408 State Hall, Department of Computer Science, Wayne State University, Detroit MI 48202
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Link to Intelligent Systems and Bioinformatics Laboratory

 

Books
Chapters
Journal Articles
Peer-reviewed Conference Publications
Invited Papers
Technical Reports
Invited Seminars and Talks
Invited Conference Tutorials
Patent Applications
Articles reviewing our research

 

Books (top)

  1. Sorin Draghici, Data Analysis Tools for DNA Microarrays, Chapman and Hall/CRC Press, 2003.

Order from Chapman & Hall /CRC Press.

Chapters (top)

  1. Sorin Draghici. – Data Analysis and Visualization in DNA Microarrays. In S. Krawetz and D. Womble, editors, Introduction to Bioinformatics,  Humana Press, 2002.

  2. Sorin Draghici. - VLSI Friendly Neural Networks for Classification Problems, in Razvan Andonie (Ed.), Neural Research Priorities in Data Transmission and EDA, 1997.

  3. Stephen A. Krawetz, Sorin Draghici, Robert Goodrich, Zhandong Liu and G. Charles Ostermeier. In silico and wet-bench identificatio of nuclear matrix attachment regions. In Andrew H. Baker and Jerome Fennell, editors, Methods in Molecular Medicine: Molecular Methods in Hypertension. Humana Press 2003.

  4. Anton Petrov, Shishir Shah, Sorin Draghici and Soheil Shams. Microarray image processing and quality control. In Gerda Kamberova and Shishir Shah, editors, DNA Array Image Analysis: nuts and bolts. DNA Press, 2002.

  5. Sorin Draghici. Global functional profiling of gene expression data. In D.P. Berar, W. Dubitzky and M. Granzow, editors, A Practical Approach to Microarray Data Analysis. Kluwer, 2002.

  6. Michael Johnson, Farshad Fotouhi and Sorin Draghici. Query-by-structure approach for the web. In John Wang, editor, Data Mining: Opportunities and Challenges, 2002.

Journal Articles (top)

  1. Pourabdollah S, Muzik O, Juhasz, C, Chugani DC, Janisse J, Draghici S. Application of an objective method for localizing bilateral cortical FDG PET abnormalities to guide the resection of epileptic foci. IEEE TBME 2004 (in press).

  2. S. Draghici, D. Chen, and J. Reifman. Applications and Challenges of DNA Microarray Technology in Military Medical Research. Military Medicine, 169 (8): 654 - 659, 2004.

  3. Michael Johnson, Farshad Fatouhi, Sorin Draghici, Ming Dong and Duo Xu. Discovering Document Semantics QBYS: A System for Querying the WWW by Semantics. Multimedia Tools and Applications, 24 (2): 155-188, November 2004.

  4. Bin Yao, Sanjay N Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici and Jeffery A Loeb. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. BMC Bioinformatics 2004, 5:99 (23 July 2004). (Citing Articles)

  5. Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa and Sorin Draghici. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Research, 32:W449-W456, July 2004.

  6. Harvey I. Pass, Zhandong Liu, Anil Wali, Raphael Bueno, Susan Land, Daniel Lott, Fauzia Siddiq, Fulvio Lonardo, Michele Carbone, and Sorin Draghici. Gene Expression Profiles Predict Survival and Progression of Pleural Mesothelioma. Clinical Cancer Research 2004 10: 849-859.(Citing Articles)

  7. Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen Krawetz and Michael A. Tainsky. Onto-Tools, The toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Research, 31(13):3775-81, July 2003. (Citing Articles)

  8. G. Charles Ostermeier, Zhandong Liu, Rui Pires Martins, Sorin Draghici and Stephen A. Krawetz. Nuclear matrix association of the human ß-globin locus utilizing a novel approach to quantitative real-time PCR. Nucleic Acids Research, 31 (12):3257-66, June 2003. (Citing Articles)

  9. Olga I. Kulaeva, Sorin Draghici, Lin Tang, Janice M. Kraniak, Susan J. Land and Michael Tainsky. Epigenetic silencing of multiple interferon pathway genes after cellular immortalization. Oncogene,  22(26):4118-27, June 2003. (Citing Articles)

  10. Sorin Draghici, Olga Kulaeva, Anton Petrov, Bruce Hoff,  Alexander Kuklin, Soheil Shams and Michael Tainsky. Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays. Bioinformatics, 19(11):1348-59, July 2003. (Citing Articles)

  11. Sorin Draghici, Frank Graziano, Samira Kettoola, Ishwar Sethi and George Towfic. Mining HIV dynamics using Independent Component Analysis. Bioinformatics, 19(8):981-986, May 2003.

