Viktor Stolc

Summary

Affiliation: NASA Ames Research Center
Country: USA

Publications

  1. pmc Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes
    Viktor Stolc
    Genome Research Facility, National Aeronautic and Space Administration, Ames Research Center, Moffett Field, CA 94035, USA
    Proc Natl Acad Sci U S A 102:3703-7. 2005
  2. pmc Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays
    Lei Li
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Genome Biol 9:R57. 2008
  3. pmc Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
    Lei Li
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Genome Biol 6:R52. 2005
  4. pmc Adaptation of organisms by resonance of RNA transcription with the cellular redox cycle
    Viktor Stolc
    NASA Ames Research Center, Moffett Field, California, United States of America
    PLoS ONE 6:e25270. 2011
  5. doi request reprint NASA Radiation Biomarker Workshop, September 27-28, 2007
    Tore Straume
    NASA Ames Research Center, Moffett Field, California 94035, B Columbia University, New York, New York 10032, USA
    Radiat Res 170:393-405. 2008
  6. pmc Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway
    Manoj Pratim Samanta
    Genome Research Facility, National Aeronautics and Space Administration Ames Research Center, Moffet Field, CA 94035, USA
    Proc Natl Acad Sci U S A 103:4192-7. 2006
  7. ncbi request reprint Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays
    David C Nelson
    Biotechnology Center and Biochemistry Department, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
    FEBS Lett 581:3363-70. 2007
  8. ncbi request reprint In-depth query of large genomes using tiling arrays
    Manoj Pratim Samanta
    Systemix Institute, Cupertino, CA, USA
    Methods Mol Biol 377:163-74. 2007
  9. pmc High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression
    Xueyong Li
    National Institute of Biological Sciences, Beijing 102206, China
    Plant Cell 20:259-76. 2008
  10. pmc Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development
    Jungeun Lee
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520 8104, USA
    Plant Cell 19:731-49. 2007

Collaborators

  • William F Blakely
  • Sally A Amundson
  • Tore Straume
  • Fredric J Burns
  • Wallace Marshall
  • NICHOLAS J DAINIAK
  • Michael P Snyder
  • ROBERT ANDREW CAMERON
  • Deyou Zheng
  • HARMEN BUSSEMAKER
  • Waraporn Tongprasit
  • Lei Li
  • Xing Wang Deng
  • Xiangfeng Wang
  • Manoj Pratim Samanta
  • Xueyong Li
  • Manoj P Samanta
  • Ning Su
  • Songgang Li
  • Joel S Rozowsky
  • Sherman Weissman
  • Thomas E Royce
  • Paul Bertone
  • Hang He
  • Kun He
  • Olof Emanuelsson
  • David C Nelson
  • Jungeun Lee
  • Jun Wang
  • Alexander E Urban
  • Manoj Samanta
  • Mark Gerstein
  • Jiming Jiang
  • Yeqin Ma
  • William Terzaghi
  • Nevin D Young
  • Sulan Bai
  • Juan Zhang
  • Oliver Yu
  • Weiwei Jin
  • Pablo Figueroa
  • Michael R Sussman
  • Ilha Lee
  • Horim Lee
  • Zheng Lian
  • Matthew J Rodesch
  • Jiang Du
  • Hongyu Zhao
  • Ying Gao
  • Dana J Wohlbach
  • Ugrappa Nagalakshmi
  • Mark B Gerstein
  • Dongfen Zhang
  • Zhukuan Cheng
  • Qiang Tu
  • Chen Shan Chin
  • Eric H Davidson
  • Himanshu Sethi
  • Sorin Istrail
  • Zhiyu Peng
  • Xiping Wang
  • Mian Xia
  • John L Rinn
  • Xiaowei Zhu

Detail Information

Publications18

  1. pmc Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes
    Viktor Stolc
    Genome Research Facility, National Aeronautic and Space Administration, Ames Research Center, Moffett Field, CA 94035, USA
    Proc Natl Acad Sci U S A 102:3703-7. 2005
    ....
  2. pmc Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays
    Lei Li
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Genome Biol 9:R57. 2008
    ..The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery...
  3. pmc Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
    Lei Li
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Genome Biol 6:R52. 2005
    ..Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes...
  4. pmc Adaptation of organisms by resonance of RNA transcription with the cellular redox cycle
    Viktor Stolc
    NASA Ames Research Center, Moffett Field, California, United States of America
    PLoS ONE 6:e25270. 2011
    ..This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation...
  5. doi request reprint NASA Radiation Biomarker Workshop, September 27-28, 2007
    Tore Straume
    NASA Ames Research Center, Moffett Field, California 94035, B Columbia University, New York, New York 10032, USA
    Radiat Res 170:393-405. 2008
    ..A summary of conclusions is provided at the end of the report...
  6. pmc Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway
    Manoj Pratim Samanta
    Genome Research Facility, National Aeronautics and Space Administration Ames Research Center, Moffet Field, CA 94035, USA
    Proc Natl Acad Sci U S A 103:4192-7. 2006
    ..A class of ncRNAs, located antisense to coding regions of verified protein-coding genes, is discussed in this article. One member, HRA1, is likely involved in 18S rRNA maturation...
  7. ncbi request reprint Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays
    David C Nelson
    Biotechnology Center and Biochemistry Department, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
    FEBS Lett 581:3363-70. 2007
    ..While the artifact affected transcript discovery with tiling arrays, it showed only a minor impact on measurements of gene expression using commercially available 'gene-only' expression arrays...
  8. ncbi request reprint In-depth query of large genomes using tiling arrays
    Manoj Pratim Samanta
    Systemix Institute, Cupertino, CA, USA
    Methods Mol Biol 377:163-74. 2007
    ..This chapter discusses computational tools and techniques necessary to successfully conduct genome tiling array experiments...
  9. pmc High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression
    Xueyong Li
    National Institute of Biological Sciences, Beijing 102206, China
    Plant Cell 20:259-76. 2008
    ..Collectively, this study provides insights into the rice epigenomes and their effect on gene expression and plant development...
  10. pmc Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development
    Jungeun Lee
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520 8104, USA
    Plant Cell 19:731-49. 2007
    ..Our data thus support a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis...
  11. pmc Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:886-97. 2007
    ..Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments...
  12. ncbi request reprint The transcriptome of the sea urchin embryo
    Manoj P Samanta
    Systemix Institute, Los Altos, CA 94024, USA
    Science 314:960-2. 2006
    ..The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process...
  13. ncbi request reprint Genome-wide transcription analyses in rice using tiling microarrays
    Lei Li
    National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
    Nat Genet 38:124-9. 2006
    ..Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome...
  14. ncbi request reprint A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray
    Viktor Stolc
    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Plant Mol Biol 59:137-49. 2005
    ..These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation...
  15. pmc Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    Thomas E Royce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Genet 21:466-75. 2005
    ..We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology...
  16. pmc Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
    Viktor Stolc
    Genome Research Facility, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035, USA
    Proc Natl Acad Sci U S A 102:4453-8. 2005
    ..Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage...
  17. ncbi request reprint Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
    ..A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins...
  18. ncbi request reprint A gene expression map for the euchromatic genome of Drosophila melanogaster
    Viktor Stolc
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 306:655-60. 2004
    ..Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted...