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Perry L. Miller, MD, PhD
Curriculum Vitae
Education
AB
MS
PhD
MD
Harvard University, 1966, Physics and Chemistry
University of California, Berkeley, 1969, EE & CS
Massachusetts Institute of Technology, 1973, Computer Science
University of Miami, 1978
Employment
1966-68 IBM, Systems Engineer, Boston, MA & London, England
1969-75 Massachusetts Institute of Technology
1969-1973 Research Assistant
1973-1975 Research Staff
1975-76 Boston College, Assistant Professor, Computer Sciences
1978-81 Hospital of the University of Pennsylvania, Resident, Anesthesiology
1981Yale University
1981-1987 Assistant Professor, Anesthesiology
1987-1992 Associate Professor, Anesthesiology
1992-2016 Professor, Anesthesiology
2016Professor Emeritus and Senior Research Scientist, Anesthesiology
1982-1984 Section Chief, General Anesthesia Group
1985-2014 Director, Yale Biomedical Informatics Research Training Program
1991-2016 Director, Yale Center for Medical Informatics
2001-2014 Professor, Molecular, Cellular & Developmental Biology
2003-2011 Co-Director, Bioinformatics, Yale Center for Genomics and Proteomics
2003-2012 Co-Director for Graduate Studies, Interdepartmental PhD Program
in Computational Biology and Bioinformatics
2006Director, Biomedical Informatics, Yale Center for Clinical Investigation
2011-2016 Co-Director, Clinical Informatics Pathway, Master of Health Science (MHS)
Program
2009VA Connecticut Healthcare System, Staff Physician researcher
Books and Monographs
1.
Miller PL: Automatic Creation of a Code Generator from a Machine Description. MAC-TR-85,
Project MAC, MIT, May 1971.
2.
Miller PL: A Locally-Organized Parser for Spoken Input. TR-503, MIT Lincoln Laboratory, May
1973.
3.
Miller PL: A Critiquing Approach to Expert Computer Advice: ATTENDING. London/Boston:
Pitman, 1984.
4.
Miller PL: Expert Critiquing Systems: Practice-Based Medical Consultation by Computer. New
York: Springer-Verlag, 1986.
5.
Miller PL (Ed.): Selected Topics in Medical Artificial Intelligence. New York: Springer-Verlag,
1988.
Perry L. Miller, MD, PhD
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Curriculum Vitae
Journal Articles
1.
Miller PL: A locally-organized parser for spoken input. Communications of the Association for
Computing Machinery 17:621-630, 1974.
2.
Miller PL: An adaptive natural language parser. Proceedings of the Association for Computational
Linguistics Conference, 1975; American Journal of Computational Linguistics Fall 1975.
3.
Miller PL: ATTENDING: Critiquing a physician's management plan. IEEE Transactions on Pattern
Analysis and Machine Intelligence PAMI-5:449-461, 1983.
4.
Miller PL: Critiquing anesthetic management: The "ATTENDING" computer system.
Anesthesiology 58:362-369, 1983.
5.
Miller PL, Black HR: Medical plan-analysis by computer: Critiquing the pharmacologic
management of essential hypertension. Computers and Biomedical Research 17:38-54, 1984.
6.
Miller PL: Medical plan-analysis by computer. Computer Programs in Biomedicine 18:15-20,
1984.
7.
Miller PL: Training for a research career in Medical Information Science: How much is enough?
Medical Informatics 9:301-304, 1984.
8.
Miller PL, Blumenfrucht SJ, Black HR: An expert system which critiques patient workup:
Modeling conflicting expertise. Computers and Biomedical Research 17:554-569, 1984.
9.
Miller PL, Black HR: HT-ATTENDING: Critiquing the pharmacologic management of essential
hypertension. Journal of Medical Systems 8:181-187, 1984.
10.
Miller PL: Goal-directed critiquing by computer: Ventilator management. Computers and
Biomedical Research 18:422-438, 1985.
11.
Miller PL: Building an expert critiquing system: ESSENTIAL-ATTENDING. Methods of
Information in Medicine 25:71-78, 1986. Republished in Methods of Information in Medicine,
Special Issue 1988: 297-304.
12.
Miller PL: Critiquing: A different approach to computer-based advice in medicine. Medical
Informatics 11:29-38, 1986.
13.
Tanner GE, Angers DG, Barash PG, Mulla A, Miller PL, Rothstein P: Effect of left-to-right, mixed
left-to-right, and right-to-left shunts on inhalational anesthetic induction in children: A computer
model. Anesth Analg 64:101-107, 1985.
14.
Miller PL: Extending computer-based critiquing to a new domain: ATTENDING, ESSENTIALATTENDING, and VQ-ATTENDING. International Journal of Clinical Monitoring and Computing
2:135-142, 1986.
15.
Miller PL, Shaw C, Rose JR, Swett HA: Critiquing the process of radiologic differential diagnosis.
Computer Methods and Programs in Biomedicine 22:12-25, 1986.
16.
Miller PL: The evaluation of artificial intelligence systems in medicine. Computer Methods and
Programs in Biomedicine 22:5-11, 1986.
Perry L. Miller, MD, PhD
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Curriculum Vitae
17.
Rennels GD, Shortliffe EH, Miller PL: Choice and explanation in medical management: A multiattribute model of artificial intelligence approaches. Medical Decision Making 7:22-31, 1987.
18.
Rennels GD, Miller PL: Artificial intelligence research in anesthesia and intensive care. Journal of
Clinical Monitoring 4:274-289, 1988.
19.
Miller PL, Rennels GD: Prose generation from expert systems: An applied computational linguistics
approach. AI Magazine 9;3:37-44, 1988.
20.
Mars NJI, Miller PL: Knowledge acquisition and verification tools for medical expert systems.
Medical Decision Making 7:6-11, 1987.
21.
Miller PL, Blumenfrucht SJ, Rose JR, Rothschild M, Swett HA, Weltin G, Mars NJI: HYDRA: A
knowledge acquisition tool for expert systems which critique medical workup. Medical Decision
Making 7:12-21, 1987.
22.
Frolich M, Morrow J, Miller PL: Modeling differential diagnosis as "dynamic competition" between
systematic analysis and disease directed deduction. Computers and Biomedical Research 23:449513, 1990.
23.
Swett HA, Miller PL: ICON: A computer-based approach to differential diagnosis in radiology.
Radiology 163:555-558, 1987.
24.
Rothschild M, Swett HA, Fisher PR, Weltin G, Miller PL: Exploring subjective vs. objective issues
in the validation of computer-based critiquing advice. Computer Methods and Programs in
Biomedicine 31:11-18, 1990.
25.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: A computational model of reasoning from the
clinical literature. Computer Methods and Programs in Biomedicine 24:139-149, 1987.
26.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: A structured representation of the clinical
literature and its use in a medical management advice system. Bulletin du Cancer 74:215-220, 1987.
27.
Miller PL, Barwick KW, Morrow JS, Powsner SM, Riely CA: Semantic relationships and medical
bibliographic retrieval: A preliminary assessment. Computers and Biomedical Research 21:64-77,
1988.
28.
Miller PL: Exploring the critiquing approach: Clinical practice-based feedback by computer.
Biomedical Measurement, Informatics and Control 2:108-112, 1988.
29.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: A computational model of reasoning from the
clinical literature. AI Magazine 10(1):49-57, 1988.
30.
Miller PL, Morrow JS, Powsner SM, Riely CA: Semantically assisted medical bibliographic
retrieval: An experimental computer system. Bulletin of the Medical Library Association 76:131136, 1988.
31.
Swett HA, Rothschild M, Weltin GG, Fisher PR, Miller PL: Optimizing radiologic workup: An
artificial intelligence approach. Journal of Digital Imaging 2:15-20, 1989.
32.
Miller PL, Smith P, Morrow JS, Riely CA, Powsner SM: Capturing the semantic relationship
Perry L. Miller, MD, PhD
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Curriculum Vitae
between clinical terms with current MeSH bibliographic coding. Computer Methods and Programs
in Biomedicine 27:205-211, 1988.
33.
Powsner SM, Barwick KW, Morrow JS, Riely CA, Miller PL: Automated bibliographic retrieval
based on current topics in hepatology: HEPATOPIX. Computers and Biomedical Research 22:552564, 1989.
34.
Cohn AI, Fisher PR, Mutalik P, Miller PL, Swett HA: AXON: Knowledge-based retrieval of
radiographic studies using "axes" of clinical relevance. Computers and Biomedical Research
23:199-221, 1990.
35.
Cohn AI, Rosenbaum SH, Factor M, Miller PL: DYNASCENE: An approach to computer-based
intelligent cardiovascular monitoring using sequential clinical "scenes". Methods of Information in
Medicine 29:122-131, 1990.
36.
Swett HA, Fisher PR, Miller PL, Mutalik PG: Expert system controlled image display. Radiology
172:487-493, 1989.
37.
Miller PL, Sittig DF: The evaluation of clinical decision support systems: What is necessary vs.
what is interesting. Medical Informatics 15:185-190, 1990.
38.
Factor M, Sittig DF, Cohn AI, Gelernter D, Miller PL, Rosenbaum SH: A parallel software
architecture for building intelligent medical monitors. International Journal of Clinical Monitoring
& Computing 7:117-128, 1990.
39.
Berger M, Gelfand R, Miller PL: Combining statistical, rule-based and physiologic model-based
methods to assist in the management of diabetes mellitus. Computers and Biomedical Research
23:346-357, 1990.
40.
Miller PL, Nadkarni PM, Carriero NM: Parallel computation and FASTA: Confronting the
problems of parallel database search for a fast sequence comparison algorithm. Computer
Applications in the Biosciences 7:71-78, 1991.
41.
Factor M, Gelernter D, Kolb C, Miller PL, Sittig DF: Real-time data fusion in the ICU. IEEE
Computer 24:45-54, 1991.
42.
Sittig DF, Foulser D, Carriero N, McCorkle G, Miller PL: A parallel computing approach to genetic
sequence comparison: The master-worker paradigm with interworker communication. Computers
and Biomedical Research 24:152-169, 1991.
43.
Clyman JI, Issacsohn J, Gelfand RA, Miller PL: LIPID-ADVISOR: A computer program to help in
the management of hyperlipidemia. Journal of Medical Practice Management 6:186-192, 1991.
44.
Ball SS, Mah VH, Miller PL: SENEX: A computer-based representation of the cellular signal
transduction processes in the central nervous system. Computer Applications in the Biosciences
7:175-187, 1991.
45.
Miller PL, Nadkarni P, Gelernter JE, Carriero N, Pakstis AJ, Kidd KK: Parallelizing genetic linkage
analysis: A case study for applying parallel computation in molecular biology. Computers and
Biomedical Research 24:234-248, 1991. Also published in: van Bemmel JH, McCray AT:
Yearbook 92 of Medical Informatics Stuttgart: Schattauer, 1992, pp. 478-492.
Perry L. Miller, MD, PhD
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Curriculum Vitae
46.
Goradia TM, Lange K, Miller PL, Nadkarni PM: Fast computation of genetic likelihoods on human
pedigree data. Human Heredity 42:42-62, 1992.
47.
Shifman MA, Windemuth A, Schulten K, Miller PL: Molecular dynamics on a network of
workstations using a machine-independent parallel programming language. Computers and
Biomedical Research 25:168-180, 1992.
48.
Miller PL, Nadkarni PM, Pearson WR: Comparing machine-independent vs. machine-specific
parallelization of a software platform for biological sequence comparison. Computer Applications
in the Biosciences 8:167-175, 1992.
49.
Miller PL, Nadkarni PN, Bercovitz P: Harnessing networked workstations as a powerful parallel
machine: A general paradigm illustrated using three programs for genetic linkage analysis.
Computer Applications in the Biosciences 8:141-147, 1992.
50.
Sittig DF, Shifman MA, Nadkarni P, Miller PL: Parallel computation for medicine and biology:
Experience with Linda at Yale University. International Journal of Supercomputing Applications
6:147-163, 1992.
51.
Miller PL, Paton JA, Clyman JI, Powsner SM: Prototyping an institutional IAIMS/UMLS
information environment for an academic medical center. Bulletin of the Medical Library
Association 80:281-287, 1992. Also published in: van Bemmel JH, McCray AT: Yearbook 93 of
Medical Informatics Stuttgart: Schattauer, 1993, pp. 133-139.
52.
Jachna J, Miller PL, Powsner SM: Augmenting Grateful Med with the UMLS metathesaurus: An
initial evaluation with psychiatric consultation cases. Bulletin of the Medical Library Association
81:20-28, 1993.
53.
Powsner SM, Miller PL: Automated online transition from the medical record to the psychiatric
literature. Methods of Information in Medicine 31:169-174, 1992. Also published in: van Bemmel
JH, McCray AT: Yearbook 93 of Medical Informatics Stuttgart: Schattauer, 1993, pp. 234-239.
54.
Clyman JI, Powsner SM, Paton JA, Miller PL: Using the UMLS information sources map to access
online reference materials. Bulletin of the Medical Library Association 8:207-216. 1993.
55.
Berman L, Cullen MR, Miller PL: Automated integration of external databases: A knowledge-based
approach to enhancing rule-based expert systems. Computers and Biomedical Research 26:230-241,
1993.
56.
Wright LW, Lichter JB, Shifman MA, Kidd KK, Miller PL: Computer-assisted restriction mapping:
An integrated approach to handling experimental uncertainty. Computer Applications in the
Biosciences 10:435-442, 1994.
57.
Board of Directors of the American Medical Informatics Association (Ackerman MJ, Ball MJ,
Clayton PD, Frisse ME, Gardner RM, Greenes RA, Hammond WE, Kingsland LC, McDonald CJ,
Masys DR, Miller PL, Miller RA, Mitchell JA, Ozbolt JG, Stead WW): Standards for medical
identifiers, codes and messages needed to create an efficient computer-stored medical record.
Journal of the American Medical Informatics Association 1:1-7, 1994.
58.
Miller PL, Frawley SJ: Tradeoffs in producing patient-specific recommendations from a computerbased clinical guideline: A case study. Journal of the American Medical Informatics Association
2:238-242, 1995.
Perry L. Miller, MD, PhD
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Curriculum Vitae
59.
Miller PL, Frawley SJ, Wright L, Roderer NK, Powsner SM: Lessons learned from a pilot
implementation of the UMLS information sources map. Journal of the American Medical
Informatics Association 2:102-115, 1995.
60.
Schippits MG, Miller PL, Perrino AC, Rosenblatt W, Smith W: MUPIT: Helping clinicians build
computer-based multimedia applications. MD Computing 12:215-225, 1995.
61.
Krauter K, Montgomery K, Yoon SJ, LeBlanc-Straceski J, Renault B, Marondel I, Herdman V,
Banks A, Lieman J, Menninger J, Bray-Ward P, Nadkarni P, Weissenbach J, Chumakov I, Cohen
D, Miller P, Ward D, Kucherlapati R: A second generation physical map of human chromosome 12.
Nature 377 Suppl.:321-333, 1995.
62.
