Perry Miller
From Rutgers Medical Informatics History Project
Name: Perry Miller
Elected ACMI Fellow: 1985
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Curriculum Vitae:
Selected Publications:
ustavich LF, Miller P, Kidd KK, Zhao H. Using a pharmacokinetic model to relate an individual's susceptibility to alcohol dependence to genotypes. Hum Hered. 2010;70(3):177-93. Epub 2010 Aug 12. Marenco L, Wang R, Shepherd GM, Miller PL. The NIF DISCO Framework: facilitating automated integration of neuroscience content on the web. Neuroinformatics. 2010 Jun;8(2):101-12. Samwald M, Chen H, Ruttenberg A, Lim E, Marenco L, Miller P, Shepherd G, Cheung KH. Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artif Intell Med. 2010 Jan;48(1):21-8. Epub 2009 Dec 16. Samwald M, Lim E, Masiar P, Marenco L, Chen H, Morse T, Mutalik P, Shepherd G, Miller P, Cheung KH. Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research. Stud Health Technol Inform. 2009;150:317-21. Bernstam EV, Hersh WR, Johnson SB, Chute CG, Nguyen H, Sim I, Nahm M, Weiner MG, Miller P, DiLaura RP, Overcash M, Lehmann HP, Eichmann D, Athey BD, Scheuermann RH, Anderson N, Starren J, Harris PA, Smith JW, Barbour E, Silverstein JC, Krusch DA, Nagarajan R, Becich MJ; CTSA Biomedical Informatics Key Function Committee. Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs. Acad Med. 2009 Jul;84(7):964-70. Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, Morse TM, Mutalik P, Shepherd GM, Miller PL. Approaches to neuroscience data integration. Brief Bioinform. 2009 Jul;10(4):345-53. Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL. The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers. Neuroinformatics. 2008 Sep;6(3):219-27. Epub 2008 Oct 31. Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME. Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics. 2008 Sep;6(3):205-17. Epub 2008 Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL. Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework. Neuroinformatics. 2008 Sep;6(3):229-39. Epub 2008 Oct 25. Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW. The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics. 2008 Sep;6(3):149-60. Epub 2008 Oct 23. Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung KH, Miller PL, Williams K. X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. J Proteome Res. 2008 Jan;7(1):293-9. Epub 2007 Sep 29. Liu N, Xu F, Miller PL, Shepherd GM. OdorMapComparer: an application for quantitative analyses and comparisons of fMRI brain odor maps. Neuroinformatics. 2007 Summer;5(2):105-14. Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR. YPED: a web-accessible database system for protein expression analysis. J Proteome Res. 2007 Oct;6(10):4019-24. Epub 2007 Sep 15. Dinu V, Zhao H, Miller PL. Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. J Biomed Inform. 2007 Dec;40(6):750-60. Epub 2007 Jun 10. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM. SenseLab: new developments in disseminating neuroscience information. Brief Bioinform. 2007 May;8(3):150-62. Epub 2007 May 17. Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics. 2007 May 9;8 Suppl 3:S4. Crasto CJ, Masiar P, Miller PL. NeuroExtract: facilitating neuroscience-oriented retrieval from broadly-focused bioscience databases using text-based query mediation. J Am Med Inform Assoc. 2007 May-Jun;14(3):355-60. Epub 2007 Feb 28. Dinu V, Miller PL, Zhao H. Evidence for association between multiple complement pathway genes and AMD. Genet Epidemiol. 2007 Apr;31(3):224-37. Lam HY, Marenco L, Shepherd GM, Miller PL, Cheung KH. Using web ontology language to integrate heterogeneous databases in the neurosciences. AMIA Annu Symp Proc. 2006:464-8. Corwin J, Silberschatz A, Miller PL, Marenco L. Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems. J Am Med Inform Assoc. 