Publications

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All papers

(1) Rahib, et al (2020) Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma. Presented at the AACR Precision Medicine Conference, January 2020
[ask]
(2) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(3) Shrager (2019) ELIZA in BASIC; Ch. 4 in Stefan Holtgen and Marianna Baranovska (Eds.) Hello, I'm Eliza. http://www.computerarchaeologie.de
[pdf]
(4) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(5) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(6) Roitman, Shrager, Winograd (2017) A Comparative Analysis of Augmented Reality Technologies and their Marketability in the Consumer Electronics Segment. J Biosens Bioelectron 8:236. doi: 10.4172/2155- 6210.1000236
[openpub]
(7) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(8) Aleyasen, Starov, Au, Schiffman, and Shrager (Oct. 2015) On the Privacy Practices of Just Plain Sites. Presented at WPES 2015 (Workshop on Privacy in the Electronic Society). Denver, CO. (Also: arXiv:1507.00790 [cs.CY])
[arxiv]
(9) Shrager, J (2015) Demandance. ArXiv:1507.01882.
[arxiv]
(10) Chaudhri, V et al. (2014) Inconsistency Monitoring in a Large Scientific Knowledge Base. In Proceedings of the 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW). Linkoping, Sweden.
[pdf]
(11) Kang, Y, Shrager, J, Schiffman, A (2014b) RAPPD: A language and prototype for recipient-accountable private personal data. IEEE-S&P 2014 DUMA Workshop.
[pdf]
(12) Shrager, J, Tenenbaum, JM (2014a) Rapid Learning Precision Oncology. Nature Reviews Clinical Oncology 11, 109-118.
[pdf] [journal-site]
(13) Shrager, J (2013d) Theoretical Issues for Global Cumulative Treatment Analysis (GCTA). arXiv:1308.1066.
[arxiv] [video]
(14) Travers, M, et al. (2013c) Groups: Knowledge Spreadsheets for Symbolic Biocomputing. Database, bat061.
[open@pmc]
(15) A Baquero, A Schiffman, J Shrager (2013b) Blend me in: Privacy-Preserving Input Generalization for Personalized Online Services. In proceeding of PST2013, the International Conference on Privacy, Security and Trust. Tarragona, Catalonia, July 10-12, 2013.
[pdf]
(16) J Stevovic, et al. (2013a) Adding Individual Patient Case Data to The Melanoma Targeted Therapy Advisor. Presented at the 7th International Conference on Pervasive Computing Technologies for Healthcare. May, 2013, Venice, Italy.
[pdf]
(17) West L, Vidwans SJ, Campbell NP, Shrager J, Simon GR, et al. (2012c) A Novel Classification of Lung Cancer into Molecular Subtypes. PLoS ONE 7(2): e31906. doi:10.1371/journal.pone.0031906
[open@plos]
(18) Shrager, J. (2012b). Simulating Discovery and Education in a Soccer Science World. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[pdf]
(19) Carver, S. M., & Shrager, J. (2012a). The Psychology of Science, Science Education, and the Impact of David Klahr. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[ask]
(20) Berg, GM, Shrager, J, et al. (2011d) Responses of hli, ptox and psbA genes to changes in irradiance in marine Synechococcus and Prochlorococcus. Aquatic Microbial Ecology. Vol. 65: 1 14, 2011 doi: 10.3354/ame01528
[pdf]
(21) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(22) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(23) Vidwans, et al. (2011a) A Melanoma Molecular Disease Model. PLoS ONE 6(3): e18257. doi:10.1371/journal.pone.0018257
[open@plos]
(24) Mocellin, S., Shrager, J. et al. (2010d) Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. PLoS ONE, 5(8): e11965. doi:10.1371/journal.pone.0011965.
[open@plos]
(25) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(26) Shrager, J. (2010b) The Promise and Perils of Pre-publication Review: A Multi-agent Simulation of Biomedical Discovery Under Varying Levels of Review Stringency. PLoS ONE 5(5): e10782. doi:10.1371/journal.pone.0010782.
[open@plos]
(27) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(28) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(29) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(30) Theobald, M., Shah, N., Shrager, J. (2009b). Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
[pdf]
(31) D Billman, G Convertino, J Shrager, JP Massar, P Pirolli (2009a) Collaborative intelligence analysis with cache and its effects on information gathering and cognitive bias. Computer Supported Cooperative Work (CSCW), 17, 353-393.
[pdf]
(32) GM Berg, et al. (2008e) Understanding nitrogen limitation in Aureococcus Anophagefferens (Pelagophyceae) through cDNA analysis. J. Phycology. 44(5). DOI: 10.1111/j.1529-8817.2008.00571.x
[pdf]
(33) Bernstein, M, Shrager, J, Winograd, T (2008d) Taskpose: Exploring Fluid Boundaries in an Associative Window Visualization. UIST2008.
[pdf]
(34) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]
(35) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(36) S Bailey, et al. (2008a) Alternative photosynthetic electron flow to oxygen in marine synechococcus. BBA - Bioenergetics, 1777(3), 269-276.
[journal-site]
(37) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(38) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(39) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(40) M Jain, J Shrager, E Harris, R Holbrook, A Grossman, and O Vallon (2007a) EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Research; doi: 10.1093/nar/gkm081
[open@nar]
(41) P Langley, O Shiran, J Shrager, L Todorovski, A Pohorille (2006d) Constructing explanatory process models from biological data and knowledge. AI in Medicine, 37, 191-201.
[journal-site]
(42) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(43) M Jain, H Holz, J Shrager, O Vallon, C Hauser, and A Grossman, (2006b) A Hybrid, Recursive Algorithm for Clustering Expressed Sequence Tags in Chlamydomonas reinhardtii. 18th International Conference on Pattern Recognition (ICPR'06) 404-407
[pdf]
(44) R Labiosa, et al. (2006a) Examination of diel changes in global transcript accumulation in Synechocystis. J. Phycology, 42(3), 622-636.
[pdf]
(45) S Eberhard, et al. (2005d) Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Current Genetics. 03/2006; 49(2):106-24.
[journal-site]
(46) N Fedoroff, S Racunas and J Shrager (2005c) Tools for Thought in the Age of Biological Knowledge. The Scientist, 19(11), 20-21.
[pdf]
(47) M Travers, JP Massar, and J Shrager (June 2005b) The (Re)Birth of the Knowledge Operating System. International Lisp Conference, Stanford, CA.
[pdf]
(48) JP Massar, M Travers, J Elhai, and J Shrager (2005a) BioLingua: A programmable knowledge environment for biologists. Bioinformatics. 21(2), 199-207.
[link]
(49) ME Gorman, JF Groves, J Shrager (2004g) Societal dimensions of nanotechnology as a Trading Zone: Results from a Pilot Project. In D. Baird, et al. (Eds.) Discovering the Nanocale. Amsterdam: IOS Press. 63-73.
[pdf]
(50) CJ Tu, J Shrager, RL Burnap, BL Postier, AR Grossman (2004f) Consequences of a Deletion in dspA on Transcript Accumulation in Synechocystis sp. Strain PCC6803. J. Bacteriol. 186: 3889-3902.
[link]
(51) Z Zhang, J Shrager, M Jain, C-W Chang, O Vallon, AR Grossman (2004e) Insights into Global Effects of Sulfur Depletion on Wild-Type and Mutant Chlamydomonas reinhardtii. Eukaryot Cell. 2004 October; 3(5): 1331.1348.
[link]
(52) P Langley, J Shrager, N Asghargeygi, S Bay (2004d) Inducing explanatory process models from biological time series. Ninth Workshop on Intelligent Data Analysis and Data Mining.
[ask]
(53) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(54) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(55) Shrager, J. (2005). On being and becoming a molecular biologist: Notes from the diary of an insane cell mechanic. In M. E. Gorman, R. D. Tweney, D. C. Gooding & A. P. Kincannon (Eds.), Scientific and technological thinking. Mahwah, NJ: Erlbaum.
[pdf] [link]
(56) K Saito, D George, S Bay, J Shrager (2003g) Inducing biological models from temporal gene expression data. Lecture Notes in Computer Science v. 2843, Berlin: Springer.
[ask]
(57) A Grossman, EE Harris, C Hauser, PA Lefebvre, D Martinez, D Rokhsar, J Shrager, CD Silflow, D Stern, O Vallon, Z Zhang (2003f) Chlamydomonas reinhardtii at the Crossroads of Genomics Grossman et al. Eukaryotic Cell.2003; 2: 1137-1150.
[link]
(58) J Shrager (2003e) The fiction of function. Bioinformatics, 19: 1934-1936.
[link]
(59) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003d) Chlamydomonas reinhardtii Genome Project. A Guide to the Generation and Use of the cDNA Information. Plant Physiology 2003; 131:401-408.
[link]
(60) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003c) The generation and organization of Chlamydomonas cDNA information.
[link]
(61) C-S Im, Z-D Zhang, J Shrager, C-W Chang, & A Grossman (2003b). Analysis of Light and CO2 Regulation in Chlamydomonas reinhardtii Using Genome-Wide Approaches. Photosynthesis Research, 75: 111-125.
[link]
(62) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(63) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(64) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(65) J Shrager (2002-B-2010) Introduction to Intelligent Computational Biology.
[link]
(66) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]
(67) K Crowley, et al. (2001b) Shared scientific thinking in everyday parent-child activity. Science Education, 85(6): 712-732.
[pdf]
(68) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(69) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(70) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(71) Shrager, J., Worden, M., Smith, T., Noll, D. C., Hahn, M., and Schneider, W. (1997d). Cortical dynamics during skill acquisition: fMRI of task-specific and management regions in multiple paradigms. Journal of Cognitive Neuroscience, 1997S.
[ask]
(72) Schneider, W, Shrager, J. (1997c). Skill acquisition and brain imaging. Presented at Winter Cognitive Psychology conference, Jackson Hole, WY.
[ask]
(73) Shrager, J., Worden, M. Wellington, R., Vaughn, G., Smith, T., Hahn, M., Noll, D., & Schneider, W. (1997b). fMRI of cortical control areas in early skill acquisition. Presented at the Cognitive Neuroscience Conference, Boston.
[ask]
(74) Crowley, K., Shrager, J., & Siegler, R.S. (1997a). Strategy discovery as competitive negotiation between metacognitive and associative mechanisms. Developmental Review, 17: 462-489.
[pdf]
(75) Shrager, J., Worden, M., Wellington,R., Vaughn, G., Smith, T., Hahn, M., Noll, D.C., and Schneider, W. (1996c). fMRI of cortical control areas in early skill acquisition. Presented at the 37th Annual Meeting of the Psychonomic Society. Chicago, IL.
[ask]
(76) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(77) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(78) Elkind, J., & Shrager, J. (1995c). Modeling and analysis of dyslexic writing using speech and other modalities. In A. D. N. Edwards (Ed.) Extra-ordinary human-computer interaction. Cambridge U. Press.
[pdf]
(79) M Callanan, J Shrager, J Moore (1995b) Parent-child collaborative explanations: Methods of identification and analysis. J. of the Learning Sciences 4(1): 105-129.
[pdf]
(80) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(81) J Pinto, J Shrager, BI Berthenthal (1992b). Developmental Changes in Infants' Perceptual Processing of Biomechanical Motions. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, pages 60-65, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(82) Sibun, P, Shrager, J (1992a) Collaborative Mediation of the Setting of Activity. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, 1116-1121, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(83) Jordan, D, Shrager, J (1991b) The Role of Physical Properties in Understanding the Functionality of Objects. Program of the Thirteenth Annual Conference of the Cognitive Science Society: 7-10 August 1991, Chicago, Illinois.
[pdf]
(84) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(85) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(86) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(87) Agre, P., & Shrager, J. (1990a). Routine evolution as the microgenetic basis of skill acquisition. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(88) Chen, F. R., & Shrager, J. (1989b). Automatic discovery of contextual factors describing phonological variation. DARPA Speech & Natural Language Workshop. Philadelphia, PA.
[pdf]
(89) Shrager, J. (1989a). Reinterpretation and the perceptual microstructure of conceptual knowledge: Cognition considered as a perceptual skill. Proc. Annual Conf. of the Cognitive Science Society. Ann Arbor, MI.
[ask]
(90) K Downing, J Shrager (1988c) Causes to clauses: Managing assumptions in qualitative medical diagnosis. Int. J. of AI in Engineering, 3(4): 192-199.
[pdf]
(91) J Shrager (1988b) Continued monitoring of the state of qualitative physics. Int. J. of AI in Engineering, 3(4): 182-184.
[pdf]
(92) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(93) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(94) Shrager, J., et al. (1987b). Issues in the pragmatics of qualitative modeling: Lessons learned from a xerographics modeling project. CACM, 30(22): 1036-1047.
[pdf]
(95) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(96) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(97) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(98) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]
(99) Siegler, R. S. & Shrager, J. (1984a). Strategy choices in addition and subtraction: How do children know what to do? In C. Sophian (Ed.), Origins of cognitive skills. Hillsdale, NJ: Erlbaum.
[pdf]
(100) Shrager, J., & Hartman, L. G., (1983a). An APL batch scheduler improves service and system management. Proceedings of the National Conference on APL. Washington, DC. Washington, DC: Association for Computing Machinery.
[pdf]
(101) Shrager, J., Klahr, D., & Chase, W. (1982b). Segmentation and quantification of random dot patterns. Paper presented at the 23rd annual meeting of the Psychonomics Society.
[ask]
(102) Shrager, J., & ; Finin, T. (1982a). An expert system that volunteers advice. In Proc. of the Annual Conference of the American Assoc. for Artificial Intelligence. 339-340.
[pdf] [press]
(103) Shrager, J., & Bagley, S. (1981a). Learning Lisp. Prentice Hall: Gnosis. [Also in French, as: Apprendre Lisp.]
[link]
(104) Otto, G, et al., (1980a) APL.MS Users Guide. Univ. of Penn., and Univac Corp.
[ask]
(105) Contributions to the DECUS PDP-8 Library
[pdf]
(106) Shrager, J. (1973a/1977a) Eliza. A BASIC version of Weizenbaum's ELIZA program.
[pdf]