Miller PL, Nadkarni PM, Kidd KK, Cheung K, Ward DC, Banks A, Bray-Ward P, Cupelli L,
Herdman V, Marondel I, Montgomery K, Renault B, Yoon S, Krauter KS, Kucherlapati R: Internetbased support for biomedical research: A collaborative genome center for human chromosome 12.
Journal of the American Medical Informatics Association 2:351-364, 1995.
63.
Miller PL: Medical informatics in clinical medicine and the biosciences. Nature Medicine 1:93-94,
1995.
64.
Nadkarni PM, Banks A, Montgomery K, LeBlanc-Straceski J, Miller P, Krauter K: CONTIGEXPLORER: Interactive marker content map assembly. Genomics 31:301-310, 1996.
65.
Kannry JL, Wright L, Shifman M, Silverstein S, Miller PL: Portability issues for a structured
clinical vocabulary: Mapping from Yale to the Columbia Medical Entities Dictionary. Journal of the
American Medical Informatics Association 3:66-78, 1996.
66.
Cheung KH, Nadkarni P, Silverstein S, Kidd JR, Pakstis AJ, Miller P, Kidd KK: PhenoDB: An
integrated client/server database for linkage and population genetics. Computers and Biomedical
Research 29:327-337, 1996.
67.
Nadkarni P, Cheung KH, Castiglione C, Miller P, Kidd K: DNA Workbench: A database to manage
regional mapping. Journal of Computational Biology 3:319-329, 1996.
68.
Miller DW, Frawley SJ, Miller PL: Using semantic constraints to help verify the completeness of a
computer-based clinical guideline for childhood immunization. Computer Methods and Programs in
Biomedicine 58:267-280, 1999.
69.
Peterson BE, Healy M, Nadkarni P, Shepherd GM, Miller PL: ModelDB: An environment for
running and storing computer models and their results applied to computational neuroscience.
Journal of the American Medical Informatics Association 6:389-398, 1996.
70.
Brandt C, Frawley SJ, Powsner SM, Shiffman RN, Miller PL: Visualizing the logic of a clinical
guideline: A case study in childhood immunization. Methods of Information in Medicine 36:179183, 1997.
71.
Grajek SE, McKay J, Miller PL, Paton JA, Roderer NK: Evaluating IAIMS at Yale: Information
access. Journal of the American Medical Informatics Association 4:138-149, 1997.
72.
Healy MD, Smith JE, Singer MS, Nadkarni PM, Miller PL, Shepherd GM: Olfactory receptor
database (ORDB): A resource for sharing and analyzing published and unpublished data. Chemical
Perry L. Miller, MD, PhD
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Curriculum Vitae
Senses 22:321-326, 1997.
73.
Miller PL: Aspects of IAIMS implementation that require further research. Journal of the American
Medical Informatics Association 4:S52-S61, 1997.
74.
Panzer S, Cooley L, Miller PL: Using explicitly defined biological relationships for database
navigation and searching via the World-Wide Web. Computer Applications in the Biosciences
13:281-290, 1997.
75.
Miller PL, Frawley SJ, Sayward FG, Yasnoff WA, Duncan L, Fleming D: Combining tabular, rulebased and procedural knowledge in computer-based guidelines for childhood immunization.
Computers and Biomedical Research 30:211-231, 1997.
76.
Miller PL: Tools for immunization guideline knowledge maintenance I: Automated generation of
the logic “kernel” for immunization forecasting. Computers and Biomedical Research 31:172-189,
1998.
77.
Miller PL, Frawley SJ, Brandt C, Sayward FG: Tools for immunization guideline knowledge
maintenance II: Automated Web-based generation of user-customized test cases. Computers and
Biomedical Research 31:190-208, 1998.
78.
Nadkarni PM, Brandt C, Frawley SJ, Sayward FG, Einbinder R, Zelterman D, Schacter L, Miller
PL: Managing attribute-value clinical trials data using the ACT/DB client-server database system.
Journal of the American Medical Informatics Association 5:139-151, 1998.
79.
Mirsky JS, Nadkarni PM, Healy MD, Miller PL, Shepherd GM: Database tools for integrating and
searching membrane property data correlated with neuronal morphology. Journal of Neuroscience
Methods 82:105-121, 1998.
80.
Shepherd GM, Mirsky JS, Healy MD, Singer MS, Skoufos E, Hines MS, Nadkarni PM, Miller PL:
The Human Brain Project: Neuroinformatics tools for integrating, searching, and modeling
multidisciplinary neuroscience data. Trends in Neuroscience 21:460-468, 1998.
81.
Skoufos E, Healy MD, Singer MS, Nadkarni PM, Miller PL, Shepherd GM: Olfactory receptor
database: A database of the largest eukaryotic gene family. Nucleic Acids Research 27:343-345,
1999.
82.
Chen RS, Nadkarni PM, Levin FL, Miller PL, Erdos J, Rosenheck R: Using a computer database to
monitor compliance with pharmacotherapeutic guidelines for schizophrenia. Psychiatric Services
51:791-794, 2000.
83.
Stein HD, Nadkarni P, Erdos J, Miller PL: Exploring the degree of concordance of coded and
textual data in answering clinical queries from a clinical data repository. Journal of the American
Medical Informatics Association 7:42-54, 2000.
84.
Ross-Macdonald P, Roemer T, Coelho P, des Etages S, Sheehan A, Symoniatis D, Jansen R,
Umansky L, Nelson K, Agarwal S, Hagar K, Cheung K, Miller P, Kanada D, Roeder S, Snyder M:
Large scale analysis of the yeast genome by transposon tagging and disruption. Nature 402:413-418,
1999.
85.
Miller PL, Frawley SJ, Sayward FG: IMM/Scrub: A domain-specific tool for the deduplication of
vaccination history records in childhood immunization registries. Computers and Biomedical
Perry L. Miller, MD, PhD
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Curriculum Vitae
Research 33:126-143, 2000.
86.
Mattie ME, Staib L, Stratmann E, Tagare HD, Duncan J, Miller PL: PathMaster: Content-based cell
image retrieval using automated feature extraction. Journal of the American Medical Informatics
Association 7:404-415, 2000.
87.
Nadkarni P, Marenco L, Chen R, Skoufos E, Shepherd G, Miller P: Organization of heterogeneous
scientific data using the EAV/CR representation. Journal of the American Medical Informatics
Association 6:478-493, 1999.
88.
Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: An allele frequency
database for diverse populations and DNA polymorphisms. Nucleic Acids Research 28:361-363,
2000.
89.
Kumar A, Cheung KH, Ross-Macdonald P, Coelho PSR, Miller P, Snyder M: TRIPLES: A
database of transposon mutagenesis in S. cervisiae. Nucleic Acids Research 28:81-84, 2000.
90.
Skoufos E, Marenco L, Nadkarni PM, Miller PL, Shepherd, GM: Olfactory receptor database: A
sensory chemoreceptor resource. Nucleic Acids Research 28:341-343, 2000.
91.
Chen RS, Nadkarni P, Marenco L, Miller PL: Exploring performance issues for a clinical database
organized using an entity-attribute-value representation. Journal of the American Medical
Informatics Association 7:475-487, 2000.
92.
Cheung KH, Kumar A, Snyder M, Miller P: An integrated Web interface for large-scale
characterization of sequence data. Functional and Integrative Genomics 1:70-75, 2000.
93.
Brandt CA, Nadkarni P, Marenco L, Karras BT, Lu C, Fisk JM, Miller PL: Re-engineering a
database for clinical trials management: Lessons of systems architects. Controlled Clinical Trials
21:440-461, 2000.
94.
Miller PL, Nadkarni P, Singer M, Marenco L, Hines M, Shepherd G: Integration of
multidisciplinary sensory data: a pilot model of the human brain project approach. Journal of the
American Medical Informatics Association 8:34-48, 2001.
