SMI HOMe

featured projects

SMI-2007-1253
N. F. Noy, A. Chugh, H. Alani. The CKC Challenge: Exploring Tools for Collaborative Knowledge . 2007.

SMI-2007-1252
D. Riano, J. Al. Lopez, S. W. Tu. Mining Hospital Data to Learn SDA* Clinical Algorithms. 11th Conference on Artificial Intelligence in Medicine, From Knowledge to Global Care Workshop, Amsterdam, 2007.

SMI-2007-1251
S. W. Tu, J. R. Campbell, J. Glasgow, M. A. Nyman, R. McClure, J. McClay, C. Parker, K. M. Hrabak, D. Berg, T. Weida, J. G. Mansfield, M. A. Musen, R. M. Abarbanel. The SAGE Guideline Model: Achievements and Overview. Journal of American Medical Informatics Association,(JAMIA), 14(5):589-598. 2007

SMI-2007-1250
K. M. Hrabak, J. R. Campbell, S. W. Tu, R. McClure, T. Weida. Creating Interoperable Guidelines: Requirements of Vocabulary Standards in Immunization Decision Support. Medinfo, Brisbane, Australia, 2007.

SMI-2007-1249
N. H. Shah, D. L. Rubin, I. Espinosa, K. Montgomery, M. A. Musen. Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics,8:296. 2007

SMI-2007-1247
N. H. Shah, M. A. Musen. Which Annotation did you mean?. 2007.

SMI-2007-1246
J. Shi, M. G. Walker. Gene Set Enrichment Analysis (GSEA) for Interpreting Gene Expression Profiles . Current Bioinformatics,2(2):133-137. 2007

SMI-2007-1245
M. J. O'Connor, R. D. Shankar, S. W. Tu, C. Nyulas, D. B. Parrish, M. A. Musen, A. K. Das. Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. 11th Conference on Artificial Intelligence in Medicine (AIME 07), Amsterdam, Netherlands, 2007.

SMI-2007-1244
M. J. O'Connor, R. D. Shankar, S. W. Tu, C. Nyulas, A. K. Das, M. A. Musen. Efficiently Querying Relational Databases using OWL and SWRL. The First International Conference on Web Reasoning and Rule Systems, Innsbruck, Austria, LNCS 4524, 361-363, 2007.

SMI-2007-1242
N. H. Shah, M. A. Musen. UMLS-Query: A Perl Module for Querying the UMLS . 2007.

SMI-2007-1237
R. D. Shankar, S. Martins, M. J. O'Connor, D. B. Parrish, A. K. Das. An Ontology-based Architecture for Integration of Clinical Trials Management Applications. AMIA Annual Symposium, Chicago, IL, 2007.

SMI-2007-1236
M. J. O'Connor, R. D. Shankar, D. B. Parrish, A. K. Das. Knowledge-Level Querying of Temporal Patterns in Clinical Research Systems. 12th World Congress on Medical Informatics (Medinfo2007), Brisbane, Australia, 2007.

SMI-2007-1235
R. D. Shankar, S. Martins, M. J. O'Connor, D. B. Parrish, A. K. Das. An Ontological Approach to Temporal Constraint Reasoning in the Management of Clinical Trials . 2007.

SMI-2007-1234
N. F. Noy, D. L. Rubin. Translating the Foundational Model of Anatomy into OWL. 2007.

SMI-2007-1073
S. W. Tu, S. Condamoor, T. Mather, R. Hall, N. Jones, M. A. Musen. Document-Oriented Views of Guideline Knowledge Bases. 11th Conference on Artificial Intelligence in Medicine (AIME 07), Amsterdam, 2007.

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Reports Published in 2006

SMI-2006-1248
N. H. Shah, M. A. Musen, N. V. Fedoroff. Clench2.0: Cluster enrichment analysis and visualization of expression, annotation and transcription factor binding site data. 2006.

SMI-2006-1243
S. W. Tu, J. Glasgow. The SAGE Guideline Model Technical Specification. 2006.

SMI-2006-1233
N. H. Shah, D. L. Rubin, K. S. Supekar, M. A. Musen. Ontology-based Annotation and Query of Tissue Microarray Data. AMIA Annual Symposium, Washington DC, 2006.

SMI-2006-1232
A. J. Butte, R. O. Chen. Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. Annual Symposium of the American Medical Informatics Association, Washington, D.C., 2006.

SMI-2006-1231
O. Dameron, M. A. Musen, B. Gibaud. Using Semantic Dependencies for Consistency Management of an Ontology of Brain-Cortex Anatomy. 2006.

SMI-2006-1230
S. Liu. Understanding alternative splicing from the perspectives of regulatory mechanisms and functional consequences. PhD Thesis. Stanford University,2006

SMI-2006-1229
S. Saxonov. Genome-scale analysis of DNA regulatory sequences. PhD Thesis. Stanford University,2006

SMI-2006-1228
L. Tennakoon, A. K. Das. A Systematic Review of Caregiver Burden in the Relatives of Schizophrenic People. 2006.

SMI-2006-1227
R. D. Shankar, S. B. Martins, M. J. O'Connor, D. B. Parrish, A. K. Das. Epoch: an Ontological Framework to Support Clinical Trials Management. International Workshop on Health Information and Knowledge Management (HIKM 2006), Arlington, VA, 2006.

SMI-2006-1226
R. D. Shankar, S. B. Martins, M. J. O'Connor, D. B. Parrish, A. K. Das. Towards Semantic Interoperability in a Clinical Trials Management System. The 5th International Semantic Web Conference (ISWC 2006), Athens, GA, 2006.

SMI-2006-1225
S. M. Falconer, N. F. Noy, M. Storey. Towards understanding the needs of cognitive support for ontology mapping. International Workshop on Ontology Matching (OM 2006) at ISWC 2006, Athens, GA, 2006.

SMI-2006-1224
N. F. Noy, A. Chugh, W. Liu, M. A. Musen. A Framework for Ontology Evolution in Collaborative Environments. 5th International Semantic Web Conference, Athens, GA, 2006.

SMI-2006-1218
A. Tellez, S. Crowder, J. F. Spangnolo, A. A. Thompson, O. B. Peersen, D. L. Brutlag, K. Kirkegaard. Nucleotide Channel of RNA-dependen RNA Polymerase used for Intermolecular Uridylylation of Protein Primer. J Mol Biol,2006

SMI-2006-1211
G. C. Scott, R. D. Shachter, L. A. Lenert. Using Decision Models to Automate and Individualize Interactive Patient-Oriented Decision Support Aids. American Medical Informatics Association Fall Symposium, 2001, 2006.

SMI-2006-1205
S. Saxonov, P. Berg, D. L. Brutlag. Genome-Wide Analysis of CpG Dinucleotides Indicates that Distinct Classes of Promoters. Proc. Natl. Acad. Sci. USA,2006

SMI-2006-1186
D. Fleishmann, G. D. Rubin, D. S. Paik, S. Y. Yen, P. R. Hilfiker, C. F. Beaulieu, S. Napel. Stair-Step Artifacts with Single Versus Multiple Detector-Row Helical CT. Radiology,2006

SMI-2006-1171
B. S. Srinivasan, A. Novak, J. Flannick, S. Batzoglou, H. H. Adams. Integrated Protein Interaction Networks for 11 Microbes. Research in Computational Molecular Biology (RECOMB 2006),2006

SMI-2006-1169
J. Ma, A. B. Campbell, S. Karlin. Correlations Between Shine-Dalgarno Sequences and Gene Features Such As Predicted Expression Levels and Operon Structures. J. Bacteriol,2006

SMI-2006-1159
J. M. Irish, N. Kotecha, G. P. Nolan. Mapping Normal and Cancer Cell Signalling Networks: Towards Single-Cell Proteomics. Nature Reviews Cancer 6,2006

SMI-2006-1148
D. L. Rubin, E. S. Burnside, R. Shachter. Sainfort, F., Brandeau, M.L., and W.P. Pierskalla, Eds., Handbook of Operations Research and Health Care: Methods and Applications: A Bayesian Network to Assist Mammography Interpretation. Kluwer Academic Publishers, 2006

SMI-2006-1147
E. S. Burnside, J. Y. Park. The Use of Batch Reading to Improve the Performance of Screening Mammography null null, null, 2006

SMI-2006-1145
R. S. Aga, E. Fair, N. F. Abernethy, K. DeRiemer, E. Paz, L. Kawamura, P. M. Small, M. Kato-Maeda. Micro-evolution of the Direct Repeat Locus of MYcobacterium tuberculosis in a prevalent stain in San Francisco. Journal of Clinical Microbiology,2006

SMI-2006-1142
H. Lewen, K. S. Supekar, N. F. Noy, M. A. Musen. Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation. Workshop on Evaluation of Ontologies for the Web (EON2006) at the 15th International World Wide Web Conference (WWW 2006), Edinburgh, UK, 2006.

SMI-2006-1141
R. S. Lin, S. Rhee, R. W. Shafer, A. K. Das. A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history. Computational Systems Bioinformatics, Stanford, 2006.

SMI-2006-1140
A. K. Das, B. A. Ahmed, Y. Garten, J. I. Robin, M. K. Goldstein. Knowledge-Based Method for Building Patient Decision-Analytic Tools. 2006.

SMI-2006-1134
J. Shi, P. R. Romero, G. K. Schoolnik, A. M. Spormann, P. D. Karp. Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests. Nucleic Acids Research,(NAR), 34(8):2438-2444. 2006

SMI-2006-1119
D. L. Rubin, O. Dameron, Y. Bashir, D. Grossman, P. Dev, M. A. Musen. Using ontologies linked with geometric models to reason about penetrating injuries.. Artificial Intelligence in Medicine,(AIIM), 37:167 - 176. 2006

SMI-2006-1118
D. L. Rubin, S. E. Lewis, C. J. Mungall, S. Misra, M. Westerfield, M. Ashburner, I. Sim, C. G. Chute, H. Solbrig, M. A. Storey, B. Smith, J. D. Richter, N. F. Noy, M. A. Musen. The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge.. OMICS: A Journal of Integrative Biology,:(in press). 2006

SMI-2006-1104
M. J. O'Connor, R. D. Shankar, A. K. Das. An Ontology-Driven Mediator for Querying Time-Oriented Biomedical Data. 19th IEEE International Symposium on Computer-Based Medical Systems, Salt Lake City, Utah, 2006.