Artificial Intelligence

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Shrager (2019) ELIZA in BASIC; Ch. 4 in Stefan Holtgen and Marianna Baranovska (Eds.) Hello, I'm Eliza. http://www.computerarchaeologie.de
[pdf]
(3) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(4) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(5) Chaudhri, V et al. (2014) Inconsistency Monitoring in a Large Scientific Knowledge Base. In Proceedings of the 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW). Linkoping, Sweden.
[pdf]
(6) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(7) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(8) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(9) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(10) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(11) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(12) Theobald, M., Shah, N., Shrager, J. (2009b). Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
[pdf]
(13) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]
(14) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(15) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(16) P Langley, O Shiran, J Shrager, L Todorovski, A Pohorille (2006d) Constructing explanatory process models from biological data and knowledge. AI in Medicine, 37, 191-201.
[journal-site]
(17) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(18) M Travers, JP Massar, and J Shrager (June 2005b) The (Re)Birth of the Knowledge Operating System. International Lisp Conference, Stanford, CA.
[pdf]
(19) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(20) K Saito, D George, S Bay, J Shrager (2003g) Inducing biological models from temporal gene expression data. Lecture Notes in Computer Science v. 2843, Berlin: Springer.
[ask]
(21) J Shrager (2003e) The fiction of function. Bioinformatics, 19: 1934-1936.
[link]
(22) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(23) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(24) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(25) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]
(26) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(27) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(28) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(29) Chen, F. R., & Shrager, J. (1989b). Automatic discovery of contextual factors describing phonological variation. DARPA Speech & Natural Language Workshop. Philadelphia, PA.
[pdf]
(30) K Downing, J Shrager (1988c) Causes to clauses: Managing assumptions in qualitative medical diagnosis. Int. J. of AI in Engineering, 3(4): 192-199.
[pdf]
(31) J Shrager (1988b) Continued monitoring of the state of qualitative physics. Int. J. of AI in Engineering, 3(4): 182-184.
[pdf]
(32) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(33) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(34) Shrager, J., et al. (1987b). Issues in the pragmatics of qualitative modeling: Lessons learned from a xerographics modeling project. CACM, 30(22): 1036-1047.
[pdf]
(35) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(36) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(37) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(38) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]
(39) Shrager, J., & ; Finin, T. (1982a). An expert system that volunteers advice. In Proc. of the Annual Conference of the American Assoc. for Artificial Intelligence. 339-340.
[pdf] [press]
(40) Shrager, J. (1973a/1977a) Eliza. A BASIC version of Weizenbaum's ELIZA program.
[pdf]