95.
Miller PL, Brandt C, Cheung K, Mattie M, Nadkarni P, Shiffman RN: The Yale Center for Medical
Informatics: Clinical, neuro- and genomic informatics. MD Computing 17(4):29-32, 2000.
96.
Miller PL: The opportunities at the intersection of bioinformatics and health informatics: A case
study. Journal of the American Medical Informatics Association 7:431-438, 2000.
97.
Miller PL: Domain-constrained generation of clinical condition sets to help test computer-based
clinical guidelines. Journal of the American Medical Informatics Association 8:131-145, 2001.
98.
Miller PL, Sayward FG, Frawley SJ: Exploring the utility of demographic data and vaccination
history data in the deduplication of immunization registry patient records. Journal of Biomedical
Informatics 34(1):37-50, 2001.
99.
Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: An allele frequency
database for diverse populations and DNA polymorphisms - an update. Nucleic Acids Research
29:317-319, 2001.
Perry L. Miller, MD, PhD
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Curriculum Vitae
100. Miller PL, Sayward FG, Frawley SJ: Issues in computer-based decision support in public health
illustrated using a set of related projects involving childhood immunization. Journal of Public
Health Management Practice 7:75-86, 2001.
101. Miller PL, Sayward FG, Frawley SJ: Maintaining and incrementally revalidating a computer-based
clinical guideline: A case study. Journal of Biomedical Informatics 34:99-111, 2001.
102. Amari SI, 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, Pulkkinen P, Ravindranath V, Ritz R, Ruotsalainen U, Sebestra V,
Subramaniam S, Toga AW, Usui S, van Pelt J, Verschure P, Willshaw D, Wrobel A, Yiyuan T:
Neuroinformatics: The integration of shared databases and tools towards integrative neuroscience.
Journal of Integrative Neuroscience 1:117-28, 2002.
103. Eckersley P, Egan GF, Amari SI, 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, Yiyuan T: Neuroscience data
and tool sharing: A legal and policy framework for neuroinformatics. Neuroinformatics 1:149-165,
2003.
104. 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 1:289-95, 2003.
105. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S,
Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M: Global analysis of protein
activities using proteome chips. Science 293:2101-2105, 2001.
106. 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. Journal of the American Medical
Informatics Association 9(5):491-9, 2002.
107. 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 Research 30:354360, 2002.
108. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: An allele frequency
database for anthropology. American Journal of Physical Anthropology 119:77-83, 2002.
109. Kumar A, Afarwal S, Hayman JA, Matson S, Heidtman M, Piccirillo S, Unamskyu L, Drawid A,
Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M: Subcellular localization
of the yeast proteome. Genes and Development 16:707-19, 2002.
110. 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. Nature Biotechnology 20:58-63,
2002.
111. 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 Research 30:73-5, 2002.
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Curriculum Vitae
112. Rajeevan H, Osier MV, Cheung K, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ,
Tosches NP, Yeh C, Miller PL, Kidd K: ALFRED - The ALelle FREquency Database - update.
Nucleic Acids Research 31:270-1, 2003.
113. 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. International Journal of Medical Informatics 65(3):225-41, 2002.
114. 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 and Development 17:529-40, 2003.
115. Crasto CJ, Marenco LM, Migliore M, Mao B, Nadkarni PM, Perry Miller P, Shepherd GM: Text
mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics 1:215237, 2003.
116. 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. Journal of
the American Medical Informatics Association 10:444-453, 2003.
117. Zhao X, Ma M, Liu J, Crasto C, Marenco L, Migliore M, Miller PL, Shepherd GM: Tools,
strategies and concepts for genomics and proteomics of the brain: The olfactory system as a model.
(submitted).
118. 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 2:3-18, 2004.
119. 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. Journal of Biomedical
Informatics 35:306-312, 2002.
120. 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: A case study. Journal
of the American Medical Informatics Association 11:294-299, 2004.
121. Martone R, Euskirchen G, Bertone P, Hartman S, Royce T, Luscombe NM, Rinn JL, Nelson K,
Miller P, Gerstein M, Weissman S, Snyder M: Distribution of NF-kB-binding sites across human
chromosome 22. Proceedings of the National Academy of Sciences 100:12247-52, 2003.
122. Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH,
Stormo GD, Szczepaniak MC, Tuck D, and Jeffrey Williamson J: Training the next generation of
informaticians: The impact of "BISTI" and bioinformatics—A report from the American College of
Medical Informatics. Journal of the American Medical Informatics Association 11:167-172, 2004.
123. 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 24:3804-14, 2004.
124. 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
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Curriculum Vitae
Res 32(Web Server issue):W441-4, 2004.
125. Brandt CA, Cohen DB, Shifman MA, Miller PL, Nadkarni PM, Frawley SJ: Approaches and
informatics tools to assist in the integration of similar clinical research questionnaires. Methods of
Information in Medicine 43:156-62, 2004.
126. Marenco L, Wang TY, Shepherd G, Miller PL, Nadkarni P: QIS: A framework for biomedical
database federation. Journal of the American Medical Informatics Association 11:423-434, 2004.
127. Carriero N, Osier MV, Cheung K, Miller PL, Gerstein M, Zhao H, Rifkin S, Chang J, Zhang H,
White K, Kenneth Williams K, Schultz M: A high productivity/low maintenance approach to high
performance computation for biomedicine: Four case studies. Journal of the American Medical
Informatics Association 12:90-98, 2005.
128. Gerstein M, Greenbaum D, Cheung K, Miller PL: An interdepartmental Ph.D. program in
Computational Biology and Bioinformatics: The Yale perspective. Journal of Biomedical
Informatics 40:73-9, 2007.
129. Bruce C, Shifman MA, Miller P, Gulcicek EE: Probabilistic enrichment of phosphopeptides by their
mass defect in tandem mass spectrometry. Anal Chem 78:4374-82, 2006.
130. Dinu V, Miller PL, Zhao H: Integrating domain knowledge with statistical and data mining methods
for high-density genomic SNP disease association analysis. Journal of Biomedical Informatics
20:750-60, 2007.
131. Liu N, Marenco L, Miller P: ResourceLog: An embeddable tool for dynamically monitoring the
usage of Web-based bioscience resources. Journal of the American Medical Informatics Association
13:432-437, 2006.
132. Liu N, Xu F, Miller PL, Shepherd GM: OdorMapComparer: An application for quantitative
analyses and comparisons of fMRI brain odor maps. Neuroinformatics 5:105-14, 2007.
133. Corwin J, Silberschatz A, Miller PL, Marenco L: Dynamic tables: An architecture for managing
evolving, heterogeneous biomedical data in relational database management systems. Journal of the
American Medical Informatics Association 14:86-93, 2007.
134. Rozowsky J, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng
D, Guigo R, Gingeras T, Weissman S, Miller P, Snyder M, Gerstein M: The DART classification of
unannotated transcription within the ENCODE regions: associating transcription with known and
novel loci. Genome Research 2007 Jun;17(6):732-45.
135. Crasto CJ, Masiar P, Shepherd GM, Miller PL: NeuroExtract: Facilitating Neuroscience-Oriented
Retrieval from Broadly-Focused Bioscience Databases using Text-based Query Mediation. Journal
of the American Medical Informatics Association 14:355-60, 2007.
136. Dinu V, Miller PL, Zhao H: Evidence for association between multiple complement pathway genes
and AMD. Genet Epidemiol 31:224-37, 2007.
137. 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. Briefings in Bioinformatics 8(3):150-62, 2007.