SMI-2006-1102
R. D. Shankar, S. B. Martins, M. J. O'Connor, D. B. Parrish, A. K. Das. A Knowledge-Based System for Managing Clinical Trials. 19th IEEE International Symposium on Computer-Based Medical Systems, Salt Lake City, Utah, 2006.

SMI-2006-1099
S. W. Tu, K. M. Hrabak, J. R. Campbell, J. Glasgow, M. A. Nyman, R. McClure, M. James, R. M. Abarbanel, J. G. Mansfield, S. M. Martins, M. K. Goldstein, M. A. Musen. Use of Declarative Statements in Creating and Maintaining Computer-Interpretable Knowledge Bases for Guideline-Based Care. AMIA 2006 Annual Symposium, Washington DC, 2006.

SMI-2006-1096
R. D. Shankar, S. W. Tu, M. A. Musen. Medical Arguments in an Automated Health Care System . AAAI 2006 Spring Symposia, Stanford University, 2006.

SMI-2006-1093
I. Balboni, S. M. Chan, M. Kattah, J. Tenenbaum, A. J. Butte, P. J. Utz. Multiplexed Protein Array Platforms for Analysis of Autoimmune Diseases. Annual Review of Immunology,(Annu. Rev. Immunol.), 24:391–418. 2006

SMI-2006-1090
A. J. Butte, I. S. Kohane. Creation and implications of a phenome-genome network. Nature Biotechnology,24(1):55 - 62. 2006

SMI-2006-1088
M. Peleg, S. W. Tu. Reinhold Haux, Casimir Kulikowski, Stuttgart, Germany. 2006 IMIA Yearbook of Medical Informatics: Decision Support, Knowledge Representation and Management in Medicine. Schattauer, 2006

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Reports Published in 2005

SMI-2005-1220
R. Zeiger. Towards Continuous Medical Education. J Gen Intern Med,2005

SMI-2005-1219
R. Zeiger, C. Stave, F. Schmitzberger, L. M. Fagan. Modeling the Relationship Between Search Terms in Clinical Queries. Proc AMIA Symposium, 2005.

SMI-2005-1207
G. C. Scott, R. D. Shachter. Individualizing Generic Decision Models Using Assessmetns As Evidence. J Biomed Inform,2005

SMI-2005-1193
N. A. Dye, Z. S. Pincus, J. A. Theriot, L. Shapiro, Z. Gitai. Two Independent Spiral Structures Control Cell Shape In Caulobacter. Proc Natl Acad Sci USA,2005

SMI-2005-1172
G. D. Rubin, J. K. Lyo, D. S. Paik, A. J. Sherbondy, L. C. Chow, A. N. Leung, R. Mindelzun, P. K. Schraedley-Desmond, S. E. Zinck, D. P. Naidich, S. Napel. Pulmonary Nodules on Multi-Detector Row CT Scans: Performance Comparison of Radiologists and Computer-Aided Detection. Radiology,2005

SMI-2005-1170
A. Novak, J. Flannick, B. S. Srinivasan, H. H. McAdams, S. Batzoglou. Nuke: Scalable and General Pairwise and Multiple Network Alignmnet. Cold Springs Harbor Laboratories Conference on Genome Informatics, 2005.

SMI-2005-1168
J. Ma, D. Morrow, V. Walbot. Coomparative Transcriptome Profiling of Maize Inbred Lines Genome Biology null, null, 2005

SMI-2005-1167
S. Karlin, J. Mrazek, J. Ma, L. Brocchieri. Predicted Highly Expressed Genes in Archaeal Genomes. Proc Natl Acad Sci USA,2005

SMI-2005-1162
R. B. Altman, Z. Lin, A. B. Owen. Protecting Privacy of Human Subjects (Letters). Science,2005

SMI-2005-1161
T. M. Phuong, Z. Lin, R. B. Altman. Choosing SNPs Using Feature Selection. Proceeding IEEE System Bioinformatics Conference, 2005.

SMI-2005-1160
S. D. Mooney, M. P. Liang, R. Deconde, R. B. Altman. Structural Characterization of Proteins Using Residue Environments. Protein,2005

SMI-2005-1158
I. V. Sharakhov, A. C. Serazin, O. G. Grushko, A. N. Dana, N. F. Lobo, M. E. Hillenmeyer, R. Westerman, J. Romero-Severson, C. Constantini, N. Sagon, F. H. Collins, N. J. Besansky. Inversions and Gene Order Shuffling in Anopheles Gambiae and A. Funestus. Science,2005

SMI-2005-1157
A. N. Dana, Y. S. Hong, M. K. Kern, M. E. Hillenmeyer, B. W. Harker, N. F. Lobo, J. R. Hogan, P. Romans, F. H. Collins. Gene Expression Patterns Associated With Blood-Feeding in the Malaria Mosquito Anopheles Gambiae. BMC Genomics,2005

SMI-2005-1156
A. M. Deutschbauer, D. F. Jaramillo, M. Proctor, J. Kumm, M. E. Hillenmeyer, R. W. Davis, C. Nislow, G. Giaever. Mechanisms of Haploin Sufficiency Revealed by Genome-Wide Profiling in Yeast. Genetics,2005

SMI-2005-1155
Y. Garten, S. Kaplan, Y. Pilpel. Extraction of Transcription Regulatory Signals From Genome-Wide DNA-Protein Interaction Data. Nucleic Acid Res.,2005

SMI-2005-1144
H. Eriksson, S. W. Tu, M. A. Musen. Semantic Clinical Guideline Documents. AMIA Symposium, Washington, D.C., 2005.

SMI-2005-1143
H. Eriksson, S. W. Tu, M. A. Musen. Semantic Clinical Guideline Documents. AMIA Symposium, Washington, D.C., 2005.

SMI-2005-1117
C. Golbreich, O. Bierlaire, O. Dameron, B. Gibaud. Use case: Ontology with rules for identifying brain anatomical structures.. W3C Workshop on Rule Languages for Interoperability, 2005.

SMI-2005-1116
C. Golbreich, O. Bierlaire, O. Dameron, B. Gibaud. What reasoning support for ontology and rules? the brain anatomy case study: workshop on Protégé and rules . 8th International Protégé Conference, 2005.

SMI-2005-1115
D. L. Rubin, O. Dameron, M. A. Musen. Using OWL and Description Logics based classification for reasoning in biomedical applications.. 8th International Protégé Conference, Madrid, Spain, 2005.

SMI-2005-1114
M. A. Musen, M. Crubezy, M. J. O'Connor, D. L. Buckeridge. Knowledge-Based Syndromic Surveillance for Bioterrorism.. 2005 AAAI Spring Symposium on AI Technologies for Homeland Security, Stanford, CA, 2005.

SMI-2005-1113
N. F. Noy. Representing Classes As Property Values on the Semantic Web: W3C Technical Report. 2005.

SMI-2005-1112
N. F. Noy, R. V. Guha, M. A. Musen. User ratings of ontologies: Who will rate the raters?. Proceedings of the AAAI 2005 Spring Symposium on Knowledge Collection from Volunteer Contributors, Stanford, CA, 2005.

SMI-2005-1111
P. Mitra, N. F. Noy, A. R. Jaiswal. Ontology Mapping Discovery with Uncertainty. Fourth International Conference on the Semantic Web (ISWC-2005), Galway, Ireland, 2005.

SMI-2005-1110
H. Knublauch, M. Horridge, M. A. Musen, A. L. Rector, R. Stevens, N. Drummond, P. Lord, N. F. Noy, J. Seidenberg, H. Wang. The Protege OWL Experience: workshop on OWL: Experiences and Directions. Fourth International Semantic Web Conference (ISWC2005), Galway, Ireland, 2005.

SMI-2005-1109
N. F. Noy. Order from Chaos: How can ontologies and the Semantic Web help us structure the world's semi-structured information?

SMI-2005-1100
D. L. Rubin, O. Dameron, M. A. Musen. Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries. AMIA 2005 Symposium Proceedings, 2005.

SMI-2005-1097
N. F. Abernethy. Automating Social Network Models for Tuberculosis Contact Investigation. PhD Thesis. Stanford University,2005

SMI-2005-1095
M. P. Liang. Integrating Sequence and Structure Data for Identifying Functional Sites on Protein Structures.. PhD Thesis. Stanford University,2005

SMI-2005-1094
Y. Liu. COMPUTATIONAL IDENTIFICATION OF EUKARYOTIC REGULATORY ELEMENTS AND ITS APPLICATION IN CAENORHABDITIS ELEGANS. PhD Thesis. Stanford University,2005

SMI-2005-1092
Y. Huang, H. J. Lowe, D. A. Klein, R. J. Cucina. Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon. J Am Med Inform Assoc,(JAMIA), (12) :275-285. 2005

SMI-2005-1089
J. Huang, J. Shi, V. Molle, B. Sohlberg, D. Weaver, M. J. Bibb, N. Karoonuthaisiri, C. Lih, C. M. Kao, S. N. Cohen. Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Molecular Microbiology,58(5):1276-87. 2005

SMI-2005-1087
C. J. Wolfe, I. S. Kohane, A. J. Butte. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.. BMC Bioinformatics,6(227)2005

SMI-2005-1086
M. J. O'Connor, A. K. Das. A Knowledge-Based Mediator for Temporal Pattern Discovery in Biomedical Databases. 2005.

