Stuart K Kim

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. ncbi request reprint Polarized signaling: basolateral receptor localization in epithelial cells by PDZ-containing proteins
    S K Kim
    Department of Developmental Biology, Stanford University Medical Center, CA 94305 5427, USA
    Curr Opin Cell Biol 9:853-9. 1997
  2. ncbi request reprint Cell biology. Proteins that promote long life
    Stuart K Kim
    Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305 5329, USA
    Science 317:603-4. 2007
  3. ncbi request reprint Common aging pathways in worms, flies, mice and humans
    Stuart K Kim
    Department of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305 5329, USA
    J Exp Biol 210:1607-12. 2007
  4. ncbi request reprint A gene expression map for Caenorhabditis elegans
    S K Kim
    Department of Developmental Biology and Genetics, Stanford University Medical School, Stanford, CA 94305, USA
    Science 293:2087-92. 2001
  5. ncbi request reprint Http://C. elegans: mining the functional genomic landscape
    S K Kim
    Department of Developmental Biology, Stanford University Medical School, Stanford, California 94305, USA
    Nat Rev Genet 2:681-9. 2001
  6. ncbi request reprint Functional genomics: the worm scores a knockout
    S K Kim
    Department of Developmental Biology, Stanford University, California, Stanford 94305, USA
    Curr Biol 11:R85-7. 2001
  7. ncbi request reprint A gene-coexpression network for global discovery of conserved genetic modules
    Joshua M Stuart
    Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
    Science 302:249-55. 2003
  8. pmc Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans
    Eric L Van Nostrand
    Department of Genetics, Stanford University Medical Center, Stanford, California, USA
    PLoS Genet 9:e1003325. 2013
  9. ncbi request reprint Transcriptional profile of aging in C. elegans
    James Lund
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Curr Biol 12:1566-73. 2002
  10. doi request reprint An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans
    Yelena V Budovskaya
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Cell 134:291-303. 2008

Research Grants

  1. Functional Genomics:Complex Biological Systems
    Stuart Kim; Fiscal Year: 2003
  2. Mechanisms of Aging in C elegans
    Stuart Kim; Fiscal Year: 2007