Bioinformatics and Computational Biology

(1) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(2) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(3) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(4) Chaudhri, V et al. (2014) Inconsistency Monitoring in a Large Scientific Knowledge Base. In Proceedings of the 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW). Linkoping, Sweden.
[pdf]
(5) Shrager, J, Tenenbaum, JM (2014a) Rapid Learning Precision Oncology. Nature Reviews Clinical Oncology 11, 109-118.
[pdf] [journal-site]
(6) Shrager, J (2013d) Theoretical Issues for Global Cumulative Treatment Analysis (GCTA). arXiv:1308.1066.
[arxiv] [video]
(7) Travers, M, et al. (2013c) Groups: Knowledge Spreadsheets for Symbolic Biocomputing. Database, bat061.
[open@pmc]
(8) J Stevovic, et al. (2013a) Adding Individual Patient Case Data to The Melanoma Targeted Therapy Advisor. Presented at the 7th International Conference on Pervasive Computing Technologies for Healthcare. May, 2013, Venice, Italy.
[pdf]
(9) West L, Vidwans SJ, Campbell NP, Shrager J, Simon GR, et al. (2012c) A Novel Classification of Lung Cancer into Molecular Subtypes. PLoS ONE 7(2): e31906. doi:10.1371/journal.pone.0031906
[open@plos]
(10) Berg, GM, Shrager, J, et al. (2011d) Responses of hli, ptox and psbA genes to changes in irradiance in marine Synechococcus and Prochlorococcus. Aquatic Microbial Ecology. Vol. 65: 1 14, 2011 doi: 10.3354/ame01528
[pdf]
(11) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(12) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(13) Vidwans, et al. (2011a) A Melanoma Molecular Disease Model. PLoS ONE 6(3): e18257. doi:10.1371/journal.pone.0018257
[open@plos]
(14) Mocellin, S., Shrager, J. et al. (2010d) Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. PLoS ONE, 5(8): e11965. doi:10.1371/journal.pone.0011965.
[open@plos]
(15) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(16) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(17) Theobald, M., Shah, N., Shrager, J. (2009b). Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
[pdf]
(18) GM Berg, et al. (2008e) Understanding nitrogen limitation in Aureococcus Anophagefferens (Pelagophyceae) through cDNA analysis. J. Phycology. 44(5). DOI: 10.1111/j.1529-8817.2008.00571.x
[pdf]
(19) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(20) S Bailey, et al. (2008a) Alternative photosynthetic electron flow to oxygen in marine synechococcus. BBA - Bioenergetics, 1777(3), 269-276.
[journal-site]
(21) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(22) M Jain, J Shrager, E Harris, R Holbrook, A Grossman, and O Vallon (2007a) EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Research; doi: 10.1093/nar/gkm081
[open@nar]
(23) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(24) M Jain, H Holz, J Shrager, O Vallon, C Hauser, and A Grossman, (2006b) A Hybrid, Recursive Algorithm for Clustering Expressed Sequence Tags in Chlamydomonas reinhardtii. 18th International Conference on Pattern Recognition (ICPR'06) 404-407
[pdf]
(25) R Labiosa, et al. (2006a) Examination of diel changes in global transcript accumulation in Synechocystis. J. Phycology, 42(3), 622-636.
[pdf]
(26) S Eberhard, et al. (2005d) Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Current Genetics. 03/2006; 49(2):106-24.
[journal-site]
(27) N Fedoroff, S Racunas and J Shrager (2005c) Tools for Thought in the Age of Biological Knowledge. The Scientist, 19(11), 20-21.
[pdf]
(28) JP Massar, M Travers, J Elhai, and J Shrager (2005a) BioLingua: A programmable knowledge environment for biologists. Bioinformatics. 21(2), 199-207.
[link]
(29) CJ Tu, J Shrager, RL Burnap, BL Postier, AR Grossman (2004f) Consequences of a Deletion in dspA on Transcript Accumulation in Synechocystis sp. Strain PCC6803. J. Bacteriol. 186: 3889-3902.
[link]
(30) Z Zhang, J Shrager, M Jain, C-W Chang, O Vallon, AR Grossman (2004e) Insights into Global Effects of Sulfur Depletion on Wild-Type and Mutant Chlamydomonas reinhardtii. Eukaryot Cell. 2004 October; 3(5): 1331.1348.
[link]
(31) P Langley, J Shrager, N Asghargeygi, S Bay (2004d) Inducing explanatory process models from biological time series. Ninth Workshop on Intelligent Data Analysis and Data Mining.
[ask]
(32) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(33) Shrager, J. (2005). On being and becoming a molecular biologist: Notes from the diary of an insane cell mechanic. In M. E. Gorman, R. D. Tweney, D. C. Gooding & A. P. Kincannon (Eds.), Scientific and technological thinking. Mahwah, NJ: Erlbaum.
[pdf] [link]
(34) K Saito, D George, S Bay, J Shrager (2003g) Inducing biological models from temporal gene expression data. Lecture Notes in Computer Science v. 2843, Berlin: Springer.
[ask]
(35) A Grossman, EE Harris, C Hauser, PA Lefebvre, D Martinez, D Rokhsar, J Shrager, CD Silflow, D Stern, O Vallon, Z Zhang (2003f) Chlamydomonas reinhardtii at the Crossroads of Genomics Grossman et al. Eukaryotic Cell.2003; 2: 1137-1150.
[link]
(36) J Shrager (2003e) The fiction of function. Bioinformatics, 19: 1934-1936.
[link]
(37) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003d) Chlamydomonas reinhardtii Genome Project. A Guide to the Generation and Use of the cDNA Information. Plant Physiology 2003; 131:401-408.
[link]
(38) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003c) The generation and organization of Chlamydomonas cDNA information.
[link]
(39) C-S Im, Z-D Zhang, J Shrager, C-W Chang, & A Grossman (2003b). Analysis of Light and CO2 Regulation in Chlamydomonas reinhardtii Using Genome-Wide Approaches. Photosynthesis Research, 75: 111-125.
[link]
(40) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(41) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(42) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(43) J Shrager (2002-B-2010) Introduction to Intelligent Computational Biology.
[link]
(44) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]