SMI-2005-1085
D. L. Rubin, C. F. Thorn, T. E. Klein, R. B. Altman. A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc,(JAMIA), 12(2):121-129. 2005

SMI-2005-1084
D. L. Rubin, O. Dameron, Y. Bashir, D. Grossman, P. Dev, M. A. Musen. Using an ontology of human anatomy to inform reasoning with geometric models. Stud Health Technol Inform,111:429-35. 2005

SMI-2005-1083
J. K. Ichikawa, S. B. English, M. C. Wolfgang, R. Jackson, A. J. Butte, S. Lory. Genome-wide analysis of host responses to the Pseudomonas aeruginosa yields synergistic effects. Cellular Microbiology,7(11):1635–1646. 2005

SMI-2005-1082
D. L. Buckeridge. A Method for Evaluating Outbreak Detection in Public Health Surveillance Systems that use Administrative Data. PhD Thesis. Stanford Univeristy,2005

SMI-2005-1081
M. I. Rafiq, M. J. O'Connor, A. K. Das. Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases. IEEE Computational Systems Bioinformatics Conference (CSB2005), Stanford, CA, USA, 2005.

SMI-2005-1080
M. J. O'Connor, H. Knublauch, S. W. Tu, B. Grossof, M. Dean, W. E. Grosso, M. A. Musen. Supporting Rule System Interoperability on the Semantic Web with SWRL. Fourth International Semantic Web Conference (ISWC2005), Galway, Ireland, 2005.

SMI-2005-1072
M. Crubezy, M. J. O'Connor, D. L. Buckeridge, Z. S. Pincus, M. A. Musen. Ontology-Centered Syndromic Surveillance for Bioterrorism. IEEE Intelligent Systems,20(5):26-35. 2005

SMI-2005-1068
O. Dameron. Keeping modular and platform-independent software up-to-date: benefits from the Semantic Web. 8th International Protege conference, Madrid, Spain, 2005.

SMI-2005-1067
O. Dameron, D. L. Rubin, M. A. Musen. Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. AMIA, Washington DC, 2005.

SMI-2005-1057
J. Pollard, A. J. Butte, S. Hoberman, M. Joshi, J. Levy, J. Pappo. A Computational Model to Define the Molecular Causes of Type 2 Diabetes Mellitus. DIABETES TECHNOLOGY & THERAPEUTICS,7(2):323-336. 2005

SMI-2005-1029
Y. Tseng, A. J. Butte, E. Kokkotou, V. K. Yechoor, C. M. Taniguchi, K. M. Kriauciunas, A. M. Cypess, M. Niinobe, K. Yoshikawa, M. E. Patti, C. Kahn. Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. NATURE CELL BIOLOGY,7(6):601-614. 2005

SMI-2005-1024
R. B. Altman. Editorial: Annual progress in bioinformatics. Briefings in Bioinformatics,6(1):4-5. 2005

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Reports Published in 2004

SMI-2004-1222
M. Pignone, S. Sheridan, Y. Z. Lee, J. Kuo, C. Phillips, C. Mulrow, R. Zeiger. Heart to Heart: A Computer Decision Aid for Assesment of Coronary Heart Disease Risk and teh Impact of Risk-Reduction Interventions for Primary Prevention. Preventive Cardiology,2004

SMI-2004-1221
M. Pignone, S. Sheridan, Y. Z. Lee, J. Kuo, C. Phillips, C. Mulrow, R. Zeiger. Heart to Heart: A Computer Decision Aid for Assesment of Coronary Heart Disease Risk and teh Impact of Risk-Reduction Interventions for Primary Prevention. Preventive Cardiology,2004

SMI-2004-1206
Q. J. Su, S. Saxonov, D. L. Brutlag. eBLOCKs: Enumerating Conserved Protein Blocks to Achieve Maximal Sensitivity and Specificity. Nucleic Acids Research,2004

SMI-2004-1200
C. A. Brandt, R. Gadagkar, C. Rodriguez, P. M. Nadkarni. Managing Complex Change In Clinical Stufy Metadata. J Am Med Inform Assoc,2004

SMI-2004-1176
A. Mani, S. Napel, D. S. Paik, R. B. Jeffery Jr, J. Yee, E. W. Olcott, R. Prokesch, M. Davila, R. Schraedly-Desmond, C. F. Beaulieu. Computed Tomography Colonography: Feasibility of Computer-Aided polyp Detection in a "First Reader" Paradigm. J Comput Assist Tomogr,2004

SMI-2004-1175
D. S. Paik, C. F. Beaulieu, G. D. Rubin, B. Acar, R. B. Jeffrey Jr, J. Yee, J. Dey, S. Napel. Surface Normal Overlap: A Computer-Aided Detection Algorithm With Application to Colonic Polyps and Lung Nodules in Helical CT. IEEE Trans Med Imaging,2004

SMI-2004-1174
P. Li, S. Napel, B. Acar, D. S. Paik, R. B. Jeffrey Jr, C. F. Beaulieu. Registration of Central Paths and Colonic Polyps Between Supine and Prone Scans in Computed Tomography Colonography: Pilot Study. Med Phys,2004

SMI-2004-1173
P. Li, S. Napel, B. Acar, D. S. Paik, R. B. Jeffrey Jr, C. F. Beaulieu. Registration of Central Paths and Colonic Polyps Between Supine and Prone Scans in Computed Tomograph Colonography: Pilot Study. Med Phys,2004

SMI-2004-1165
Y. Liu, X. S. Liu, L. Wei, R. B. Altman, S. Batzoglou. Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics. Genome Resource,2004

SMI-2004-1164
Z. Lin, A. B. Owen, R. B. Altman. Point of View: Approaches for Protecting Privacy in the Genomic Era. Genetic Engineering News,2004

SMI-2004-1163
E. Froelicher Sivarajan, N. H. Miller, D. J. Christopherson, K. Martin, K. M. Parker, M. Amonetti, Z. Lin, M. Sohn, N. Benowitz, C. B. Taylor, P. Bacchetti. High Rates of Sustained Smoking Cessation in Women Hospitalized with Cardiovascular Disease: The Women's Initiative for Nonsmoking (WINS). Circulation,2004

SMI-2004-1154
S. Handler, D. Nace, S. Studenski, D. B. Fridsma. Medication Error Reporting in Long Term Care. Am J Geriatr Pharmacother,2004

SMI-2004-1151
E. S. Burnside, C. Kahn. A Tutorial on Artificial Intelligence Techniques used for Computer-Aided Decision Support in Radiology. Diagn Imaging,2004

SMI-2004-1150
Y. Pan, E. S. Burnside. The effects of training parameters on learning a probabilistic expert system for mammography. International Congress Series,(Proc Compuer Assisted Radiology and Surgery) 2004

SMI-2004-1149
E. S. Burnside, D. L. Rubin, R. Shachter. Using Mayesian Network to Predict the Probability and Type of Breast Cancer Represented by Microcalcifications on Mammography. . Medinfo,2004

SMI-2004-1131
N. F. Noy, D. L. Rubin, M. A. Musen. Making Biomedical Ontologies and Ontology Repositories Work. IEEE Intelligent Systems,19(6):78-81. 2004

SMI-2004-1130
N. F. Noy, A. L. Rector. Defining N-ary Relations on the Semantic Web: Use With Individuals (Working Draft). 2004.

SMI-2004-1129
N. F. Noy. Semantic Integration: A Survey Of Ontology-Based Approaches. SIGMOD Record, Special Issue on Semantic Integration,33(4)2004

SMI-2004-1128
N. F. Noy, M. A. Musen. Specifying Ontology Views by Traversal. Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan, 2004.

SMI-2004-1127
N. F. Noy, S. Kunnatur, M. Klein, M. A. Musen. Tracking Changes During Ontology Evolution. Third International Conference on the Semantic Web, Hiroshima, Japan, 2004.

SMI-2004-1126
P. Mitra, N. F. Noy, A. R. Jaiswal. OMEN: A Probabilistic Ontology Mapping Tool. Workshop on Meaning coordination and negotiation at the Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan, 2004.

SMI-2004-1125
N. F. Noy, M. A. Musen. Using PROMPT Ontology-Comparison Tools in the EON Ontology Alignment Contest . Workshop on Evaluation of Ontology-based Tools (EON2004) at the Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan, 2004.

SMI-2004-1124
Y. Sure, A. Gomez-Perez, W. Daelemans, M. Reinberger, N. Guarino, N. F. Noy. Why Evaluate Ontology Technologies? Because It Works! . IEEE Intelligent Systems,19(4):Trends & Controversies, pp. 74-81. 2004

SMI-2004-1123
C. J. Hou, M. A. Musen, N. F. Noy. Environment for Composing Constraint Axioms by Instantiating Templates. International Journal of Human-Computer Studies,2004

SMI-2004-1108
E. S. Burnside, D. L. Rubin, R. Shachter, R. E. Sohlich, E. A. Sickles. Improving a bayesian network's ability to predict the probability of malignancy of microcalcifications on mammography. Computer Assisted Radiology and Surgery, Chicago, 2004.

SMI-2004-1107
E. S. Burnside, D. L. Rubin, R. Shachter, R. E. Sohlich, E. A. Sickles. A probabilistic expert system that provides automated mammographic-histologic correlation: initial experience. American Journal of Roentgenology,182(2):481-8. 2004

SMI-2004-1098
R. D. Shankar, S. W. Tu, M. A. Musen. Kwiz, a Knowledge-Acquisition Framework to Encode Guidelines. 2004.

SMI-2004-1071
O. Dameron. JOT: a scripting environment for creating and managing ontologies. 7th International Protégé Conference, Bethesda, MD (USA), 2004.

SMI-2004-1070
O. Dameron, N. F. Noy, H. Knublauch, M. A. Musen. Accessing and manipulating ontologies using web services.. Third International Semantic Web Conference (ISWC2004), Hiroshima, Japan, 2004.

SMI-2004-1069
O. Dameron, B. Gibaud, M. A. Musen. Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy. First International Workshop on Formal Biomedical Knowledge Representation KRMED04, Whistler, Canada, 2004.