Collaborators

Detail Information

Publications44

  1. ncbi request reprint Polarized signaling: basolateral receptor localization in epithelial cells by PDZ-containing proteins
    S K Kim
    Department of Developmental Biology, Stanford University Medical Center, CA 94305 5427, USA
    Curr Opin Cell Biol 9:853-9. 1997
    ..Exciting recent reports suggest that receptor localization to neuronal synapses and the basolateral membrane domains of epithelia may involve a common molecular mechanism involving localization by PDZ-containing proteins...
  2. ncbi request reprint Cell biology. Proteins that promote long life
    Stuart K Kim
    Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305 5329, USA
    Science 317:603-4. 2007
  3. ncbi request reprint Common aging pathways in worms, flies, mice and humans
    Stuart K Kim
    Department of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305 5329, USA
    J Exp Biol 210:1607-12. 2007
    ..Evolutionary theories of aging provide a basis to understand how age regulation of a genetic pathway might be preserved between distantly related species...
  4. ncbi request reprint A gene expression map for Caenorhabditis elegans
    S K Kim
    Department of Developmental Biology and Genetics, Stanford University Medical School, Stanford, CA 94305, USA
    Science 293:2087-92. 2001
    ....
  5. ncbi request reprint Http://C. elegans: mining the functional genomic landscape
    S K Kim
    Department of Developmental Biology, Stanford University Medical School, Stanford, California 94305, USA
    Nat Rev Genet 2:681-9. 2001
    ..These high-capacity approaches to studying gene function will provide new insights into invertebrate and vertebrate biology...
  6. ncbi request reprint Functional genomics: the worm scores a knockout
    S K Kim
    Department of Developmental Biology, Stanford University, California, Stanford 94305, USA
    Curr Biol 11:R85-7. 2001
    ....
  7. ncbi request reprint A gene-coexpression network for global discovery of conserved genetic modules
    Joshua M Stuart
    Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
    Science 302:249-55. 2003
    ..By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules...
  8. pmc Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans
    Eric L Van Nostrand
    Department of Genetics, Stanford University Medical Center, Stanford, California, USA
    PLoS Genet 9:e1003325. 2013
    ..These results illustrate how unc-62 regulation of intestinal gene expression is responsible for limiting lifespan during the normal aging process...
  9. ncbi request reprint Transcriptional profile of aging in C. elegans
    James Lund
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Curr Biol 12:1566-73. 2002
    ..Several distinct mechanisms including an altered rate of aging, increased resistance to stress, decreased metabolic rate, or alterations in a program causing organismic aging and death have been proposed to underlie these mutants...
  10. doi request reprint An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans
    Yelena V Budovskaya
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Cell 134:291-303. 2008
    ..These results identify a transcriptional circuit that guides the rapid aging process in C. elegans and indicate that this circuit is driven by drift of developmental pathways rather than accumulation of damage...
  11. ncbi request reprint Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans
    Florencia Pauli
    Department of Genetics, Stanford University, Stanford, CA 94305, USA
    Development 133:287-95. 2006
    ..We experimentally verified these results by showing that the GATA motif is required in cis and that GATA transcription factors are required in trans for expression of these intestinal genes...
  12. pmc The GATA transcription factor egl-27 delays aging by promoting stress resistance in Caenorhabditis elegans
    Xiao Xu
    Cancer Biology Program and Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 8:e1003108. 2012
    ..These results identify egl-27 as a novel factor that links stress and aging pathways...
  13. pmc A transcriptional profile of aging in the human kidney
    Graham E J Rodwell
    Division of Nephrology, Stanford University Medical Center Stanford, California, USA
    PLoS Biol 2:e427. 2004
    ..Finally, the set of aging-regulated kidney genes suggests specific mechanisms and pathways that may play a role in kidney degeneration with age...
  14. pmc AGEMAP: a gene expression database for aging in mice
    Jacob M Zahn
    Department of Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
    PLoS Genet 3:e201. 2007
    ..However, we saw no overall correlation of age regulation between mice and humans, suggesting that aging processes in mice and humans may be fundamentally different...
  15. pmc Transcriptional profiling of aging in human muscle reveals a common aging signature
    Jacob M Zahn
    Department of Developmental Biology, Stanford University Medical Center, Stanford, California, USA
    PLoS Genet 2:e115. 2006
    ....
  16. pmc Systems biology of aging in four species
    Jacob M Zahn
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Curr Opin Biotechnol 18:355-9. 2007
    ..Finally, genes in the mitochondrial electron transport chain group decrease expression with age in the human, mouse, fly, and worm...
  17. pmc Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging
    Heather E Wheeler
    Department of Genetics, Stanford University Medical Center, Stanford, California, USA
    PLoS Genet 5:e1000685. 2009
    ..6 x 10(-5), empirical p = 0.01) that explains 1%-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans...
  18. pmc Aging mice show a decreasing correlation of gene expression within genetic modules
    Lucinda K Southworth
    Biomedical Informatics, Stanford University, Stanford, California, United States of America
    PLoS Genet 5:e1000776. 2009
    ..Our results conclude that there is a modular decline in co-expression with age in mice. They also indicate that factors relating to both chromosome domains and specific transcription factors may contribute to the decline...
  19. pmc Variable pathogenicity determines individual lifespan in Caenorhabditis elegans
    Adolfo Sánchez-Blanco
    Department of Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
    PLoS Genet 7:e1002047. 2011
    ....
  20. pmc Seeing elegance in gene regulatory networks of the worm
    Eric L Van Nostrand
    Department of Genetics, Stanford University Medical Center, Stanford, CA, USA
    Curr Opin Genet Dev 21:776-86. 2011
    ..Integration of these datasets has yielded novel insights into evolution, gene expression regulation, and the link between sequence and phenotype...
  21. ncbi request reprint Global analysis of dauer gene expression in Caenorhabditis elegans
    John Wang
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
    Development 130:1621-34. 2003
    ..Homologs of C. elegans dauer-enriched genes may be involved in the disease process in parasitic nematodes...
  22. pmc TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental program
    Jinkuk Choi
    Department of Medicine, Stanford School of Medicine, Stanford, California, United States of America
    PLoS Genet 4:e10. 2008
    ..These data show that TERT controls tissue progenitor cells via transcriptional regulation of a developmental program converging on the Myc and Wnt pathways...
  23. ncbi request reprint Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans
    Peter J Roy
    Department of Developmental Biology, Stanford University Medical Center, California 94305, USA
    Nature 418:975-9. 2002
    ..These observations reveal a higher-order organization of the structure of the genome, in which the order of the genes along the chromosome id correlated with their expression in specific tissues...
