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2014

Luo Z, Pelfrey C, Zhang GQ.
Visualizing and Evaluating the Growth of Multi-Institutional Collaboration Based on Research Network Analysis, AMIA Clinical Research Informatics Summit, 2014, San Francisco (In press)


Cui L, Carter R, Zhang GQ.
Evaluation of a Novel Conjunctive Exploratory Navigation Interface for Consumer Health Information: A Crowdsourced Comparative Study." Journal of Medical Internet Research, 2014;16(2):e45.


Sahoo S, Lhatoo S, Gupta D, Cui L, Zhao M, Jayapadian C, Bozorgi A, Zhang GQ.
Epilepsy and Seizure Ontology: Towards an Epilepsy Informatics Infrastructure for Clinical Research and Patient Care. Journal of American Medical Informatics Association, 2014 Jan 1;21(1):82-9. [PMID: 23686934]


Carter R, DiFeo A, Bogie K, Zhang GQ, Sun J.
Crowdsourcing Awareness: Exploration of the Ovarian Cancer Knowledge Gap through Amazon Mechanical Turk. PLOS ONE 9, no. 1 (2014):e85508.


Xu R, Wang Q
Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection. BMC Bioinformatics 2014, 15:17. DOI: 10.1186/10.1186/1471-2105-15-17 [1].

2013

Zhang GQ, Cui L, Teagno J, Kaebler D, Koroukian S, Xu R.
Merging Ontology Navigation with Query Construction for Web-based Medicare Data Exploration. AMIA Summit on Clinical Research Informatics (CRI) 2013, pp. 285-289. [PMID: 24303282; PMCID: PMC3845758]


Cui L, Mueller R, Sahoo SS, Zhang GQ.
Querying Complex Federated Clinical Data Using Ontological Mapping and Subsumption Reasoning. IEEE International Conference on Healthcare Informatics 2013 (ICHI 2013), pp. 351-360.


Luo L, Mejino J, Zhang GQ.
An Analysis of FMA Using Structural Self-Bisimilarity. Journal of Biomedical Informatics 2013;46(3):497–505.


Luo L, Xu R, Zhang GQ.
Dissecting the Ambiguity of FMA Concept Names Using Taxonomy and Partonomy Structural Information. AMIA Summits Transl Sci Proc. 2013; 2013:157–161. [PMC3845762]


Luo L, Rowbottom J, Craker J, Xu R, Zhang GQ.
VINSIA: Visual Navigator for Surgical Information Access. Military Medicine 2013;178(7):746-752. [PMID: 23820348]


Sahoo S, Zhang GQ, Lhatoo S.
Epilepsy Informatics and an Ontology-driven Infrastructure for Large Database Research and Patient Care in Epilepsy. Epilepsia 2013;54(8):1335–1341. [PMID: 23647220; PMCID: PMC3774789]


Sahoo S, Jayapandian C, Garg G, Kaffashi F, Chung S, Bozorgi A, Chen CH, Loparo K, Lhatoo SD, and Zhang GQ.
Heart beats in the cloud: distributed analysis of electrophysiological 'big data' using cloud computing for epilepsy clinical research. Journal of the American Medical Informatics Association (2013). [PMID: 24326538]


Jayapandian CP, Chen CH, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS.
Cloudwave: Distributed Processing of “Big Data” from Electrophysiological Recordings for Epilepsy Clinical Research Using Hadoop. American Medical Informatics Association (AMIA) Annual Symposium, 2013. pp. 691-700.


Bozorgi A, Chung S, Kaffashi F, Loparo K, Sahoo S, Zhang GQ, Kaiboriboon K, Lhatoo S.
Significant postictal hypotension: Expanding the spectrum of seizure‐induced autonomic dysregulation. Epilepsia 2013;54(9):e127–e130. [PMID: 23758665; PMCID: PMC3769446]


Chen Y, Ren XF, Zhang GQ, Xu R.
Ontology-Guided Organ Detection to Retrieve Web Images of Disease Manifestation: Towards the Construction of a Consumer-based Health Image Library. Journal of the American Medical Informatics Association (JAMIA) 2013 Nov-Dec;20(6):1076-81. [PMID: 23792805; PMCID: PMC3822108]


Luo ZH, Zhang GQ, Xu R.
Mining Patterns Among Adverse Events in Clinical Trials - An Exploratory Study. AMIA Summits Transl Sci Proc 2013:112–116. [PMID: 24303317; PMCID: PMC3814483]


Lebo T, Sahoo SS, McGuinness D. (eds.)
PROV-O: The PROV Ontology. 30 April 2013, W3C Recommendation. URL: http://www.w3.org/TR/prov-o/


Asiaee AH, Doshi P, Minning T, Sahoo SS, Parikh P, Sheth A, Tarleton RL.
From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data. The 9th International Conference on Data Integration in the Life Sciences (DILS), 2013. pp. 38-45.


