Susan M Sunkin

Summary

Affiliation: Allen Institute for Brain Science
Country: USA

Publications

  1. ncbi request reprint Towards the integration of spatially and temporally resolved murine gene expression databases
    Susan M Sunkin
    Allen Institute for Brain Science, 551 N 34th St, Seattle, WA 98103, USA
    Trends Genet 22:211-7. 2006
  2. pmc Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain
    Stefan E Seemann
    Center for non coding RNA in Technology and Health, University of Copenhagen, Denmark
    BMC Genomics 13:214. 2012
  3. pmc Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
    Susan M Sunkin
    Allen Institute for Brain Science, 551 North 34th Street, Seattle, WA 98103, USA
    Nucleic Acids Res 41:D996-D1008. 2013
  4. ncbi request reprint Insights from spatially mapped gene expression in the mouse brain
    Susan M Sunkin
    Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA
    Hum Mol Genet 16:R209-19. 2007
  5. doi request reprint Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex
    Lydia Ng
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Methods 50:55-62. 2010
  6. pmc An anatomically comprehensive atlas of the adult human brain transcriptome
    Michael J Hawrylycz
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nature 489:391-9. 2012
  7. doi request reprint Areal and laminar differentiation in the mouse neocortex using large scale gene expression data
    Mike Hawrylycz
    Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA
    Methods 50:113-21. 2010
  8. pmc Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
    Chang Kyu Lee
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Genome Biol 9:R23. 2008
  9. pmc Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates
    Jeremy A Miller
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Development 140:4633-44. 2013
  10. pmc Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures
    Hongkui Zeng
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Cell 149:483-96. 2012

