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Dr. Wren:

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Arthritis and Immunology Research Program

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OMRF receives $26 million for two federal research grants

Jonathan D. Wren, Ph.D. Assistant Member, Arthritis and Immunology Research Program

Selected Peer-Reviewed Publications
(1)  O'Brien KM, Wren JD, Dave VK, Bai D, Anderson RD, Rayner S, Evans G, Dabiri AE, Garner HR, "ASTRAL, a hyperspectral imaging DNA sequencer", Review of Scientific Instruments 1998 May; 9(5), 2141-6 [link]

(2)  Fondon JW 3rd, Mele GM, Cummings D, Pande A, Wren J, O'Brien KM, Kupfer KC, Lerman M, Minna JD and Garner HR, "Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog", Proceedings of the National Academy of Sciences 1998 Jun 23; 95(13):7514-9 [PDF]

(3) Wren JD, Forgacs E, Fondon JW 3rd, Pertsemlidis A, Cheng S, Gallardo T, Williams RS, Shohet RV, Minna JD, and Garner HR "Repeat polymorphisms within gene regions: Phenotypic and evolutionary implications", American Journal of Human Genetics 2000 Aug; 67(2): 345-56 [PDF]

(4) Forgacs E, Wren JD, Kamibayashi C, Kondo M, Xu XL, Markowitz S, Tomlinson GE, Muller CY, Gazdar AF, Garner HR and Minna JD "Searching for microsatellite mutations in coding regions in lung, breast, ovarian and colorectal cancers", Oncogene 2001 Feb 22; 20(8): 1005-9 [PubMed]

(5) Wren JD, Mittleman D, Garner HR "SIGNAL - Sequence Information and GeNomic AnaLysis" Computer Methods and Programs in Biomedicine 2002 May; 68(2): 177-81 [PubMed]

(6) Wren JD, Kulkarni A, Joslin J, Butow R and Garner HR "Cross-hybridization on PCR spotted microarrays" IEEE Engineering in Medicine and Biology 2002 Mar-Apr; 21(2): 71-5. [link]

(7) Kulkarni AV, Williams NS, Lian Y, Wren JD, Mittleman D, Persemlidis A, Garner HR "ARROGANT: An application to manipulate large gene collections" Bioinformatics 2002 Nov; 18(11): 1410-7 [PDF]

(8) Wren JD, Garner HR "Heuristics for identification of acronym-definition patterns within text: Towards an automated construction of comprehensive acronym-definition dictionaries" Methods of Information in Medicine 2002; 41(5): 426-34 [PubMed]
......... (8a) Leslie M, "TOOLS: Acronym Soup" Science 2004 Jul 9; Vol 305: p. 157 [link]

(9) Wren JD "The IRIDESCENT System: An Automated Data-Mining Method to Identify, Evaluate, and Analyze Sets of Relationships Within Textual Databases" Ph.D. Dissertation, University of Texas Southwestern Medical Center, January 2003 [link]

(10) Wren JD, Garner HR "Shared Relationship Analysis: Ranking set cohesion and commonalities within a literature-derived relationship network" Bioinformatics 2004 Jan; 20(2): 191-8 [PDF]

(11) Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR "Knowledge discovery by automated identification and ranking of implicit relationships" Bioinformatics 2004 Feb; 20(3): 389-98 [PDF]

(12) Wren JD "404 Not Found: The Stability and Persistence of URLs Published in MEDLINE" Bioinformatics 2004 Mar; 20(5): 668-72 [PDF]
.........(12a) Schilling LM, Wren JD, Dellavalle RP "Bioinformatics leads charge by publishing more Internet addresses
.........in abstracts than any other journal" Bioinformatics 2004 Nov 22; 20(17):2903 (Letter) [PubMed]
.........(12b) Whitfield J "Web links leave abstracts going nowhere" Nature 2004 Apr 8; Vol. 428: p. 592 [PubMed]
.........(12c) Carlson, S "Here today, gone tomorrow: Studying how online footnotes vanish" Chronicle of Higher Education 2004
.........Apr 30th; 50(34): p. A33 [link]

(13) Wren JD "The emerging In-Silico scientist: How text-based bioinformatics is bridging biology and artificial intelligence" IEEE Engineering in Medicine and Biology 2004 Mar-Apr; 23(2): 87-93 [link]

(14) Wren JD "Extending the mutual information measure to rank inferred literature relationships" BMC Bioinformatics 2004 Oct 7; 5(1): 145 [Open Access]