Parchman AJ, Zhang GQ, Mergler P, Barnholtz-Sloan J, Lanese R, Miller DW, Opper C, Sahoo SS, Tao S, Teagno J, Warfe J, Meropol NJ.
Trial prospector: An automated clinical trials eligibility matching program. Proceedings of the American Society of Clinical Oncology (ASCO) Annual Meeting. 2013.


Chen Y, Zhang X, Zhang GQ and Xu R
Creation and Comparative Analysis of a Novel Disease Phenotype Network Based on Clinical Manifestation. Annual American Medical Informatics Association Symposium (Accepted for Late-breaking oral presentation).


Xu R, Wang Q
Automatic signal prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). J Biomed Inform (in press).


Xu R, Li L, Wang Q
Towards building a disease-phenotype relationship knowledge base: large scale extraction of disease-manifestation relationship from literature. Bioinformatics 2013; doi: 10.1093/bioinformatics/btt359 [2].


Xu R, Wang Q
A Semi-Supervised Pattern-Learning Approach to Extract Pharmacogenomics-Specific Drug-Gene Pairs from Biomedical Literature. J Pharmacogenom Pharmacoproteomics 4: 117. doi:10.4172/2153-0645.1000117


Xu R, Wang Q
Toward creation of a cancer drug toxicity knowledge base: automatically extracting cancer drug side effect relationships from literature. Journal of the American Medical Informatics Association (JAMIA), 2014;21:1 90-96. [3].


Xu R, Wang Q
A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. J Biomed Inform 2013. [4].


Xu R, Wang Q
Large-scale extraction of drug-disease treatment pairs from biomedical literature for drug repurposing. BMC Bioinformatics, 2013, 14(1), 181. [5]


Xu R, Wang Q
An iterative searching and ranking algorithm for prioritizing pharmacogenomics genes. Int J Comput Biol Drug Des. 2013;6(1-2):18-31. [6]

2012

Chen Y, Ren XF, Zhang GQ, Xu R.
Ontology Guided Approach to Retrieving Disease Manifestation Images for Health Image Base Construction. IEEE HISB 2012 (Best Research Paper Award).


Jayapandian CP, Chen CH, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS.
Electrophysiological Signal Analysis and Visualization using Cloudwave for Epilepsy Clinical Research. Studies in health technology and informatics 192 (2012): 817-821. [PMID: 23920671]


Guo-Qiang Zhang, Lhatoo S, Sahoo S (2012)
From classification to epilepsy ontology and informatics. Epilepsia, 53;28-32. [PMID: 23647220; PMCID: PMC3398997]


Jayapandian C, Zhao M, Ewing R, Guo-Qiang Zhang, Sahoo S (2012)
A semantic proteomics dashboard (SemPoD) for proteomics data management in translational research. BMC Systems Biology 2012;6:S20. [PMID: 23282161; PMCID: PMC3524316]


Guo-Qiang Zhang, Luo L, Ogbuji C, Joslyn C, Mejino J, Sahoo S (2012)
An analysis of multi-type relational interactions in FMA using graph motifs. AMIA Ann. Symposium Proc 2012. [PMID: 23304382; PMCID: PMC3540524]


Cui L, Bozorgi A, Lhatoo S.D, Guo-Qiang Zhang, Sahoo S (2012)
EpiDEA: Extracting Structured Epilepsy and Seizure Information from Patient Discharge Summaries for Cohort Identification. AMIA Annu Symp Proc. 2012, pp. 1191-1200. [PMID: 23304396; PMCID: PMC3540531]


Sahoo S, Zhao M, Luo L, Guo-Qiang Zhang (2012).
OPIC: Ontology-driven Patient Information Capturing System for Epilepsy. AMIA Annu Symp Proc. 2012:799-808. [PMID: 23304354; PMCID: PMC3540561]


Yang Chen, Guo-Qiang Zhang and Rong Xu (2012).
Semi-supervised Image Classification for Automatic Construction of a Health Image Library, ACM SIGHIT Annual Symposium on Health Informatics. [7]


Licong Cui, Guo-Qiang Zhang (2012).
A generalized non-pumping lemma for regular languages. WSPC - Proceedings


Parikh PP, Zheng J, Logan-Klumper F, Stoeckert Jr. CJ, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS.
The Ontology for Parasite Lifecycle (OPL): Towards a Consistent Vocabulary of Lifecycle Stages in Parasitic Organisms. Journal Biomedical Semantics (JBMS), 2012. Vol. 23; 3(1): 5. PMID: 22621763. (pdf)


Zhang GQ, Sahoo SS, Lhatoo SD.
From Classification to Epilepsy Ontology and Informatics. Epilepsia, 2012. Vol. 53(Suppl. 2). pp. 28-32. PMID: 22765502.