  12. Pascale Anderle, Manuel Duval, Sorin Draghici, Alexander Kuklin, Timothy G. Littlejohn, Juan F. Medrano, David Vilanova and Matthew Alan Roberts. Gene expression databases and data Mining. BioTechniques, Microarrays and Cancer: Research and Applications, March 2003. (Citing Articles)

  13. Sorin Draghici, Purvesh Khatri, Abhik Shah and Michael Tainsky. Assessing the functional bias of commercial microarrays using the Onto-Compare database. BioTechniques, Microarrays and Cancer: Research and Applications, March 2003. (Citing Articles)

  14. Sorin Draghici, Purvesh Khatri, Rui P. Martins, G. Charles Ostermeier and Stephen A. Krawetz. Global functional profiling of gene expression. Genomics 81(2):98-104, Feb 2003. (Citing Articles)

  15. Sorin Draghici and Brian Potter. Predicting HIV drug resistance with neural networks. Bioinformatics, 19(1):98-107, Jan 2003. (Citing Articles)

  16. Sorin Draghici. - Statistical intelligence: effective analysis of high-density microarray data, Drug Discovery Today  7(11):S55-S63, 2002. (Citing Articles)

  17. Sorin Draghici. - On the capabilities of neural networks using limited precision weights, Neural Networks,  15(3): 395-414, 2002. (Citing Articles)

  18. David Sprecher and Sorin Draghici. – Space-filling curves and Kolmogorov superposition-based neural networks, Neural Networks, 15(1):57-67, 2002. 

  19. Purvesh Khatri, Sorin Draghici, G. Charles Ostermeier, Stephen A. Krawetz - Profiling Gene Expression Utilizing Onto-Express, Genomics, 79(2):266-270, Feb 2002. (Citing Articles)

  20. Sorin Draghici, Kuklin A., Hoff B. Shams S. - Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays. Current Opinion in Drug Discovery & Development, 4(3):332-337, 2001.

  21. Sorin Draghici - The Constraint Based Decomposition (CBD) training architecture, Neural Networks 14(4-5):527-550, 2001.

  22. Sorin Draghici - Neural Networks in Analog Hardware - Design and Implementation Issues, Intl. Journal of Neural Systems, 10(1):1-25, February 2000.

  23. Valeriu Beiu, Sorin Draghici, T. De Pauw - A constructive approach to calculating lower entropy bounds, Neural Processing Letters, 9(1):1-12, February 1999.

  24. Sorin Draghici - Improving the speed of some constructive algorithms by using a locking detection mechanism, Neural Network World, 6(4):563-575, 1996.

  25. Sorin Draghici - A neural network based artificial vision system for licence plate recognition, International Journal of Neural Systems, 8(1):113-126, February 1997. (Citing Articles)

Peer-reviewed Conference Publications (top)

  1. Siamak Pourabdollah, Otto Muzik and Sorin Draghici. A Back Propagation Neural Network for Localizing Abnormal Cortical Regions in FDG PET Images in Epileptic Children. In Jose Mira,editor, Lecture Notes in Computer Science, Claustro del Carmen, Menorca, Balearic Islands, Spain, June 3-6 2003.

  2. Sorin Draghici, Korkut Uygun and Michael A. Tainsky. Cancer prediction by protein microarray profiling. In O. Castillo and J. M. Zurada, editors, Proc. of Neural Networks and Computational Intelligence NCI, Cancun, Mexico, 19-21, May 2003.