Biomedicine

(1) Rahib, et al (2020) Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma. Presented at the AACR Precision Medicine Conference, January 2020
[ask]
(2) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(3) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(4) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(5) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(6) Shrager, J, Tenenbaum, JM (2014a) Rapid Learning Precision Oncology. Nature Reviews Clinical Oncology 11, 109-118.
[pdf] [journal-site]
(7) Shrager, J (2013d) Theoretical Issues for Global Cumulative Treatment Analysis (GCTA). arXiv:1308.1066.
[arxiv] [video]
(8) J Stevovic, et al. (2013a) Adding Individual Patient Case Data to The Melanoma Targeted Therapy Advisor. Presented at the 7th International Conference on Pervasive Computing Technologies for Healthcare. May, 2013, Venice, Italy.
[pdf]
(9) West L, Vidwans SJ, Campbell NP, Shrager J, Simon GR, et al. (2012c) A Novel Classification of Lung Cancer into Molecular Subtypes. PLoS ONE 7(2): e31906. doi:10.1371/journal.pone.0031906
[open@plos]
(10) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(11) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(12) Vidwans, et al. (2011a) A Melanoma Molecular Disease Model. PLoS ONE 6(3): e18257. doi:10.1371/journal.pone.0018257
[open@plos]
(13) Mocellin, S., Shrager, J. et al. (2010d) Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. PLoS ONE, 5(8): e11965. doi:10.1371/journal.pone.0011965.
[open@plos]
(14) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(15) Theobald, M., Shah, N., Shrager, J. (2009b). Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
[pdf]
(16) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]
(17) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(18) K Downing, J Shrager (1988c) Causes to clauses: Managing assumptions in qualitative medical diagnosis. Int. J. of AI in Engineering, 3(4): 192-199.
[pdf]

NIL

(1) Rahib, et al (2020) Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma. Presented at the AACR Precision Medicine Conference, January 2020
[ask]
(2) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(3) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(4) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(5) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(6) Shrager, J, Tenenbaum, JM (2014a) Rapid Learning Precision Oncology. Nature Reviews Clinical Oncology 11, 109-118.
[pdf] [journal-site]
(7) J Stevovic, et al. (2013a) Adding Individual Patient Case Data to The Melanoma Targeted Therapy Advisor. Presented at the 7th International Conference on Pervasive Computing Technologies for Healthcare. May, 2013, Venice, Italy.
[pdf]
(8) West L, Vidwans SJ, Campbell NP, Shrager J, Simon GR, et al. (2012c) A Novel Classification of Lung Cancer into Molecular Subtypes. PLoS ONE 7(2): e31906. doi:10.1371/journal.pone.0031906
[open@plos]
(9) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(10) Vidwans, et al. (2011a) A Melanoma Molecular Disease Model. PLoS ONE 6(3): e18257. doi:10.1371/journal.pone.0018257
[open@plos]
(11) Mocellin, S., Shrager, J. et al. (2010d) Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. PLoS ONE, 5(8): e11965. doi:10.1371/journal.pone.0011965.
[open@plos]
(12) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]

Cognitive Neuroscience

(1) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(2) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(3) Shrager, J., Worden, M., Smith, T., Noll, D. C., Hahn, M., and Schneider, W. (1997d). Cortical dynamics during skill acquisition: fMRI of task-specific and management regions in multiple paradigms. Journal of Cognitive Neuroscience, 1997S.
[ask]
(4) Schneider, W, Shrager, J. (1997c). Skill acquisition and brain imaging. Presented at Winter Cognitive Psychology conference, Jackson Hole, WY.
[ask]
(5) Shrager, J., Worden, M. Wellington, R., Vaughn, G., Smith, T., Hahn, M., Noll, D., & Schneider, W. (1997b). fMRI of cortical control areas in early skill acquisition. Presented at the Cognitive Neuroscience Conference, Boston.
[ask]
(6) Shrager, J., Worden, M., Wellington,R., Vaughn, G., Smith, T., Hahn, M., Noll, D.C., and Schneider, W. (1996c). fMRI of cortical control areas in early skill acquisition. Presented at the 37th Annual Meeting of the Psychonomic Society. Chicago, IL.
[ask]
(7) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(8) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(9) Elkind, J., & Shrager, J. (1995c). Modeling and analysis of dyslexic writing using speech and other modalities. In A. D. N. Edwards (Ed.) Extra-ordinary human-computer interaction. Cambridge U. Press.
[pdf]
(10) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(11) J Pinto, J Shrager, BI Berthenthal (1992b). Developmental Changes in Infants' Perceptual Processing of Biomechanical Motions. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, pages 60-65, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(12) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(13) Shrager, J. (1989a). Reinterpretation and the perceptual microstructure of conceptual knowledge: Cognition considered as a perceptual skill. Proc. Annual Conf. of the Cognitive Science Society. Ann Arbor, MI.
[ask]
(14) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(15) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]

Cognitive Psychology

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Shrager, J (2015) Demandance. ArXiv:1507.01882.
[arxiv]
(3) Shrager, J. (2012b). Simulating Discovery and Education in a Soccer Science World. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[pdf]
(4) Carver, S. M., & Shrager, J. (2012a). The Psychology of Science, Science Education, and the Impact of David Klahr. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[ask]
(5) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(6) Shrager, J. (2010b) The Promise and Perils of Pre-publication Review: A Multi-agent Simulation of Biomedical Discovery Under Varying Levels of Review Stringency. PLoS ONE 5(5): e10782. doi:10.1371/journal.pone.0010782.
[open@plos]
(7) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(8) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(9) D Billman, G Convertino, J Shrager, JP Massar, P Pirolli (2009a) Collaborative intelligence analysis with cache and its effects on information gathering and cognitive bias. Computer Supported Cooperative Work (CSCW), 17, 353-393.
[pdf]
(10) Bernstein, M, Shrager, J, Winograd, T (2008d) Taskpose: Exploring Fluid Boundaries in an Associative Window Visualization. UIST2008.
[pdf]
(11) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(12) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(13) Shrager, J. (2005). On being and becoming a molecular biologist: Notes from the diary of an insane cell mechanic. In M. E. Gorman, R. D. Tweney, D. C. Gooding & A. P. Kincannon (Eds.), Scientific and technological thinking. Mahwah, NJ: Erlbaum.
[pdf] [link]
(14) K Crowley, et al. (2001b) Shared scientific thinking in everyday parent-child activity. Science Education, 85(6): 712-732.
[pdf]
(15) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(16) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(17) Shrager, J., Worden, M., Smith, T., Noll, D. C., Hahn, M., and Schneider, W. (1997d). Cortical dynamics during skill acquisition: fMRI of task-specific and management regions in multiple paradigms. Journal of Cognitive Neuroscience, 1997S.
[ask]
(18) Schneider, W, Shrager, J. (1997c). Skill acquisition and brain imaging. Presented at Winter Cognitive Psychology conference, Jackson Hole, WY.
[ask]
(19) Shrager, J., Worden, M. Wellington, R., Vaughn, G., Smith, T., Hahn, M., Noll, D., & Schneider, W. (1997b). fMRI of cortical control areas in early skill acquisition. Presented at the Cognitive Neuroscience Conference, Boston.
[ask]
(20) Crowley, K., Shrager, J., & Siegler, R.S. (1997a). Strategy discovery as competitive negotiation between metacognitive and associative mechanisms. Developmental Review, 17: 462-489.
[pdf]
(21) Shrager, J., Worden, M., Wellington,R., Vaughn, G., Smith, T., Hahn, M., Noll, D.C., and Schneider, W. (1996c). fMRI of cortical control areas in early skill acquisition. Presented at the 37th Annual Meeting of the Psychonomic Society. Chicago, IL.
[ask]
(22) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(23) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(24) Elkind, J., & Shrager, J. (1995c). Modeling and analysis of dyslexic writing using speech and other modalities. In A. D. N. Edwards (Ed.) Extra-ordinary human-computer interaction. Cambridge U. Press.
[pdf]
(25) M Callanan, J Shrager, J Moore (1995b) Parent-child collaborative explanations: Methods of identification and analysis. J. of the Learning Sciences 4(1): 105-129.
[pdf]
(26) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(27) J Pinto, J Shrager, BI Berthenthal (1992b). Developmental Changes in Infants' Perceptual Processing of Biomechanical Motions. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, pages 60-65, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(28) Jordan, D, Shrager, J (1991b) The Role of Physical Properties in Understanding the Functionality of Objects. Program of the Thirteenth Annual Conference of the Cognitive Science Society: 7-10 August 1991, Chicago, Illinois.
[pdf]
(29) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(30) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(31) Agre, P., & Shrager, J. (1990a). Routine evolution as the microgenetic basis of skill acquisition. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(32) Shrager, J. (1989a). Reinterpretation and the perceptual microstructure of conceptual knowledge: Cognition considered as a perceptual skill. Proc. Annual Conf. of the Cognitive Science Society. Ann Arbor, MI.
[ask]
(33) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(34) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(35) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(36) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(37) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(38) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]
(39) Siegler, R. S. & Shrager, J. (1984a). Strategy choices in addition and subtraction: How do children know what to do? In C. Sophian (Ed.), Origins of cognitive skills. Hillsdale, NJ: Erlbaum.
[pdf]
(40) Shrager, J., Klahr, D., & Chase, W. (1982b). Segmentation and quantification of random dot patterns. Paper presented at the 23rd annual meeting of the Psychonomics Society.
[ask]