Parikh PP, Minning TA, Nguyen V, Lalithsena S, Asiaee AH, Sahoo SS, Doshi P, Tarleton R, Sheth AP.
A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi. PLoS Neglected Tropical Diseases, 2012. Vol. 6(1): e1458. PMID: 22272365.(pdf)


Teagno J, Kiefer RC, Pathak J, Zhang GQ, Sahoo SS.
A Distributed Semantic Web Approach for Cohort Identification. Proceedings of the American Medical Informatics Association (AMIA) Annual Symposium, 2012; pp. 1969


Ogbuji C, Xu R, (2012) Integrating large, disparate biomedical ontologies to boost organ development network connectivity. Data Integration in the Life Sciences 2012 (DILS 2012).


Xu R, Wang Q, (2012) A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text, J Biomed Inform. 2012 Oct;45(5):827-34. [8]

2011

Guo-Qiang Zhang, Xiangnan Zhou, Robert Fraser, Licong Cui.
Concatenation and Kleene Star on Deterministic Finite Automata. WSPC - Proceedings concatenation-star.pdf LICS 2011 (short presentation: slides)


Sahoo, S, Ogbuji, C,, Luo, L, Dong, X, Cui, L, Redline, S, Guo-Qiang Zhang (2011).
MiDas: Automatic Extraction of a Common Domain of Discourse in Sleep Medicine for Multi-center Data Integration, AMIA Annu Symp Proc. 2011. [PMID: 22195180; PMCID: PMC3243207]


Guo, L, Huang, F, Li, Q, Guo-Qiang Zhang (2011).
Power contexts and their concept lattices. pdf Discrete Mathematics 311 (18-19): 2049-2063.


Tran, V, Johnson, N, Redline, S, Guo-Qiang Zhang (2011).
OnWARD: Ontology-driven Web-based framework for multi-center studies. Journal of Biomedical Informatics, Dec 2011, 1:S48-53. [PMID: 21924379; PMCID: PMC3251701]


Huang F, Narayan S, Wilson D, Johnson D, Guo-Qiang Zhang (2011).
A Fast Iterated Conditional Modes Algorithm for Water-Fat Decomposition in MRI. IEEE Trans Med Imaging Vol. 30(8) pp. 1480-92. [PMID: 21402510; PMCID: PMC3651048]


Narayan S, Huang F, Johnson D, Guo-Qiang Zhang, Wilson D (2011).
Fast Lipid And Water Levels by Extraction with Spatial Smoothing (FLAWLESS): Three-dimensional volume fat/water separation at 7 Tesla, Journal of Magnetic Resonance Imaging Volume 33, Issue 6, June 2011. [PMID: 21591017; PMCID: PMC3285449]


Sahoo SS, Nguyen V, Bodenreider O, Parikh PP, Minning T, Sheth AP.
A unified framework for managing provenance information in translational research. BMC Bioinformatics, 2011. Vol. 12:461. PMID: 22126369. (pdf)


Zhao J, Sahoo SS, Missier P, Sheth AP, Goble C.
Extending Semantic Provenance into the Web of Data. IEEE Internet Computing, 2011. Vol. 15(1). pp. 40-48.(pdf)


Sahoo SS.
Towards Desiderata for Provenance Ontologies in Biomedicine, International Conference on Biomedical Ontologies (ICBO), 2011. pp. 269-272. (pdf)


Mueller R, Sahoo SS, Dong X, Redline S, Arabandi S, Luo L, Zhang GQ.
Mapping multi-institution data sources to domain ontology for data federation: the PhysioMIMI approach. AMIA Clinical Research Informatics Summit (CRI), 2011.


Zhang GQ, Mueller R, Jonhson N, Arabandi S, Sahoo SS, Redline S.
Online Exploration of Case-control Study Designs in VISAGE. AMIA Clinical Research Informatics Summit (CRI), 2011.

2010

Guo-Qiang Zhang and Olivier Bodenreider (2010).
Large-scale, exhaustive lattice-based structural auditing of SNOMED CT. pdf AMIA Annual Symp Proc 2010, pp. 922-926 (Distinguished Paper Award). [PMID: 21347113; PMCID: PMC3041382]


Guo-Qiang Zhang and Olivier Bodenreider (2010).
Using SPARQL to test for lattices: application to quality assurance in biomedical ontologies. pdf Proceedings of the 9th International Semantic Web Conference (ISWC 2010) 2010, Lecture Notes in Computer Science Vol. 6497 (Best Paper Award Finalist).