Perry L. Miller, MD, PhD
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Curriculum Vitae
138. 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 8 Suppl 3:S4, 2007.
139. 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. Journal of Proteome
Research 6:4019-24, 2007.
140. Bjornson R, Shifman M, Miller P. Carriero N: X!!Tandem, an improved method for running
X!Tandem in parallel on collections of commodity computers. Journal of Proteome Research 7:2939, 2008.
141. 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 6(3):205-217, 2008.
142. Gardner D, Akil H, Ascoli GA, Bowden DM, BugW, 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: The Neuroscience Information
Framework: A data and knowledge environment for neuroscience. Neuroinformatics 6(3):149-160,
2008.
143. 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 6(3):229-239, 2008.
144. Marenco L, Giorgio A. Ascoli GA, Martone ME, Shepherd GM, Miller PL: The NIF LinkOut
Broker: A web resource to facilitate federated data integration using NCBI identifiers.
Neuroinformatics 6(3):219-227, 2008.
145. 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 and Translational
Science Award programs. Acad Med. 2009 Jul;84(7):964-70. PMID: 19550198; PMCID:
PMC2884382.
146. 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. PMID: 19505888; PMCID: PMC2691938.
147. 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. PMID: 20006477; PMCID: PMC3131218.
148. 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.
PMID: 20387131.
149. Mustavich LF, Miller P, Kidd KK, Zhao H. Using a pharmacokinetic model to relate an individual's
Perry L. Miller, MD, PhD
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Curriculum Vitae
susceptibility to alcohol dependence to genotypes. Hum Hered. 2010;70(3):177-93. PMID:
20714161; PMCID: PMC3164201.
150. Marenco LN, Bahl G, Hyland L, Shi J, Wang R, Lai PC, Miller PL, Shepherd GM, Crasto CJ.
Databases in SenseLab for the genomics, proteomics, and function of olfactory receptors. Methods
Mol Biol. 2013;1003:3-22. PMID: 23585030.
151. Harvey PD, Siever LJ, Huang GD, Muralidhar S, Zhao H, Miller P, Aslan M, Mane S, McNamara
M, Gleason T, Brophy M, Przygodszki R, O'Leary TJ, Gaziano M, Concato J. The genetics of
functional disability in schizophrenia and bipolar illness:Methods and initial results for VA
cooperative study #572. Am J Med Genet B Neuropsychiatr Genet. 2014 Jun;165B(4):381-9.
PMID: 24798943.
152. Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL. Extending the NIF
DISCO framework to automate complex workflow: coordinating the harvest and integration of data
from diverse neuroscience information resources. Front Neuroinform. 2014 May 28;8:58. PMID:
25018728; PMCID: PMC4071641.
153. Miller PL, Phipps M, Chatterjee S, Rajeevan N, Levin F, Frawley S, Tokuno H. Exploring a
clinically friendly web-based approach to clinical decision support linked to the electronic health
record: Design philosophy, prototype implementation, and framework for assessment. JMIR Med
Inform. 2014;2(2):e20. PMID: 25580426; PMCID: PMC4288105.
154. Colangelo C, Shifman M, Cheung K, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T,
Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller P, Williams KR. YPED: An integrated
bioinformatics suite and database for mass spectrometry based proteomics research. Genomics,
Proteomics & Bioinformatics. 2015 13(1):25-35. PMID: 25712262.
155. Niehoff KM, Rajeevan N, Charpentier PA, Miller PL, Goldstein MK, Fried TR. Development of the
tool to reduce inappropriate medications (TRIM): A clinical decision support system to improve
medication prescribing for older adults. Pharmacotherapy. 2016 Jun;36(6):694-701. PMID:
27041466.
156. Benin AL, Fodeh SJ, Lee K, Koss M, Miller P, Brandt C. Electronic approaches to making sense of
the text in the adverse event reporting system. Journal of Healthcare Risk Management. (in press).
Conference Proceedings Papers
1.
Miller PL: An adaptive natural language system that listens, asks, and learns. Proceedings of the
Fourth International Joint Conference on Artificial Intelligence, Tbilisi, 1975, pp. 406-413.
2.
Miller PL: ATTENDING: A system which critiques an anesthetic management plan. Proceedings of
the American Medical Informatics Association Congress-82, San Francisco, May 1982, pp. 36-40.
3.
Miller PL: PROSENET: Facilitating machine generation of prose analysis of medical management.
Proceedings of MEDCOMP 82, Philadelphia, September 1982, pp. 460-464.
4.
Miller PL: A heuristic approach to risk analysis in computer-assisted medical management.
Proceedings of the Sixth Symposium of Computer Applications in Medical Care, Washington,
D.C., November 1982, pp. 697-701.
5.
Miller PL: The ATTENDING system. Proceedings of MEDCOMP 82, Philadelphia, September
Perry L. Miller, MD, PhD
14
Curriculum Vitae
1982, pp. 409-412.
6.
Miller PL, Angers D, Marks P, Sudan N, Tanner G: Teaching with "ATTENDING": A practical
way to "debug" an expert knowledge base. Proceedings of the American Association for Medical
Systems and Informatics Congress-83, May 1983, pp. 87-91 (received Award as one of three best
papers).
7.
Miller PL: Medical plan-analysis: The ATTENDING system. Proceedings of the Eighth
International Joint Conference on Artificial Intelligence, Karlsruhe, Germany, 1983, pp. 239-241.
8.
Miller PL: Medical plan-analysis by computer. Proceedings of the Fourth World Conference on
Medical Informatics MEDINFO-83, Amsterdam, 1983, pp. 592-596 (received Gold Medal as one of
three best papers).
9.
Miller PL, Black HR: HT-ATTENDING: Critiquing the pharmacologic management of essential
hypertension. Proceedings of the Seventh Symposium on Computer Applications in Medical Care,
Baltimore, October 1983, pp. 824-827.
10.
Miller PL, Black HR: Medical plan-analysis and the management of essential hypertension.
Proceedings of the AAMSI Second Annual Conference, Baltimore, October 1983, pp. 72-74.
11.
Miller PL: Critiquing as a modality for computer advice in medical management and work-up.
Proceedings of the Seventh Symposium on Computer Applications in Medical Care, Baltimore,
October 1983, pp. 842-843 (session chairman's paper).
12.
Miller PL: Critiquing as a modality for explanation: Three systems. Proceedings of the American
Association for Medical Systems and Informatics Congress-84, San Francisco, May 1984, pp. 105109 (session chairman's paper).
13.
Miller PL: Critiquing: A different approach to computer-based advice in medicine. Proceedings of
the Eighth Symposium on Computer Applications in Medical Care, Washington DC, November
1984, pp. 17-23.
14.
Marks PS, Bowen RW, Miller PL: An expert system for critiquing ventilator management.
Proceedings of the American Association for Medical Systems and Informatics Congress-84, San
Francisco, May 1984, pp. 172-175.
15.
Miller PL, Blumenfrucht SJ, Black HR: An expert system which critiques the work-up of
pheochromocytoma. Proceedings of the American Association for Medical Systems and
Informatics Congress-85, San Francisco, May 1985, pp. 297-300 (session chairman's paper).
16.
Miller PL, Shaw C, Rose JR, Swett HA: Critiquing the process of radiologic differential diagnosis.
Proceedings of the Ninth Symposium on Computer Applications in Medical Care, Baltimore MD,
November 1985, pp. 182-185.
17.
Miller PL: Issues in the evaluation of artificial intelligence systems in medicine. Proceedings of the
Ninth Symposium on Computer Applications in Medical Care, Baltimore MD, November 1985, pp.
281-286.
18.
Miller PL: Medical information science: What academic role should it play? Proceedings of the
Ninth Symposium on Computer Applications in Medical Care, Baltimore MD, November 1985, pp.