Models of Scientific Reasoning and Discovery

(1) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(2) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(3) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(4) Shrager, J, Tenenbaum, JM (2014a) Rapid Learning Precision Oncology. Nature Reviews Clinical Oncology 11, 109-118.
[pdf] [journal-site]
(5) Shrager, J (2013d) Theoretical Issues for Global Cumulative Treatment Analysis (GCTA). arXiv:1308.1066.
[arxiv] [video]
(6) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(7) P Langley, O Shiran, J Shrager, L Todorovski, A Pohorille (2006d) Constructing explanatory process models from biological data and knowledge. AI in Medicine, 37, 191-201.
[journal-site]
(8) P Langley, J Shrager, N Asghargeygi, S Bay (2004d) Inducing explanatory process models from biological time series. Ninth Workshop on Intelligent Data Analysis and Data Mining.
[ask]
(9) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(10) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(11) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(12) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(13) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]
(14) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(15) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(16) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(17) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]

Developmental Psychology

(1) Shrager, J. (2012b). Simulating Discovery and Education in a Soccer Science World. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[pdf]
(2) Carver, S. M., & Shrager, J. (2012a). The Psychology of Science, Science Education, and the Impact of David Klahr. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[ask]
(3) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]
(4) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(5) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(6) Crowley, K., Shrager, J., & Siegler, R.S. (1997a). Strategy discovery as competitive negotiation between metacognitive and associative mechanisms. Developmental Review, 17: 462-489.
[pdf]
(7) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(8) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(9) M Callanan, J Shrager, J Moore (1995b) Parent-child collaborative explanations: Methods of identification and analysis. J. of the Learning Sciences 4(1): 105-129.
[pdf]
(10) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(11) J Pinto, J Shrager, BI Berthenthal (1992b). Developmental Changes in Infants' Perceptual Processing of Biomechanical Motions. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, pages 60-65, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(12) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(13) Siegler, R. S. & Shrager, J. (1984a). Strategy choices in addition and subtraction: How do children know what to do? In C. Sophian (Ed.), Origins of cognitive skills. Hillsdale, NJ: Erlbaum.
[pdf]

Human Learning

(1) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(2) Shrager, J. (2005). On being and becoming a molecular biologist: Notes from the diary of an insane cell mechanic. In M. E. Gorman, R. D. Tweney, D. C. Gooding & A. P. Kincannon (Eds.), Scientific and technological thinking. Mahwah, NJ: Erlbaum.
[pdf] [link]
(3) K Crowley, et al. (2001b) Shared scientific thinking in everyday parent-child activity. Science Education, 85(6): 712-732.
[pdf]
(4) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(5) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(6) Shrager, J., Worden, M., Smith, T., Noll, D. C., Hahn, M., and Schneider, W. (1997d). Cortical dynamics during skill acquisition: fMRI of task-specific and management regions in multiple paradigms. Journal of Cognitive Neuroscience, 1997S.
[ask]
(7) Schneider, W, Shrager, J. (1997c). Skill acquisition and brain imaging. Presented at Winter Cognitive Psychology conference, Jackson Hole, WY.
[ask]
(8) Shrager, J., Worden, M. Wellington, R., Vaughn, G., Smith, T., Hahn, M., Noll, D., & Schneider, W. (1997b). fMRI of cortical control areas in early skill acquisition. Presented at the Cognitive Neuroscience Conference, Boston.
[ask]
(9) Crowley, K., Shrager, J., & Siegler, R.S. (1997a). Strategy discovery as competitive negotiation between metacognitive and associative mechanisms. Developmental Review, 17: 462-489.
[pdf]
(10) Shrager, J., Worden, M., Wellington,R., Vaughn, G., Smith, T., Hahn, M., Noll, D.C., and Schneider, W. (1996c). fMRI of cortical control areas in early skill acquisition. Presented at the 37th Annual Meeting of the Psychonomic Society. Chicago, IL.
[ask]
(11) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(12) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(13) M Callanan, J Shrager, J Moore (1995b) Parent-child collaborative explanations: Methods of identification and analysis. J. of the Learning Sciences 4(1): 105-129.
[pdf]
(14) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(15) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(16) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(17) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(18) Agre, P., & Shrager, J. (1990a). Routine evolution as the microgenetic basis of skill acquisition. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]
(19) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(20) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(21) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(22) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(23) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(24) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]

