Patrik D'haeseleer

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. ncbi request reprint What are DNA sequence motifs?
    Patrik D'haeseleer
    Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, PO Box 808, L 448, Livermore, California 94551, USA
    Nat Biotechnol 24:423-5. 2006
  2. pmc Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass
    Patrik D'haeseleer
    Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 8:e68465. 2013
  3. ncbi request reprint How does gene expression clustering work?
    Patrik D'haeseleer
    Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, PO Box 808, L 448, Livermore, California 94551, USA
    Nat Biotechnol 23:1499-501. 2005
  4. pmc Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization
    Michael J Dougherty
    The Joint Bioenergy Institute, Emeryville, USA
    BMC Biotechnol 12:38. 2012
  5. pmc From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis
    Ryan P McAndrew
    Joint BioEnergy Institute, Emeryville, California 94608, USA
    J Biol Chem 288:14985-92. 2013
  6. pmc A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels
    Joshua I Park
    Joint BioEnergy Institute JBEI, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 7:e37010. 2012
  7. pmc Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus
    Jane I Khudyakov
    Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Proc Natl Acad Sci U S A 109:E2173-82. 2012
  8. pmc Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses
    Amitha P Reddy
    Joint BioEnergy Institute, Emeryville, California, United States of America Biological and Agricultural Engineering, University of California Davis, Davis, California, United States of America
    PLoS ONE 8:e77985. 2013
  9. pmc Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community
    Yongqin Jiao
    Physical and Life Sciences, LLNL, 7000 East Ave, L 452, Livermore, CA 94550, USA
    Appl Environ Microbiol 77:5230-7. 2011
  10. pmc Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community
    Martin Allgaier
    Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 5:e8812. 2010

Collaborators

Detail Information

Publications11

  1. ncbi request reprint What are DNA sequence motifs?
    Patrik D'haeseleer
    Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, PO Box 808, L 448, Livermore, California 94551, USA
    Nat Biotechnol 24:423-5. 2006
    ..How do we define sequence motifs, and why should we use sequence logos instead of consensus sequences to represent them? Do they have any relation with binding affinity? How do we search for new instances of a motif in this sea of DNA?..
  2. pmc Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass
    Patrik D'haeseleer
    Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 8:e68465. 2013
    ..These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction. ..
  3. ncbi request reprint How does gene expression clustering work?
    Patrik D'haeseleer
    Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, PO Box 808, L 448, Livermore, California 94551, USA
    Nat Biotechnol 23:1499-501. 2005
    ..Clustering is often one of the first steps in gene expression analysis. How do clustering algorithms work, which ones should we use and what can we expect from them?..
  4. pmc Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization
    Michael J Dougherty
    The Joint Bioenergy Institute, Emeryville, USA
    BMC Biotechnol 12:38. 2012
    ....
  5. pmc From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis
    Ryan P McAndrew
    Joint BioEnergy Institute, Emeryville, California 94608, USA
    J Biol Chem 288:14985-92. 2013
    ..Arg-587 and Phe-598 from the C-terminal domain of the opposing monomer are shown to interact with bound ligands in the D261N structure. Enzyme assays confirmed that these residues are absolutely essential for full catalytic activity...
  6. pmc A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels
    Joshua I Park
    Joint BioEnergy Institute JBEI, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 7:e37010. 2012
    ..This cocktail will enable the development of novel biomass to biofuel bioprocessing configurations that may overcome some of the barriers to production of inexpensive cellulosic biofuels...
  7. pmc Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus
    Jane I Khudyakov
    Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Proc Natl Acad Sci U S A 109:E2173-82. 2012
    ..These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance...
  8. pmc Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses
    Amitha P Reddy
    Joint BioEnergy Institute, Emeryville, California, United States of America Biological and Agricultural Engineering, University of California Davis, Davis, California, United States of America
    PLoS ONE 8:e77985. 2013
    ..Furthermore, these discoveries warrant future research to determine if exoglucanases with CBM2 represent thermostable enzymes tolerant to the process conditions expected to be encountered during industrial biofuel production...
  9. pmc Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community
    Yongqin Jiao
    Physical and Life Sciences, LLNL, 7000 East Ave, L 452, Livermore, CA 94550, USA
    Appl Environ Microbiol 77:5230-7. 2011
    ..Compared to the differences between EPS and cellular fractions, the relative differences in the EPS proteomes between DS1 and DS2 were smaller and consistent with expected physiological changes during biofilm development...
  10. pmc Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community
    Martin Allgaier
    Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
    PLoS ONE 5:e8812. 2010
    ....
  11. pmc Microbial genotype-phenotype mapping by class association rule mining
    Makio Tamura
    Lawrence Livermore National Laboratory, Computing Applications and Research Department Chemistry, Materials, Earth and Life Sciences Department, Microbial Systems Biology Group, Livermore, CA 94550, USA
    Bioinformatics 24:1523-9. 2008
    ..netCAR takes into account the phylogenetic co-occurrence graph between COGs to restrict hypothesis space, and uses mutual information to evaluate the biconditional relation...