Guo-Qiang Zhang, Siegler T, Saxman P, Sandberg N, Mueller R, Johnson N, Hunscher D, Arabandi S.
VISAGE: A Query Interface for Clinical Research. Proceedings of the 2010 AMIA Clinical Research Informatics Summit, San Francisco, March 12-13, 2010, pp. 76-80. [PMID: 21347154; PMCID: PMC3041531]


Ogbuji, C., Arabandi, S., Zhang, S., Guo-Qiang Zhang.
Segmenting and Merging Domain-specific Ontology Modules for Clinical Informatic. Formal Ontology in Information Systems, proceedings of the 6th international conference, Volume 209, Frontiers in Artificial Intelligence and Applications, Edited by: A. Galton and R. Mizoguchi. IOS Press, pages 414-427


Guo-Qiang Zhang and Licong Cui.
A set coverage problem. pdf Information Processing Letters, Vol 110, Issue 4, pages 158-159, 2010.


Barga R, Simmhan Y, Chinthaka-Withana E, Sahoo SS, Jackson J, Araujo N.
Provenance for Scientific Workflows Towards Reproducible Research. IEEE Data Engineering Bulletin, 2010. Vol. 33(3). pp. 50-58. (pdf)


Sahoo SS, Bodenreider O, Hitzler P, Sheth AP, Thirunarayan K.
Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM), 2010. pp. 461-470. (pdf)


Missier P, Sahoo SS, Zhao J, Goble C, Sheth A.
Janus: from workflows to semantic provenance and linked open data. The 3rd International Provenance and Annotation Workshop (IPAW), Lecture Notes in Computer Science, Vol. 6378/2010, 2010. pp. 129-141. (pdf)


Deus H, Zhao J, Sahoo SS, Samwald M, Prud’hommeaux E, Miller M, Marshall MS, Cheung K.
Provenance of Microarray Experiments for a Better Understanding of Experiment Results. The 2nd International Workshop on Role of Semantic Web in Provenance Management (SWPM 2010), co-located with ISWC, 2010. (pdf)


Patni H, Sahoo SS, Henson C, Sheth A.
Provenance Aware Linked Sensor Data, The 2nd International Workshop on Trust and Privacy on the Social and Semantic Web, co-located with ESWC, 2010. (pdf)


Sahoo SS, Groth P, Hartig O, Miles S, Coppens S, Myers J, Gil Y, Moreau L, Zhao J, Panzer M, Garijo D.
Provenance Vocabulary Mappings. W3C Provenance Incubator Group Report, 2010.


Xu R, Musen M, Shah N, (2010) A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. Annual American Medical Informatics Association Symposium 2010. pp. 907-911.[9]


Parai, PK, Jonquet C, Xu R, Musen M, Shah N, (2010) The Lexicon Builder Web Service: Building Custom Lexicons from Two Hundred Biomedical Ontologies. Annual American Medical Informatics Association Symposium 2010. pp. 587–591.[10]

2009

Guo-Qiang Zhang.
Closures in binary partial algebras. Electronic Notes in Theoretical Computer Science Volume 257, Pages 3-18, 2009. pdf


Manfred Droste and Guo-Qiang Zhang.
Bifinite Chu spaces. Logical Methods in Computer Science, Vol 6, Issue 1, Paper 3, 2010. pdf


Remo Mueller, Van Anh Tran and Guo-Qiang Zhang.
A scalable parametric-RBAC architecture for the propagation of MIMI. The 11th International Conference on Enterprise Information Systems (ICEIS 2009), LNBIP 24, pp. 114-124, Springer-Verlag, 2009. pdf


Jie Dai, Remo Mueller, Jacek Szymanski and Guo-Qiang Zhang.
Towards "WYDISYS" for MIMI using concept analysis. The 24th Annual ACM Symposium on Applied Computing, pp. 91-97, ACM Press, 2009. pdf


Sahoo SS, Weatherly DB, Mutharaju R, Anantharam P, Sheth AP, Tarleton RL.
Ontology-driven Provenance Management in eScience: an Application in Parasite Research. The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE), 2009. pp. 992-1009. pdf


Sahoo SS, Sheth A.
Provenir ontology: Towards a Framework for eScience Provenance Management. Microsoft eScience Workshop, 2009. pdf


Sahoo SS, Halb W, Hellmann S, Idehen K, Thibodeau Jr. T, Auer S, Sequeda J, Ezzat A.
A Survey of Current Approaches for Mapping of Relational Databases to RDF. W3C RDB2RDF Incubator Group Report, 2009. pdf


Xu R, Das A, Garber AM, (2009) Unsupervised Method for Extracting Machine Understandable Medical Knowledge from a Large Free Text Collection. Annual American Medical Informatics Association Symposium, 2009. pp. 709-713.[11] (Student Paper Finalist)


Xu R, Morgan A, Das A, Garber AM, (2009) Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon. Association for Computational Linguistics BioNLP Workshop, 2009. pp. 63-70. [12]

2008

Manfred Droste and Guo-Qiang Zhang.
Random event structures. Int J Software Informatics, Vol.2, No.1, pp. 77-88, 2008. pdf


Fangping Huang, Manfred Droste and Guo-Qiang Zhang.
A monoidal category of bifinite Chu spaces. Electronic Notes in Theoretical Computer Science, Vol. 212, 285-297, 2008.


Sahoo SS, Sheth AP, Henson C.
Semantic Provenance for eScience: ‘Meaningful’ Metadata to Manage the Deluge of Scientific Data. IEEE Internet Computing, Web-Scale Workflow Track, M.B. Blake and M. Huhns (Eds.), 2008. Vol. 12(4). pp.46-54. (Featured in Association of Computing Machinery (ACM) TechNews 2008) pdf


Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP.
An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence. Journal of Biomedical Informatics (Special Issue: Semantic Mashup of Biomedical Data), 2008. Vol. 41(5). pp. 752-65. PMID: 18395495.


Sheth A, Henson C, Sahoo SS.
Semantic Sensor Web. IEEE Internet Computing, 2008. Vol. 12(4). pp. 78-83. pdf


Valerio MD, Sahoo SS, Barga RS, Jackson JJ.
Capturing Workflow Event Data for Monitoring, Performance Analysis, and Management of Scientific Workflows. SWBES08, co-located with the 4th IEEE International Conference on eScience, 2008. pp. 626-33. pdf


Xu R, Supekar K, Morgan A, Das A, Garber AM, (2008) Unsupervised Method for Automatic Construction of a Disease Dictionary from a Large Free Text Collection. Annual American Medical Informatics Association Symposium, 2008. pp. 820-824.[13]

2007

Adam Troy and Guo-Qiang Zhang.
Beyond PubMed and Google Scholar: using vertical digital library portals to enhance exploratory biomedical literature mining.

Adam Troy and Guo-Qiang Zhang.
Enhancing relevance scoring with chronological term rank. SIGIR'07: Proceedings of the 30th Annual International ACM SIGIR Conference, pages 599-606, 2007. pdf


Jacek Szymanski, David L. Wilson and Guo-Qiang Zhang.
MIMI: Multimodality, Multiresource, Information Integration Environment for Biomedical Core Facilities. Journal of Digital Imaging, Vol. 22, pp. 535-47.


Ying Jiang and Guo-Qiang Zhang.
Weakly distributive domains (II). Frontiers of Computer Science in China, Vol 1, No. 4, pages 373-384, Springer, 2007.


Adam Troy, Guo-Qiang Zhang and Ye Tian.
Faster concept analysis. ICCS'07: 15th International Conference on Conceptual Structures, Lecture Notes in Artificial Intelligence, Vol. 4604, pages 206-219, 2007. pdf


Guo-Qiang Zhang.
Mediating secure information-flow policies. Information and Computation,Vol 205, issue 9, pages 1413-1425, 2007. pdf


Manfred Droste and Guo-Qiang Zhang.
Bifinite Chu spaces. CALCO'07: 2nd Conference on Algebra and Coalgebra in Computer Science, Lecture Notes in Computer Science, Vol. 4624, pages 179-193, 2007. pdf


Ying Jiang and Guo-Qiang Zhang.
Weakly distributive domains. TLCA'07: Typed Lambda Calculi and Applications, Lecture Notes in Computer Science, Vol. 4583, pages 194-206, 2007. pdf


Sahoo SS, Zeng K, Bodenreider O, Sheth AP.
From ‘glycosyltransferase’ to ‘congenital muscular dystrophy’: Integrating knowledge from NCBI Entrez Gene and the Gene Ontology. The 12th World Congress on Health (Medical) Informatics (Medinfo), 2007. pp. 1260–64. PMID: 17911917. pdf


Sahoo SS, Bodenreider O, Zeng K, Sheth AP.
An experiment in integrating large biomedical knowledge resources with RDF: Application to associating genotype and phenotype information. International Workshop on Health Care and Life Sciences Data Integration for the Semantic Web, co-located with WWW2007, 2007. pdf


Sahoo SS, Sheth A, Hunter B, York WS.
SemBOWSER–Adding Semantics to biological Web services registry. Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Baker CJO, Cheung KO (Eds.), Springer, 2007. pp. 317–40. pdf


Xu R, Garten Y, Supekar K, Altman RB, Garber AM, (2007) Extracting Subject Demographics From Abstracts of Randomized Clinical Trials. World Congress on Medical and Health Informatics(MEDINFO), 2007. pp. 824-828.[14]