Molecular Biology

(1) Rahib, et al (2020) Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma. Presented at the AACR Precision Medicine Conference, January 2020
[ask]
(2) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(3) Shrager (Sep. 2016) Precision medicine: Fantasy meets reality. Letters; Science 353(6305)
[pdf]
(4) West L, Vidwans SJ, Campbell NP, Shrager J, Simon GR, et al. (2012c) A Novel Classification of Lung Cancer into Molecular Subtypes. PLoS ONE 7(2): e31906. doi:10.1371/journal.pone.0031906
[open@plos]
(5) Berg, GM, Shrager, J, et al. (2011d) Responses of hli, ptox and psbA genes to changes in irradiance in marine Synechococcus and Prochlorococcus. Aquatic Microbial Ecology. Vol. 65: 1 14, 2011 doi: 10.3354/ame01528
[pdf]
(6) Vidwans, et al. (2011a) A Melanoma Molecular Disease Model. PLoS ONE 6(3): e18257. doi:10.1371/journal.pone.0018257
[open@plos]
(7) GM Berg, et al. (2008e) Understanding nitrogen limitation in Aureococcus Anophagefferens (Pelagophyceae) through cDNA analysis. J. Phycology. 44(5). DOI: 10.1111/j.1529-8817.2008.00571.x
[pdf]
(8) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(9) S Bailey, et al. (2008a) Alternative photosynthetic electron flow to oxygen in marine synechococcus. BBA - Bioenergetics, 1777(3), 269-276.
[journal-site]
(10) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(11) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(12) M Jain, J Shrager, E Harris, R Holbrook, A Grossman, and O Vallon (2007a) EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Research; doi: 10.1093/nar/gkm081
[open@nar]
(13) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(14) M Jain, H Holz, J Shrager, O Vallon, C Hauser, and A Grossman, (2006b) A Hybrid, Recursive Algorithm for Clustering Expressed Sequence Tags in Chlamydomonas reinhardtii. 18th International Conference on Pattern Recognition (ICPR'06) 404-407
[pdf]
(15) R Labiosa, et al. (2006a) Examination of diel changes in global transcript accumulation in Synechocystis. J. Phycology, 42(3), 622-636.
[pdf]
(16) S Eberhard, et al. (2005d) Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Current Genetics. 03/2006; 49(2):106-24.
[journal-site]
(17) N Fedoroff, S Racunas and J Shrager (2005c) Tools for Thought in the Age of Biological Knowledge. The Scientist, 19(11), 20-21.
[pdf]
(18) JP Massar, M Travers, J Elhai, and J Shrager (2005a) BioLingua: A programmable knowledge environment for biologists. Bioinformatics. 21(2), 199-207.
[link]
(19) CJ Tu, J Shrager, RL Burnap, BL Postier, AR Grossman (2004f) Consequences of a Deletion in dspA on Transcript Accumulation in Synechocystis sp. Strain PCC6803. J. Bacteriol. 186: 3889-3902.
[link]
(20) Z Zhang, J Shrager, M Jain, C-W Chang, O Vallon, AR Grossman (2004e) Insights into Global Effects of Sulfur Depletion on Wild-Type and Mutant Chlamydomonas reinhardtii. Eukaryot Cell. 2004 October; 3(5): 1331.1348.
[link]
(21) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(22) K Saito, D George, S Bay, J Shrager (2003g) Inducing biological models from temporal gene expression data. Lecture Notes in Computer Science v. 2843, Berlin: Springer.
[ask]
(23) A Grossman, EE Harris, C Hauser, PA Lefebvre, D Martinez, D Rokhsar, J Shrager, CD Silflow, D Stern, O Vallon, Z Zhang (2003f) Chlamydomonas reinhardtii at the Crossroads of Genomics Grossman et al. Eukaryotic Cell.2003; 2: 1137-1150.
[link]
(24) J Shrager (2003e) The fiction of function. Bioinformatics, 19: 1934-1936.
[link]
(25) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003d) Chlamydomonas reinhardtii Genome Project. A Guide to the Generation and Use of the cDNA Information. Plant Physiology 2003; 131:401-408.
[link]
(26) J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z Zhang, AR Grossman (2003c) The generation and organization of Chlamydomonas cDNA information.
[link]
(27) C-S Im, Z-D Zhang, J Shrager, C-W Chang, & A Grossman (2003b). Analysis of Light and CO2 Regulation in Chlamydomonas reinhardtii Using Genome-Wide Approaches. Photosynthesis Research, 75: 111-125.
[link]
(28) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(29) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(30) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(31) J Shrager (2002-B-2010) Introduction to Intelligent Computational Biology.
[link]
(32) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]

Machine Learning

(1) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(2) P Langley, O Shiran, J Shrager, L Todorovski, A Pohorille (2006d) Constructing explanatory process models from biological data and knowledge. AI in Medicine, 37, 191-201.
[journal-site]
(3) K Saito, D George, S Bay, J Shrager (2003g) Inducing biological models from temporal gene expression data. Lecture Notes in Computer Science v. 2843, Berlin: Springer.
[ask]
(4) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(5) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(6) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(7) J Shrager, P Langley, A Pohorille (2002a) Guiding revision of regulatory models with expression data. Proc. of the Pacific Symposium on BioComputing. World Scientific Press.
[pdf]
(8) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(9) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(10) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(11) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(12) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(13) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(14) Chen, F. R., & Shrager, J. (1989b). Automatic discovery of contextual factors describing phonological variation. DARPA Speech & Natural Language Workshop. Philadelphia, PA.
[pdf]
(15) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(16) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(17) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(18) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(19) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(20) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]

Sociology/Anthropology

(1) Shrager (2019) ELIZA in BASIC; Ch. 4 in Stefan Holtgen and Marianna Baranovska (Eds.) Hello, I'm Eliza. http://www.computerarchaeologie.de
[pdf]
(2) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(3) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(4) ME Gorman, JF Groves, J Shrager (2004g) Societal dimensions of nanotechnology as a Trading Zone: Results from a Pilot Project. In D. Baird, et al. (Eds.) Discovering the Nanocale. Amsterdam: IOS Press. 63-73.
[pdf]
(5) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]

Psychology of Science

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Shrager, J. (2010b) The Promise and Perils of Pre-publication Review: A Multi-agent Simulation of Biomedical Discovery Under Varying Levels of Review Stringency. PLoS ONE 5(5): e10782. doi:10.1371/journal.pone.0010782.
[open@plos]
(3) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(4) Collins, H, Sanders, G (2007d) They give you the keys and say 'drive it!' Managers, referred expertise, and other expertises (co-authored appendix: 'More on the definition of referred expertise')
[pdf]
(5) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(6) Shrager, J. (2005). On being and becoming a molecular biologist: Notes from the diary of an insane cell mechanic. In M. E. Gorman, R. D. Tweney, D. C. Gooding & A. P. Kincannon (Eds.), Scientific and technological thinking. Mahwah, NJ: Erlbaum.
[pdf] [link]
(7) K Crowley, et al. (2001b) Shared scientific thinking in everyday parent-child activity. Science Education, 85(6): 712-732.
[pdf]
(8) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(9) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(10) J Shrager, P Langley (1990b) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]

Computer Simulation

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Shrager (2019) ELIZA in BASIC; Ch. 4 in Stefan Holtgen and Marianna Baranovska (Eds.) Hello, I'm Eliza. http://www.computerarchaeologie.de
[pdf]
(3) Shrager, J. (2012b). Simulating Discovery and Education in a Soccer Science World. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[pdf]
(4) Carver, S. M., & Shrager, J. (2012a). The Psychology of Science, Science Education, and the Impact of David Klahr. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[ask]
(5) Shrager, J. (2010b) The Promise and Perils of Pre-publication Review: A Multi-agent Simulation of Biomedical Discovery Under Varying Levels of Review Stringency. PLoS ONE 5(5): e10782. doi:10.1371/journal.pone.0010782.
[open@plos]
(6) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(7) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(8) P Langley, J Shrager, N Asghargeygi, S Bay (2004d) Inducing explanatory process models from biological time series. Ninth Workshop on Intelligent Data Analysis and Data Mining.
[ask]
(9) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(10) Shrager, J. & Siegler, R. S. (1999a). SCADS: A model of strategy choice and strategy discovery. Psychological Science.
[pdf]
(11) Johnson, M., Oliver, A., & Shrager, J. (1998a). The paradox of plasticity: A constrained plasticity approach to the emergence of representation in the neocortex. Cognitive Studies, 5(2): 5-24.
[pdf]
(12) Crowley, K., Shrager, J., & Siegler, R.S. (1997a). Strategy discovery as competitive negotiation between metacognitive and associative mechanisms. Developmental Review, 17: 462-489.
[pdf]
(13) Oliver, A., Johnson, M., Shrager, J. (1996b). The emergence of hierarchical clustered representations in a Hebbian neural network model that simulates aspects of development in the neocortex. Network: Computation in Neural Systems, 7(2), 291-299.
[ask]
(14) Shrager, J. & Johnson, M. H. (1996a). Factors influencing the emergence of function in a simple cortical network. Neural Networks, 9(6), 1119-1129.
[pdf]
(15) Shrager, J., Johnson, M. H. (1995a). Timing in the development of cortical function: A computational approach. In B. Julesz & I. Kovacs (Eds.), Maturational windows and adult cortical plasticity. New York: Addison-Wesley.
[pdf]
(16) J Shrager (1990c) Commonsense perception and the psychology of theory formation. In Shrager & Langley (Eds.) Computational models of scientific discovery and theory formation. San Mateo, CA: Morgan Kaufmann.
[pdf]
(17) K Downing, J Shrager (1988c) Causes to clauses: Managing assumptions in qualitative medical diagnosis. Int. J. of AI in Engineering, 3(4): 192-199.
[pdf]
(18) J Shrager (1988b) Continued monitoring of the state of qualitative physics. Int. J. of AI in Engineering, 3(4): 182-184.
[pdf]
(19) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(20) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]
(21) Shrager, J., et al. (1987b). Issues in the pragmatics of qualitative modeling: Lessons learned from a xerographics modeling project. CACM, 30(22): 1036-1047.
[pdf]
(22) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(23) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(24) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(25) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]
(26) Siegler, R. S. & Shrager, J. (1984a). Strategy choices in addition and subtraction: How do children know what to do? In C. Sophian (Ed.), Origins of cognitive skills. Hillsdale, NJ: Erlbaum.
[pdf]

