Jean Marie Rouillard

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, H H Dow, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 31:3057-62. 2003
  2. pmc OligoArrayDb: pangenomic oligonucleotide microarray probe sets database
    Jean Marie Rouillard
    Chemical Engineering Department, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 37:D938-41. 2009
  3. pmc Gene2Oligo: oligonucleotide design for in vitro gene synthesis
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
    Nucleic Acids Res 32:W176-80. 2004
  4. doi request reprint Target concentration dependence of DNA melting temperature on oligonucleotide microarrays
    Ayse Bilge Ozel
    Dept of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
    Biotechnol Prog 28:556-66. 2012
  5. ncbi request reprint OligoArray: genome-scale oligonucleotide design for microarrays
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 2136, USA
    Bioinformatics 18:486-7. 2002
  6. ncbi request reprint Signal-amplifying conjugated polymer-DNA hybrid chips
    Kangwon Lee
    Department of Materials Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, USA
    Angew Chem Int Ed Engl 46:4667-70. 2007
  7. pmc On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes
    Lukas M Wick
    National Food Safety and Toxicology Center, Michigan State University, East Lansing, MI, USA
    Nucleic Acids Res 34:e26. 2006
  8. ncbi request reprint Integrating cancer genomics and proteomics in the post-genome era
    Samir M Hanash
    University of Michigan Medical Center, Ann Arbor, MI 48109 0656, USA
    Proteomics 2:69-75. 2002
  9. pmc Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas
    Rong Wu
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    Am J Pathol 162:1603-10. 2003
  10. pmc Colloids with high-definition surface structures
    Hsien Yeh Chen
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 104:11173-8. 2007

Research Grants

  1. Parallel high sensitivity gene expression monitoring
    Jean Marie Rouillard; Fiscal Year: 2007

Collaborators

Detail Information

Publications17

  1. pmc OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, H H Dow, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 31:3057-62. 2003
    ..OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts...
  2. pmc OligoArrayDb: pangenomic oligonucleotide microarray probe sets database
    Jean Marie Rouillard
    Chemical Engineering Department, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 37:D938-41. 2009
    ..Probe sequences, in addition to a comprehensive set of annotations can be downloaded from this database. OligoArrayDb is publicly accessible online at http://berry.engin.umich.edu/oligoarraydb...
  3. pmc Gene2Oligo: oligonucleotide design for in vitro gene synthesis
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
    Nucleic Acids Res 32:W176-80. 2004
    ..We have successfully designed and used a set of oligonucleotides to synthesize the Saccharomyces cerevisiae cytochrome b5 by using both LCR and assembly PCR...
  4. doi request reprint Target concentration dependence of DNA melting temperature on oligonucleotide microarrays
    Ayse Bilge Ozel
    Dept of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
    Biotechnol Prog 28:556-66. 2012
    ..At very low target concentrations, a multi-melting process was observed in low temperature domains of the curves. This was attributed to the presence of truncated or mismatch probes...
  5. ncbi request reprint OligoArray: genome-scale oligonucleotide design for microarrays
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 2136, USA
    Bioinformatics 18:486-7. 2002
    ..OligoArray is a program that computes gene specific and secondary structure free oligonucleotides for genome-scale oligonucleotide microarray construction or other applications...
  6. ncbi request reprint Signal-amplifying conjugated polymer-DNA hybrid chips
    Kangwon Lee
    Department of Materials Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, USA
    Angew Chem Int Ed Engl 46:4667-70. 2007
  7. pmc On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes
    Lukas M Wick
    National Food Safety and Toxicology Center, Michigan State University, East Lansing, MI, USA
    Nucleic Acids Res 34:e26. 2006
    ..These results have broad implications for hybridization data obtained from complex mixtures of nucleic acids...
  8. ncbi request reprint Integrating cancer genomics and proteomics in the post-genome era
    Samir M Hanash
    University of Michigan Medical Center, Ann Arbor, MI 48109 0656, USA
    Proteomics 2:69-75. 2002
    ..Our current approach is illustrated with findings stemming from our studies of human gliomas...
  9. pmc Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas
    Rong Wu
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    Am J Pathol 162:1603-10. 2003
    ..The data implicate L-MYC gene amplification and/or overexpression in human OvCa pathogenesis...
  10. pmc Colloids with high-definition surface structures
    Hsien Yeh Chen
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 104:11173-8. 2007
    ....
  11. pmc Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice
    Chad Creighton
    Bioinformatics Program, Human Genetics, and Public Health, University of Michigan, Ann Arbor, MI 48109, USA
    Genome Biol 4:R46. 2003
    ..Global gene-expression profiles of the tumors were determined, based on analysis of expression of human genes, and compared with expression profiles of the cell lines grown in culture...
  12. pmc From design to screening: a new antimicrobial peptide discovery pipeline
    Saadet Albayrak Guralp
    Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 8:e59305. 2013
    ....
  13. pmc Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli
    Jeremy J Minty
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
    Microb Cell Fact 10:18. 2011
    ..We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases of adaptation to exogenous isobutanol stress...
  14. pmc Cytophobic surface modification of microfluidic arrays for in situ parallel peptide synthesis and cell adhesion assays
    Suparna Mandal
    Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109 2136, USA
    Biotechnol Prog 23:972-8. 2007
    ..Sequence-specific binding was observed on incubation with fluorescently labeled, intact murine B lymphoma cells, and key residues for binding were identified by deletional analysis...
  15. pmc An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
    Kevin Le Brigand
    CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, UMR6097, 660, route des Lucioles, F 06560 Sophia Antipolis, France
    Nucleic Acids Res 34:e87. 2006
    ..All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE...
  16. ncbi request reprint Amplification and overexpression of the IGF2 regulator PLAG1 in hepatoblastoma
    Andrea Zatkova
    Institut für Medizinische Biologie, Universitat Wien, Vienna, Austria
    Genes Chromosomes Cancer 39:126-37. 2004
    ....
  17. ncbi request reprint Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs
    Syed A Hashsham
    Department of Civil and Environmental Engineering, Michigan State University, A 126 Research Complex Engineering, East Lansing, MI 48824, USA
    Biosens Bioelectron 20:668-83. 2004
    ..Data illustrating selected probe design issues for detecting multiple targets in mixed microbial systems is presented. Challenges with respect to cost, time, and ease of use compared to other methods are also summarized...

Research Grants1

  1. Parallel high sensitivity gene expression monitoring
    Jean Marie Rouillard; Fiscal Year: 2007
    ..Further validation will be by conducting new experiments to detect weakly expressed genes involved in adipogenesis, and to monitor bacterial gene expression in infected host cells. ..