Jonathan D Wren

Summary

Affiliation: University of Oklahoma
Country: USA

Publications

  1. pmc A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
    Zengjun Xu
    Division of Neurotoxicology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S8. 2005
  2. ncbi request reprint Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman, 73019, USA
    OMICS 10:15-27. 2006
  3. ncbi request reprint Markov model recognition and classification of DNA/protein sequences within large text databases
    Jonathan D Wren
    Advanced Center for Genome Technology, Stephenson Research and Technology Center, Department of Botany and Microbiology, The University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    Bioinformatics 21:4046-53. 2005
  4. pmc Automating genomic data mining via a sequence-based matrix format and associative rule set
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, 101 David L, Boren Blvd, Rm 2025
    BMC Bioinformatics 6:S2. 2005
  5. pmc Open access and openly accessible: a study of scientific publications shared via the internet
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    BMJ 330:1128. 2005
  6. pmc Biomedical term mapping databases
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    Nucleic Acids Res 33:D289-93. 2005
  7. ncbi request reprint Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons
    Jonathan D Wren
    Advanced Center for Genome Technology, The University of Oklahoma, Norman, Oklahoma 73019, USA
    DNA Cell Biol 23:695-700. 2004
  8. pmc Extending the mutual information measure to rank inferred literature relationships
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 101 David L, Boren Blvd, Rm 2025, Norman 73019, USA
    BMC Bioinformatics 5:145. 2004
  9. ncbi request reprint The emerging in-silico scientist: how text-based bioinformatics is bridging biology and artificial intelligence
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman 73019, USA
    IEEE Eng Med Biol Mag 23:87-93. 2004
  10. ncbi request reprint 404 not found: the stability and persistence of URLs published in MEDLINE
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:668-72. 2004