SMI-2004-1063
R. J. Radmer, T. E. Klein. Severity of osteogenesis imperfecta and structure of a collagen-like peptide modeling a lethal mutation site.. Biochemistry,(Bried Bioinform), 43(18):5314-23. 2004

SMI-2004-1062
R. J. Radmer, T. E. E, M. Woon, J. F. Conroy, T. E. Klein. Severity of osteogenesis imperfecta and structure of a collagen-like peptide modeling a lethal mutation site.. 2004

SMI-2004-1061
D. L. Rubin, M. W. Carillo, M. Woon, J. F. Conroy, T. E. Klein, R. B. Altman. A resource to acquire and summarize pharmacogenetics knowledge in the literature.. Medinfo,(Bried Bioinform), 11(2):793-7. 2004

SMI-2004-1058
R. B. Altman. Building Successful Biological Databases. Brief Bioinformatics,(Bried Bioinform), 5(1):4-5. 2004

SMI-2004-1056
D. E. Oliver, G. Bhalotia, A. S. Schwartz, R. B. Altman, M. A. Hearst. Tools for loading MEDLINE into a local relational database. BMC Bioinformatics,5:146. 2004

SMI-2004-1045
A. T. Kho, Q. Zhao, Z. Cai, A. J. Butte, J. Y. Kim, S. L. Pomeroy, D. H. Rowitch, I. S. Kohane. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. GENES & DEVELOPMENT,18:629-640. 2004

SMI-2004-1043
A. B. Csoka, S. B. English, C. P. Simkevich, D. G. Ginzinger, A. J. Butte, G. P. Schatten, F. G. Rothman, J. M. Sedivy. Genome-scale expression profiling of Hutchinson–Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell,:1-9. 2004

SMI-2004-1031
M. K. Goldstein, R. W. Coleman, S. W. Tu, R. D. Shankar, M. J. O'Connor, M. A. Musen, S. B. Martins, P. W. Lavori, M. G. Shilpak, E. Z. Oddone, A. Advani, P. Gholami, B. B. Hoffman. Translating research into practice: organizational issues in implementing automated decision support for hypertension in three medical centers. Journal of the American Medical Informatics Association,(JAMIA), 11(5):368-376. 2004

SMI-2004-1030
D. J. Allocco, I. S. Kohane, A. J. Butte. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics,5(18)2004

SMI-2004-1028
J. M. Stuart. PREDICTING GENE FUNCTION USING DNA. Doctoral. Stanford University,2004

SMI-2004-1027
J. T. Chang, R. B. Altman. Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics,14(9):577-586. 2004

SMI-2004-1025
R. Das, A. Laederach, S. M. Pearlman, D. Herschlag, R. B. Altman. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.. RNA,11(3):344-354. 2004

SMI-2004-1023
Z. Lin, R. B. Altman. Finding haplotype tagging SNPs by use of principal components analysis.. The American Journal of Human Genetics,(Am J Hum Genet), 75:850-861. 2004

SMI-2004-1022
D. L. Buckeridge, M. J. O'Connor, H. Xu, M. A. Musen. A knowledge-based framework for deploying surveillance problem solvers. Proceedings of the 2004 International Conference on Information and Knowledge Engineering (IKE'04). June 21-24, 2004, Las Vegas, NV, 2004.

SMI-2004-1021
A. Garg. Comparing automatic and manually generated trees of protein structures. Masters Thesis. Stanford University,2004

SMI-2004-1016
D. Wang, M. Peleg, S. W. Tu, A. A. Boxwala, O. Ogunyemi, Q. T. Zeng, R. A. Greenes, V. L. Patel, E. H. Shortliffe. Design and Implementation of the GLIF3 Guideline Execution Engine. Journal of Biomedical Informatics,(JBI), :In Press. 2004

SMI-2004-1015
S. W. Tu, J. R. Campbell, M. A. Musen. K. Kaiser, S. Miksch and S. W. Tu, Amsterdam. Computer-Based Support for Clinical Guidelines and Protocols: Proceedings of the Symposium on Computerized Guidelines and Protocols (CGP-2004): SAGE Guideline Modeling: Motivations and Methodology. IOS Press, 167-171. 2004

SMI-2004-1013
A. L. Rector, N. Drummond, M. Horridge, J. Rogers, H. Knublauch, R. Stevens, H. Wang, C. Wroe. OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns. 14th International Conference on Knowledge Engineering and Knowledge Management (EKAW), Whittlebury Hall, UK, 2004.

SMI-2004-1012
H. Knublauch. Ontology-Driven Software Development in the Context of the Semantic Web: An Example Scenario with Protégé/OWL. International Workshop on the Model-Driven Semantic Web, Monterey, CA, 2004.

SMI-2004-1011
H. Knublauch, R. W. Fergerson, N. F. Noy, M. A. Musen. The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. Third International Semantic Web Conference, Hiroshima, Japan, 2004.

SMI-2004-1010
Z. Lin, A. B. Owen, R. B. Altman. Genomic research and human subject privacy. Science,305(5681):183. 2004

SMI-2004-1008
D. Wang, M. Peleg, S. W. Tu, A. A. Boxwala, O. Ogunyemi, Q. T. Zeng, R. A. Greenes, V. L. Patel, E. H. Shortliffe. Design and Implementation of the GLIF3 Guideline Execution Engine. 2004.

SMI-2004-1007
H. Knublauch, M. A. Musen, A. L. Rector. Editing Description Logic Ontologies with the Protégé OWL Plugin. International Workshop on Description Logics (DL2004), Whistler, Canada, 2004.

SMI-2004-1006
H. Knublauch, O. Dameron, M. A. Musen. Weaving the Biomedical Semantic Web with the Protégé OWL Plugin. First International Workshop on Formal Biomedical Knowledge Representation, Whistler, Canada, 2004.

SMI-2004-1005
I. Yeh, T. Hanekamp, S. Tsoka, P. D. Karp, R. B. Altman. Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery. Genome Resources,(Genome Res.), (April 12, 2004) :epub ahead of print. 2004

SMI-2004-0995
J. M. Dugan, R. B. Altman. Using surface envelopes for discrimination of molecular models. Protien Science,13(January 2004):15-24. 2004

SMI-2004-0993
J. T. Chang, H. Schutze, R. B. Altman. GAPSCORE: finding gene and protein names one word at a time. Bioinformatics,Vol.20 no.2(January 22):216-225. 2004

SMI-2004-0982
Y. Liu, X. S. Liu, L. Wei, R. B. Altman, S. Batzoglou. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Resource,3(March 14, 2004):451-458. 2004

SMI-2004-0981
C. P. Friedman, R. B. Altman, I. S. Kohane, K. A. McCormick, P. L. Miller, J. G. Ozbolt, E. H. Shortliffe, G. D. Stormo, M. C. Szczepaniak, D. Tuck, J. Williamson. Training the Next Generation of Informaticians: The Impact of 'BISTI' and Bioinformatics; A Report from the American College of Medical Informatics. Journal of American Medical Informatics Association,(JAMIA), (Feb 2004) 2004

SMI-2004-0980
A. A. Boxwala, M. Peleg, S. W. Tu, O. Ogunyemi, Q. T. Zeng, D. Wang, V. L. Patel, R. A. Greenes, E. H. Shortliffe. GLIF3: A Representation Format for Sharable Computer-Interpretable Clinical Practice. Journal of Biomedical Informatics,(JBI), 37(3):147-161. 2004

SMI-2004-0979
A. S. Chan, R. W. Coleman, S. B. Martins, A. Advani, M. A. Musen, H. B. Bosworth, E. Z. Oddone, M. G. Shlipak. Evaluating Provider Adherence in a Trial of a Guideline-Based Decision Support System for Hypertension. MedInfo 2004, San Francisco, California, Sept 7 - 11, 2004.

SMI-2004-0977
C. H. Cain. REPRESENTING AND REASONING ABOUT CONTEXTUALLY CHANGING ORGANIZATIONAL BEHAVIOR USING SIMULATION MODELS OF MEDICAL WORK. Doctoral dissertation. Stanford University. 2004

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Reports Published in 2003

SMI-2003-1223
E. Rose, R. Zeiger, S. Corley, P. Gorman, T. Yackel, W. R. Hersh. Development Methodology for a "Next Generation" Medical Informatics Curriculum for Clinicians. Proc AMIA Symposium, 2003.

SMI-2003-1202
J. M. Fidler, K. Li, C. Chung, K. Wei, J. A. Ross, M. Gao, G. D. Rosen. PG490-88, A Derivative of Triptolode, Causes Tumor Regression and Sensitizes Tumors to Chemotherapy. Mol Cancer Ther,2003

SMI-2003-1201
C. A. Brandt, A. M. Deshpande, C. Lu, G. Ananth, K. Sun, R. Gadagkar, R. Morse, C. Rodriguez, P. L. Miller, P. M. Nadkarni. Center for Medical Informations. TrialDB: A Web-Based Clinical Study Data Management System. AMIA Annual Symp Proc, 2003.

SMI-2003-1194
M. J. O'Connor, D. L. Buckeridge, M. K. Choy, M. Crubezy, Z. S. Pincus, M. A. Musen. BioSTORM: A System for Automated Surveillance of Diverse Data Sources. AMIA Annu Symp Proc,2003

SMI-2003-1177
P. Sundaram, C. F. Beaulieu, D. S. Paik, P. K. Schraedley-Desmond, S. Napel. CT Colonography: Does Improved Z Resolution Help Computer-Aided Polyp Detection?. Med Phys,2003

SMI-2003-1166
S. Liu, S. Lin, M. Woon, T. E. Klein, R. B. Altman. A Personlized and AUtomated dbSNP Surveillance System. CSB,2003

SMI-2003-1153
C. Cheng, M. K. Goldstein, E. Geller, R. E. Levitt. The Effects of CPOE on ICU workflow: An Observational Study. AMIA 2003 Fall Symposium, 2003.

SMI-2003-1122
N. F. Noy. S.Staab and R. Studer, Handbook on Ontologies: Tools for Mapping and Merging Ontologies. Springer-Verlag, 365-384. 2003

SMI-2003-1121
N. F. Noy, M. Klein. Tracking Complex Changes During Ontology Evolution . Second International Semantic Web Conference (ISWC-2003), Sanibel Island, Florida, 2003.