(15) Wren JD, Yao M, Langer M, Conway T "Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons" DNA and Cell Biology 2004 Oct; 23(10): p. 695-700 [PubMed]

(16) Jennings SF, Ptitsyn AA, Wilkins D, Bruhn RE, Slikker W, Wren JD "Regional societies: Fostering competitive research through virtual infrastructures" PLoS Biology 2004 Dec; 2(12): e372-3 [Open Access]

(17) Wren JD, Chang JT, Pustejovsky J, Adar E, Garner HR, Altman RB "Biomedical term mapping databases" Nucleic Acids Research 2005 Jan; 3(Database Issue): D289-293 [Open Access]

(18) Mizumoto N, Hui F, Edelbaum D, Weil MR, Wren JD, Shalhevet D, Matsue H, Liu L, Garner HR, Takashima A "Differential activation profiles of multiple transcription factors during dendritic cell maturation" Journal of Investigative Dermatology 2005 Apr; 124(4): 718-24 [PubMed]

(19) Wren JD "Open access and openly accessible: A study of scientific publications shared via the Internet" British Medical Journal 2005 May 14; 330(7500):1128-31 [PDF (long version)] - posted with permission from BMJ  ;)
.........(19a) Suber P "Open access, impact and demand" BMJ 2005 May 14; 330(7500):1104 [PubMed]

(20) Wren JD "Automating literature-based lead discovery", in Frontiers in Drug Design and Discovery (eds. GW Caldwell, A Rahman and BA Springer), Bentham Science Publishers, 2005; Volume 1, p.267-86. [link]

(21) Wren JD, Garner HR "Data-mining analysis suggests an epigenetic pathogenesis for Type II Diabetes" Journal of Biomedicine and Biotechnology 2005 Jun; 2005(2): 104-12 [Open Access]

(22) Wren JD and Slikker W "Proceedings of the Midsouth Computational Biology and Bioinformatics Society 2004 Conference" BMC Bioinformatics 2005 Jul 15; 6(Suppl 2):S1  [Open Access] (editorial)

(23) Wren JD, Johnston DK, Gruenwald L "Automating genomic data mining via a sequence-based matrix format and associative rule set" BMC Bioinformatics 2005 Jul 15; 6(Suppl 2):S2 [Open Access]

(24) Xu Z, Patterson TA, Wren JD, Han T, Shi L, Duhart H, Ali SF, Slikker W "A microarray study of MPP+-treated PC12 cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools" BMC Bioinformatics 2005 Jul 15; 6(Suppl 2):S8  [Open Access]

(25) Wren JD, Hildebrand WH, Chandrasekaran S, Melcher UK "Markov model recognition and classification of DNA/Protein sequences within large text databases" Bioinformatics 2005 Nov 1; 21(21): 4046-53 [PubMed]

(26) Wren JD "Truth, probability, and frameworks" PLoS Medicine 2005 Nov; 2(11):e361 [Open Access] (letter)

(27) Wren JD "Using Fuzzy Set Theory and scale-free network properties to relate MEDLINE terms" Soft Computing 2006 Feb; 10(4): 374-81 [link] [Supplementary_Info]

(28) Wren JD, Grissom JE, Conway T "Email decay rates among MEDLINE corresponding authors" EMBO Reports 2006 Feb; 7(2): 122-7 [Open Access]

(29) Wren JD, Conway T "Meta-analysis of published transcriptional and translational fold-changes reveals a preference for low-fold inductions" OMICS 2006 Feb; 10(1) 15-27 [PubMed]

(30) Wren JD, Roossinck MJ, Nelson RS, Scheets K, Palmer MW, Melcher U "Plant virus biodiversity and ecology" PLoS Biology 2006 Mar;4(3):e80 [Open Access]

(31) Flood EM, Kumar RS, Shah R, Amos Q, Wren JD, Shohet RV, Garner HR "Melatonin administration does not affect isoproterenol-induced LVH" IEEE Engineering in Medicine and Biology 2006 May-Jun 25(3):84-7 [PubMed]

(32) Wren JD "Theory and reality for software patents: Good in concept, not so good in practice" Bioinformatics 2006 Jul 1;22(13):1543-5 [PubMed] (editorial)

(33) Wren JD, Ptitsyn AA, Gusev Y, Winters-Hilt S "Proceedings of the 2006 Midsouth Computational Biology and Bioinformatics Society Conference" BMC Bioinformatics 2006 Sep 26; 7(Suppl 2):S1 (editorial) [Open Access]