2006

Guo-Qiang Zhang and Gongqin Shen.
Approximable Concepts, Chu spaces, information systems. In V. De Paiva and V. Pratt (edts.) Theory and Applications of Categories Special Volume on Chu Spaces: Theory and Applications, Vol. 17, No. 5, pp. 80-102, 2006. pdf


Pascal Hitzler, Markus Krotzsch, Guo-Qiang Zhang.
A categorical view on algebraic lattices in FCA. Fundamenta Informaticae, Volume 74 (2-3), pp. 301 - 328, 2006. pdf


Jeff Stuckman and Guo-Qiang Zhang.
Mastermind is NP-Complete. INFOCOMP Journal of Computer Science, Vol 5, pp. 25 - 28, 2006. pdf


Sahoo SS, Thomas C, Sheth AP, York WS, Tartir S.
Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies. The 15th International World Wide Web (WWW) Conference, 2006. pp. 317-26。 pdf


Sahoo SS, Sheth A.
Bioinformatics applications of Web Services, Web Processes and role of Semantics. Semantic Web Processes and Their Applications. Cardoso J, Sheth A (Eds.), Springer, 2006. pp. 305–22.


Xu R, Supekar K, Huang Y, Das A, Garber AM, Combining Text Classification and Hidden Markov Modeling Techniques for Structuring Randomized Clinical Trial Abstracts (2006), Annual American Medical Informatics Association Symposium, 2006. pp. 824-828.[15]

2005

Guo-Qiang Zhang, Lee White, C. Hesse, M. Buchner, M. Mehregany.
Roadmap for a departmental website. Educause Quarterly, Volume 28, Number 3, 2005. pdf


Guo-Qiang Zhang, Adam D. Troy, Keith Bourgoin.
Bootstrapping ontology learning for information retrieval using FCA and information anchors. 14th International Conference on Conceptual Structures, Aalborg, Denmark, July 2006. pdf


Adam D. Troy, Guo-Qiang Zhang, Mehran Mehregany.
Evolution of the Hilton Head Workshop research community. Education Technical Digest of Sensors, Actuators and Microsystems Workshop, Hilton Head, SC, June 2006. pdf


Guo-Qiang Zhang and Ying Jiang.
On an open problem of Amadio and Curien: the finite antichain condition. Information and Computation, Vol. 202, pp. 87 - 103, 2005. pdf


Yixiang Chen and Guo-Qiang Zhang.
Maximality and totality of stable functions in the category of stable bifinite domains. Computers and Mathematics with Applications, Vol 51, pp. 1011-1020, 2006. pdf


Guo-Qiang Zhang, Gongqin Shen, Ye Tian, and Jiayang Sun.
Concept analysis as a formal method for menu design. Springer Lecture Notes in Computer Science, Vol. 3941 (Proceedings of the 12th International Workshop on Design, Specification and Verification of Interactive Systems, Newcastle-upon-Tyne, England, July 13-15, 2005.) pdf


Guo-Qiang Zhang and Devin Tian.
ACOSys: an experimental system for automated content organization. Proceedings of the 13th International Conference on Conceptual Structures July 18-22, 2005, Kassel, Germany. pdf


Markus Krotzsch, Pascal Hitzler, Guo-Qiang Zhang.
Morphisms in Context. Proceedings of the 13th International Conference on Conceptual Structures July 18-22, 2005, Kassel, Germany. pdf


Sahoo SS, Thomas C, Sheth AP, Henson C, York WS.
GLYDE-An expressive XML standard for the representation of glycan structure. Carbohydrate Research, 2005. Vol. 340(18). pp.2802-7. PMID: 16242678 pdf


Atwood III J, Sahoo SS, Alvarez-Manilla G, Weatherly DB, Kolli K, Orlando R, York WS.
Simple modification of a protein database for mass spectral identification of N-linked glycopeptides. Rapid Communications Mass Spectrometry, 2005. Vol. 19(21). pp.3002-6. PMID: 16196021. pdf


Alvarez-Manilla G, Atwood. III J, Sahoo SS, Guo Y, Warren NL, York WS, Orlando R, Pierce M.
Tools for glycoproteomic analysis: size-exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation site. Glycobiology 15(1208), 2005.


