Bobbie Jo M Webb-Robertson

Summary

Affiliation: Pacific Northwest National Laboratory
Country: USA

Publications

  1. doi request reprint Spectral signatures for the classification of microbial species using Raman spectra
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, 902 Battelle Blvd, J4 33, Richland, WA 99352, USA
    Anal Bioanal Chem 404:563-72. 2012
  2. doi request reprint A feature vector integration approach for a generalized support vector machine pairwise homology algorithm
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Comput Biol Chem 32:458-61. 2008
  3. pmc Measuring global credibility with application to local sequence alignment
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Comput Biol 4:e1000077. 2008
  4. doi request reprint A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory
    Bioinformatics 24:1503-9. 2008
  5. ncbi request reprint Current trends in computational inference from mass spectrometry-based proteomics
    Bobbie Jo M Webb-Robertson
    Department of Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    Brief Bioinform 8:304-17. 2007
  6. ncbi request reprint A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, USA
    Bioinformatics 26:1677-83. 2010
  7. pmc Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Proteome Res 9:5748-56. 2010
  8. ncbi request reprint SVM-BALSA: remote homology detection based on Bayesian sequence alignment
    Bobbie Jo Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Comput Biol Chem 29:440-3. 2005
  9. pmc A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, USA
    Proteomics 11:4736-41. 2011
  10. pmc Physicochemical property distributions for accurate and rapid pairwise protein homology detection
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    BMC Bioinformatics 11:145. 2010

