1998, The Journal of clinical investigation.

[58]  A. McMahon,et al.  Noggin-mediated antagonism of BMP signaling is required for growth and patterning of the neural tube and somite. , 1998, Genes & development.

[59]  R. Behringer,et al.  Mouse gastrulation: the formation of a mammalian body plan , 1997, Mechanisms of Development.

[60]  B. Hogan,et al.  The winged helix transcription factor MFH1 is required for proliferation and patterning of paraxial mesoderm in the mouse embryo. , 1997, Genes & development.

[61]  Elizabeth J. Robertson,et al.  Left-Right Asymmetry , 1997, Science.

[62]  D. Melton,et al.  Vertebrate Embryonic Cells Will Become Nerve Cells Unless Told Otherwise , 1997, Cell.

[63]  N. Brown,et al.  Cell proliferation in mammalian gastrulation: The ventral node and notochord are relatively quiescent , 1996, Developmental dynamics : an official publication of the American Association of Anatomists.

[64]  T. Davies,et al.  Staging of gastrulating mouse embryos by morphological landmarks in the dissecting microscope. , 1993, Development.

[65]  M. Snow Gastrulation in the mouse: Growth and regionalization of the epiblast , 1977 .

[66]  T. Kume The cooperative roles of Foxc1 and Foxc2 in cardiovascular development. , 2009, Advances in experimental medicine and biology.

[67]  Ravindra K. Ahuja,et al.  Network Flows: Theory, Algorithms, and Applications , 1993 .

[68]  R. Pedersen,et al.  Clonal analysis of cell fate during gastrulation and early neurulation in the mouse. , 1992, Ciba Foundation symposium.

[69]  R. Beddington,et al.  The formation of mesodermal tissues in the mouse embryo during gastrulation and early organogenesis. , 1987, Development.

[70]  Karl Theiler,et al.  The House Mouse: Atlas of Embryonic Development , 1972 .