169-171 (panel chair paper).
Perry L. Miller, MD, PhD
15
Curriculum Vitae
19.
Swett HA, Shaw C, Rose JR, Miller PL: ICON: An expert system for critiquing radiologic
differential diagnosis. Proceedings of the American Association for Medical Systems and
Informatics Congress-85, San Francisco, May 1985, pp. 202-206.
20.
Miller PL: ESSENTIAL-ATTENDING: A domain independent tool for building critiquing systems.
Proceedings of the American Association for Medical Systems and Informatics Congress-86,
Anaheim, May 1986, pp. 9-13 (session chairman's paper).
21.
Miller PL: Current research topics in medical artificial intelligence. Proceedings of the American
Association for Medical Systems and Informatics Congress-86, Anaheim, May 1986, pp. 263-267
(panel chairman's paper).
22.
Miller PL: Exploring the critiquing approach: Sophisticated practice-based feedback by computer.
Proceedings of the Fifth World Conference on Medical Informatics MEDINFO-86, Washington
DC, October 1986, pp. 2-6.
23.
Mars NJI, Miller PL: Tools for knowledge acquisition and verification in medicine. Proceedings of
the Tenth Symposium on Computer Applications in Medical Care, Washington DC, October 1986,
pp. 36-42.
24.
Swett HA, Rothschild M, Weltin G, Miller PL: Expert system knowledge validation: ESSENTIALATTENDING's knowledge exerciser program. Proceedings of the American Association for
Medical Systems and Informatics Congress-86, Anaheim, May 1986, pp. 14-18.
25.
Miller PL, Blumenfrucht SJ, Rose JR, Rothschild M, Weltin G, Swett HA, Mars NJI: Expert system
knowledge acquisition for domains of medical workup: An augmented transition network model.
Proceedings of the Tenth Symposium on Computer Applications in Medical Care, Washington DC,
October 1986, pp. 30-35.
26.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: Reasoning from the clinical literature: A
"distance" metric. Proceedings of the American Association for Medical Systems and Informatics
Congress-86, Anaheim, May 1986, pp. 19-23.
27.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: Reasoning from the clinical literature: The
Roundsman system. Proceedings of the Fifth World Conference on Medical Informatics
MEDINFO-86, Washington DC, October 1986, pp. 771-775.
28.
Swett HA, Shaw C, Rose JR, Miller PL: An expert system for critiquing radiologic differential
diagnosis. Proceedings of the Twelfth Northeast Bioengineering Conference, New Haven, March
1986, pp. 194-197.
29.
Weltin G, Rothschild M, Swett HA, Miller PL: X-CON: A critiquing system for the imaging
workup of jaundice. Proceedings of the Twelfth Northeast Bioengineering Conference, New Haven,
March 1986, pp. 190-193.
30.
Miller PL, Blumenfrucht SJ, Rose JR, Rothschild M, Mars NJI: Knowledge acquisition for an
expert critiquing system: An augmented transition network model. Proceedings of the Twelfth
Northeast Bioengineering Conference, New Haven, March 1986, pp. 186-189.
31.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: Updating an expert knowledge base as
medical knowledge evolves: Examples from oncology management. Proceedings of the American
Perry L. Miller, MD, PhD
16
Curriculum Vitae
Association of Medical Systems and Informatics Congress-87, San Francisco, May 1987, pp. 228232.
32.
Fisher PR, Miller PL, Swett HA: A script-based representation of medical knowledge involving
multiple perspectives. Proceedings of the American Association of Medical Systems and
Informatics Congress-87, San Francisco, May 1987, pp. 233-237.
33.
Miller PL: Expert consultation systems in medicine: A complex and fascinating domain.
Proceedings of the Annual Meeting of the IEEE (Electro-87), New York, April 1987, pp. 1/2:1-4
(invited paper).
34.
Miller PL, Fisher PR: Causal models in medical artificial intelligence. Proceedings of the Eleventh
Symposium on Computer Applications in Medical Care, Washington DC, November 1987, pp. 1722.
35.
Powsner SM, Barwick KW, Morrow JS, Riely CA, Miller PL: Coding semantic relationships for
medical bibliographic retrieval: A preliminary study. Proceedings of the Eleventh Symposium on
Computer Applications in Medical Care, Washington DC, November 1987, pp. 108-112.
36.
Swett HA, Miller PL: Critiquing systems in medicine. Proceedings of the 9th Annual Conference of
the IEEE Engineering in Medicine and Biology Society, Boston, November 1987, 3:1523-1524.
37.
Miller PL, Barwick KW, Morrow JS, Powsner SM, Riely CA: Towards a conceptual schema of
medical knowledge: Facilitating transition between different computer-based forms of clinical
information. Proceedings of the American Association of Medical Systems and Informatics
Congress-88, San Francisco, May 1988, pp. 77-82.
38.
Miller PL, Smith P, Morrow JS, Riely CA, Powsner SM: Semantic relationships and MeSH.
Proceedings of the Twelfth Symposium on Computer Applications in Medical Care, Washington,
D.C., November 1988, pp. 174-179.
39.
Rothschild M, Miller PL, Fisher PR, Weltin G, Swett HA: Confronting subjective criteria in the
evaluation of computer-based critiquing advice. Proceedings of the Twelfth Symposium on
Computer Applications in Medical Care, Washington, D.C., November 1988, pp. 220-224.
40.
Fisher PR, Miller PL, Swett HA: Great expectations: Expectation-based reasoning for medical
differential diagnosis. Proceedings of the Twelfth Symposium on Computer Applications in
Medical Care, Washington, D.C., November 1988, pp. 38-42.
41.
Mutalik P, Fisher PR, Swett HA, Miller PL: Using INTERNIST-like diagnostic strategies to
structure explanation in an expert critiquing system. Proceedings of the Twelfth Symposium on
Computer Applications in Medical Care, Washington, D.C., November 1988, pp. 26-31.
42.
Miller PL, Factor M, Gelernter D, Sittig DF, Cohn AI, Rosenbaum S: A parallel process lattice
model for an intelligent cardiovascular monitor. Proceedings of the American Association of
Medical Systems and Informatics Congress-89, San Francisco, May 1989, pp. 121-125.
43.
Cohn AI, Fisher PR, Mutalik P, Miller PL, Swett HA: AXON: A computer-based approach to
intelligent retrieval of radiographic images using "axes" of clinical relevance. Proceedings of
MEDINFO-89, Singapore, December 1989, pp. 432-436.
44.
Cohn AI, Rosenbaum SH, Factor M, Gelernter D, Sittig DF, Miller PL: Sequential clinical "scenes":
Perry L. Miller, MD, PhD
17
Curriculum Vitae
A paradigm for computer-based intelligent hemodynamic monitoring. Proceedings of the Thirteenth
Symposium on Computer Applications in Medical Care, Washington, D.C., November 1989, pp. 510.
45.
Miller PL, Ball S, Kidd KK: The Human Gene Mapping Library database: Representational
challenges posed by new bioscience technologies and by evolving biomedical knowledge.
Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care, Washington,
D.C., November 1989, pp. 81-84.
46.
Powsner SM, Miller PL: Linking bibliographic retrieval to clinical reports: PsychTopix.
Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care, Washington,
D.C., November 1989, pp. 431-435.
47.
Clyman JI, Black HR, Miller PL: Assessing practice conformance for hypertension management
using an expert system. Proceedings of the Thirteenth Symposium on Computer Applications in
Medical Care, Washington, D.C., November 1989, pp. 124-128.
48.