Aleman-Meza A, Halaschek-Wiener C, Sahoo SS, Sheth A, Arpinar B.
Template Based Semantic Similarity for Security Applications. The IEEE Intl. Conference on Intelligence and Security Informatics (ISI-2005), 2005. pp: 621-622. pdf


Sahoo SS, Sheth AP, York WS, Miller JA.
Semantic Web Services for N-glycosylation Process. International Symposium on Web Services for Computational Biology and Bioinformatics, 2005. pdf

2004

Guo-Qiang Zhang and William Rounds.
Reasoning with power defaults. Theoretical Computer Science, Vol. 323/1-3, pp 321-350, 2004. pdf


Guo-Qiang Zhang, Josh Staiger, Gongqin Shen, Adam Troy, J Sun.
Web-menu design using formal concept analysis. Position paper. In Pfeiffer Wolff and Delugach (Eds.) Conceptual Structures at Work, Shaker Verlag, ISBN 3-8322-2950-7, pp 141 - 145, 2004. pdf


Pascal Hitzler and Guo-Qiang Zhang.
A cartesian closed category of approximating concepts. Proceedings of 12th International Conference on Conceptual Structures, ICCS 2004, Huntsville, AL, July 2004, Lecture Notes in Artificial Intelligence Vol 3127, pp 170 - 185, 2004. pdf


Guo-Qiang Zhang.
Compact coverages generate spectral frames. Electronic Notes in Theoretical Computer Science, Vol. 83, 7 pages, 2004. pdf


Guo-Qiang Zhang.
Chu spaces, concept lattices, and domains. 19th Conference on the Mathematical Foundations of Programming Semantics, Montreal, Canada, March 19-22, 2003, Electronic Notes in Theoretical Computer Science, Vol. 83, 17 pages, 2004. pdf pdf


Sheth A, York WS, Thomas C, Nagarajan M, Miller JA, Kochut K, Sahoo SS, Yi X.
Semantic Web technology in support of Bioinformatics for Glycan Expression. W3C Workshop on Semantic Web for Life Sciences, 2004. pdf

2003 And Earlier

Thierry Coquand and Guo-Qiang Zhang.
A representation of stably compact spaces, and patch topology. Theoretical Computer Science, Vol. 305, pp 77-84, 2003. pdf


Manfred Droste and Guo-Qiang Zhang.
On transformations of formal power series. Information and Computation, Vol. 184, pp 369-383, 2003. pdf


Guo-Qiang Zhang.
Domain mu-calculus. Theoretical Informatics and Applications, Vol 37, pp 337 - 364, 2003 (postscript format) (slides presented at the Summer Topology Conference in DC, July 12, 2003. journal pdf


Guo-Qiang Zhang.
Logic, semantics and computer science: some fundamental ideas. Advances in Mathematics, Vol 31, No. 5, October 2002, pages 389-402. pdf


Guo-Qiang Zhang.
Axiomatic aspects of default inference. In Decker et al. pages 17-32. Paraconsistent Computational Logic'02, CoRR (Computing Research Repository). pdf


Guo-Qiang Zhang.
Decidable fragments of domain mu-calculus: an automata-theoretic perspective. In Esik and Ingolfsdottir, Fixed Points In Computer Science Copenhagen,B Denmark, July 20-21, 2002.


Bill Rounds and Guo-Qiang Zhang.
Clausal logic and logic programming in algebraic domains. Information and Computation vol 171:183-200, December 2001. pdf


T. Coquand and Guo-Qiang Zhang.
Sequents, frames, and completeness. Computer Science Logic 2000, Lecture Notes in Computer Science, 1862, 277-291. Abstract Postscript pdf


Guo-Qiang Zhang and Bill Rounds.
Semantics of logic programs and representation of Smyth powerdomain. In: (Keimel et al eds.) Domains and Processes, Kluwer Academic Publishers, 2001, 151-179. Postscript


G.-Q. Zhang and L. Smith.
A collection of functional libraries for theory of computation. Proceedings of the 39th ACM-SE Conference, ACM PRESS, May 2001, 83-90.


M. Droste and G.-Q. Zhang.
Rational transformations of formal power series. In: Automata, Languages and Programming (28th ICALP, Crete), Lecture Notes in Computer Science vol 2076, Springer 2001, 555 - 566. pdf


G.-Q. Zhang and Y. Chen.
A category of graphs. Journal of Computer Science and Technology. December 2001.


Eric Klavins, W. Rounds and Guo-Qiang Zhang.
Experimenting with power default reasoning. AAAI'98. Abstract Postscript


Guo-Qiang Zhang.
Automata, Boolean matrices, and ultimate periodicity. Information and Computation, Vol. 152, Number 1, pages 138-154, July 1999. Abstract Postscript PDF


W. Rounds and Guo-Qiang Zhang.
Logical considerations of default semantics. Annals of Mathematics and Artificial Intelligence. vol 20, 1997, 195-226. Abstract Postscript


W. Rounds and Guo-Qiang Zhang.
Nonmonotonic consequences of default domain theory. Annals of Mathematics and Artificial Intelligence. vol 20,1997, 227-265. Abstract Postscript