  24. pmc An engineering approach to extending lifespan in C. elegans
    Dror Sagi
    Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
    PLoS Genet 8:e1002780. 2012
    ..Using engineering to add novel functions and to tune endogenous functions provides a new framework for lifespan extension that goes beyond the constraints of the worm genome...
  25. pmc Properties of balanced permutations
    Lucinda K Southworth
    Biomedical Informatics, Stanford University, Stanford, California 94305, USA
    J Comput Biol 16:625-38. 2009
    ..In particular the observed test statistic can be larger than that of all B balanced permutations of a data set with a probability much higher than 1/(B + 1), even under the null hypothesis...
  26. ncbi request reprint Downstream targets of let-60 Ras in Caenorhabditis elegans
    Béatrice Romagnolo
    Department of Developmental Biology and Genetics, Stanford University Medical School, California 94305, USA
    Dev Biol 247:127-36. 2002
    ..We have used DNA microarrays to identify 708 genes that change expression in response to activated let-60 Ras...
  27. doi request reprint The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit
    Xiao Xu
    Cancer Biology Program and Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Rev Genet 12:793-801. 2011
    ..These developments both enhance the worm as a model for studying processes such as development and ageing and make it an attractive model in areas such as neurobiology and behaviour...
  28. doi request reprint Analysis of cell fate from single-cell gene expression profiles in C. elegans
    Xiao Liu
    Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
    Cell 139:623-33. 2009
    ..These results demonstrate insights that become possible using computational approaches to analyze quantitative expression from many genes in parallel using a digital gene expression atlas...
  29. pmc The modular era of functional genomics
    Eran Segal
    Computer Science Department, Stanford University, Stanford, CA 94305, USA
    Genome Biol 4:317. 2003
    ..A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003...
  30. pmc Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
    Eric L Van Nostrand
    Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 23:941-53. 2013
    ..We experimentally showed that two of the new candidate aging regulators can extend lifespan when overexpressed, indicating that this approach can identify novel functional regulators of complex processes...
  31. pmc Genetics and genomics of human ageing
    Heather E Wheeler
    Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
    Philos Trans R Soc Lond B Biol Sci 366:43-50. 2011
    ..New human genetics technologies are continually in development and may lead to additional breakthroughs in human ageing in the near future...
  32. ncbi request reprint A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life span
    Mohan Viswanathan
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Dev Cell 9:605-15. 2005
    ..1-mediated repression of ER stress genes. Our findings demonstrate that abu-11 and other members of its ER stress gene family are positive determinants of C. elegans life span...
  33. ncbi request reprint A global analysis of Caenorhabditis elegans operons
    Thomas Blumenthal
    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Box B121, 4200 E 9th Avenue, Denver, Colorado 80262, USA
    Nature 417:851-4. 2002
    ..elegans genes. Numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal previously unknown functional relationships...
  34. ncbi request reprint Delayed development and lifespan extension as features of metabolic lifestyle alteration in C. elegans under dietary restriction
    Nathaniel J Szewczyk
    NASA Ames Research Center, M S 239 11, Moffett Field, CA 94035 1000, USA
    J Exp Biol 209:4129-39. 2006
    ..Our observations introduce a powerful system for automation of experimentation on healthy C. elegans and for systematic analysis of the profound impact of diet on animal physiology...
  35. ncbi request reprint Identification of genes expressed in C. elegans touch receptor neurons
    Yun Zhang
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Nature 418:331-5. 2002
    ..Using regions 5' of the start codon of the first 20 genes, we have also identified an over-represented heptanucleotide, AATGCAT, that is needed for the expression of touch receptor genes...
  36. pmc Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans
    Tammie Bishop
    The Henry Wellcome Building of Genomic Medicine, University of Oxford, Oxford, United Kingdom
    PLoS Biol 2:e289. 2004
    ....
  37. ncbi request reprint Coordinate activation of maternal protein degradation during the egg-to-embryo transition in C. elegans
    Jason Pellettieri
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Dev Cell 5:451-62. 2003
    ..We propose that MBK-2 functions as a temporal regulator of protein stability, and that coordinate activation of maternal protein degradation is one of the mechanisms that drives the transition from symmetric egg to patterned embryo...
  38. ncbi request reprint Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline
    Albertha J M Walhout
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Curr Biol 12:1952-8. 2002
    ..Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other organisms, including humans...
  39. ncbi request reprint Transcriptional instability is not a universal attribute of aging
    Luigi A Warren
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Aging Cell 6:775-82. 2007
    ..We conclude that large-scale regulatory destabilization is not a universal concomitant of aging, and may be of significance as an aging mechanism primarily in nonrenewing tissues...
  40. ncbi request reprint Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegans
    Chuan Shen
    Department of Genetics, Development, and Cell Biology, Iowa State University, Ames 50011, USA
    J Biol Chem 280:20580-8. 2005
    ..The microarray data presented herein also provide clear evidence for an HIF-1-independent pathway for hypoxia response, and this pathway regulates the expression of multiple heat shock proteins and several transcription factors...
  41. ncbi request reprint The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
    Dee R Denver
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nat Genet 37:544-8. 2005
    ..elegans expressed sequences...
  42. ncbi request reprint Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans
    Fabio Piano
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Curr Biol 12:1959-64. 2002
    ..We find that phenoclusters correlate well with sequence-based functional predictions and thus may be useful in predicting functions of uncharacterized genes...
  43. ncbi request reprint X-chromosome silencing in the germline of C. elegans
    William G Kelly
    Biology Department, Emory University, Atlanta, GA 30322, USA
    Development 129:479-92. 2002
    ..Silencing of the sex chromosome during early meiosis is a conserved feature throughout the nematode phylum, and is not limited to hermaphroditic species...
  44. pmc Straightening Caenorhabditis elegans images
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 24:234-42. 2008
    ..For example, worm bodies usually curve significantly in images. Thus one must 'straighten' the worms if they are to be compared under a canonical coordinate system...

Research Grants2

  1. Functional Genomics:Complex Biological Systems
    Stuart Kim; Fiscal Year: 2003
    ..The goal of the meeting is to integrate advances in human disease, modeling of genetic networks, quantitative trait mapping, and data mining techniques. ..
  2. Mechanisms of Aging in C elegans
    Stuart Kim; Fiscal Year: 2007
    ....