SMI-2003-1091
Y. Huang, H. J. Lowe, W. R. Hersh. A Pilot Study of Contextual UMLS Indexing to Improve the Precision of Concept-based Representation in XML-structured Clinical Radiology Reports. J. Am. Med. Inform. Assoc.,(JAMIA), (10) :580-587. 2003

SMI-2003-1054
D. L. Weiner, A. J. Butte, P. L. Hibberd, G. R. Fleisher. Computerized Recruiting for Clinical Trials in Real Time. ANNALS OF EMERGENCY MEDICINE,41(2):242-246. 2003

SMI-2003-1050
M. E. Patti, A. J. Butte, S. Crunkhorn, K. Cusi, R. Berria, S. Kashyap, Y. Miyazaki, I. S. Kohane, M. Costello, R. Saccone, E. J. Landaker, A. B. Goldfine, E. Mun, R. DeFronzo, J. Finlayson, C. Kahn, L. J. Mandarino. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proceedings of the National Academy of Sciences,(PNAS), 100(14):8466–8471. 2003

SMI-2003-1048
A. Nimgaonkar, D. Sanoudou, A. J. Butte, J. N. Haslett, H. M. Kunkel, A. H. Beggs, I. S. Kohane. Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics,4:1-12. 2003

SMI-2003-1047
K. Y. Lee, I. S. Kohane, A. J. Butte. PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications. BIOINFORMATICS APPLICATIONS NOTE,19(6):778-779. 2003

SMI-2003-1020
J. Quackenbush. Microarrays - Guilt by Association. Science,302(5643):240-241. 2003

SMI-2003-1017
A. B. Owen, J. M. Stuart, K. Mach, A. M. Villeneuve, S. K. Kim. A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans. Genome Res.,13(8):1828-37. 2003

SMI-2003-1014
J. M. Stuart, E. Segal, D. Koller, S. K. Kim. A gene co-expression network for global discovery of conserved genetic modules. Science,302(5643):249-55. 2003

SMI-2003-1009
Z. Lin, A. B. Owen, R. B. Altman. Fundamental tensions between genomic research and human subject privacy. 2003.

SMI-2003-1001
R. B. Altman, J. M. Dugan. Defining bioinformatics and structural bioinformatics. Methods of Biochemical Analysis,(Methods Biochem Anal), 44(April 2003):3-14. 2003

SMI-2003-1000
R. B. Altman. Complexities of managing biomedical information. (OMICS), 1(Spring 7, 2003):127-129. 2003

SMI-2003-0999
R. B. Altman. Genetic sequence data for pharmacogenomics. Current Opinion in Drug Discovery & Development,3(May 6,2003):297-303. 2003

SMI-2003-0998
S. Raychaudhuri, J. T. Chang, F. Imam, R. B. Altman. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Research,31(August 1, 2003):4553-4560. 2003

SMI-2003-0997
N. C. Denko, L. A. Fontana, K. M. Hudson, P. D. Sutphin, S. Raychaudhuri, R. B. Altman, A. J. Giaccia. Investigating hypoxic tumor physiology through gene expression patterns. Oncogene,22(September 1, 2003):5907-5914. 2003

SMI-2003-0989
I. Yeh, P. D. Karp, N. F. Noy, R. B. Altman. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics,2(January 22):241-8. 2003

SMI-2003-0988
R. B. Altman, D. A. Flockhart, S. T. Sherry, D. E. Oliver, D. L. Rubin, T. E. Klein. Indexing pharmacogenetic knowledge on the World Wide Web. Pharmacogenetics,1(January 2003):3-5. 2003

SMI-2003-0987
S. Raychaudhuri, R. B. Altman. A literature-based method for assessing the functional coherence of a gene group. Bioinfomatics,3(February 12, 2003):396-401. 2003

SMI-2003-0986
S. D. Mooney, T. E. Klein, R. B. Altman, M. A. Trifiro, B. Gottlieb. A functional analysis of disease-associated mutations in the androgen receptor gene. Nucleic Acids Research,31(April 2003):e42. 2003

SMI-2003-0985
M. P. Liang, D. R. Banatao, T. E. Klein, D. L. Brutlag, R. B. Altman. WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Research,13(July 1, 2003):3324-3327. 2003

SMI-2003-0984
O. G. Troyanskaya, K. Dolinski, A. B. Owen, R. B. Altman, D. Botstein. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) . Proceedings of the National Academy of Sciences,(PNAS), 14(July 1, 2003):8348-8353. 2003

SMI-2003-0983
D. R. Banatao, R. B. Altman, T. E. Klein. Microenvironment analysis and identification of magnesium . Nucleic Acids Research,31(August 1, 2003):4450-4460. 2003

SMI-2003-0978
M. Crubezy, Z. S. Pincus, M. A. Musen. Mediating Knowledge between Application Components. 2003.

SMI-2003-0976
C. H. Cain, M. K. Goldstein, E. Geller, R. E. Levitt. The effects of CPOE on ICU workflow: an observational study. 2003.

SMI-2003-0974
I. S. Gabashvili, M. Whirl-Carrillo, M. Bada, D. R. Banatao, R. B. Altman. Ribosomal Dynamics Inferred from Variations in Experimental Measurements. RNA,9(2003):1301-1307. 2003

SMI-2003-0973
N. F. Noy, M. A. Musen. The PROMPT Suite: Interactive Tools For Ontology Merging And Mapping. International Journal of Human-Computer Studies,2003

SMI-2003-0972
C. Parker, R. Rocha, J. R. Campbell, S. W. Tu, S. M. Huff. Detailed Clinical Models for Sharable, Executable Guidelines. 2003.

SMI-2003-0971
P. Ram, D. Berg, S. W. Tu, J. G. Mansfield, Q. Ye, R. M. Abarbanel. Executing Clinical Practice Guidelines using the SAGE Execution Engine. 2003.

SMI-2003-0970
S. W. Tu, M. A. Musen, R. D. Shankar, J. R. Campbell, K. M. Hrabak, J. McClay, S. M. Huff, R. McClure, C. Parker, R. Rocha, R. M. Abarbanel, N. Beard, J. Glasgow, J. G. Mansfield, P. Ram, Q. Ye, E. Mays, T. Weida, C. G. Chute, K. McDonald, D. Mohr, M. A. Nyman, S. M. Scheitel, H. Solbrig, D. Zill, M. K. Goldstein. Modeling Guidelines for Integration into Clinical Workflow. 2003.

SMI-2003-0969
S. Liu, R. B. Altman. Large scale study of protein domain distribution in the context of alternative splicingthe context of alternative splicing. Nucleic Acids Research,31(16):4828-4835. 2003

SMI-2003-0968
M. Peleg, A. A. Boxwala, S. W. Tu, Q. T. Zeng, O. Ogunyemi, D. Wang, V. L. Patel, R. A. Greenes, E. H. Shortliffe. The InterMed Approach to Sharable Computer-Interpretable Guidelines: a Review. Journal of the American Medical Informatics Association,2003

SMI-2003-0967
M. Peleg, R. Kantor. Approaches for Guideline Versioning Using GLIF. 2003.

SMI-2003-0966
S. W. Tu, J. R. Campbell, M. A. Musen. The Structure of Guideline Recommendations: A Synthesis. 2003.

SMI-2003-0965
D. B. Fridsma. Organizational Simulation of Medical Work: An Information-processing Approach. Doctoral dissertation. Stanford University,2003

SMI-2003-0964
D. L. Buckeridge, M. A. Musen, P. Switzer, M. Crubezy. An Analytic Framework for Space­Time Aberrancy Detection in Public Health Surveillance Data. 2003.

SMI-2003-0963
S. Khambata-Ford, Y. Liu, C. Gleason, M. Dickson, R. B. Altman, S. Batzoglou, R. M. Myers. Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay. Genome Research,13(7):1765-1774. 2003

SMI-2003-0962
J. R. Campbell, S. W. Tu, J. G. Mansfield, J. I. Boyer, J. McClay, C. Parker, P. Ram, S. M. Scheitel, K. McDonald. The SAGE Guideline Model: A Knowledge Representation Framework for Encoding Interoperable Clinical Practice Guidelines. 2003.

SMI-2003-0961
N. F. Noy, M. A. Musen. Ontology Versioning as an Element of an Ontology-Evolution Framework. IEEE Intelligent Systems,2003

SMI-2003-0960
M. Klein, N. F. Noy. A Component-Based Framework for Ontology Evolution. 2003.

SMI-2003-0959
L. Wei, R. B. Altman. RECOGNIZING COMPLEX, ASYMMETRIC FUNCTIONAL SITES IN PROTEIN STRUCTURES USING A BAYESIAN SCORING FUNCTION. Journal of Bioinformatics and Computational Biology,1:119-138. 2003

SMI-2003-0958
M. Crubezy, E. Motta, W. Lu, M. A. Musen. Configuring Online Problem-Solving Resources with the Internet Reasoning Service. IEEE Intelligent Systems,2(March-April):34-42. 2003

SMI-2003-0957
M. Crubezy, M. A. Musen. Ontologies in Support of Problem Solving. 2003

SMI-2003-0956
Z. S. Pincus, M. A. Musen. Contextualizing Heterogeneous Data for Integration. 2003.

SMI-2003-0954
A. Advani, M. K. Goldstein, Y. Shahar, M. A. Musen. Developing Quality Indicators and Auditing Protocols from Formal Guideline Models: Knowledge Representation and Transformations. 2003.

SMI-2003-0952
D. L. Buckeridge, M. A. Musen, P. Switzer, M. Crubezy. A Modular Framework for Automated Space-Time Surveillance Analysis of Public Health Data. 2003.

SMI-2003-0951
M. P. Liang, D. L. Brutlag, R. B. Altman. Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structure. 2003.

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Reports Published in 2002

SMI-2002-1210
G. C. Scott, R. D. Shachter, G. D. Sanders, L. A. Lenert. Design and Pilot Evaluation of an Automated Individualized Patient Decision Support Framework. Society for Medical Decision Making Annual Meeting, 2002.