  3. Aviva Fridman, Fatimah Nahhas, Lin Tang, Olga Kulaeva, Janice Kraniak, Sorin Draghici and Michael A. Tainsky. Mechanisms of genomic instability and epigenetic silencing leading to cellular immortalization. In Proc. of 94-th American Association for Cancer Research Conference, Toronto, Canada, April 2003. Paper 5180.

  4. M. Johnson, F. Fotouhi, S. Draghici and M. Dong. Enhancing query-by-structure neural network net approach. In Proc. of Workshop on Multimedia Semantics (in conjunction with SOFSEM), Milovy, Czech Republic, November 24-25, 2002.

  5. Anil Wali, Jason Mussman, Julia Sluchak-Carlsen, Sunita Sharma, Sorin Draghici, Raymond Reeves, Maurizio Bocchetta, Michele Carbone and Harvey I. Pass. Differential expression profile of methylated genes in simian virus 40 tranformed mesothelial cells. In Proc. of 93rd American Association for Cancer Research Conference, San Francisco, April 6-10, 2002. Paper 5532.

  6. Michael Johnson, Farshad Fotouhi and Sorin Draghici. Query-by-structure approach for the web. In John Wang, editor, Data Mining: Opportunities and Challenges. 2002.

  7. Olga Studitskaia, Sorin Draghici, Michael Tainsky - Gene expression changes related to cellular immortalization. In Proc. of 93rd American Association for Cancer Research Conference, San Franscisco, April 6-10, 2002.

  8. Brain Potter, Sorin Draghici - A SOFM Approach to Predicting HIV Drug Resistance. In Proc. of Pacific Symposium on Biocomputing, PSB 2002, pages 77-87, Kaua'i Marriott, Kaua'i, Hawaii, January 2-7, 2002.

  9. Farshad Fotouhi, Michael Johnson, Sorin Draghici - A Neural Network Net Query-by-Structure Approach, in Proc. of IRMA 2001: Information Resources Management Association International Conference, Toronto Marriott-Eaton Hotel, Toronto, Canada, May 20-23, 2001.

  10. Sorin Draghici, R. P. Martins and Stephen A. Krawetz – Expressed Sequence Tag Data Mining: The reality of virtual gene expression. In Proc. of the Atlantic Symposium on Computational Biology, and Genome Information Systems and Technology, 18-19 December, pages 440-451, Regal University Center, Durham, NC, 18-19 December, 2001.

  11. Sorin Draghici, Lonnie Cumberland and Ladislau C. Kovari - Correlation of HIV protease structure with Indinavir resistance: a data mining and neural network approach. In Proc. of SPIE, volume 4057, Orlando, Florida, 2000.

  12. Sorin Draghici - Some new results on the capabilities of integer weights neural networks in classification problems, Paper #308, Session 3.4 in Proc. Of IEEE-INNS International Joint Conference on Neural Networks IJCNN'99 (electronic format), Washington, DC, 1999.

  13. Sorin Draghici - On the computational power of limited precision weight neural networks in classification problems: How to calculate the weight range so that a solution will exist, Proc. of IWANN’99, Alicante, Spain, Lecture Notes in Comp. Science, vol 1606, pp. 401-412, Springer-Verlag, 1999.

  14. Sorin Draghici, Damon Miller - A VLSI neural network classifier based on integer-valued weights. In Proc. of IEEE-INNS International Joint Conference of Neural Networks IJCNN’99, Washington, DC, 1999.

  15. Sorin Draghici - On the complexity-capabilities relationship of adaptive systems based on VLSI friendly Neural Networks. In Lecture Notes in Artificial Intelligence, Proc. of XII Canadian Conference on Artificial Intelligence AI'98 volume 1418, pages 285-297, Springer-Verlag, 18-20 June, 1998.

  16. Sorin Draghici - Using Information Entropy Bounds for the Design and Implementation of VLSI Friendly Neural Networks. In Proc. of 1998 IEEE World Congress on Computational Intelligence IJCNN'98, pages 547-552. IEEE Press, 4-9 May, 1998.