Factor M, Sittig D, Cohn A, Gelernter D, Miller P, Rosenbaum S: A parallel software architecture
for building intelligent medical monitors. Proceedings of the Thirteenth Symposium on Computer
Applications in Medical Care, Washington, D.C., November 1989, pp. 11-16.
49.
Ball S, Wright L, Miller P: SENEX: An object-oriented biomedical knowledge base. Proceedings of
the Thirteenth Symposium on Computer Applications in Medical Care, Washington, D.C.,
November 1989, pp. 85-89.
50.
Miller PL, Gelernter D: Machine-independent model-based tools for parallel computation in
biomedicine. Proceedings of the Fourteenth Symposium on Computer Applications in Medical
Care, Washington, D.C., November 1990, pp. 262-265.
51.
Nadkarni P, Gelernter JE, Carriero N, Pakstis AJ, Kidd KK, Miller PL: Parallelizing genetic linkage
analysis: A case study for applying parallel computation in molecular biology. Proceedings of the
Fourteenth Symposium on Computer Applications in Medical Care, Washington, D.C., November
1990, pp. 104-108.
52.
Sittig DF, Foulser D, Carriero N, McCorkle G, Miller PL: A parallel computing approach to genetic
sequence comparison: The master-worker paradigm. Proceedings of the Fourteenth Symposium on
Computer Applications in Medical Care, Washington, D.C., November 1990, pp. 109-113.
53.
Paton JA, Clyman JI, Lynch P, Miller PL, Sittig DF, Berson BB: Strategic planning for IAIMS:
Prototyping as a catalyst for change. Proceedings of the Fourteenth Symposium on Computer
Applications in Medical Care, Washington, D.C., November 1990, pp. 709-713.
54.
Clyman JI, Miller PL: An environment for building and testing advice-giving systems for medicine.
Proceedings of the Fourteenth Symposium on Computer Applications in Medical Care, Washington,
D.C., November 1990, pp. 584-588.
55.
Shifman MA, Windemuth A, Schulten K, Miller PL: Molecular dynamics on a network of
workstations using a machine-independent parallel programming language. Proceedings of the
Fifteenth Symposium on Computer Applications in Medical Care, Washington, D.C., November
1991, pp. 414-418.
56.
Powsner SM, Miller PL: From patient records to bibliographic retrieval: A Meta-1 front-end.
Perry L. Miller, MD, PhD
18
Curriculum Vitae
Proceedings of the Fifteenth Symposium on Computer Applications in Medical Care, Washington,
D.C., November 1991, pp. 526-530.
57.
Miller PL, Shifman MA, Kidd KK: Modeling uncertainty in a database for physical gene mapping
data. Proceedings of the Fifteenth Symposium on Computer Applications in Medical Care,
Washington, D.C., November 1991, pp. 409-413.
58.
Nadkarni PM, Miller PL: Parallel computation for biological sequence comparison: Comparing a
portable model to the native model for the Intel Hypercube. Proceedings of the Fifteenth
Symposium on Computer Applications in Medical Care, Washington, D.C., November 1991, pp.
404-408.
59.
Miller PL, Wright LW, Frawley SJ, Clyman JI, Powsner SM: Selecting relevant information
resources in a network-based environment: The UMLS information sources map. MEDINFO-92,
Geneva, Switzerland, September 1992, pp. 1512-1517.
60.
Sittig DF, Shifman MA, Nadkarni P, Miller PL: Parallel computation for medicine and biology:
Experience with LINDA. MEDINFO-92, Geneva, Switzerland, September 1992, pp. 14-19.
61.
Shifman MA, Nadkarni P, Miller PL: PFGE Mapper and PFGE Reader: Two tools to aid in the
analysis and data input of pulse field gel electrophoresis maps. Proceedings of the Sixteenth
Symposium on Computer Applications in Medical Care, Baltimore, MD, November 1992, pp. 361365.
62.
Nadkarni PM, Reeders ST, Shifman MA, Miller PL: Chrominfo: A database for viewing and editing
top-level chromosome data. Proceedings of the Sixteenth Symposium on Computer Applications in
Medical Care, Baltimore, MD, November 1992, pp. 366-370.
63.
Berman L, Cullen MR, Miller PL: Automated integration of external databases: A knowledge-based
approach to enhancing rule-based expert systems. Proceedings of the Sixteenth Symposium on
Computer Applications in Medical Care, Baltimore, MD, November 1992, pp. 227-233.
64.
Paton JA, Belanger A, Cheung K, Grajek S, Branch KA, Ikeda N, Sette L, Miller PL, Fryer RK: Online bibliographic information: Integration into an emerging IAIMS environment. Proceedings of
the Sixteenth Symposium on Computer Applications in Medical Care, Baltimore, MD, November
1992, pp. 605-609.
65.
Shifman MA, Clyman JI, Paton JA, Powsner SM, Roderer NK, Miller PL: NetMenu: Experience in
the implementation of an institutional menu of information sources. Proceedings of the Seventeenth
Symposium on Computer Applications in Medical Care, Washington DC, November 1993, pp. 554558.
66.
Silverstein SM, Miller PL, Cullen MR: An information sources map for occupational and
environmental medicine: Guidance to network-based information through domain-specific
indexing. Proceedings of the Seventeenth Symposium on Computer Applications in Medical Care,
Washington DC, November 1993, pp. 616-620.
67.
Miller PL, Nadkarni PM, Kucherlapati R, Krauter KS, Kidd KK, Ward DC, Shepherd GM,
Berkowicz D: Network-based informatics support of research collaboration in the Human Genome
Project and the Human Brain Project. MEDINFO-95, Vancouver, July 1995, pp. 1541-1544.
68.
Miller PL, Frawley SJ, Sayward FG, Yasnoff WA, Duncan L, Fleming D: IMM/Serve: A rule-based
Perry L. Miller, MD, PhD
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Curriculum Vitae
program for childhood immunization. Proceedings of the 1996 AMIA Annual Fall Symposium
(Formerly SCAMC), Washington DC, October 1996, pp. 184-188.
69.
Frawley SJ, Miller PL, Sayward FG, Yasnoff WA: Towards the systematic maintenance of different
versions of rule-based immunization guideline logic. Proceedings of the 1997 AMIA Annual Fall
Symposium, Nashville TN, October 1997, CD-ROM file D003990.
70.
Miller PL, Frawley SJ, Brandt C, Sayward FG: A prototype web site for immunization knowledge
maintenance. Proceedings of the 1997 AMIA Annual Fall Symposium, Nashville TN, October
1997, pp. 293-297.
71.
Poljak A, Miller PL: Comparing the data model of the MLP vocabulary to SNOMED III for
capturing history and physical exam data at point of care. Proceedings of the 1997 AMIA Annual
Fall Symposium, Nashville TN, October 1997, CD-ROM file D004033.
72.
Brandt C, Fernandes L, Powsner SM, Miller PL: Using coded semantic relationships to retrieve and
structure clinical reference information. Proceedings of the 1997 AMIA Annual Fall Symposium,
Nashville TN, October 1997, CD-ROM file D004058.
73.
Miller PL, Frawley SJ, Sayward FG: Issues in accommodating national changes and local variation
in a computer-based guideline for childhood immunization and in related knowledge maintenance
tools. Proceedings of the 1998 AMIA Annual Fall Symposium, Orlando FL, November 1998, pp.
563-567.
74.
Cheung KH, Miller P, Nadkarni P, Shin DG: Automatic query mapping among genomic databases:
A pilot exploration. Proceedings of the 1998 AMIA Annual Fall Symposium, Orlando FL,
November 1998, pp. 942-946.
75.