Educational Psychology and Technology

(1) Shrager, J. (2012b). Simulating Discovery and Education in a Soccer Science World. In S. Carver & J. Shrager (Eds.), The journey from child to scientist: Integrating cognitive development and the education sciences. Washington, D.C.: American Psychological Association.
[pdf]
(2) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(3) J Shrager (1986b) The acquisition of device models in instructionless learning. In JL Kolodner and CK Riesbeck (Eds.) Experience, Memory, and Reasoning. Hillsdale, NJ: Lawrence Erlbaum Assoc. pp. 167-176.
[ask]
(4) J Shrager, D Klahr (1986a) Instructionless learning about a complex device: The paradigm and observations. Int. J. of Man-Machine Studies, 25: 153-189.
[pdf]
(5) J Shrager (1985) Instructionless learning about a complex device. CMU PhD Thesis.
[zip]
(6) Siegler, R. S. & Shrager, J. (1984a). Strategy choices in addition and subtraction: How do children know what to do? In C. Sophian (Ed.), Origins of cognitive skills. Hillsdale, NJ: Erlbaum.
[pdf]

Programming Languages

(1) N Fedoroff, S Racunas and J Shrager (2005c) Tools for Thought in the Age of Biological Knowledge. The Scientist, 19(11), 20-21.
[pdf]
(2) JP Massar, M Travers, J Elhai, and J Shrager (2005a) BioLingua: A programmable knowledge environment for biologists. Bioinformatics. 21(2), 199-207.
[link]
(3) J Shrager (2002-B-2010) Introduction to Intelligent Computational Biology.
[link]
(4) Shrager, J., & Bagley, S. (1981a). Learning Lisp. Prentice Hall: Gnosis. [Also in French, as: Apprendre Lisp.]
[link]
(5) Otto, G, et al., (1980a) APL.MS Users Guide. Univ. of Penn., and Univac Corp.
[ask]

Usability and Human Machine Interaction

(1) Roitman, Shrager, Winograd (2017) A Comparative Analysis of Augmented Reality Technologies and their Marketability in the Consumer Electronics Segment. J Biosens Bioelectron 8:236. doi: 10.4172/2155- 6210.1000236
[openpub]
(2) Shrager, J (2015) Demandance. ArXiv:1507.01882.
[arxiv]
(3) Travers, M, et al. (2013c) Groups: Knowledge Spreadsheets for Symbolic Biocomputing. Database, bat061.
[open@pmc]
(4) J Stevovic, et al. (2013a) Adding Individual Patient Case Data to The Melanoma Targeted Therapy Advisor. Presented at the 7th International Conference on Pervasive Computing Technologies for Healthcare. May, 2013, Venice, Italy.
[pdf]
(5) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(6) D Billman, G Convertino, J Shrager, JP Massar, P Pirolli (2009a) Collaborative intelligence analysis with cache and its effects on information gathering and cognitive bias. Computer Supported Cooperative Work (CSCW), 17, 353-393.
[pdf]
(7) Bernstein, M, Shrager, J, Winograd, T (2008d) Taskpose: Exploring Fluid Boundaries in an Associative Window Visualization. UIST2008.
[pdf]
(8) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(9) Elkind, J., & Shrager, J. (1995c). Modeling and analysis of dyslexic writing using speech and other modalities. In A. D. N. Edwards (Ed.) Extra-ordinary human-computer interaction. Cambridge U. Press.
[pdf]
(10) Shrager, J., & ; Finin, T. (1982a). An expert system that volunteers advice. In Proc. of the Annual Conference of the American Assoc. for Artificial Intelligence. 339-340.
[pdf] [press]

Mathematics (esp. Non-linear Graph Theory)

(1) Shrager, J (2013d) Theoretical Issues for Global Cumulative Treatment Analysis (GCTA). arXiv:1308.1066.
[arxiv] [video]
(2) Mocellin, S., Shrager, J. et al. (2010d) Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. PLoS ONE, 5(8): e11965. doi:10.1371/journal.pone.0011965.
[open@plos]
(3) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(4) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(5) Shrager, J., Hogg, T. and Huberman, B. A. (1987c). Observation of phase transitions in spreading activation networks. Science, 236: 1092-1094.
[pdf]

Privacy and Security

(1) Aleyasen, Starov, Au, Schiffman, and Shrager (Oct. 2015) On the Privacy Practices of Just Plain Sites. Presented at WPES 2015 (Workshop on Privacy in the Electronic Society). Denver, CO. (Also: arXiv:1507.00790 [cs.CY])
[arxiv]
(2) Kang, Y, Shrager, J, Schiffman, A (2014b) RAPPD: A language and prototype for recipient-accountable private personal data. IEEE-S&P 2014 DUMA Workshop.
[pdf]
(3) A Baquero, A Schiffman, J Shrager (2013b) Blend me in: Privacy-Preserving Input Generalization for Personalized Online Services. In proceeding of PST2013, the International Conference on Privacy, Security and Trust. Tarragona, Catalonia, July 10-12, 2013.
[pdf]

Collaboration and Collaboration Technologies

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Sweetnam, et al (2018) Prototyping a precision oncology 3.0 rapidlearning platform. BMC Bioinformatics, 19:341 doi:10.1186/s12859-018-2374-0
[openpub]
(3) Shrager (2017) Forget Moonshots: Biomedicine Needs an Air Traffic Control System (Blog posting). CollabRx Blog (Lundberg, G, Ed.)
[html]
(4) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(5) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(6) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(7) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(8) D Billman, G Convertino, J Shrager, JP Massar, P Pirolli (2009a) Collaborative intelligence analysis with cache and its effects on information gathering and cognitive bias. Computer Supported Cooperative Work (CSCW), 17, 353-393.
[pdf]
(9) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(10) ME Gorman, JF Groves, J Shrager (2004g) Societal dimensions of nanotechnology as a Trading Zone: Results from a Pilot Project. In D. Baird, et al. (Eds.) Discovering the Nanocale. Amsterdam: IOS Press. 63-73.
[pdf]
(11) M Callanan, J Shrager, J Moore (1995b) Parent-child collaborative explanations: Methods of identification and analysis. J. of the Learning Sciences 4(1): 105-129.
[pdf]
(12) Sibun, P, Shrager, J (1992a) Collaborative Mediation of the Setting of Activity. In Proceedings of the Fourteenth Annual Conference of the Cognitive Science Society, 1116-1121, Lawrence Erlbaum Associates, Hillsdale, NJ.
[ask]
(13) Shrager, J. & Callanan, M. (1991a). Active language in the collaborative development of cooking skill. Proc. Annual Conf. of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum.
[pdf]

BioBike

(1) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(2) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(3) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(4) J Shrager (2007b) The Evolution of BioBike: Community Adaptation of a Biocomputing Platform. Studies in History and Philosophy of Science, 38, 642-656.
[pdf]
(5) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(6) N Fedoroff, S Racunas and J Shrager (2005c) Tools for Thought in the Age of Biological Knowledge. The Scientist, 19(11), 20-21.
[pdf]
(7) M Travers, JP Massar, and J Shrager (June 2005b) The (Re)Birth of the Knowledge Operating System. International Lisp Conference, Stanford, CA.
[pdf]
(8) JP Massar, M Travers, J Elhai, and J Shrager (2005a) BioLingua: A programmable knowledge environment for biologists. Bioinformatics. 21(2), 199-207.
[link]
(9) J Shrager (2002-B-2010) Introduction to Intelligent Computational Biology.
[link]