  17. Sorin Draghici - On VLSI -optimal Constructive Algorithms for Classification Problems, Proc. of EIS'98 International Symposium on Engineering of Intelligent Systems, pages 456-462.  ICSC Academic Press, 1998.

  18. Beiu V., Sorin Draghici, Makaruk H.E. - On Limited Fan-In Optimal Neural Networks. In Proc. Brazilian Symp. on Nueral Networks IV SBRN, pages 19-30, 1997.

  19. Sorin Draghici, Valeriu Beiu, Ishwar K. Sethi - A VLSI optimal constructive algorithm for classification problems. In Smart Engineering Systems: Neural Networks, Fuzzy Logic, Data Mining and Evolutionary Programming, vol 7, pages 145-151, St. Louis, 1997. ASME Press.

  20. Valeriu Beiu and Sorin Draghici - On Sparsely Connected Optimal Neural Networks. In H. Klar, A. Konig, U. Ramacher, editors, Proc. of the 6 th Intl. Conference on Microelectronics for Neural Networks, Evolutionary and Fuzzy Systems, pages 56-63, Dresden, Germany, September 24-26 1997. University of Technology Dresden and Sächsisches Verlagshaus GmbH, ISBN 3-860050190-3.

  21. Sorin Draghici and Ishwar K. Sethi - On the possibilities of the limited precision weights neural networks in classification problems. In J. Mira, R. Moreno-Diaz Biological and J. Cabestany, (editors), Biological and Artificial Computation: From Neuroscience to Technology, Lecture Notes in Computer Science, pages 753-762, Springer Verlag, 1997.

  22. Valeriu Beiu and Sorin Draghici - Limited weights neural networks: very tight entropy based bounds. In David W. Pearson, (editor), Proc. 2 nd Intl. ICSC Symp on Soft Computing SOCO'97, pages 111-118, Nimes France, 17-19 September 1997. ICSC, Academic Press (ISBN 3-906454-06-1).

  23. Sorin Draghici, Sethi, I.K. - Choosing the appropriate size network for low-cost hardware implementation: a tight lower bound for the number of bits of integer limited weights neural networks. In Proc. of the 11th International Conference on Control System and Computer Science, vol. 2, pages 95-100, Politehnica University Press, Bucharest, Romania, 1997.

  24. Sorin Draghici and Valeriu Beiu - Entropy based comparison of neural networks for classification. In Proc. of the 9th Italian Workshop on Neural Nets, pages 124-132, Springer-Verlag, 1997.

  25. Sorin Draghici, Ishwar K. Sethi - Adapting theoretical constructive algorithms to hardware implementations for classification problems. In Proc. of  International Conference on Engineering Applications of Neural Networks EANN"97, pages 303-308, Systeemitekniikan Seurary, 1997.

  26. Sorin Draghici - Security applications for a neural network based artificial vision system, in “Solving Engineering Problems with Neural Networks” - Proceedings of the International Conference on Engineering Applications of Neural Networks, London, United Kingdom, 17-19 June 1996, part II, pp. 645-648, 1996.

  27. Sorin Draghici - Enhancements of the Constraint Based Decomposition Training Architecture, Proceedings of the International Conference on Neural Networks, ICNN’96 Washington, 3-6 June 1996, vol. I, pp. 317-322, IEEE Press, 1996.

  28. Sorin Draghici - The Constraint Based Decomposition Training Architecture, Proceedings of World Congress on Neural Networks, WCNN’94 San Diego, Vol. III, pp. 545 555, 1994.

Invited Papers (top)

  1. Sorin Draghici. Reading the microarray map. Current Drug Discovery, pages 33-35, February 2002.

  2. Sorin Draghici - DNA Arrays: The Steam Engine of the 21-st Century?, ACM SIGBIO Newsletter, vol. 21, no. 1, pp. 2-9, April, 2001.

  3. Sorin Draghici. New Trends in neural networks implementations. International Journal of Neural Systems, 10(3):vii-viii, June 2000.

Technical Reports (top)

  1. Sorin Draghici, V. Beiu - Entropy based comparison of neural networks for classification, Technical Report LA-UR-97-483,Los Alamos National Laboratory, 1997

  2. Beiu V., S. Draghici - Limited weights neural networks: very tight entropy based bounds, Technical Report LA-UR-97-294, Los Alamos National Laboratory, 1997.

