LAWRENCE E HUNTER

Summary

Affiliation: University of Colorado Health Sciences Center
Country: USA

Publications

  1. pmc Corpus refactoring: a feasibility study
    Helen L Johnson
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 2:4. 2007
  2. pmc Cross-species cluster co-conservation: a new method for generating protein interaction networks
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 8:R185. 2007
  3. pmc Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 8:393. 2007
  4. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
  5. pmc A critical review of PASBio's argument structures for biomedical verbs
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    BMC Bioinformatics 7:S5. 2006
  6. pmc BioCreAtIvE task1A: entity identification with a stochastic tagger
    Shuhei Kinoshita
    Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, Colorado, USA
    BMC Bioinformatics 6:S4. 2005
  7. pmc Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
    Hannah J Tipney
    Computational Pharmacology Department, University of Colorado at Denver and Health Sciences Center, Aurora, CO, USA
    BMC Bioinformatics 10:S12. 2009
  8. pmc Semantic role labeling for protein transport predicates
    Steven Bethard
    Computer Science Department, University of Colorado at Boulder, Boulder, CO, USA
    BMC Bioinformatics 9:277. 2008
  9. pmc OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 9:78. 2008
  10. pmc An open-source framework for large-scale, flexible evaluation of biomedical text mining systems
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 3:1. 2008

Research Grants

  1. Integrated Neuroinformatics Resource for Alcoholism (IN*
    Lawrence Hunter; Fiscal Year: 2005
  2. Ontologies and Biomedical Language Processing
    Lawrence Hunter; Fiscal Year: 2007