2007 Jan-Feb;14(1):86-93. Epub 2006 Oct 26. Bruce C, Shifman MA, Miller P, Gulcicek EE. Probabilistic enrichment of phosphopeptides by their mass defect. Anal Chem. 2006 Jul 1;78(13):4374-82. Shifman MA, Sun K, Colangelo CM, Cheung KH, Miller P, Williams K. YPED: a proteomics database for protein expression analysis. AMIA Annu Symp Proc. Gerstein M, Greenbaum D, Cheung K, Miller PL. An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective. J Biomed Inform. 2007 Feb;40(1):73-9. Epub 2006 Mar 6. Liu N, Marenco L, Miller PL. ResourceLog: an embeddable tool for dynamically monitoring the usage of web-based bioscience resources. J Am Med Inform Assoc. 2006 Jul-Aug;13(4):432-7. Epub 2006 Apr 18. Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: an allele frequency database for microevolutionary studies. Evol Bioinform Online. 2007 Feb 22;1:1-10. Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. J Am Med Inform Assoc. 2005 Jan-Feb;12(1):90-8. Epub 2004 Oct 18. Marenco L, Wang TY, Shepherd G, Miller PL, Nadkarni P. QIS: A framework for biomedical database federation. J Am Med Inform Assoc. 2004 Nov-Dec;11(6):523-34. Epub 2004 Aug 6. Cheung KH, Hager J, Pan D, Srivastava R, Mane S, Li Y, Miller P, Williams KR. KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W441-4. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):38 Shifman MA, Srivastava R, Brandt CA, Li TR, White K, Miller PL. Exploring the portability of informatics capabilities from a clinical application to a bioscience application. J Am Med Inform Assoc. 2004 Jul-Aug;11(4):294-9. Epub 2004 Apr 2. Gardner D, Toga AW, Ascoli GA, Beatty JT, Brinkley JF, Dale AM, Fox PT, Gardner EP, George JS, Goddard N, Harris KM, Herskovits EH, Hines ML, Jacobs GA, Jacobs RE, Jones EG, Kennedy DN, Kimberg DY, Mazziotta JC, Miller PL, Mori S, Mountain DC, Reiss AL, Rosen GD, Rottenberg DA, Shepherd GM, Smalheiser NR, Smith KP, Strachan T, Van Essen DC, Williams RW, Wong ST. Towards effective and rewarding data sharing. Neuroinformatics. 2003;1(3):289-95. Crasto CJ, Marenco LN, Migliore M, Mao B, Nadkarni PM, Miller P, Shepherd GM. Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics. 2003;1(3):215-37. Eckersley P, Egan GF, Amari S, Beltrame F, Bennett R, Bjaalie JG, Dalkara T, De Schutter E, Gonzalez C, Grillner S, Herz A, Hoffmann KP, Jaaskelainen IP, Koslow SH, Lee SY, Matthiessen L, Miller PL, da Silva FM, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Subramaniam S, Toga AW, Usui S, van Pelt J, Verschure P, Willshaw D, Wrobel A, Tang Y; OECD Working Group on Neuroinformatics. Neuroscience data and tool sharing: a legal and policy framework for 04-14. Liu N, Xu F, Marenco L, Hyder F, Miller P, Shepherd GM. Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb: OdorMapBuilder and OdorMapDB. Neuroinformatics. 2004;2(1):3-18. Shifman MA, Srivastava R, Brandt CA, Li TR, White K, Miller PL. Exploring the portability of informatics capabilities from a clinical application to a bioscience application. J Am Med Inform Assoc. 2004 Jul-Aug;11(4):294-9. Epub 2004 Apr 2. Gardner D, Toga AW, Ascoli GA, Beatty JT, Brinkley JF, Dale AM, Fox PT, Gardner EP, George JS, Goddard N, Harris KM, Herskovits EH, Hines ML, Jacobs GA, Jacobs RE, Jones EG, Kennedy DN, Kimberg DY, Mazziotta JC, Miller PL, Mori S, Mountain DC, Reiss AL, Rosen GD, Rottenberg DA, Shepherd GM, Smalheiser NR, Smith KP, Strachan T, Van Essen DC, Williams RW, Wong ST. Towards effective and rewarding data sharing. Neuroinformatics. 2003;1(3):289-95. Crasto CJ, Marenco LN, Migliore M, Mao B, Nadkarni PM, Miller P, Shepherd GM. Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics. 2003;1(3):215-37. Eckersley P, Egan GF, Amari S, Beltrame F, Bennett R, Bjaalie JG, Dalkara T, De Schutter E, Gonzalez C, Grillner S, Herz A, Hoffmann KP, Jaaskelainen IP, Koslow SH, Lee SY, Matthiessen L, Miller PL, da Silva FM, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Subramaniam S, Toga AW, Usui S, van Pelt J, Verschure P, Willshaw D, Wrobel A, Tang Y; OECD Working Group on Neuroinformatics. Neuroscience data and tool sharing: a legal and policy framework for neuroinformatics. Neuroinformatics. 