Jonas Warringer

Summary

Country: Sweden

Publications

  1. pmc High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
    Gianni Liti
    Institute of Research on Cancer and Ageing of Nice IRCAN, CNRS UMR 7284 INSERM U1081, Universite de Nice Sophia Antipolis, 06107, Nice Cedex 2, France
    BMC Genomics 14:69. 2013
  2. pmc Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Bioinformatics 13:327. 2012
  3. pmc Exploration of multivariate analysis in microbial coding sequence modeling
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
    BMC Bioinformatics 13:97. 2012
  4. pmc A Partial Least Squares based algorithm for parsimonious variable selection
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    Algorithms Mol Biol 6:27. 2011
  5. pmc Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide
    Eun Hee Park
    Laboratory of Gene Regulation and Development, Eunice K, Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    BMC Genomics 12:68. 2011
  6. pmc Mining for genotype-phenotype relations in Saccharomyces using partial least squares
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    BMC Bioinformatics 12:318. 2011
  7. pmc Trait variation in yeast is defined by population history
    Jonas Warringer
    Department of Cell and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
    PLoS Genet 7:e1002111. 2011
  8. pmc PROPHECY--a yeast phenome database, update 2006
    Luciano Fernandez-Ricaud
    Department of Cell and Molecular Biology, Lundberg Laboratory, Goteborg University, Medicinaregatan 9c SE 41390 Göteborg, Sweden
    Nucleic Acids Res 35:D463-7. 2007
  9. doi request reprint A role for Myh1 in DNA repair after treatment with strand-breaking and crosslinking chemotherapeutic agents
    Kristina Jansson
    Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, SE 405 30, Goteborg, Sweden
    Environ Mol Mutagen 54:327-37. 2013
  10. pmc PROPHECY--a database for high-resolution phenomics
    Luciano Fernandez-Ricaud
    Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University Medicinaregatan 9c, 41390 Goteborg, Sweden
    Nucleic Acids Res 33:D369-73. 2005