SMI-2002-1209
G. C. Scott, R. D. Shachter, L. A. Lenert. Treating the Patient As Qwll As The Disease: Evidence-Based Reasoning About Patient Parameters. Society for Medical Decision Making Annual Meeting, 2002.

SMI-2002-1208
G. C. Scott, R. D. Shachter, L. A. Lenert. An Approach to Automate and Individualize Interactive Decision Support for Patients. American Medical INformations Assocaition Fall Symposium, 2002.

SMI-2002-1203
J. A. Ross, G. D. Rosen. The Molecular Biology of Lung Cancer. Curr Opin Pulm Med,2002

SMI-2002-1180
P. W. Hung, D. S. Paik, S. Napel, J. Yee, R. B. Jeffrey Jr, A. Steinauer-Gebauer, J. Min, A. Jathavedam, C. F. Beaulieu. Quantification of Distention in CT Colonogrpahy: Development and Validation of Three Computer Alogrithms . Radiology,2002

SMI-2002-1179
S. Napel, H. Xu, D. S. Paik, B. A. Ross, T. S. Sumanaweera, J. A. Hossack, R. B. Jeffrey Jr. Carotid Disease: Automted Analysis With Cardiac-Gated Three-Dimensional US Technique and Preliminary Results. Radiology,2002

SMI-2002-1178
B. Acar, C. F. Beaulieu, S. B. Gokturk, C. Tomasi, D. S. Paik, R. B. Jeffrey Jr, J. Yee, S. Napel. Edge Displacement Field-Based Calssification for Improved Detection of Polyps in CT Colonography. IEEE Trans Med Imaging,2002

SMI-2002-1077
A. J. Butte. Automated Assessments in Health Care Quality. Improving the Quality of Primary Care,32:50-62. 2002

SMI-2002-1066
D. E. Oliver, D. L. Rubin, M. Hewett, T. E. Klein, R. B. Altman. Ontology development for a pharmacogenetics knowledge base.. Pac Symp Biocomput,:65-76. 2002

SMI-2002-1065
D. L. Rubin, M. Hewett, D. E. Oliver, T. E. Klein, R. B. Altman. Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput,:88-99. 2002

SMI-2002-1064
S. D. Mooney, T. E. Klein. Structural models of osteogenesis imperfecta-associated variants in the COL1A1 gene.. Mol Cell Proteomics,1(11):868-75. 2002

SMI-2002-1049
P. J. Park, A. J. Butte, I. S. Kohane. Comparing expression profiles of genes with similar promoter regions. BIOINFORMATICS,18(12):1576–1584. 2002

SMI-2002-1046
W. P. Kuo, T. Jenssen, A. J. Butte, L. Ohno-Machado, I. S. Kohane. Analysis of matched mRNA measurements from two different microarray technologies. BIOINFORMATICS,0(0):1-9. 2002

SMI-2002-1036
A. J. Butte, L. Bao, B. Y. Reis, T. W. Watkins, I. S. Kohane. Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics. Journal of Biomedical Informatics,34:396-405. 2002

SMI-2002-1034
A. J. Butte. THE USE AND ANALYSIS OF MICROARRAY DATA. Nature Reviews: Drug Discovery,1:951-960. 2002

SMI-2002-1018
P. J. Roy, J. M. Stuart, J. Lund, S. K. Kim. Chromosomal clustering of muscle-expressed genes in C. elegans.. Nature,418:975-9. 2002

SMI-2002-1002
J. T. Chang, R. B. Altman. Promises of text processing: natural language processing meets AI . Drug Discovery Today,(Drug Discov Today), 19(October 1, 2002):992-993. 2002

SMI-2002-0991
D. L. Rubin, F. Shafa, D. E. Oliver, M. Hewett, R. B. Altman. Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Bioinformatics,18(July 2002):207-15. 2002

SMI-2002-0990
O. G. Troyanskaya, M. E. Garber, P. O. Brown, D. Botstein, R. B. Altman. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformtics,11(November, 2002):1454-61. 2002

SMI-2002-0975
A. K. Das. COMPUTERS IN PSYCHIATRY: A REVIEW OF PAST PROGRAMS AND AN ANALYSIS OF HISTORICAL TRENDS. Psychiatric Quarterly - Winter 2002,73(4):351-365. 2002

SMI-2002-0953
A. Advani, M. K. Goldstein, M. A. Musen. A Framework For Evidence-Adaptive Quality Assessment That Unifies Guideline-Based And Performance-Indicator Approaches. 2002.

SMI-2002-0950
A. Waugh, P. Gendron, R. B. Altman, J. W. Brown, D. Case, D. Gautheret, S. C. Harvey, N. Leontis, J. Westbrook. RNAML: A Standard Syntax for Exchanging RNA Informatio. 2002.

SMI-2002-0949
Z. Lin, M. Hewett, R. B. Altman. Using Binning to Maintain Confidentiality of Medical Data. 2002.

SMI-2002-0948
S. Raychaudhuri, H. Schutze, R. B. Altman. Using Text Analysis to Identify Functionally Coherent Gene Groups. 2002.

SMI-2002-0947
S. D. Mooney, T. E. Klein. The functional importance of disease-associated mutation. 2002.

SMI-2002-0946
D. L. Buckeridge, J. Graham, M. J. O'Connor, M. K. Choy, S. W. Tu, M. A. Musen. Knowledge-Based Bioterrorism Surveillance. AMIA Annual Symposium, San Antonio, TX, 2002.

SMI-2002-0945
D. M. Bravata, D. K. Owens, D. L. Buckeridge, C. Haberland, C. Rydzak, M. Schleinitz, W. M. Smith, H. Szeto, M. A. Musen. Bioterrorism Preparedness and Response: Use of Information Technologies and Decision Support Systems. 2002.

SMI-2002-0944
R. D. Shankar, S. W. Tu, M. A. Musen. Use of Protégé-2000 to Encode Clinical Guidelines. 2002.

SMI-2002-0943
J. Gennari, M. A. Musen, R. W. Fergerson, W. E. Grosso, M. Crubezy, H. Eriksson, N. F. Noy, S. W. Tu. The Evolution of Protégé: An Environment for Knowledge-Based Systems Development. 2002.

SMI-2002-0942
J. T. Chang, S. Raychaudhuri. Towards Incorporating Scientific Literature into Biological Algorithms. 2002.

SMI-2002-0941
M. J. O'Connor, S. W. Tu, M. A. Musen. The Chronus II Temporal Database Mediator. AMIA Annual Symposium, San Antonio, TX, 2002.

SMI-2002-0940
J. H. Nguyen, M. G. Kahn, C. A. Broverman, M. A. Musen. Protocol Design Patterns: Domain-Oriented Abstractions to Support the Authoring Of Computer-Executable Clinical Trials. 2002.

SMI-2002-0939
J. T. Chang, H. Schutze, R. B. Altman. Creating an Online Dictionary of Abbreviations from MEDLINE. 2002.

SMI-2002-0938
J. Han, R. B. Altman, V. Kumar, H. Mannila, D. Pregibon. Emerging Scientific Applications in Data Mining. 2002.

SMI-2002-0937
C. HF. Cheng. Representing and reasoning about contextuallychanging organizational behavior using simulation models of medical work. 2002.

SMI-2002-0936
N. F. Noy, M. A. Musen. Evaluating Ontology-Mapping Tools: Requirements and Experience. 2002.

SMI-2002-0935
M. Peleg, S. W. Tu, J. Bury, P. Ciccarese, J. Fox, R. A. Greenes, R. Hall, P. D. Johnson, N. Jones, A. Kumar, S. Miksch, S. Quaglini, A. Seyfang, E. H. Shortliffe, M. Stefanelli. Comparing Computer-Interpretable Guideline Models: A Case-Study Approach. J Am Med Inform Assoc.,(JAMIA), 10(1):52-68. 2002

SMI-2002-0934
J. T. Chang, R. B. Altman. Promises of Text Processing: Where Natural Language Processing Meets Artificial Intelligence. 2002.

SMI-2002-0933
C. ih. Hou, N. F. Noy, M. A. Musen. A Template-Based Approach Toward Acquisition of Logical Sentences. Intelligent Information Processing 2002, World Computer Congress, Montreal, Canada. 2002.

SMI-2002-0932
M. Kivi, X. S. Liu, S. Raychaudhuri, R. B. Altman, P. M. Small. Determining the Genomic Locations of Repetitive DNA Sequenceswith a Whole-Genome Microarray: IS6110 in Mycobacterium tuberculosis. 2002.

SMI-2002-0931
M. Crubezy, W. Lu, E. Motta, M. A. Musen. Configuring Online Problem-Solving Resources with the Internet Reasoning Service. 2002.

SMI-2002-0930
I. S. Gabashvili, M. Whirl-Carrillo, M. Bada, D. R. Banatao, R. B. Altman. Mining biochemical information: Lessons taught by the ribosome. RNA (2002),3:279-289. 2002

SMI-2002-0929
D. Wang, M. Peleg, S. W. Tu, A. A. Boxwala, R. A. Greenes, V. L. Patel, E. H. Shortliffe. Representation Primitives, Process Models and Patient Data in Computer-Interpretable Clinical Practice Guidelines: A Literature Review of Guideline Representation Models. International Journal of Medical Informatics,68:59-70. 2002

SMI-2002-0928
M. Peleg, I. S. Gabashvili, R. B. Altman. Qualitative models of molecular function: linking genetic polymorphisms of tRNA to their functional sequelae. Proceedings of the IEEE,92(12):1875-1886. 2002

SMI-2002-0927
N. F. Noy, M. A. Musen. PromptDiff: A Fixed-Point Algorithm for Comparing Ontology Versions. 2002.

SMI-2002-0926
N. F. Noy, M. Klein. Ontology Evolution: Not the Same as Schema Evolution. 2002.

SMI-2002-0925
N. F. Noy, M. A. Musen, J. L. Mejino, C. Rosse. Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy. 2002.

SMI-2002-0924
V. L. Patel, T. Branch, D. Wang, M. Peleg, A. A. Boxwala. Analysis of the Process of Encoding Guidelines: An Evaluation of GLIF3. 2002.