(34) Wren JD "A scalable machine-learning approach to recognize chemical names within large text databases" BMC Bioinformatics 2006 Sep 26; 7(Suppl 2):S3 [Open Access]

(35) Wren JD, Johnson KR, Crockett DM, Heilig LF. Schilling LM, Dellavalle RP "URL decay in dermatology journals: Author attitudes and preservation practices" Archives of Dermatology 2006 Sep; 142(9):1147-52 [PubMed]

(36) Perez-Iraxeta C, Andrade MA, Wren JD "Evolving research trends in bioinformatics" Briefings in Bioinformatics 2006 Oct 31 [PubMed]

(37) Garner HR, Hicks J, Wren JD, Errami M "Medline: the knowledge buried therein, its potential, and cost" IEEE Eng Med Biol 2007 May-Jun;26(3):73-4.

(38) Errami M, Wren JD, Hicks JM, Garner HR “eTBLAST: A web server to identify expert reviewers, appropriate journals and similar publications.” Nucleic Acids Research 2007 Jul 1;35(Web Server issue):W12-5 [Open Access]

(39) Wren JD, Wu Y, Guo S "A Near-System-Wide Analysis of Differentially Expressed Genes in Ectopic and Eutopic Endometrium" Human Reproduction 2007 Aug;22(8):2093-2102

(40) Burkart MF, Wren JD, Herschkowitz JI, Perou CM, Garner HR "Clustering Microarray- Derived Gene Lists through Implicit Literature Relationships" Bioinformatics 2007 Aug 1;23(15):1995-2003

(41) Wilkins D, Gusev Y, Loganantharaj R, Bridges S, Winters-Hilt S, Wren JD "Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society" BMC Bioinformatics Nov 1, 2007; 7(Suppl 8):S1 (editorial)

(42) Wren JD, Kozak KZ, Johnson KR, Deakyne SJ, Schilling LM, Dellavalle RP "The Write Position: A survey of perceived contributions to papers based upon byline position and number of authors" EMBO Reports November 2007; 8(11): 988-91
.........(42a) Interviewed for and featured in Genome Technology cover story "Team Science v. Tenure". March 2008, p.38-42

(43) Errami M, Hicks JM, Fisher W, Trusty D, Wren JD, Long TC, Garner HR "Déjà vu - A Study of Duplicate Citations in Medline" Bioinformatics 2008 Jan 15;24(2):243-9.
.........(43a) Errami M, Garner HR "A tale of two citations" Nature. 2008 Jan 24;451(7177):397-9
.........(43b) Zizzo D "Computer Program Hunts Copycats" The Oklahoman newspaper, March 18 2008 - featured for Science & Health front page story

(44) Wang H, Kesinger JW, Zhou Q, Wren JD, Martin G, Turner S, Tang Y, Frank MB, Centola M "Identification and expression of ocular formation genes in zebrafish" Genome 2008 Mar; 51(3):222-235.

(45) Wren JD "URL decay in MEDLINE - a 4-year follow-up study" Bioinformatics 2008 Jun 1;24(11):1381-5.

(46) Wren JD, Wilkins D, Fuscoe J, Bridges S, Winters-Hilt S, Gusev Y "Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference" BMC Bioinformatics 2008 Aug 12; 9(Suppl 9): S1 (editorial)

(47) Giles CB and Wren JD "Large-scale Directional Relationship Extraction and Resolution" BMC Bioinformatics 2008 Aug 12; 9(Suppl 9): S11

(48) Wren JD, Bateman A "Databases, Data Tombs and Dust in the Wind" Bioinformatics 2008; 24(19): 2127-8 (editorial)

(49) Wren JD "The 'Open Discovery' Challenge" in Literature-Based Discovery (eds. Peter Bruza & Marc Weeber) Springer-Verlag Berlin Heidelberg 2008: pp. 39-55

(50) Webb R, Wren JD, Jeffries M, Kelly JA, Kaufman KM, Tang Y, Frank MB, Merrill J, PROFILE study group, Alarcón-Riquelme ME, James JA, Vyse TJ, Moser KL, Gilkeson GS, Harley JB, Sawalha AH "Variants within MECP2, a key transcriptional regulator, are associated with increased susceptibility to lupus and differential gene expression in lupus patients" Arthritis & Rheumatism 2009 (in press)

Mailing Address
Arthritis and Immunology Research Program, MS 58
Oklahoma Medical Research Foundation
825 N.E. 13th Street
Oklahoma City, Oklahoma 73104

Contact Information
Phone: (405) 271-6989
Fax: (405) 271-4110