Collaborators

Detail Information

Publications37

  1. pmc A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
    Zengjun Xu
    Division of Neurotoxicology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S8. 2005
    ..MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear...
  2. ncbi request reprint Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman, 73019, USA
    OMICS 10:15-27. 2006
    ..All extracted regulation and response patterns can be downloaded at the following website: www.ou.edu/microarray/ oumcf/Meta_analysis.xls...
  3. ncbi request reprint Markov model recognition and classification of DNA/protein sequences within large text databases
    Jonathan D Wren
    Advanced Center for Genome Technology, Stephenson Research and Technology Center, Department of Botany and Microbiology, The University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    Bioinformatics 21:4046-53. 2005
    ..g. keyword queries or manual searches). We describe herein a system to accurately identify and classify sequence patterns from within large corpora using an n-gram Markov model (MM)...
  4. pmc Automating genomic data mining via a sequence-based matrix format and associative rule set
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, 101 David L, Boren Blvd, Rm 2025
    BMC Bioinformatics 6:S2. 2005
    ..A prototype was developed and successful in detecting coinciding genomic features among genes, exons, repetitive elements and CpG islands...
  5. pmc Open access and openly accessible: a study of scientific publications shared via the internet
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    BMJ 330:1128. 2005
    ....
  6. pmc Biomedical term mapping databases
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 101 David L Boren Blvd, Rm 2025, Norman, OK 73019, USA
    Nucleic Acids Res 33:D289-93. 2005
    ..hpl.hp.com/research/idl/projects/abbrev.html). In addition to serving as useful computational tools, these databases serve as valuable references that help biologists keep up with an ever-expanding vocabulary of terms...
  7. ncbi request reprint Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons
    Jonathan D Wren
    Advanced Center for Genome Technology, The University of Oklahoma, Norman, Oklahoma 73019, USA
    DNA Cell Biol 23:695-700. 2004
    ..Testing SA on a published dataset, we find that it significantly reduces interexperimental variation, suggesting it holds promise to accomplish this goal...
  8. pmc Extending the mutual information measure to rank inferred literature relationships
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 101 David L, Boren Blvd, Rm 2025, Norman 73019, USA
    BMC Bioinformatics 5:145. 2004
    ..The Mutual Information Measure (MIM) is a well-established method to measure how informative an association is, but is limited to direct (i.e. observable) associations...
  9. ncbi request reprint The emerging in-silico scientist: how text-based bioinformatics is bridging biology and artificial intelligence
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman 73019, USA
    IEEE Eng Med Biol Mag 23:87-93. 2004
  10. ncbi request reprint 404 not found: the stability and persistence of URLs published in MEDLINE
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:668-72. 2004
    ..An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal...
  11. ncbi request reprint Knowledge discovery by automated identification and ranking of implicit relationships
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:389-98. 2004
    ....
  12. ncbi request reprint Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval, Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:191-8. 2004
    ....
  13. pmc A scalable machine-learning approach to recognize chemical names within large text databases
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman, Oklahoma 73019, USA
    BMC Bioinformatics 7:S3. 2006
    ....
  14. pmc E-mail decay rates among corresponding authors in MEDLINE. The ability to communicate with and request materials from authors is being eroded by the expiration of e-mail addresses
    Jonathan D Wren
    Advanced Center for Genome Technology in the Department of Botany and Microbiology at the University of Oklahoma, Norman, OK, USA
    EMBO Rep 7:122-7. 2006
  15. ncbi request reprint Uniform resource locator decay in dermatology journals: author attitudes and preservation practices
    Jonathan D Wren
    Department of Botany and Microbiology, Advanced Center for Genome Technology, University of Oklahoma, Norman, OK, USA
    Arch Dermatol 142:1147-52. 2006
    ..To describe dermatology journal uniform resource locator (URL) use and persistence and to better understand the level of control and awareness of authors regarding the availability of the URLs they cite...
  16. doi request reprint Identification and characterization of zebrafish ocular formation genes
    Han Wang
    Department of Zoology and Stephenson Research and Technology Center, University of Oklahoma, 101 David L Boren Boulevard, Norman, OK 73019, USA
    Genome 51:222-35. 2008
    ....
  17. pmc Functional characterization of the MECP2/IRAK1 lupus risk haplotype in human T cells and a human MECP2 transgenic mouse
    Kristi A Koelsch
    Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
    J Autoimmun 41:168-74. 2013
    ....
  18. ncbi request reprint SIGNAL-Sequence Information and GeNomic AnaLysis
    Jonathan D Wren
    Southwestern Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 8591, USA
    Comput Methods Programs Biomed 68:177-81. 2002
    ..The package can be accessed or downloaded at the following URL: http://innovation.swmed.edu/signal.htm...
  19. ncbi request reprint Cross-hybridization on PCR-spotted microarrays
    Jonathan D Wren
    IEEE Eng Med Biol Mag 21:71-5. 2002
  20. ncbi request reprint Déjà vu--a study of duplicate citations in Medline
    Mounir Errami
    UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390 9185, USA
    Bioinformatics 24:243-9. 2008
    ..Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts...
  21. pmc Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
    Dawn Wilkins
    Computer and Information Science Department, The University of Mississippi, University, MS, USA
    BMC Bioinformatics 8:S1. 2007
  22. pmc The write position. A survey of perceived contributions to papers based on byline position and number of authors
    Jonathan D Wren
    Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
    EMBO Rep 8:988-91. 2007
  23. pmc Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    BMC Bioinformatics 9:S1. 2008
  24. ncbi request reprint Medline: the knowledge buried therein, its potential, and cost
    Harold R Garner
    UT Southwestern Medical Center, Dallas, TX 75390 9185, USA
    IEEE Eng Med Biol Mag 26:73-4. 2007
  25. ncbi request reprint Clustering microarray-derived gene lists through implicit literature relationships
    Mark F Burkart
    Department of Internal Medicine, The McDermott Center for Human Growth and Development, Division of Translational Research, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Bioinformatics 23:1995-2003. 2007
    ..New methods that can identify functionally related genes via shared literature concepts will be useful in addressing these needs...
  26. pmc eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications
    Mounir Errami
    McDermott Center for Human Growth and Development and the Department for Translational Research, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9185, USA
    Nucleic Acids Res 35:W12-5. 2007
    ..These services are freely accessible through the Internet at http://invention.swmed.edu/etblast/etblast.shtml, where users can upload a file or paste text such as an abstract into the browser interface...
  27. ncbi request reprint ARROGANT: an application to manipulate large gene collections
    Amit V Kulkarni
    Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
    Bioinformatics 18:1410-7. 2002
    ....
  28. ncbi request reprint Evolving research trends in bioinformatics
    Carolina Perez-Iratxeta
    Ottawa Health Research Institute, Ontario, Canada
    Brief Bioinform 8:88-95. 2007
    ..Via this analysis, we were able to identify areas of rapid growth in the use of informatics to aid in curriculum planning, development of computational infrastructure and strategies for workforce education and funding...
  29. ncbi request reprint Bioinformatics leads charge by publishing more Internet addresses in abstracts than any other journal
    Lisa M Schilling
    Bioinformatics 20:2903. 2004
  30. ncbi request reprint Theory and reality for software patents: good in concept, not so good in practice
    Jonathan D Wren
    Bioinformatics 22:1543-5. 2006
  31. pmc Large-scale directional relationship extraction and resolution
    Cory B Giles
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N, E, 13th Street, Oklahoma City, Oklahoma 73104 5005, USA
    BMC Bioinformatics 9:S11. 2008
    ..Because of the size and growth of biomedical literature, it is increasingly important to be able to automate this process as much as possible...
  32. doi request reprint Databases, data tombs and dust in the wind
    Jonathan D Wren
    Bioinformatics 24:2127-8. 2008
    ..Thus, for database creators, reviewers and journal editors, there are several additional considerations to judge, prior to publication, how potentially valuable these new databases may be...
  33. doi request reprint URL decay in MEDLINE--a 4-year follow-up study
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Bioinformatics 24:1381-5. 2008
    ..Thus, a reexamination of URL growth and decay in the literature is merited to see if the problem has grown or been mitigated by any of these changes...
  34. ncbi request reprint A system-wide analysis of differentially expressed genes in ectopic and eutopic endometrium
    Jonathan D Wren
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N E 13th Street, Oklahoma City, OK 73104 5005, USA
    Hum Reprod 22:2093-102. 2007
    ..Thus, it is difficult to see 'the big picture' without first integrating these multiple, heterogeneous sources of high-quality information for analysis...
  35. ncbi request reprint Melatonin administration does not affect isoproterenol-induced LVH
    Elizabeth M Flood
    University of Texas Southwestern Medical Center, Dallas 75390 8591, USA
    IEEE Eng Med Biol Mag 25:84-7. 2006
  36. pmc Regional societies: fostering competitive research through virtual infrastructures
    Steven F Jennings
    Department of Applied Science at the University of Arkansas at Little Rock, USA
    PLoS Biol 2:e372. 2004
  37. pmc Truth, probability, and frameworks
    Jonathan D Wren
    PLoS Med 2:e361. 2005