SMI-2002-0923
M. Peleg, S. W. Tu, J. Bury, P. Ciccarese, J. Fox, R. A. Greenes, R. Hall, P. D. Johnson, N. Jones, A. Kumar, S. Miksch, S. Quaglini, A. Seyfang, E. H. Shortliffe, M. Stefanelli. Comparing Models of Data and Knowledge for Guideline-Based Decision Support: a Case-Study Approach (Part 2 of 2). 2002.

SMI-2002-0922
M. Peleg, S. W. Tu, J. Bury, P. Ciccarese, J. Fox, R. A. Greenes, R. Hall, P. D. Johnson, N. Jones, A. Kumar, S. Miksch, S. Quaglini, A. Seyfang, E. H. Shortliffe, M. Stefanelli. Comparing Models of Decision and Action for Guideline-Based Decision Support: a Case-Study Approach (Part 1 of 2). 2002.

SMI-2002-0921
M. Peleg, V. L. Patel, V. Snow, S. W. Tu, C. Mottur-Pilson, E. H. Shortliffe, R. A. Greenes. Support for Guideline Development through Error Classification and Constraint Checking. Proceedings AMIA Symposium, 2002.

SMI-2002-0920
M. Peleg, I. Yeh, R. B. Altman. Modeling Biological Processes using Workflow and Petri Net Model. 2002.

SMI-2002-0919
T. E. Klein, J. T. Chang, M. K. Cho, K. L. Easton, R. W. Fergerson, M. Hewett, Z. Lin, Y. Liu, S. Liu, D. E. Oliver, D. L. Rubin, F. Shafa, J. M. Stuart, R. B. Altman. Integrating Genotype and Phenotype Information: An . 2002.

SMI-2002-0918
S. D. Mooney, P. A. Kollman, T. E. Klein. Conformational Preferences of Substituted Prolines in the Collagen Triple Helix. 2002.

SMI-2002-0917
M. L. Green, J. R. Polansky, H. Do, T. E. Klein, T. D. Nguyen. Similarites and Difference Between the TIGR and Olfactomedin Protein Families. Investigative Ophthalmology Visual Science (IOVS. 2002.

SMI-2002-0916
M. A. Musen. Medical Informatics: Searching For Underlying Components. Methods of Information in Medicine, Stanford University, 41, 2002.

SMI-2002-0915
D. C. Berrios, R. J. Cucina, P. D. Sutphin, L. M. Fagan. Methods For Semi-Automated Indexing For High Precision Information Retrieval. 2002.

SMI-2002-0914
S. Raychaudhuri, J. T. Chang, P. D. Sutphin, R. B. Altman. Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature. Genome Research, 1, 203-21. 2002.

SMI-2002-0913
R. B. Altman. Challenges for Intelligent Systems in Biology. 2002.

SMI-2002-0912
A. Advani, Y. Shahar, M. A. Musen. Medical Quality Assessment by Scoring Adherence to Guideline Intentions. 2002.

SMI-2002-0911
S. W. Tu, P. D. Johnson, M. A. Musen. A Typology for Modeling Processes in Clinical Guidelines and Protocols. 2002.

SMI-2002-0910
M. Hewett, D. E. Oliver, D. L. Rubin, K. L. Easton, J. M. Stuart, R. B. Altman, T. E. Klein. PharmGKB: the Pharmacogenetics Knowledge Base. 2002.

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Reports Published in 2001

SMI-2001-1212
G. C. Scott, R. D. Shachter. An Interactive Approach to Individualizing Generic Medical Decision Models. Society for Medical Decision Making Annual Meeting, 2001.

SMI-2001-1204
W. T. Chang, J. J. Kang, K. Y. Lee, K. Wei, E. Anderson, S. Gotmare, J. A. Ross, G. D. Rosen. Triptolide and Chemotherapy Cooperate in Tumor Cell Apoptosis. J Biol Chem,2001

SMI-2001-1185
D. Fleishmann, T. J. Hastie, F. C. Dannegger, D. S. Paik, M. Tillich, C. K. Zarins, G. D. Rubin. Quantitative Determination of Age-Related Geometric Changes in the Normal Abdominal aorta. J Vasc Surg,2001

SMI-2001-1183
M. Tillich, R. E. Bell, D. S. Paik, D. Fleischmann, M. C. Sofilos, L. J. Logan, G. D. Rubin. Iliac Arterial Injuries After Endovascular Repair of Abdominal Aortic Aneurysms: Correlation with Iliac Curvature and Radiology. Radiology,2001

SMI-2001-1182
M. Tillich, B. B. Hill, D. S. Paik, K. Petz, S. Napel, C. K. Zarins, G. D. Rubin. Prediction of Aortoiliac Stent-Graft Length: Comparison of Measurement Methods. Radiology,2001

SMI-2001-1181
S. B. Gokturk, C. Tomasi, B. Acar, C. F. Beaulieu, D. S. Paik, R. B. Jeffrey Jr, J. Yee, S. Napel. A Statistical 3-D Pattern Processing Method for Computer-Aided Detection of Polyps in CT Colonography. IEEE Trans Med Imaging,2001

SMI-2001-1053
A. Riva, K. D. Mandl, D. Oh, D. J. Nigrin, A. J. Butte, P. Szolovits, I. S. Kohane. The Personal Internetworked Notary and Guardian. International Journal of Medical Informatics,60:27-40. 2001

SMI-2001-1052
B. Y. Reis, A. J. Butte, I. S. Kohane. Extracting Knowledge from Dynamics in Gene Expression. Journal of Biomedical Informatics,34:15-27. 2001

SMI-2001-1042
A. J. Butte. Challenges in bioinformatics: infrastructure, models and analytics. TRENDS in Biotechnology,19(5):159-160. 2001

SMI-2001-1041
A. J. Butte, J. YE, G. NIEDERFELLNER, K. RETT, H. U. HÄRING, M. F. WHITE, I. S. Kohane. DETERMINING SIGNIFICANT FOLD DIFFERENCES IN GENE EXPRESSION ANALYSIS. 2001.

SMI-2001-1038
A. J. Butte, J. S. Shaw, H. Bernstein. Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses. THE PEDIATRIC INFECTIOUS DISEASE JOURNAL,20(6):561-565. 2001

SMI-2001-1037
A. J. Butte, V. J. Dzau, S. B. Glueck. Further defining housekeeping, or “maintenance,” genes Focus on “A compendium of gene expression in normal human tissues”. Physiol Genomics,7:95-96. 2001

SMI-2001-1019
S. K. Kim, J. Lund, M. Kiraly, K. Duke, M. Jiang, J. M. Stuart, A. Eizinger, B. N. Wylie, G. S. Davidson. A gene expression map for C. elegans.. Science,293:2087-92. 2001

SMI-2001-0994
I. S. Kohane, R. B. Altman. The new peer review. Proc AMIA Symposium,(2000) :433-7. 2001

SMI-2001-0992
M. E. Garber, O. G. Troyanskaya, K. Schluens, S. Petersen, Z. Thaesler, M. Pacyna-Gengelbach, M. Van de Rijn, G. D. Rosen, C. M. Perou, R. I. Whyte, R. B. Altman, P. O. Brown, D. Botstein. Diversity of gene expression in adenocarcinoma of the lung. Proceedings of the National Academy of Sciences,(PNAS), 24(November 20, 2001):13784-9. 2001

SMI-2001-0955
R. J. Cucina, M. K. Shah, D. C. Berrios, L. M. Fagan. Empirical Formulation of a Generic Query Set for Clinical Information Retrieval Systems. MedInfo2001,10(1):181-185. 2001

SMI-2001-0909
J. McClintick, D. Koller, N. Pankratz, S. C. Kirkwood, B. Naughton, T. Forroud. Automation and Integration of Components for Generalized Semantic Markup of Electronic Medical Texts. 2001.

SMI-2001-0908
W. Pratt, L. M. Fagan. The Usefulness of Dynamically Categorizing SearchThe Usefulness of Dynamically Categorizing Search. Journal of the American Medical Informatics Association,7(6):605-617. 2001

SMI-2001-0907
S. D. Mooney, C. C. Huang, P. A. Kollman, T. E. Klein. Computed Free Energy Differences Between Point Mutations in a Collagen-Like Peptide. Biopolymers,58:347-353. 2001

SMI-2001-0906
G. A. Williams, J. M. Dugan, R. B. Altman. Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances. Journal of Computational Biology,2001

SMI-2001-0903
R. B. Altman. Biomedical Computation At Stanford University: A Larger Umbrella for the Future. MD Computing,November/December 2000:35 - 37. 2001

SMI-2001-0902
J. M. Dugan. Open Source Initiatives in Bioinformatics. 2001.

SMI-2001-0901
D. E. Oliver, M. Hewett, D. L. Rubin, J. M. Stuart, T. E. Klein, R. B. Altman. Management of Data, Knowledge, and Metadata on the Semantic Web: Experience with a Pharmacogenetics Knowledge Base. Semantic Web Working Symposium, Stanford, CA, 2001.

SMI-2001-0900
A. K. Das, M. A. Musen. A Formal Method to Resolve Temporal Mismatches in Clinical Databases. AMIA Annual Symposium, 2001.

SMI-2001-0899
S. Shiffman, G. D. Rubin, S. Napel. Medical Image Segmentation Using Analysis of Isolable-Contour Maps. IEEE Transactions on Medical Imaging,19(11):1064-1074. 2001

SMI-2001-0898
R. B. Altman, T. E. Klein. Challenges for Biomedical Informatics and Pharmacogenomics. 2001.

SMI-2001-0897
R. B. Altman, S. Raychaudhuri. Whole-genome expression analysis: challenges beyond clustering. Current Opinion in Structural Biology,11:340-347. 2001

SMI-2001-0896
A. A. Boxwala, S. W. Tu, Q. T. Zeng, M. Peleg, O. Ogunyemi, R. A. Greenes, E. H. Shortliffe, V. L. Patel. Towards a Representation Format for Sharable Clinical Guidelines. Journal of Biomedical Informatics,2001

SMI-2001-0895
M. Crubezy, W. Lu, E. Motta, M. A. Musen. The Internet Reasoning Service: Delivering Configurable Problem-Solving Components to Web Users. Submitted to the First International Conference on Knowledge Capture (K-CAP 2001),, 2001.