  3. Weir M.K., S. Draghici - A backpropagation artificial neural network using complex weights, Technical Report CS/95/4, Department of Computer Science, St Andrews University.

  4. Sorin Draghici - A CAD System for Software Engineering, Technical Report, Department of Computer Science , “Politehnica” University, 1989, Bucharest.

Invited seminars and talks (top)

  1. Data Analysis and Data Interpretation of High Throughput Gene Expression Experiments, 2nd International Conference on Bioinformatics and Computational Biology, Angra dos Reis, Rio de Janeiro, Brazil, 25--28 October, 2004.

  2. Data Analysis Tools for DNA Microarrays. Keynote talk at 2004 China International Conference of Biotechnology, Beijing, China,  May 20--22, 2004.

  3. Data Analysis of Microarray Data, Invited talk,  National Research Council, Plant Biotechnology Institute, Saskatoon, Canada, 26-27 February 2004.

  4. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto Translate. Invited talk at the Gene Ontology Users' Meeting 2004, Stanford University, Palo Alto, CA, 15 January 2004.

  5. Onto-Tools: the toolkit of the modern biologist. Invited talk at the Satellite Meeting of the 10th FAOMB Congress, Institute of Genomics and Integrative Biology, New Delhi, India, 5-6 Dec 2003.

  6. Integrated Bioinformatics Tools for the Functional Analysis of High-throughout Expression Data. Invited speaker at Cambridge Healthtech Institute's ``Microarray Data Analysis'', Baltimore, 22-23 September 2003.

  7. Bioinformatics Tools for Military Medical Research, US Army Medical Research and Materiel Command Bioinformatics Workshop, Frederick, MD., 4-6 November 2003.

  8. Data Analysis Tools for DNA Microarrays. Invited talk at Concordia University,  Montreal, Canada, 10 October, 2003.

  9. Onto-Tools: Data Analysis in the Post-Genomic Era, Invited talk at McGill University, Montreal, Canada, 8 October, 2003. .

  10. From Data Analysis to Biology. Invited speaker at Human Proteomics Organization World Congress, Montreal, Canada, 8-11 October, 2003.

  11. Onto-Tools: Data Analysis in the Post-Genomic Era, Invited talk at Cambridge Healthtech Institute's Microarray Data Analysis, September 21-23, 2003, Baltimore, Maryland.

  12. Data Analysis for Microarrays. Invited speaker at US Army Medical Research and Materiel Command, Fort Detrick, MD, 27 August, 2003.

  13. Using Onto-Tools. Invited speaker at US Army Medical Research and Materiel Command, Fort Detrick, MD, July 18, 2003.

  14. Bioinformatics Tools in the Post-Genomic Era, Dept. of Computer Science, Birmigham University, UK. June 10, 2003

  15. Data Analysis in the Post-Genomic Era. Keynote speaker at the "DNA and Protein Microarrays: Technology and Application" workshop, 7-15, April 2003, La Trobe University, Melbourne, Victoria, Australia.

  16. Onto-Tools: From data analysis to biology and back. - The Tools of the modern biologist, Invited talk at Cambridge Healthtech Institute's "Macroresults for Microarrays: An array of Possibilities", May 13-14, 2003, World Trade Center, Boston, MA.

  17. Onto-Tools: From data analysis to biology and back Invited speaker in the Distinguished Speaker Seminar Series at the National Cancer Institute, February 14, 2003, Fort Detrick, MD

  18. Onto-Express, Onto-Convert, Onto-Compare and Onto-Design. Invited talk to the Medical College of Wisconsin, November 22, 2002, Milwaukee, WI.

  19. Method for selecting differentially regulated genes. Invited talk at the Microarray Workshop, Telemedicine and Advanced Technology Research Center of the U.S. Army, August 7, 2002, Fort Detrick, MD.