Miller PL, Frawley SJ, Sayward FG: Exploring three approaches for handling incomplete patient
histories in a computer-based guideline for childhood immunization. Proceedings of the 1999
AMIA Annual Fall Symposium, Washington, DC, November 1999, pp. 878-882.
76.
Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P: Neuronal database integration: The
Senselab EAV data model. Proceedings of the 1999 AMIA Annual Fall Symposium, Washington,
DC, November 1999, pp. 102-106.
77.
Cheung KH, Miller PL, Kidd JR, Kidd KK, Osier MV, Pakstis AJ: ALFRED: A Web-assessable
allele frequency database. Proceedings of the Pacific Symposium on Biocomputing, Hawaii,
January 2000, pp. 639-50.
78.
Miller PL, Frawley SJ, Sayward FG: Informatics issues in the national dissemination of a computerbased clinical guideline: A case study in childhood immunization. Proceedings of the 2000 AMIA
Annual Fall Symposium, Los Angeles, CA, November 2000. pp. 580-584..
79.
Cheung K-H, Miller P, Sherman A, Weston S, Stratmann E, Schultz M, Snyder M, Kumar A:
Graphically-enabled integration of bioinformatics tools allowing parallel execution. Proceedings of
the 2000 AMIA Annual Fall Symposium, Los Angeles, CA, November 2000, pp. 141-145.
80.
Cheung K-H, Deshpande AM, Tosches N, Nath S, Agrawal A, Miller P, Kumar A, Snyder M: A
metadata framework for integrating heterogeneous genome data using XML. Proceedings of the
2001 AMIA Annual Fall Symposium, Washington, DC, November 2001, pp. 110-114.
Perry L. Miller, MD, PhD
20
Curriculum Vitae
81.
Cheung K-H, 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. Proceedings of the 2002 AMIA Annual Fall Symposium, San
Antonio, TX, November 2002, pp. 140-144.
82.
Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F,
Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M:
Identification of novel functional elements in the human genome. Cold Spring Harb Symp Quant
Biol. 68:317-22, 2003
83.
Liu N, Xu F, Shepherd G, Miller P: Building, databasing, analyzing and comparing rodentfMRI
odor maps. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and
Informatics, 2005, pp. 161-166.
84.
Sayward FG, Yang J, Nelson FK, Euskirchen G, Urban A, Bertone P, Rinn J, Weissman S, Gerstein
M, Snyder M, Miller PL: Design issues in implementing a portable sample tracking and analysis
research support (STARS) system for PCR based microarray research. Proceedings IEEE 40th
Annual Conference on Information Sciences and Systems, Princeton, NJ, March 2006, pp 15781598.
85.
Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger
P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the
human genome. Cold Spring Harb Symp Quant Biol. 71:111-6, 2006.
86.
Lam HY, Marenco L, Shepherd GM, Miller PL, Cheung KH: Using web ontology language to
integrate heterogeneous databases in the neurosciences. Proceedings of the 2006 AMIA Annual
Symposium, pp. 464-8.
87.
Fodeh SJ, Brandt C, Miller P, Benin AL. Feature selection improves Laplacian SVM in classifying
medical event reports to enhance patient safety. IEEE International Conference on Data Mining,
November, 2015.
Book Chapters
1.
Miller PL, Angers D, Keefer JR, Sudan N, Tanner G: Teaching with "ATTENDING": Tutorial use
of an expert system. In Prakash O (Ed.): Computers in Anesthesia and Intensive Care. Martinus
Nijhoff, 1983, pp. 193-201.
2.
Miller PL: Expert consultation systems in medicine. In Lloyd JS (Ed.): Computer Applications in
the Evaluation of Physician Competence. American Board of Medical Specialties, 1984, pp. 145154.
3.
Miller PL: Expert consultation systems in medicine. In Osswald PM (Ed.): Computers in Critical
Care and Pulmonary Medicine. New York: Springer-Verlag, 1985.
4.
Miller PL: A heuristic approach to risk analysis in computer-assisted medical management. In
Reggia JA, Tuhrim SS (Eds.): Computer-Assisted Medical Decision Making, vol. 2. New York:
Springer-Verlag, pp. 73-81, 1985.
5.
Miller PL: Artificial intelligence in medicine: An emerging discipline. In Miller PL (Ed.): Selected
Topics in Medical Artificial Intelligence. New York: Springer-Verlag, 1988, chapter 1.
Perry L. Miller, MD, PhD
21
Curriculum Vitae
6.
Miller PL: The evaluation of artificial intelligence systems in medicine. In Miller PL (Ed.):
Selected Topics in Medical Artificial Intelligence. New York: Springer-Verlag, 1988, chapter 15.
7.
Mars NJI, Miller PL: Knowledge acquisition and verification tools for medical expert systems. In
Miller PL (Ed.): Selected Topics in Medical Artificial Intelligence. New York: Springer-Verlag,
1988, chapter 11.
8.
Miller PL, Blumenfrucht SJ, Rose JR, Rothschild M, Swett HA, Weltin G, Mars NJI: HYDRA: A
knowledge acquisition tool for expert systems which critique medical workup. In Miller PL (Ed.):
Selected Topics in Medical Artificial Intelligence. New York: Springer-Verlag, 1988, chapter 14.
9.
Miller PL, Fisher PR: Causal models in medical artificial intelligence. In Miller PL (Ed.): Selected
Topics in Medical Artificial Intelligence. New York: Springer-Verlag, 1988, chapter 2.
10.
Rennels GD, Shortliffe EH, Stockdale FE, Miller PL: A computational model of reasoning from the
clinical literature. In Miller PL (Ed.): Selected Topics in Medical Artificial Intelligence. New York:
Springer-Verlag, 1988, chapter 10.
11.
Miller PL, Shiffman RN, Silverstein S, Frawley SJ, Nadkarni PM: Medical informatics training at
Yale University School of Medicine. In van Bemmel JH, McCray AT (Eds.): Yearbook of Medical
Informatics ‘96. Stuttgart: Schattauer, 1996, pp. 122-125.
12.
Shepherd GM, Healy MD, Singer MS, Peterson BE, Mirsky JS, Wright L, Smith JE, Nadkarni P,
Miller PL: SenseLab: A project in multidisciplinary, multilevel sensory integration. In Heurta MF,
Koslow SH (Eds.): Neuroscience Informatics. Mahwah, NJ: Lawrence Erlbaum, 1997, pp. 21-56.
13.
Yasnoff WA, Miller PL: Decision support and expert systems in public health. In O’Carroll PW,
Yasnoff WA, Ward ME, Ripp LH, Martin EL: Public Health Informatics and Information Systems.
New York: Springer, 2002, pp. 494-512.
14.
Miller PL, Marenco L, Shepherd G, Nadkarni P: Entity-attribute-value database approaches for
heterogeneous, evolving neuroscience data. In, Koslow SH, Subramanian S (Eds.): Databasing the
Brain: Data to Knowledge (Neuroinformatics). New York: John Wiley & Sons, 2005, Chapter 5.
15.
Marenco L, Crasto CJ, Liu N, Migliore M, Liu J, Morse TM, Hines ML, Nadkarni PM, Miller PL,
Shepherd GM. SenseLab: A decade of experience with multilevel, multidisciplinary neuroscience
databases. In, Koslow SH, Subramanian S (Eds.): Databasing the Brain: Data to Knowledge
(Neuroinformatics), New York: John Wiley & Sons, 2005, Chapter 20.
16.
Shepherd GM, Morse TM, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines
M, Perry Miller P. SenseLab: Integration of multidisciplinary neuroscience data. In, Jaeger D, Jung
R (Eds): Encyclopedia of Computational Neuroscience, Springer Science+Business Media, New
York, NY, 2013, Article ID: 348562, Chapter ID: 497.