Research Topics
Genomes and Genes | Stuart K KimSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
A transcriptional profile of aging in the human kidneyGraham 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...
Polarized signaling: basolateral receptor localization in epithelial cells by PDZ-containing proteinsS 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...- Common aging pathways in worms, flies, mice and humansStuart 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... - Cell biology. Proteins that promote long lifeStuart K Kim
Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305-5329, USA
Science 317:603-4. 2007 - A gene expression map for Caenorhabditis elegansS K Kim
Department of Developmental Biology and Genetics, Stanford University Medical School, Stanford, CA 94305, USA
Science 293:2087-92. 2001.... - Http://C. elegans: mining the functional genomic landscapeS 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... - Functional genomics: the worm scores a knockoutS K Kim
Department of Developmental Biology, Stanford University, California, Stanford 94305, USA
Curr Biol 11:R85-7. 2001.... - A gene-coexpression network for global discovery of conserved genetic modulesJoshua 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... - Transcriptional profile of aging in C. elegansJames Lund
Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
Curr Biol 12:1566-73. 2002..CONCLUSIONS: We have performed a whole-genome analysis of changes in gene expression during aging in C. elegans that provides a molecular description of C. elegans senescence... 
An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegansYelena 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...- Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegansFlorencia 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... - AGEMAP: a gene expression database for aging in miceJacob 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... 
Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney agingHeather 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...- Systems biology of aging in four speciesJacob 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... - Transcriptional profiling of aging in human muscle reveals a common aging signatureJacob M Zahn
Department of Developmental Biology, Stanford University Medical Center, Stanford, California, USA
PLoS Genet 2:e115. 2006.... - Aging mice show a decreasing correlation of gene expression within genetic modulesLucinda 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... - Variable pathogenicity determines individual lifespan in Caenorhabditis elegansAdolfo Sánchez-Blanco
Department of Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
PLoS Genet 7:e1002047. 2011.... - Seeing elegance in gene regulatory networks of the wormEric 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... - Global analysis of dauer gene expression in Caenorhabditis elegansJohn 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... - Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegansPeter 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... - TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental programJinkuk 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... - An engineering approach to extending lifespan in C. elegansDror 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... - Properties of balanced permutationsLucinda 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... - The modular era of functional genomicsEran 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... - The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkitXiao 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... - Analysis of cell fate from single-cell gene expression profiles in C. elegansXiao 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... - Downstream targets of let-60 Ras in Caenorhabditis elegansBéatrice 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... - The GATA Transcription Factor egl-27 Delays Aging by Promoting Stress Resistance in Caenorhabditis elegansXiao Xu
Cancer Biology Program and Departments of Developmental Biology and Genetics, 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... - Genetics and genomics of human ageingHeather 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... - A global analysis of Caenorhabditis elegans operonsThomas 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... - Identification of genes expressed in C. elegans touch receptor neuronsYun 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... - Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegansTammie Bishop
The Henry Wellcome Building of Genomic Medicine, University of Oxford, Oxford, United Kingdom
PLoS Biol 2:e289. 2004.... - A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life spanMohan 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... - Delayed development and lifespan extension as features of metabolic lifestyle alteration in C. elegans under dietary restrictionNathaniel 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... - The transcriptional consequences of mutation and natural selection in Caenorhabditis elegansDee R Denver
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
Nat Genet 37:544-8. 2005..elegans expressed sequences... - X-chromosome silencing in the germline of C. elegansWilliam 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... - Transcriptional instability is not a universal attribute of agingLuigi 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... - Straightening Caenorhabditis elegans imagesHanchuan Peng
Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
Bioinformatics 24:234-42. 2008..We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images... - Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germlineAlbertha 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... - Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegansFabio 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... - Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegansChuan 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... - Coordinate activation of maternal protein degradation during the egg-to-embryo transition in C. elegansJason 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...
Research Grants
- Functional Genomics:Complex Biological SystemsStuart 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. ..
- Mechanisms of Aging in C elegansStuart Kim; Fiscal Year: 2007....