  20. Functional analysis using AI tools. Invited talk at the Microarray Workshop, Telemedicine and Advanced Technology Research Center of the U.S. Army, August 7, 2002, Fort Detrick, MD.

  21. Microarray Data Analysis: How to Extract Biological Meaning from Microarray Results, Invited talk at the Cambridge Healthtech Institute's Second Annual Microarray Data Analysis, September 10-11, 2002, Washington, DC.

  22. Microarray Data Analysis: Onto-Express and Functional Analysis as a Tool for Experiment Design, Cambridge Healthtech's Data Visualization, September 12-13 2002, Washington, DC.

  23. Data Analysis Issues and Tools in DNA microarrays, August 29, 2002, Invited talks at University of Maryland, Baltimore. MD.

  24. Advanced Methods for the Analysis of Microarray Data. Invited talk at Cambridge Healthech Institute's Integrated Bioinfomatics: High-throughput Intepretation of pathways and Biology, January 16-18, 2002, Zurich, Switzerland.

  25. Data Analysis Issues and Tools in DNA Micorarrays, Invited talk at Cambridge Healthech Institute's Microarray Data Analysis Using Statistics and Standards to Navigate the Microarray Data Minefield, Nov. 12-13, 2001, Alexandria, VA.

  26. Methods for Selecting Differentially Regulated Genes – Experimental Design and Statistical Analysis in Array Technology Symposium, Harvard University, Boston, MA, 11 May 2001.

  27. Data Analysis Issues and Tools in DNA Microarrays. Starr Center for Human Genetics Seminar, Rockefeller University, New York, NY, 21 March, 2001.

  28. Data Analysis Tools for DNA Microarray data. Invited talk at Pacific Symposium of Bioinformatics, 2001,Stanford University.

  29. Image Processing and Data Analysis Issues in DNA Microarrays – Invited talk at Het Instrument 2000, Jaarbeurs Utrecht, 9-13 October, 2000.

  30. Data Mining for Microarrays. nvited talk at Display Systems, Copenhagen, Denmark, 9 October 2000.

  31. Microarray Data Analysis – Invited talk, Chiroscience R&D Inc., Seattle, WA.

  32. Algorithms and Methods for Microarray Data Analysis – 2 day workshop, UC San Diego, San Diego, November 2000.

  33. Data Analysis Workshop – 2 day workshop, BioDiscovery Inc., Holiday Inn, Boston, MA, September 2000.

  34. Software Tools for DNA Microarray Analysis – Invited talk, Rockefeller University, September 2000.

  35. HIV virtual phenotyping – Invited talk, Structural Bioinformatics Inc., San Diego, California, June, 2000

  36. Optimizing Neural Networks for VLSI Implementations - talk in the Department of Computer Science, University of Western Ontario, June, 1998.

  37. Entropy Bounds and VLSI Friendly Neural Networks. Department of Computer Science, Transilvania University, Brasov, Romania, May 1997.

  38. Constraint Based Decomposition. Department of Physiology, University of Newcastle, UK, July 1994.

Invited Conference Tutorials (top)

  1. Data Analysis Tools for DNA Microarray Data Invited Tutorial at Pacific Symposium on Biocomputing PSB2001, Hawai, 3-7 January 2001.

  2. Data Mining with Neural Networks Invited Tutorial, Data Mining in Crystallography, Summer School, Erice, Italy, 12-20 May, 1999.

Patent Applications (top)

  1. Sorin Draghici, Purvesh Khatri, Steve Krawetz, Charles Ostermeier and Rui Martines. Onto-Express: A tool for functional analysis of bioinformatics data. Wayne State University, January 2 2002. Patent Application.

  2. Michael Tainsky and Sorin Draghici. Neoepitope detection of disease using protein arrays. Wayne State University, December 3 2001. Patent Application.

  3. Sorin Draghici, Anton Petrov and Bruce Hoff. Methods for global significance analysis of cDNA and Protein microarray. Biodiscovery Inc., 2001. Patent Application.

  4. Sorin Draghici. Piecewise linearization method for the normalization of cDNA and protein microarrays in multi-channel experiment. Biodiscovery Inc., 2001. Patent Application.

 

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