Collaborators

Detail Information

Publications35

  1. pmc Corpus refactoring: a feasibility study
    Helen L Johnson
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 2:4. 2007
    ..We tracked the total time expended and the success rates of the automated steps...
  2. pmc Cross-species cluster co-conservation: a new method for generating protein interaction networks
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 8:R185. 2007
    ..We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation...
  3. pmc Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 8:393. 2007
    ..The Co-Conservation method, also known as the Phylogenetic profiles method, is a well-established computational tool for predicting functional relationships between proteins...
  4. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
    ..We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance...
  5. pmc A critical review of PASBio's argument structures for biomedical verbs
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    BMC Bioinformatics 7:S5. 2006
    ..Here, we quantitatively evaluate several dimensions of the initial PASBio propositional structure repository...
  6. pmc BioCreAtIvE task1A: entity identification with a stochastic tagger
    Shuhei Kinoshita
    Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, Colorado, USA
    BMC Bioinformatics 6:S4. 2005
    ..We participated in both the open and the closed divisions; for the open division, we made use of data from NCBI...
  7. pmc Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
    Hannah J Tipney
    Computational Pharmacology Department, University of Colorado at Denver and Health Sciences Center, Aurora, CO, USA
    BMC Bioinformatics 10:S12. 2009
    ..In contrast to unstructured gene lists, these networks often represent coherent functional groupings...
  8. pmc Semantic role labeling for protein transport predicates
    Steven Bethard
    Computer Science Department, University of Colorado at Boulder, Boulder, CO, USA
    BMC Bioinformatics 9:277. 2008
    ....
  9. pmc OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 9:78. 2008
    ....
  10. pmc An open-source framework for large-scale, flexible evaluation of biomedical text mining systems
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 3:1. 2008
    ....
  11. pmc Ontologies for programs, not people
    Lawrence Hunter
    Center for Computational Pharmacology, Department of Pharmacology, School of Medicine, University of Colorado Health Sciences Center, 4200 E, Ninth Avenue, Denver, CO 80262, USA
    Genome Biol 3:INTERACTIONS1002. 2002
    ..A response to Life sentences: Ontology recapitulates philology by Sydney Brenner, Genome Biology 2002, 3:comment1006.1-1006.2...
  12. pmc Biomedical language processing: what's beyond PubMed?
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, 80045, USA
    Mol Cell 21:589-94. 2006
  13. ncbi request reprint GEST: a gene expression search tool based on a novel Bayesian similarity metric
    L Hunter
    Center for Computational Pharmacology, Department of Pharmacology, School of Medicine, C236, University of Colorado Health Sciences Center, 4200 E Ninth Avenue, Denver CO 80206, USA
    Bioinformatics 17:S115-22. 2001
    ..We provide a computationally tractable approximation to this measure, and have implemented a database search tool based on it. We discuss implementation issues and efficiency, and we compare our new metric to other standard metrics...
  14. pmc Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation
    Alkesh Jani
    Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Physiol Genomics 44:717-27. 2012
    ....
  15. pmc Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation
    Allyson G Hindle
    Dept of Cell and Developmental Biology, PO Box 6511, MS 8010, Univ of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO 80045, USA
    Am J Physiol Regul Integr Comp Physiol 301:R1440-52. 2011
    ..This, along with winter elevation of TCA cycle enzymes, suggests that hindlimb muscles are primed for rapid energy production and that carbohydrates are an important fuel for shivering thermogenesis...
  16. pmc Protein carbonylation in a murine model for early alcoholic liver disease
    James J Galligan
    Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
    Chem Res Toxicol 25:1012-21. 2012
    ..These data suggest a major role for aldehyde adduction in the pathogenesis of ALD...
  17. pmc Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development
    Suparna A Sarkar
    Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
    Pancreas 41:962-9. 2012
    ..This study investigated the utility of advanced computational techniques to large-scale genome-based data to identify novel genes that govern murine pancreatic development...
  18. pmc Multistate proteomics analysis reveals novel strategies used by a hibernator to precondition the heart and conserve ATP for winter heterothermy
    Katharine R Grabek
    Human Medical Genetics Program, Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Physiol Genomics 43:1263-75. 2011
    ....
  19. pmc Exploring species-based strategies for gene normalization
    Karin Verspoor
    Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:462-71. 2010
    ..5 tasks...
  20. pmc The structural and content aspects of abstracts versus bodies of full text journal articles are different
    K Bretonnel Cohen
    Department of Pharmacology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
    BMC Bioinformatics 11:492. 2010
    ..However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research...
  21. pmc A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools
    Karin Verspoor
    Computational Bioscience Program, U, Colorado School of Medicine, 12801 E 17th Ave, Aurora, MS 8303, CO 80045, USA
    BMC Bioinformatics 13:207. 2012
    ..We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus...
  22. pmc Concept annotation in the CRAFT corpus
    Michael Bada
    Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    BMC Bioinformatics 13:161. 2012
    ..Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text...
  23. pmc Predicting protein linkages in bacteria: which method is best depends on task
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Bioinformatics 9:397. 2008
    ..We also review many previous treatments of these prediction methods, use the latest available annotations, and offer a number of new observations...
  24. pmc A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Hum Genomics 4:421-7. 2010
    ..In this paper, most of the well known algorithms, analysis software and the limitations of that software will be briefly reviewed...
  25. pmc Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma
    Beth A Tamburini
    Integrated Department of Immunology, University of Colorado, Denver, School of Medicine, Denver, CO, USA
    BMC Cancer 10:619. 2010
    ..The hypothesis for this study was that characteristic molecular features distinguish hemangiosarcoma from non-malignant endothelial cells, and that such features are informative for the etiology of this disease...
  26. pmc Parenthetically speaking: classifying the contents of parentheses for text mining
    K Bretonnel Cohen
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, CO, USA
    AMIA Annu Symp Proc 2011:267-72. 2011
    ..It performs at a micro-averaged accuracy of 68% and a macro-averaged accuracy of 60% on an annotated corpus. The application is available as a Java class and as a Perl module...
  27. pmc The topology of the bacterial co-conserved protein network and its implications for predicting protein function
    Anis Karimpour-Fard
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    BMC Genomics 9:313. 2008
    ..coli K12. Next, we demonstrate one way in which network connectivity measures and global and local function distribution can be exploited to predict protein function for previously uncharacterized proteins...
  28. pmc Improving protein function prediction methods with integrated literature data
    Aaron P Gabow
    Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6101, PO Box 6511, Aurora, CO 80045, USA
    BMC Bioinformatics 9:198. 2008
    ..We also quantify changes in performance as the prediction algorithms annotate with increased specificity...
  29. pmc Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences
    Weiguo Feng
    Department of Craniofacial Biology, University of Colorado Denver, Aurora, Colorado, USA
    PLoS ONE 4:e8066. 2009
    ..Overall, our studies provide a valuable resource for probing orofacial development and a robust dataset for bioinformatic analysis of spatial and temporal gene expression changes during embryogenesis...
  30. pmc Chapter 16: text mining for translational bioinformatics
    K Bretonnel Cohen
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS Comput Biol 9:e1003044. 2013
    ..Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing...
  31. pmc Regional differences in subcutaneous adipose tissue gene expression
    Charles W Rehrer
    Division of Endocrinology, Metabolism and Diabetes, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
    Obesity (Silver Spring) 20:2168-73. 2012
    ..These results in normal weight healthy women provide a new perspective on regional differences in SAT biology that may have pathophysiologic implications when adiposity increases...
  32. pmc The PhenoGen informatics website: tools for analyses of complex traits
    Sanjiv V Bhave
    Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA
    BMC Genet 8:59. 2007
    ..Managing this diverse data and integrating with other biological data are major challenges for the bioinformatics community. Comprehensive new tools are needed to store, integrate and analyze the data efficiently...
  33. pmc Metabolic cycles in a circannual hibernator
    L Elaine Epperson
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
    Physiol Genomics 43:799-807. 2011
    ..This finding provides new data that strongly support the predictions of a long-standing hypothesis that periodic arousals are necessary to restore metabolic homeostasis...
  34. pmc Profiling impaired hepatic endoplasmic reticulum glycosylation as a consequence of ethanol ingestion
    James J Galligan
    Department of Pharmacology, University of Colorado Denver, Aurora, Colorado 80045, United States
    J Proteome Res 10:1837-47. 2011
    ..Impaired TGH activity is associated with increased cellular storage of lipids and provides a potential mechanism for the observed pathologies associated with ALD...
  35. pmc Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed
    Beth A Tamburini
    Integrated Department of Immunology, University of Colorado Denver, Denver, Colorado, USA
    PLoS ONE 4:e5549. 2009
    ..Our results suggest heritable factors mold gene expression phenotypes, and consequently biological behavior in sporadic, naturally occurring tumors...

Research Grants2

  1. Integrated Neuroinformatics Resource for Alcoholism (IN*
    Lawrence Hunter; Fiscal Year: 2005
    ..We believe the INRA will greatly enhance the Dace of discovery in the area of ethanol consumption and neuroadaptation to alcohol within the INIAC as well as the general research community. ..
  2. Ontologies and Biomedical Language Processing
    Lawrence Hunter; Fiscal Year: 2007
    ....