SMI-2001-0894
A. T. Schreiber, M. Crubezy, M. A. Musen. A Case Study in Using Protege-2000 as a Tool for CommonKADS. 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France, 2001.

SMI-2001-0893
P. W. Groeneveld, J. L. Kwong, Y. Liu, A. J. Rodriguez, M. P. Jones, G. D. Sanders, A. M. Garber. The Cost-Effectiveness of Automated External Defibrillators on U.S. Airlines. 2001.

SMI-2001-0892
M. Peleg, A. A. Boxwala, E. V. Bernstam, S. W. Tu, R. A. Greenes, E. H. Shortliffe. Sharable Representation of Clinical Guidelines in GLIF: Relationship to the Arden Syntax. Journal of Biomedical Informatics,2001

SMI-2001-0891
M. A. Musen, M. J. O'Connor, D. L. Buckeridge, J. Graham, N. F. Noy, Y. Shahar, K. A. Henry. A Knowledge-Based Approach To Temporal Abstraction Of Clinical Data For Disease Surveillance. NATO Human Factors in Medicine Symposium on Operational Issues in Chemical and Biological Defense, Estoril, Portugal, May 14-17, 2001, 2001.

SMI-2001-0890
R. D. Shankar, S. W. Tu, S. B. Martins, L. M. Fagan, M. K. Goldstein, M. A. Musen. Integration of Textual Guideline Documents with Formal Guideline Knowledge Bases. AMIA 2001, 2001.

SMI-2001-0889
N. F. Noy, M. A. Musen. Anchor-PROMPT: Using Non-Local Context for Semantic Matching. Workshop on Ontologies and Information Sharing at the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-2001), Seattle, WA, 2001.

SMI-2001-0888
O. G. Troyanskaya, M. Cantor, G. Sherlock, P. O. Brown, T. J. Hastie, R. Tibshirani, D. Botstein, R. B. Altman. Missing value estimation methods for DNA microarrays. Bioinformatics,17(6):520-525. 2001

SMI-2001-0887
E. V. Bernstam. Chronic cough in immunocompetent adults. MDVista Journal of Medicine,2001

SMI-2001-0886
S. Raychaudhuri, P. D. Sutphin, J. T. Chang, R. B. Altman. Basic microarray analysis: Grouping and feature reduction. TRENDS in Biotechnology,19(5):189-193. 2001

SMI-2001-0885
D. C. Berrios. Automated Indexing for Full Text Information Retrieval. 2000 AMIA Fall Symposium, Los Angeles, CA, 2001.

SMI-2001-0884
E. V. Bernstam, N. Ash, M. Peleg, S. W. Tu, E. H. Shortliffe, R. A. Greenes. Preliminary Evaluation of a Guideline Classification System. AMIA Fall Symposium 2001, Washington DC, 2001.

SMI-2001-0883
R. C. Phillips, E. V. Bernstam, P. Mork, B. T. Karras. Modification of GEM to Accommodate Changes in a Classification Scheme. AMIA Fall Symposium 2001, Washington, DC, 2001.

SMI-2001-0882
E. V. Bernstam. Medline Query-by-Example. AMIA Fall Symposium 2001, Washington, DC, 2001.

SMI-2001-0881
E. V. Bernstam, S. D. Kamvar, F. Meric, J. M. Dugan, J. T. Chang, S. C. Chizek, C. Stave, O. G. Troyanskaya, L. M. Fagan. Oncology Patient Interface To Medline. American Society of Clinical Oncology, San Francisco, CA, 2001.

SMI-2001-0880
N. F. Noy, D. L. McGuinness. Ontology Development 101: A Guide to Creating Your First Ontology. 2001.

SMI-2001-0879
M. Peleg, O. Ogunyemi, S. W. Tu, A. A. Boxwala, Q. T. Zeng, R. A. Greenes, E. H. Shortliffe. Using Features of Arden Syntax with Object-Oriented Medical Data Models for Guideline Modeling. AMIA Annual Symposium, Washington, DC, 2001.

SMI-2001-0878
J. Q. Yin, M. Peleg, A. A. Boxwala, R. A. Greenes. Combining a Document Model and an Execution Model for Clinical Guidelines. AMIA Annual Symposium, Washington, DC, 2001.

SMI-2001-0877
M. J. O'Connor, R. D. Shankar, S. W. Tu, A. Advani, M. K. Goldstein, R. W. Coleman, M. A. Musen. A Client-Server Framework for Deploying a Decision-Support System in a Resource-Constrained Environment. 2001.

SMI-2001-0876
P. D. Johnson, S. W. Tu, M. A. Musen, I. Purves. A Virtual Medical Record for Guideline-Based Decision Support. AMIA Annual Symposium, Washington, DC, 2001.

SMI-2001-0875
M. K. Goldstein, B. B. Hoffman, R. W. Coleman, S. W. Tu, R. D. Shankar, M. J. O'Connor, S. B. Martins, A. Advani, M. A. Musen. Patient Safety in Guideline-Based Decision Support for Hypertension Management: ATHENA DSS. AMIA Annual Symposium, Washington, DC, 2001.

SMI-2001-0874
E. H. Shortliffe, A. M. Garber. Training Synergies Between Medical Informatics and Health Services Research: Successes and Challenges. 2001.

SMI-2001-0873
P. D. Johnson, S. W. Tu, N. Jones. Achieving Reuse of Computable Guideline Systems. MedInfo, London, UK, 2001.

SMI-2001-0872
N. F. Noy, M. Sintek, S. Decker, M. Crubezy, R. W. Fergerson, M. A. Musen. Creating Semantic Web Contents with Protege-2000. IEEE Intelligent Systems,16(2):60-71. 2001

SMI-2001-0871
A. A. Boxwala, P. Mehta, M. Peleg, R. Lacson, N. Ash, J. Bury, E. H. Shortliffe, R. A. Greenes. Representing guidelines using domain-level knowledge components. AMIA Annual Symposium, Los Angeles, CA, 2001.

SMI-2001-0870
Q. T. Zeng, S. W. Tu, A. A. Boxwala, M. Peleg, R. A. Greenes, E. H. Shortliffe. A Three-Layer Domain Ontology for Guideline Representation and Sharing. AMIA Annual Symposium, Los Angeles, CA, 2001.

SMI-2001-0869
S. W. Tu, M. A. Musen. Representation Formalisms and Computational Methods for Modeling Guideline-Based Patient Care. First European Workshop on Computer-based Support for Clinical Guidelines and Protocols, Leipzig, Germany, 2001.

SMI-2001-0868
S. W. Tu, M. A. Musen. Modeling Data and Knowledge in the EON Guideline Architecture. MedInfo 2001, London, UK, 2001.

SMI-2001-0867
B. E. Burnside, D. L. Rubin, R. Shachter. A Bayesian Network for Mammography. 2001.

SMI-2001-0866
R. D. Shankar, S. B. Martins, S. W. Tu, M. K. Goldstein, M. A. Musen. Building an Explanation Function for a Hypertension Decision-Support System. MedInfo2001, London, UK, 2001.

SMI-2001-0865
P. L. Elkin, M. Peleg, R. Lacson, E. V. Bernstam, S. W. Tu, A. A. Boxwala, R. A. Greenes, E. H. Shortliffe. Toward Standardization of Electronic Guidelines. MD Computing,17(6):39-44. 2001

SMI-2001-0864
C. HF. Cheng, G. D. Sanders, M. Hlatky, P. Heidenreich, K. McDonald, B. Lee, M. Larson, D. K. Owens. Cost-Effectiveness of Radiofrequency Ablation for Supraventricular Tachycardia. Annals of Internal Medicine,133(11):864-876. 2001

SMI-2001-0863
A. Waugh, G. A. Williams, L. Wei, R. B. Altman. Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases. Pacific Symposium on Biocomputing 2001, Mauna Lani, 2001.

SMI-2001-0862
J. T. Chang, S. Raychaudhuri, R. B. Altman. Improving Biological Literature Improves Homology Search. Pacific Symposium on Biocomputing 2001, Mauna Lani, HI, 2001.

SMI-2001-0861
D. Wang, M. Peleg, S. W. Tu, E. H. Shortliffe, R. A. Greenes. Representation of Clinical Practice Guidelines. Medinfo, London, UK, 2001.

SMI-2001-0860
R. A. Greenes, M. Peleg, A. A. Boxwala, S. W. Tu, V. L. Patel, E. H. Shortliffe. Sharable Computer-Based Clinical Practice Guidelines: Rationale, Obstacles, Approaches, and Prospects. Medinfo, London, UK, 2001.

SMI-2001-0859
M. Peleg, A. A. Boxwala, S. W. Tu, R. A. Greenes, E. H. Shortliffe, V. L. Patel. Handling Expressiveness and Comprehensibility Requirements in GLIF3. Medinfo, London, UK, 2001.

SMI-2001-0858
M. J. O'Connor, W. E. Grosso, S. W. Tu, M. A. Musen. RASTA: A Distributed Temporal Abstraction System to facilitate Knowledge-Driven Monitoring of Clinical Databases. Proceedings of 10th World Congress on Medical Informatics (MedInfo2001), London, 2001.

SMI-2001-0857
M. J. O'Connor, S. W. Tu, M. A. Musen. Representation of Temporal Indeterminacy in Clinical Databases. AMIA Annual Symposium, Los Angeles, CA, 2001.

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Reports Published in 2000

SMI-2000-1217
J. Shon, J. Marshall, M. A. Musen. The Impact of Displayed Awards on the Credibility and Retention of Web Site Information. Proc AMIA Symposium, 2000.

SMI-2000-1213
G. C. Scott, L. A. Lenert. What is the Next Step in Patient Decision Support?. JAMIA, 2000.

SMI-2000-1187
D