Bill Rounds and Guo-Qiang Zhang.
Clausal logic and logic programming in algebraic domains. Information and Computation vol 171:183-200, December 2001. pdf


Ilaria Castallani and Guo-Qiang Zhang.
Parallel product of event structures. Theoretical Computer Science, vol 179, Issue 1-2, 1997, 203-215. Abstract Postscript


Guo-Qiang Zhang and W. Rounds.
Defaults in domain theory. Theoretical Computer Science, vol 177, Issue 1, 1997, 155-182. Abstract Postscript


Guo-Qiang Zhang and E. Rodny Canfield.
The end of pumping?. Theoretical Computer Science, vol 174, Issue 1-2, 1997, 275-279. Abstract Postscript


Guo-Qiang Zhang and W. Rounds.
Complexity of power default reasoning, (LICS'97) Proceedings of the 12th Annual IEEE Symposium on Logic in Computer Science, 328-339, Warsaw, Poland, July 1997. Abstract Postscript


Guo-Qiang Zhang and W. Rounds.
Reasoning with power defaults (preliminary report) (LPNMR'97). Proceedings of the 4th International Conference on Logic programming and Non-monotonic Reasoning, 152-169, Dagstuhl, Germany, July 1997. Abstract Postscript


Guo-Qiang Zhang, W. Rounds, and Chang Huang.
A modal logic for reasoning about belief. Proceedings of the 30th International Conference on System Sciences, vol V, pages 383-391, Maui, Hawaii, Jan. 1997. Abstract Postscript


Guo-Qiang Zhang and W. Rounds.
Resolution in the Smyth powerdomain, (MFPS'97). Proceedings of the 13rd International Conference on Mathematical Foundations of Programming Semantics, (Carnegie-Mellon University, Pittsburgh, March 1997) ENTCS, Volume 6. Abstract Postscript


W. Rounds and Guo-Qiang Zhang.
Lecture Notes on Domain Theory and Nonmonotonic Reasoning. European Summer School in Logic, Language, and Information (ESSLLI 97). Slides


Guo-Qiang Zhang.
The largest cartesian closed category of stable domains. Theoretical Computer Science, vol 166, Issue 1-2, 1996, 203-219. Abstract Postscript


Guo-Qiang Zhang.
Quasi-prime algebraic domains. Theoretical Computer Science, Vol 155, 1996, 221-264. pdf


W. Rounds and Guo-Qiang Zhang.
Attunement to constraints in nonmonotonic reasoning. Logic, Language, and Computation, vol 1, 479--494. CSLI Lecture Notes, vol 58, CSLI Publication, Stanford, CA., 1996. Abstract Postscript


W. Rounds and Guo-Qiang Zhang.
Domain theory meets default logic. Journal of Logic and Computation, vol 5, no.1, 1995, 1-25. Abstract Postscript


Guo-Qiang Zhang.
Maximal stable functions. Theoretical Computer Science, vol 146, 1995, 331-339. Abstract Postscript


W. Rounds and Guo-Qiang Zhang.
Suggestions for a nonmonotonic feature logic. Abstract Postscript CWI Technical Report CS-R9551, ISSN 0169-118X, 1995.


Guo-Qiang Zhang.
A representation of SFP. Information and Computation, vol 110, no.1, 1994, 233-263. Abstract Postscript


Guo-Qiang Zhang.
Universal quasi-prime algebraic domains, (MFPS'94). Proceedings of the 9th International Conference on the Mathematical Foundations of Programming Semantics, Lecture Notes in Computer Science 802. Abstract Postscript


Guo-Qiang Zhang.
Some monoidal closed categories of stable domains and event structures. Mathematical Structures in Computer Science, vol 3, 1993, 259--276. Abstract Postscript


Guo-Qiang Zhang.
DI-domains as prime information systems. Information and Computation, vol 100, 1992, 151-177. Abstract Postscript


Guo-Qiang Zhang.
Stable neighborhoods. Theoretical Computer Science, vol 93, 1992, 143-157. Abstract Postscript


Guo-Qiang Zhang.
Disjunctive systems and L-domains, (ICALP'92). 19th International Colloquium on Automata, Languages, and Programming, Lecture Notes in Computer Science 623, 1992, pp. 284-295. Abstract Postscript


Guo-Qiang Zhang.
A monoidal closed category of event structures, (MFPS'91). Proceedings of the 7th International Conference on the Mathematical Foundations of Programming Semantics, Lecture Notes in Computer Science 598, 1991, pp.426--435.


Guo-Qiang Zhang.
DI-domains as information systems, (ICALP'89). 6th International Colloquium on Automata, Languages, and Programming, Lecture Notes in Computer Science 372, 1989, pp.773-788.

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