Duccio Cavalieri

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint Evidence for S. cerevisiae fermentation in ancient wine
    Duccio Cavalieri
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    J Mol Evol 57:S226-32. 2003
  2. ncbi request reprint Ecological and evolutionary genomics of Saccharomyces cerevisiae
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 15:575-91. 2006
  3. ncbi request reprint Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae
    Kyle M Brown
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Mol Ecol 17:2985-97. 2008
  4. ncbi request reprint Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
    Gene 366:343-51. 2006
  5. doi request reprint Integrating whole-genome expression results into metabolic networks with Pathway Processor
    Duccio Cavalieri
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts, USA
    Curr Protoc Bioinformatics . 2004
  6. ncbi request reprint Population genetic variation in genome-wide gene expression
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:955-63. 2003
  7. ncbi request reprint Indel arrays: an affordable alternative for genotyping
    Neeraj Salathia
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Plant J 51:727-37. 2007
  8. pmc Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks
    Paul Grosu
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 12:1121-6. 2002
  9. ncbi request reprint Fundamentals of cDNA microarray data analysis
    Yuk Fai Leung
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    Trends Genet 19:649-59. 2003
  10. doi request reprint Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion
    Luca Lotito
    Department of Biochemistry G Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
    J Mol Biol 377:311-22. 2008

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Evidence for S. cerevisiae fermentation in ancient wine
    Duccio Cavalieri
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    J Mol Evol 57:S226-32. 2003
    ..This inference has major implications for the evolution of bread and beer yeasts, since it suggests that S. cerevisiae yeast, which occurs naturally on the surface bloom of grapes, was also used as an inoculum to ferment cereal products...
  2. ncbi request reprint Ecological and evolutionary genomics of Saccharomyces cerevisiae
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 15:575-91. 2006
    ....
  3. ncbi request reprint Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae
    Kyle M Brown
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Mol Ecol 17:2985-97. 2008
    ....
  4. ncbi request reprint Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
    Gene 366:343-51. 2006
    ..We also found that genes with genetic variation for plasticity were less likely to be essential and were significantly biased towards genes that have paralogs...
  5. doi request reprint Integrating whole-genome expression results into metabolic networks with Pathway Processor
    Duccio Cavalieri
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts, USA
    Curr Protoc Bioinformatics . 2004
    ..This unit presents applications of the Pathway Processor software...
  6. ncbi request reprint Population genetic variation in genome-wide gene expression
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:955-63. 2003
    ..Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments...
  7. ncbi request reprint Indel arrays: an affordable alternative for genotyping
    Neeraj Salathia
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Plant J 51:727-37. 2007
    ..Given the ease of use of shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms...
  8. pmc Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks
    Paul Grosu
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 12:1121-6. 2002
    ..This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned...
  9. ncbi request reprint Fundamentals of cDNA microarray data analysis
    Yuk Fai Leung
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    Trends Genet 19:649-59. 2003
    ....
  10. doi request reprint Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion
    Luca Lotito
    Department of Biochemistry G Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
    J Mol Biol 377:311-22. 2008
    ..As telomere-proximal regions are known to be enriched for stress-activated genes, our findings show that Top1p can optimize transcript levels for cell growth in exponentially growing cells under a synthetic medium with glucose...
  11. ncbi request reprint An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae
    Tania Gamberi
    Dipartimento di Scienze Biochimiche, Universita degli Studi di Firenze, Viale G Morgagni, 50 I 50134 Firenze, Italy
    Biochim Biophys Acta 1774:688-700. 2007
    ..The employment of different technologies may reveal the potential and limitations of each adapted approach in a prospective application for drug screening...
  12. pmc Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains
    Elisa Giuntini
    Dipartimento di Biologia Animale e Genetica, Universita di Firenze, Via Romana 17, I 50125 Firenze, Italy
    BMC Genomics 6:158. 2005
    ....
  13. ncbi request reprint Yeast adapt to near-freezing temperatures by STRE/Msn2,4-dependent induction of trehalose synthesis and certain molecular chaperones
    Olga Kandror
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 13:771-81. 2004
    ..Thus, below 10 degrees C, yeast show an adaptive response that sustains viability at low or freezing temperatures, which are commonly encountered in natural environments and laboratory refrigerators...
  14. ncbi request reprint Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids
    Federico Sebastiani
    Department of Animal Biology and Genetics, University of Florence, Italy
    Res Microbiol 153:53-8. 2002
    ..Fertile asci could derive from allotetraploid cells generated by endomitotic events in allodiploid cells, a mechanism that enables overcoming the species barrier between S. cerevisiae and S. bayanus...
  15. ncbi request reprint Emerging treatments and gene expression profiling in high-risk medulloblastoma
    Iacopo Sardi
    Department of Pediatrics, Onco hematology and Neuro surgery Units, University of Florence Medical School, A Meyer Children s Hospital, Florence, Italy
    Paediatr Drugs 9:81-96. 2007
    ....
  16. ncbi request reprint Bioinformatic methods for integrating whole-genome expression results into cellular networks
    Duccio Cavalieri
    Department of Pharmacology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
    Drug Discov Today 10:727-34. 2005
    ....
  17. ncbi request reprint Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
    Duccio Cavalieri
    Department of Preclinical and Clinical Pharmacology, Department of Statistics, University of Florence, Florence, Italy
    Bioinformatics 23:2631-2. 2007
    ..In conclusion, Eu.Gene Analyzer is a new software application that takes advantage of information from multiple pathway databases to build a comprehensive interpretation of experimental results in a simple, intuitive environment...
  18. ncbi request reprint Extremely low-frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes
    Cristina Luceri
    Department of Pharmacology, University of Florence, Viale Pieraccini 6, 50139, Florence, Italy
    Radiat Res 164:277-85. 2005
    ..The results suggest that extremely low-frequency EMFs do not induce DNA damage or affect gene expression in these two different eukaryotic cell systems...
  19. ncbi request reprint The underlying principles of scientific publication
    Catherine A Ball
    Bioinformatics 18:1409. 2002
  20. ncbi request reprint Analysis of gene expression profiles reveals novel correlations with the clinical course of colorectal cancer
    Duccio Cavalieri
    Department of Pharmacology, University of Florence, Florence, Italy
    Oncol Res 16:535-48. 2007
    ..In this set of patients the Cox Proportional Hazard Model analysis demonstrated a significant association between increased patient survival and low expression of ITGB2 (p = 0.011) and NPR1 (p = 0.023) genes...
  21. ncbi request reprint Standards for microarray data
    Catherine A Ball
    Science 298:539. 2002