Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

[1]  David Haussler,et al.  High-resolution comparative analysis of great ape genomes , 2018, Science.

[2]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[3]  Y. Gilad,et al.  A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues , 2018, Scientific Reports.

[4]  G. Wagner,et al.  Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes , 2018, Genome biology and evolution.

[5]  David Haussler,et al.  The UCSC Genome Browser database: 2018 update , 2017, Nucleic Acids Res..

[6]  David Haussler,et al.  Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation , 2017, bioRxiv.

[7]  Alex A. Pollen,et al.  Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex , 2017, Science.

[8]  M. Gerstein,et al.  Molecular and cellular reorganization of neural circuits in the human lineage , 2017, Science.

[9]  Spyros Darmanis,et al.  Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells , 2017, Neuron.

[10]  John D. Blischak,et al.  A comparative study of endoderm differentiation in humans and chimpanzees , 2017, Genome Biology.

[11]  Daniel R. Berger,et al.  Cell diversity and network dynamics in photosensitive human brain organoids , 2017, Nature.

[12]  Alex A. Pollen,et al.  Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. , 2017, Cell stem cell.

[13]  Bradley P. Coe,et al.  Targeted sequencing identifies 91 neurodevelopmental disorder risk genes with autism and developmental disability biases , 2017, Nature Genetics.

[14]  C. Baker,et al.  The evolution and population diversity of human-specific segmental duplications , 2017, Nature Ecology &Evolution.

[15]  Di Yu,et al.  Brain Development and Akt Signaling: the Crossroads of Signaling Pathway and Neurodevelopmental Diseases , 2016, Journal of Molecular Neuroscience.

[16]  S. Pääbo,et al.  A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification , 2016, Science Advances.

[17]  W. Enard.  The Molecular Basis of Human Brain Evolution , 2016, Current Biology.

[18]  Wieland B Huttner,et al.  Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development , 2016, eLife.

[19]  Maria Teresa Dell'Anno,et al.  Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. , 2016, Cell reports.

[20]  Evan Z. Macosko,et al.  Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics , 2016, Cell.

[21]  Allan R. Jones,et al.  Comprehensive transcriptional map of primate brain development , 2016, Nature.

[22]  Hans Clevers,et al.  Modeling Development and Disease with Organoids , 2016, Cell.

[23]  F. Gage,et al.  2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size , 2016, Cell stem cell.

[24]  Eric E. Schadt,et al.  variancePartition: interpreting drivers of variation in complex gene expression studies , 2016, BMC Bioinformatics.

[25]  D. Silver.  Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex , 2016, BioEssays : news and reviews in molecular, cellular and developmental biology.

[26]  Steven J. M. Jones,et al.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma , 2016, Cell.

[27]  Madeline A. Lancaster,et al.  Human cerebral organoids recapitulate gene expression programs of fetal neocortex development , 2015, Proceedings of the National Academy of Sciences.

[28]  Alex A. Pollen,et al.  Molecular Identity of Human Outer Radial Glia during Cortical Development , 2015, Cell.

[29]  F. Gage,et al.  Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest , 2015, Cell.

[30]  R. Gordân,et al.  Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex , 2015, Current Biology.

[31]  Yoav Gilad,et al.  A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics , 2014, bioRxiv.

[32]  Alex A. Pollen,et al.  Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex , 2014, Nature Biotechnology.

[33]  Jing Zhao,et al.  An activator of mTOR inhibits oxLDL-induced autophagy and apoptosis in vascular endothelial cells and restricts atherosclerosis in apolipoprotein E-/- mice , 2014, Scientific Reports.

[34]  H. Nawa,et al.  mTOR signaling and its roles in normal and abnormal brain development , 2014, Front. Mol. Neurosci..

[35]  B. Conklin,et al.  Induced pluripotent stem cells from patients with human fibrodysplasia ossificans progressiva show increased mineralization and cartilage formation , 2013, Orphanet Journal of Rare Diseases.

[36]  M. Eiraku,et al.  Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell–derived neocortex , 2013, Proceedings of the National Academy of Sciences.

[37]  Wei Niu,et al.  Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism , 2013, Cell.

[38]  S. Horvath,et al.  Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism , 2013, Cell.

[39]  Gene W. Yeo,et al.  Differential LINE-1 regulation in pluripotent stem cells of humans and other great apes , 2013, Nature.

[40]  Carl Baker,et al.  Evolution and diversity of copy number variation in the great ape lineage , 2013, Genome research.

[41]  Madeline A. Lancaster,et al.  Cerebral organoids model human brain development and microcephaly , 2013, Nature.

[42]  Jason S. Park,et al.  A robust method to derive functional neural crest cells from human pluripotent stem cells. , 2013, American journal of stem cells.

[43]  Avi Ma'ayan,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[44]  N. Ogihara,et al.  Fetal brain development in chimpanzees versus humans , 2012, Current Biology.

[45]  Martin Kircher,et al.  Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal , 2012, Proceedings of the National Academy of Sciences.

[46]  S. Herculano‐Houzel.  The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost , 2012, Proceedings of the National Academy of Sciences.

[47]  Anirvan Ghosh,et al.  Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation , 2012, Cell.

[48]  Peter H. Sudmant,et al.  Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication , 2012, Cell.

[49]  Maria K. Lehtinen,et al.  Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations , 2012, Neuron.

[50]  S. Pääbo,et al.  Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. , 2012, Genome research.

[51]  David Haussler,et al.  Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.

[52]  Yasuko Matsumura,et al.  A more efficient method to generate integration-free human iPS cells , 2011, Nature Methods.

[53]  T. Adachi,et al.  Self-organizing optic-cup morphogenesis in three-dimensional culture , 2011, Nature.

[54]  A. Brunet,et al.  Energy metabolism in adult neural stem cell fate , 2011, Progress in Neurobiology.

[55]  Cory Y. McLean,et al.  Human-specific loss of regulatory DNA and the evolution of human-specific traits , 2011, Nature.

[56]  Peter H. Sudmant,et al.  Diversity of Human Copy Number Variation and Multicopy Genes , 2010, Science.

[57]  Katja Nowick,et al.  Lineage-specific transcription factors and the evolution of gene regulatory networks. , 2010, Briefings in functional genomics.

[58]  Lu Wang,et al.  mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells , 2009, Proceedings of the National Academy of Sciences.

[59]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[60]  Yoshiki Sasai,et al.  Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. , 2008, Cell stem cell.

[61]  S. Horvath,et al.  Functional organization of the transcriptome in human brain , 2008, Nature Neuroscience.

[62]  H. Kennedy,et al.  Making bigger brains–the evolution of neural-progenitor-cell division , 2008, Journal of Cell Science.

[63]  Jean-Loup Guillaume,et al.  Fast unfolding of communities in large networks , 2008, 0803.0476.

[64]  S. Pääbo,et al.  Accelerated Evolution of Conserved Noncoding Sequences in Humans , 2006, Science.

[65]  A. Kriegstein,et al.  Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion , 2006, Nature Reviews Neuroscience.

[66]  D. Haussler,et al.  An RNA gene expressed during cortical development evolved rapidly in humans , 2006, Nature.

[67]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[68]  P. Rakic.  Developmental and evolutionary adaptations of cortical radial glia. , 2003, Cerebral cortex.

[69]  Henry Kennedy,et al.  Unique morphological features of the proliferative zones and postmitotic compartments of the neural epithelium giving rise to striate and extrastriate cortex in the monkey. , 2002, Cerebral cortex.

[70]  Evan E. Eichler,et al.  Positive selection of a gene family during the emergence of humans and African apes , 2001, Nature.

[71]  H. Okano,et al.  Asymmetric Inheritance of Radial Glial Fibers by Cortical Neurons , 2001, Neuron.

[72]  T. Weissman,et al.  Neurons derived from radial glial cells establish radial units in neocortex , 2001, Nature.

[73]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[74]  P. Rakic.  A small step for the cell, a giant leap for mankind: a hypothesis of neocortical expansion during evolution , 1995, Trends in Neurosciences.

[75]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.