Collaborators

Detail Information

Publications27

  1. doi request reprint Spectral signatures for the classification of microbial species using Raman spectra
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, 902 Battelle Blvd, J4 33, Richland, WA 99352, USA
    Anal Bioanal Chem 404:563-72. 2012
    ....
  2. doi request reprint A feature vector integration approach for a generalized support vector machine pairwise homology algorithm
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Comput Biol Chem 32:458-61. 2008
    ..97 versus 0.73 and 0.70 for PSI-BLAST and Basic Local Alignment Search Tool (BLAST), respectively...
  3. pmc Measuring global credibility with application to local sequence alignment
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Comput Biol 4:e1000077. 2008
    ....
  4. doi request reprint A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory
    Bioinformatics 24:1503-9. 2008
    ..It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic)...
  5. ncbi request reprint Current trends in computational inference from mass spectrometry-based proteomics
    Bobbie Jo M Webb-Robertson
    Department of Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    Brief Bioinform 8:304-17. 2007
    ..This review presents an overview of recently developed methods and their impact on these core computational challenges currently facing proteomics...
  6. ncbi request reprint A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, USA
    Bioinformatics 26:1677-83. 2010
    ..It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic)...
  7. pmc Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Proteome Res 9:5748-56. 2010
    ..We use three LC-MS data sets to demonstrate the robustness and sensitivity of the IMD-ANOVA approach...
  8. ncbi request reprint SVM-BALSA: remote homology detection based on Bayesian sequence alignment
    Bobbie Jo Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Comput Biol Chem 29:440-3. 2005
    ..The SVM-BALSA algorithms returns a higher area under the receiver operating characteristic (ROC) curves for 37 of the 54 families and achieves an improved overall performance curve at a significance level of 0.07...
  9. pmc A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, USA
    Proteomics 11:4736-41. 2011
    ....
  10. pmc Physicochemical property distributions for accurate and rapid pairwise protein homology detection
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    BMC Bioinformatics 11:145. 2010
    ....
  11. ncbi request reprint Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool
    Susan L Havre
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    IEEE Eng Med Biol Mag 24:50-7. 2005
    ..Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods...
  12. pmc Improved quality control processing of peptide-centric LC-MS proteomics data
    Melissa M Matzke
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Bioinformatics 27:2866-72. 2011
    ..g. analysis of variance (ANOVA)] rely upon accurate estimates of sample variance, and their results are influenced by extreme values...
  13. ncbi request reprint Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data
    William R Cannon
    Computational Biology and Bioinformatics Group, Computational and Information Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Proteome Res 4:1687-98. 2005
    ..The results are shown to reduce the misidentification rate significantly when compared to a benchmark cross-correlation based approach...
  14. ncbi request reprint Integrating subcellular location for improving machine learning models of remote homology detection in eukaryotic organisms
    Anuj R Shah
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Comput Biol Chem 31:138-42. 2007
    ..Combining these two approaches in the application SVM-SimLoc resulted in identification of significantly more remote homologs (p-value<0.006) than using either sequence similarity or subcellular location independently...
  15. pmc Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics
    Stephen J Callister
    Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
    J Proteome Res 5:277-86. 2006
    ..Nevertheless, this study serves as an important step for evaluating approaches that address systematic biases related to relative quantification and label-free proteomics...
  16. pmc Diet-induced obesity reprograms the inflammatory response of the murine lung to inhaled endotoxin
    Susan C Tilton
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Toxicol Appl Pharmacol 267:137-48. 2013
    ..These data show obesity may increase sensitivity to further insult and that co-occurrence of environmental stressors result in complex biosignatures that are not predicted from analysis of individual exposures...
  17. doi request reprint Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
    Biotechniques 54:165-8. 2013
    ..Our results demonstrate that this approach generates robust and informative low-dimensional data representations compared to commonly used imputation approaches...
  18. pmc VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
    Elena S Peterson
    Scientific Data Management, Pacific Northwest National Laboratory, Richland, WA, USA
    BMC Genomics 13:131. 2012
    ....
  19. ncbi request reprint A study of spectral integration and normalization in NMR-based metabonomic analyses
    Bobbie Jo M Webb-Robertson
    Pacific Northwest National Laboratory, P O Box 999, K7 90, Richland, WA 99352, USA
    J Pharm Biomed Anal 39:830-6. 2005
    ..Of the top 10 latent variables for the ANIT dataset the auto-scale normalization has standard deviations larger than the total-scale in seven cases. In the case of the elastase all standard deviations are larger for the auto-scaling...
  20. pmc Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp. novicida
    Susan M Varnum
    Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
    J Proteome Res 11:3690-703. 2012
    ..Finally, this study identifies several candidate biomarkers, including Chitinase 3-like-1 (CHI3L1 or YKL-40) and peroxiredoxin 1, that are associated with F. tularensis ssp. novicida but not P. aeruginosa infection...
  21. pmc VIBE 2.0: visual integration for bayesian evaluation
    Nathaniel Beagley
    Computational Mathematics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Bioinformatics 26:280-2. 2010
    ....
  22. pmc A semiautomated framework for integrating expert knowledge into disease marker identification
    Jing Wang
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Dis Markers 35:513-23. 2013
    ..However, a recurring problem in deriving biological information from large data sets is how to best incorporate expert knowledge into the biomarker selection process...
  23. ncbi request reprint PQuad--a visual analysis platform for proteomic data exploration of microbial organisms
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
    Bioinformatics 23:1705-7. 2007
    ..PQuad requires Java 1.5 and has been tested to run across different operating systems. Availability: http://ncrr.pnl.gov/software...
  24. pmc Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size
    Haizhen Zhang
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proteomics 11:4569-77. 2011
    ..The comprehensive quantitative proteomics results obtained in this study provide rich data for computational modeling and have potential implications towards predicting nanoparticle biocompatibility...
  25. doi request reprint Support vector machines for improved peptide identification from tandem mass spectrometry database search
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
    Methods Mol Biol 492:453-60. 2009
    ..In practice, following the database search routine, a peptide is denoted in its vector representation and the SVM generates a single statistical score that is then used to classify presence or absence in the sample...
  26. doi request reprint The effects of low-dose irradiation on inflammatory response proteins in a 3D reconstituted human skin tissue model
    Susan M Varnum
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Radiat Res 178:591-9. 2012
    ..Overall, these results indicate that there are subtle changes in the inflammatory protein levels after exposure to low-dose radiation and this response is a subset of what is seen after a high dose in a human skin tissue model...
  27. pmc Plasma biomarkers for detecting Hodgkin's lymphoma in HIV patients
    Susan M Varnum
    Department of Cell Biology and Biochemistry, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS ONE 6:e29263. 2011
    ..The relationship of these novel candidate biomarkers with cancer and inflammation suggests that they are truly associated with HL and therefore may be useful for the early detection of this cancer in susceptible populations...