Collaborators

Detail Information

Publications24

  1. pmc High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
    Gianni Liti
    Institute of Research on Cancer and Ageing of Nice IRCAN, CNRS UMR 7284 INSERM U1081, Universite de Nice Sophia Antipolis, 06107, Nice Cedex 2, France
    BMC Genomics 14:69. 2013
    ..Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate...
  2. pmc Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Bioinformatics 13:327. 2012
    ..Results were compared to PLS-based procedures, where no background information was used...
  3. pmc Exploration of multivariate analysis in microbial coding sequence modeling
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
    BMC Bioinformatics 13:97. 2012
    ..Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties...
  4. pmc A Partial Least Squares based algorithm for parsimonious variable selection
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    Algorithms Mol Biol 6:27. 2011
    ..abstract:..
  5. pmc Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide
    Eun Hee Park
    Laboratory of Gene Regulation and Development, Eunice K, Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    BMC Genomics 12:68. 2011
    ....
  6. pmc Mining for genotype-phenotype relations in Saccharomyces using partial least squares
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    BMC Bioinformatics 12:318. 2011
    ..We introduce a methodology based on a BLAST approach for extracting information from genomic sequences and Soft- Thresholding Partial Least Squares (ST-PLS) for mapping genotype-phenotype relations...
  7. pmc Trait variation in yeast is defined by population history
    Jonas Warringer
    Department of Cell and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
    PLoS Genet 7:e1002111. 2011
    ..Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism...
  8. pmc PROPHECY--a yeast phenome database, update 2006
    Luciano Fernandez-Ricaud
    Department of Cell and Molecular Biology, Lundberg Laboratory, Goteborg University, Medicinaregatan 9c SE 41390 Göteborg, Sweden
    Nucleic Acids Res 35:D463-7. 2007
    ..We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics...
  9. doi request reprint A role for Myh1 in DNA repair after treatment with strand-breaking and crosslinking chemotherapeutic agents
    Kristina Jansson
    Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, SE 405 30, Goteborg, Sweden
    Environ Mol Mutagen 54:327-37. 2013
    ..These observations indicate a wider role of Myh1 in DNA repair and DNA damage-induced checkpoint activation than previously thought...
  10. pmc PROPHECY--a database for high-resolution phenomics
    Luciano Fernandez-Ricaud
    Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University Medicinaregatan 9c, 41390 Goteborg, Sweden
    Nucleic Acids Res 33:D369-73. 2005
    ..PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se...
  11. pmc The HOG pathway dictates the short-term translational response after hyperosmotic shock
    Jonas Warringer
    Department of Cell and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S 40530 Göteborg, Sweden
    Mol Biol Cell 21:3080-92. 2010
    ..Our results show the importance of translational control for fine tuning of the adaptive responses...
  12. pmc mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress
    Claes Molin
    Department of Cell and Molecular Biology, University of Gothenburg, Sweden
    RNA 15:600-14. 2009
    ..Conversely, stabilization of stress-repressed mRNAs permits their rapid accumulation in the recovery phase. Our results show that mRNA turnover is coordinated with transcriptional induction...
  13. pmc Sulfate assimilation mediates tellurite reduction and toxicity in Saccharomyces cerevisiae
    Lars Göran Ottosson
    Department of Cell and Molecular Biology, University of Gothenburg, Sweden
    Eukaryot Cell 9:1635-47. 2010
    ..The results reported here represent a robust base from which to attack the mechanistic details of Te(IV) toxicity and reduction in a eukaryotic organism...
  14. ncbi request reprint Genetic pleiotropy in Saccharomyces cerevisiae quantified by high-resolution phenotypic profiling
    Elke Ericson
    Department of Cell and Molecular Biology, Goteborg University, Medicinaregatan 9C, Box 462, 40530, Goteborg, Sweden
    Mol Genet Genomics 275:605-14. 2006
    ..Thus, the here reported features of pleiotropy both have implications on our understanding of evolutionary processes as well as the mechanisms underlying disease...
  15. doi request reprint Quantitative proteomics of yeast post-Golgi vesicles reveals a discriminating role for Sro7p in protein secretion
    Annabelle Forsmark
    Department of Cell and Molecular Biology, Microbiology, University of Gothenburg, Box 462, SE 405 30 Gothenburg, Sweden
    Traffic 12:740-53. 2011
    ....
  16. doi request reprint The Ashbya gossypii EF-1α promoter of the ubiquitously used MX cassettes is toxic to Saccharomyces cerevisiae
    Roja Babazadeh
    Department of Cell and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
    FEBS Lett 585:3907-13. 2011
    ..Toxicity could be eliminated by promoter replacement or exclusion of the marker cassette. To our knowledge, this is the first report of toxicity caused by introduction of a heterologous promoter alone...
  17. pmc Evolutionary constraints on yeast protein size
    Jonas Warringer
    Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University Medicinaregatan 9c, 41390 Goteborg, Sweden
    BMC Evol Biol 6:61. 2006
    ..Data on yeast protein size was compared to global experimental data on protein expression, phenotypic pleiotropy, protein-protein interactions, protein evolutionary rate and biochemical classification...
  18. pmc Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping
    Jonathan Esguerra
    Department of Cell and Molecular Biology, Goteborg University, 405 30 Goteborg, Sweden
    RNA 14:649-56. 2008
    ..Our data indicate that individual rRNA ribose methylations can play either distinct or general roles in the workings of the ribosome...
  19. pmc Physiological importance and identification of novel targets for the N-terminal acetyltransferase NatB
    Robert Caesar
    Department of Cell and Molecular Biology, Lundberg Laboratory, Goteborg University, Medicinaregatan 9C, 413 90 Goteborg, Sweden
    Eukaryot Cell 5:368-78. 2006
    ..By this procedure we predicted functional importance of the N-terminal acetylation for 31 proteins...
  20. pmc High-resolution yeast phenomics resolves different physiological features in the saline response
    Jonas Warringer
    Department of Cell and Molecular Biology, Göteborg University Medicinaregatan 9c, 41390 Goteborg, Sweden
    Proc Natl Acad Sci U S A 100:15724-9. 2003
    ..In contrast, no correlation was found between gene dispensability and gene expression. It is proposed that high-resolution phenomics will be instrumental in systemwide descriptions of intragenomic functional networks...
  21. ncbi request reprint Involvement of yeast YOL151W/GRE2 in ergosterol metabolism
    Jonas Warringer
    Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University Medicinaregatan 9c, 41390 Goteborg, Sweden
    Yeast 23:389-98. 2006
    ....
  22. pmc Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway
    Marcus Krantz
    Department of Cell and Molecular Biology, University of Gothenburg, Goteborg, Sweden
    Mol Syst Biol 5:281. 2009
    ..Thus, in vivo robustness data can be used to discriminate and improve mathematical models...
  23. doi request reprint The tumor suppressor homolog in fission yeast, myh1(+), displays a strong interaction with the checkpoint gene rad1(+)
    Kristina Jansson
    Department of Cell and Molecular Biology, Lundberg Laboratory, Goteborg University, P O Box 462, Göteborg SE 405 30, Sweden
    Mutat Res 644:48-55. 2008
    ..Our results implicate fission yeast Myh1 in repair of a wider range of DNA damage than previously thought, and functionally link it to the checkpoint pathway...
  24. ncbi request reprint Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae
    Jonas Warringer
    Department of Cell and Molecular Biology, Lundberg Laboratory, Goteborg University, Medicinaregatan 9C, 413 90 Goteborg, Sweden
    Yeast 20:53-67. 2003
    ..We propose the utilization of this methodology in large-scale screening of the complete collection of yeast deletion mutants...