2003;1(2):149-65. Amari S, Beltrame F, Bjaalie JG, Dalkara T, De Schutter E, Egan GF, Goddard NH, Gonzalez C, Grillner S, Herz A, Hoffmann KP, Jaaskelainen I, Koslow SH, Lee SY, Matthiessen L, Miller PL, Da Silva FM, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Sebestra V, Subramaniam S, Tang Y, Toga AW, Usui S, Van Pelt J, Verschure P, Willshaw D, Wrobel A; OECD Neuroinformatics Working Group. Neuroinformatics: the integration of shared databases and tools towards integrative neuroscience. J Integr Neurosci. 2002 Dec;1(2):117-28. Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH, Stormo GD, Szczepaniak MC, Tuck D, Williamson J; American College of Medical Informatics. Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc. 2004 May-Jun;11(3):167-72. Epub 2004 Feb 5. Crasto CJ, Morse TM, Migliore M, Nadkarni P, Hines M, Brash DE, Miller PL, Shepherd GM. Creating knowledgebases to text-mine clustering techniques. AMIA Annu Symp Proc. 2003:821. Cohen DB, Frawley SJ, Shifman MA, Miller PL, Brandt C. The integration of similar clinical research data collection instruments. AMIA Annu Symp Proc. 2003:817. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3. Cheung KH, Hager J, Nelson K, White K, Li Y, Snyder M, Williams K, Miller P. A dynamic approach to mapping coordinates between microplates and microarrays. J Biomed Inform. 2002 Oct-Dec;35(5-6):306-12. Miller PN, Lawrence RJ, Powell RC. Discrete varieties of care in the clinical pastoral tradition: continuing the dialogue. J Pastoral Care Counsel. 2003 Summer;57(2):111-6. Marenco L, Tosches N, Crasto C, Shepherd G, Miller PL, Nadkarni PM. Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances. J Am Med Inform Assoc. 2003 Sep-Oct;10(5):444-53. Epub 2003 Jun 4. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of human Chromosome 22. Genes Dev. 2003 Feb 15;17(4):529-40. Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K. YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002:140-4. Brandt CA, Morse R, Matthews K, Sun K, Deshpande AM, Gadagkar R, Cohen DB, Miller PL, Nadkarni PM. Metadata-driven creation of data marts from an EAV-modeled clinical research database. Int J Med Inform. 2002 Nov 12;65(3):225-41. Shifman MA, Sayward FG, Mattie ME, Miller PL. Exploring issues of quality of service in a Next Generation Internet testbed: a case study using PathMaster. J Am Med Inform Assoc. 2002 Sep-Oct;9(5):491-9. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: An allele frequency database for anthropology. Am J Phys Anthropol. 2002 Sep;119(1):77-83. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M. Subcellular localization of the yeast proteome. Genes Dev. 2002 Mar 15;16(6):707-19. Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. An integrated approach for finding overlooked genes in yeast. Nat Biotechnol. 2002 Jan;20(1):58-63. Crasto C, Marenco L, Miller P, Shepherd G. Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Res. 2002 Jan 1;30(1):354-60. Kumar A, Cheung KH, Tosches N, Masiar P, Liu Y, Miller P, Snyder M. The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Res. 2002 Jan 1;30(1):73-5.
Books
Main title: Selected topics in medical artificial intelligence / Perry
L. Miller, editor.
Published/Created: New York : Springer-Verlag, c1988.
Related names: Miller, Perry L.
ISBN: 038796701X
Personal name: Miller, Perry L.
Main title: A critiquing approach to expert computer advice--ATTENDING
/ Perry L. Miller.
Published/Created: Boston : Pitman, 1984.
ISBN: 0273086650 : $18.00
Personal name: Miller, Perry L.
Main title: Expert critiquing systems : practice-based medical
consultation by computer / Perry L. Miller.
Published/Created: New York : Springer-Verlag, c1986.
ISBN: 0387962913 : $37.00 (est.)
Series: Computers and medicine
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