Computer Science

(1) Shrager, Shapiro, Hoos (2019) Is Cancer Solvable? Towards Efficient and Ethical Biomedical Science. J Law Med and Ethics, 47 (2019): 362-368. DOI: 10.1177/1073110519876164
[pdf]
(2) Shrager (2019) ELIZA in BASIC; Ch. 4 in Stefan Holtgen and Marianna Baranovska (Eds.) Hello, I'm Eliza. http://www.computerarchaeologie.de
[pdf]
(3) Aleyasen, Starov, Au, Schiffman, and Shrager (Oct. 2015) On the Privacy Practices of Just Plain Sites. Presented at WPES 2015 (Workshop on Privacy in the Electronic Society). Denver, CO. (Also: arXiv:1507.00790 [cs.CY])
[arxiv]
(4) Chaudhri, V et al. (2014) Inconsistency Monitoring in a Large Scientific Knowledge Base. In Proceedings of the 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW). Linkoping, Sweden.
[pdf]
(5) Kang, Y, Shrager, J, Schiffman, A (2014b) RAPPD: A language and prototype for recipient-accountable private personal data. IEEE-S&P 2014 DUMA Workshop.
[pdf]
(6) A Baquero, A Schiffman, J Shrager (2013b) Blend me in: Privacy-Preserving Input Generalization for Personalized Online Services. In proceeding of PST2013, the International Conference on Privacy, Security and Trust. Tarragona, Catalonia, July 10-12, 2013.
[pdf]
(7) Tenenbaum, M., and Shrager, J. (2011c) Cancer: A computational disease that AI can cure. AI Magazine, Summer 2011 volume.
[pdf]
(8) Shrager, J, Tenenbaum, JM (2011b) Cancer Commons: Biomedicine in the internet age. In S. Elkin, et al. (Eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons.
[pdf]
(9) Shrager, J (2010c) From Wizards to Trading Zones: Computers in Scientific Collaboration. In M. Gorman (Ed.) Trading Zones and Interactional Expertise. MIT Press.
[publisher-site] [draft]
(10) Cornel, R, St. Amant, R, Shrager, J (2010a) Collaboration and Modeling Support in CogLaborate. The 19th Behavior Representation in Modeling & Simulation (BRIMS) Conference; March 22-25, 2010; Charleston, SC. (Received one of several Best Paper awards at the conference.)
[ask]
(11) Shrager, J., et al. (2009d) Soccer science and the Bayes community: Exploring the cognitive implications of modern scientific communication. Topics in Cognitive Science, 2(1), 53-72.
[pdf]
(12) Elhai, J., Taton, A., Massar, J.P., Myers, J.K., Travers, M., Casey, J., Slupesky, M., Shrager, J. (2009c) BioBIKE: A Web-based, programmable, integrated biological knowledge base. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp354
[open@nar]
(13) Theobald, M., Shah, N., Shrager, J. (2009b). Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
[pdf]
(14) Bernstein, M, Shrager, J, Winograd, T (2008d) Taskpose: Exploring Fluid Boundaries in an Associative Window Visualization. UIST2008.
[pdf]
(15) Collins, H., Clark, A., Shrager, J. (2008c). Keeping the collectivity in mind? Phenom Cogn Sci.
[pdf]
(16) Waldinger, R, Shrager, J (2008b) Answering Science Questions: Deduction with Answer Extraction and Procedural Attachment. AAAI Spring Symposium: Semantic Scientific Knowledge Integration. Stanford, CA.
[pdf]
(17) Shrager J, Waldinger R, Stickel M, Massar J (2007c) Deductive Biocomputing. PLoS ONE 2(4): e339. doi:10.1371/journal.pone.0000339
[link]
(18) M Jain, J Shrager, E Harris, R Holbrook, A Grossman, and O Vallon (2007a) EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Research; doi: 10.1093/nar/gkm081
[open@nar]
(19) P Langley, O Shiran, J Shrager, L Todorovski, A Pohorille (2006d) Constructing explanatory process models from biological data and knowledge. AI in Medicine, 37, 191-201.
[journal-site]
(20) R Waldinger and J Shrager (2006c) Deductive Discovery and Composition of Resources. Reasoning on the Web Conference (RoW2006). May 22, 2006, Edinburgh, Scotland.
[pdf]
(21) M Travers, JP Massar, and J Shrager (June 2005b) The (Re)Birth of the Knowledge Operating System. International Lisp Conference, Stanford, CA.
[pdf]
(22) S Bay, L Chrisman, A Pohorille, J Shrager (2004c) Temporal aggregation bias and inference of causal regulatory networks. J Computational Biology, 11(5), 971-985.
[pdf]
(23) Thompson, CA, Goker, MH, Langley, P (2004b) A Personalized System for Conversational Recommendations J. AI Res., 21, 393-428.
[pdf]
(24) J Shrager (2003e) The fiction of function. Bioinformatics, 19: 1934-1936.
[link]
(25) L Chrisman, et al. (2003a) Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Proc. of the Pacific Symposium on Biocomputing (PSB2003). Hawaii.
[ask]
(26) S Bay, J Shrager, A Pohorille, P Langley (2002d) Revising regulatory networks: From expression data to linear causal models. J Biomed Informatics, 35: 289-297.
[link]
(27) P Langley, J Shrager, K Saito (2002c) Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, C. Pizzi (Eds), Logical and Computational Aspects of Model-Based Reasoning. Dordrecht: Kluwer Academic Pubs.
[ask]
(28) J Shrager (2001a) High throughput discovery: Search and interpretation on the path to new drugs. In K. Crowley, et al. (Eds.) Design for Science. Hillsdale, NJ: Lawrence Erlbaum. 325-348.
[pdf]
(29) Chen, F. R., & Shrager, J. (1989b). Automatic discovery of contextual factors describing phonological variation. DARPA Speech & Natural Language Workshop. Philadelphia, PA.
[pdf]
(30) K Downing, J Shrager (1988c) Causes to clauses: Managing assumptions in qualitative medical diagnosis. Int. J. of AI in Engineering, 3(4): 192-199.
[pdf]
(31) J Shrager (1988b) Continued monitoring of the state of qualitative physics. Int. J. of AI in Engineering, 3(4): 182-184.
[pdf]
(32) Shrager, J., Hogg, T. and Huberman, B. A. (1988a). A graph-dynamic models of the power-law of practice and the problem-solving fan effect. Science, 242: 414-416.
[pdf]
(33) Shrager, J., et al. (1987b). Issues in the pragmatics of qualitative modeling: Lessons learned from a xerographics modeling project. CACM, 30(22): 1036-1047.
[pdf]
(34) J Shrager (1987a) Theory change via view application in instructionless learning. Machine Learning, 2: 247-276.
[pdf]
(35) Shrager, J., & Hartman, L. G., (1983a). An APL batch scheduler improves service and system management. Proceedings of the National Conference on APL. Washington, DC. Washington, DC: Association for Computing Machinery.
[pdf]
(36) Shrager, J., & ; Finin, T. (1982a). An expert system that volunteers advice. In Proc. of the Annual Conference of the American Assoc. for Artificial Intelligence. 339-340.
[pdf] [press]
(37) Shrager, J., & Bagley, S. (1981a). Learning Lisp. Prentice Hall: Gnosis. [Also in French, as: Apprendre Lisp.]
[link]
(38) Otto, G, et al., (1980a) APL.MS Users Guide. Univ. of Penn., and Univac Corp.
[ask]
(39) Contributions to the DECUS PDP-8 Library
[pdf]
(40) Shrager, J. (1973a/1977a) Eliza. A BASIC version of Weizenbaum's ELIZA program.
[pdf]

Open Jeff's Vita