Detail Information

Publications29

  1. ncbi request reprint Towards the integration of spatially and temporally resolved murine gene expression databases
    Susan M Sunkin
    Allen Institute for Brain Science, 551 N 34th St, Seattle, WA 98103, USA
    Trends Genet 22:211-7. 2006
    ..Here, the various projects for collecting and mining this information are reviewed, some challenges in data set comparisons are discussed, and some basic proposals are made for overcoming the challenges...
  2. pmc Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain
    Stefan E Seemann
    Center for non coding RNA in Technology and Health, University of Copenhagen, Denmark
    BMC Genomics 13:214. 2012
    ..However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts...
  3. pmc Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
    Susan M Sunkin
    Allen Institute for Brain Science, 551 North 34th Street, Seattle, WA 98103, USA
    Nucleic Acids Res 41:D996-D1008. 2013
    ..In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal...
  4. ncbi request reprint Insights from spatially mapped gene expression in the mouse brain
    Susan M Sunkin
    Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA
    Hum Mol Genet 16:R209-19. 2007
    ....
  5. doi request reprint Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex
    Lydia Ng
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Methods 50:55-62. 2010
    ....
  6. pmc An anatomically comprehensive atlas of the adult human brain transcriptome
    Michael J Hawrylycz
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nature 489:391-9. 2012
    ..This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function...
  7. doi request reprint Areal and laminar differentiation in the mouse neocortex using large scale gene expression data
    Mike Hawrylycz
    Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA
    Methods 50:113-21. 2010
    ..Surface-based mapping and visualization techniques are used as a representation to clarify these relationships...
  8. pmc Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
    Chang Kyu Lee
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Genome Biol 9:R23. 2008
    ....
  9. pmc Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates
    Jeremy A Miller
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Development 140:4633-44. 2013
    ....
  10. pmc Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures
    Hongkui Zeng
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Cell 149:483-96. 2012
    ....
  11. doi request reprint A comprehensive transcriptional map of primate brain development
    Trygve E Bakken
    Allen Institute for Brain Science, Seattle, Washington 98109, USA
    Nature 535:367-75. 2016
    ..Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey. ..
  12. doi request reprint Neuroinformatics of the Allen Mouse Brain Connectivity Atlas
    Leonard Kuan
    The Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA Electronic address
    Methods 73:4-17. 2015
    ..Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases. ..
  13. doi request reprint Exploration and visualization of connectivity in the adult mouse brain
    David Feng
    Allen Institute for Brain Science, Seattle, WA 98103, United States Electronic address
    Methods 73:90-7. 2015
    ..These tools offer convenient access to detailed axonal projection information in the adult mouse brain and the ability to perform data analysis and visualization of projection fields and neuroanatomy in an integrated manner. ..
  14. doi request reprint An anatomic gene expression atlas of the adult mouse brain
    Lydia Ng
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nat Neurosci 12:356-62. 2009
    ..The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea)...
  15. doi request reprint Large-scale neuroinformatics for in situ hybridization data in the mouse brain
    Lydia L Ng
    Allen Institute for Brain Science, Seattle, Washington, USA
    Int Rev Neurobiol 104:159-82. 2012
    ..Scalable techniques for processing and presenting these data for maximum utility in viewing and analysis are key for end user value. We describe methods and use cases for the Allen Brain Atlas resources of the adult and developing mouse...
  16. pmc Spatiotemporal dynamics of the postnatal developing primate brain transcriptome
    Trygve E Bakken
    Allen Institute for Brain Science, Seattle, WA, USA
    Hum Mol Genet 24:4327-39. 2015
    ..This network was enriched for genes associated with axon guidance and interneuron differentiation, consistent with a disruption in the formation of functional cortical circuitry in ASD. ..
  17. doi request reprint Organization of the connections between claustrum and cortex in the mouse
    Quanxin Wang
    Allen Institute for Brain Science, Seattle, Washington, 98109
    J Comp Neurol . 2016
    ..J. Comp. Neurol., 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc...
  18. pmc Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
    Bosiljka Tasic
    Allen Institute for Brain Science, Seattle, Washington, USA
    Nat Neurosci 19:335-46. 2016
    ....
  19. pmc Transcriptional architecture of the primate neocortex
    Amy Bernard
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Neuron 73:1083-99. 2012
    ..These data provide a unique resource detailing neocortical transcription patterns in a nonhuman primate with great similarity in gene expression to human...
  20. pmc Comprehensive cellular-resolution atlas of the adult human brain
    Song Lin Ding
    Allen Institute for Brain Science, Seattle, Washington, 98109
    J Comp Neurol 524:3127-481. 2016
    ..J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. ..
  21. pmc A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain
    Carol L Thompson
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Neuron 83:309-23. 2014
    ..The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org)...
  22. ncbi request reprint Genome-wide atlas of gene expression in the adult mouse brain
    Ed S Lein
    Allen Institute for Brain Science, Seattle, Washington 98103, USA
    Nature 445:168-76. 2007
    ..This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function...
  23. pmc A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
    Linda Madisen
    Allen Institute for Brain Science, Seattle, Washington, USA
    Nat Neurosci 13:133-40. 2010
    ..Our expression data are displayed in a public online database to help researchers assess the utility of various Cre-driver lines for cell-type-specific genetic manipulation...
  24. doi request reprint The Allen Brain Atlas: 5 years and beyond
    Allan R Jones
    Allen Institute for Brain Science, 551 North 34th Street, Seattle, Washington 98103, USA
    Nat Rev Neurosci 10:821-8. 2009
    ..Having overcome these challenges, it is now a fundamental tool for neuroscientists worldwide and has set the stage for the creation of other similar open resources. Nevertheless, there are many untapped opportunities for exploration...
  25. pmc Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance
    Linda Madisen
    Allen Institute for Brain Science, 551 N 34 th Street, Seattle, WA 98103, USA
    Neuron 85:942-58. 2015
    ..High functionality was shown in example mouse lines for GCaMP6, YCX2.60, VSFP Butterfly 1.2, and Jaws. These novel transgenic lines greatly expand the ability to monitor and manipulate neuronal activities with increased specificity...
  26. pmc CTCF regulates ataxin-7 expression through promotion of a convergently transcribed, antisense noncoding RNA
    Bryce L Sopher
    Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
    Neuron 70:1071-84. 2011
    ..Discovery of this pathway underscores the importance of altered epigenetic regulation for disease pathology at repeat loci exhibiting bidirectional transcription...
  27. doi request reprint Genomic anatomy of the hippocampus
    Carol L Thompson
    Allen Institute for Brain Science, Seattle, WA 98103, USA
    Neuron 60:1010-21. 2008
    ..This complex, discrete molecular architecture provides a novel paradigm for predicting functional differentiation across the full septotemporal extent of the hippocampus...
  28. pmc Specific expression of long noncoding RNAs in the mouse brain
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Proc Natl Acad Sci U S A 105:716-21. 2008
    ..Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs...
  29. pmc Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Genome Res 18:1433-45. 2008
    ..Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery...