413 State Hall, Department of Computer Science, Wayne State University, Detroit MI 48202
Phone: (313) 577-5070 Fax: (313) 577-6868

Link to Dr. Sorin Draghici's home page

 

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 (First Print), 2005 (Second Print)

Order from Chapman & Hall /CRC Press.

Chapters (top)

  1. Adi L. Tarca, Sorin Draghici, Roberto Romero, and Michael Tainsky. Spatial Detrending and Normalization Methods for Two-channel DNA and Protein Microarray Data. In: Methods in Microarray Normalization. Taylor and Francis CRC Press, 2008.

  2. Purvesh Khatri and Sorin Draghici. Ontological analysis of gene expression data. In Encyclopedia of Genetics, Proteomics and Bioinformatics. John Wiley and Sons, 2005.

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

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

  5. Stephen A. Krawetz, Sorin Draghici, Robert Goodrich, Zhandong Liu and G. Charles Ostermeier. In silicoand 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.

  6. 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.

  7. Sorin Draghici and Stephen Krawetz. 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.

  8. 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. Stephen A. Krawetz, Adele Kruger, Claudia Lalancette, Rebecca Tagett, Ester Anton, Sorin Draghici and Michael Diamond: A survey of small RNAs RNAs in human sperm. Human Reproduction 2011 (accepted for publication).

  2. Duccio Cavalieri, Damariz Rivero, Luca Beltrame, Sonja I. Buschow, Enrica Calura, Lisa Rizzetto, Sandra Gessani, Maria C. Gauzzi, Walter Reith, Andreas Baur, Roberto Bonaiuti, Marco Brandizi, Carlotta De Filippo, Ugo D'Oro, Sorin Draghici, Isabelle Dunand-Sauthier, Evelina Gatti, Francesca Granucci, Michaela Gundel, Matthijs Kramer, Mirela Kuka, Arpad Lanyi, Cornelis J. M.K. Melief, Nadine van Montfoort, Renato Ostuni, Philippe Pierre, Razvan Popovici, Eva Rajnavolgyi, Stephan Schierer, Gerold Schuler: DC-ATLAS, a Systems Biology Resource to Dissect Receptor Specific Signal Transduction in Dendritic Cells. Immunome Research 2010, 6:10.

  3. Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A: NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010 Jan 12;11(1):R3

  4. Gabor Than N, Romero R, Tarca AL, Draghici S, Erez O, Chaiworapongsa T, Mee Kim Y, Kim SK, Vaisbuch E, Tromp G: Mitochondrial manganese superoxide dismutase mRNA expression in human chorioamniotic membranes and its association with labor, inflammation, and infection. Journal of Maternal-Fetal and Neonatal Medicine. 2009 Jul 1:1-14

  5. Tarca AL, Draghici S, Romero R: Developing classifiers for the detection of cancer using multi-analytes. Methods in Molecular Biology. 2009;520:259-72

  6. Kim MJ, Romero R, Kim CJ, Tarca AL, Chhauy S, LaJeunesse C, Lee DC, Draghici S, Gotsch F, Kusanovic JP, Hassan SS, and Kim JS: Villitis of unknown etiology is associated with a distinct pattern of chemokine up-regulation in the feto-maternal and placental compartments: implications for conjoint maternal allograft rejection and maternal anti-fetal graft-versus-host disease. J Immunol 15 Mar 2009 182(6): p. 3919

  7. Montenegro D, Romero R, Kim SS, Tarca AL, Draghici S, Kusanovic JP, Kim JS, Lee DC, Erez O, Gotsch F, Hassan SS, Kim CJ: Expression patterns of microRNAs in the chorioamniotic membranes: a role for microRNAs in human pregnancy and parturition. The Journal of Pathology, Oct 1st 2008

  8. Tarca AL, Draghici S, Khatri P, Hassan S, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R: A Novel Signaling Pathway Impact Analysis (SPIA). Bioinformatics 2009 25(1):75-82

  9. Tarca AL, Draghici S, Romero R, Tainsky MA: Spatial Detrending and Normalization Methods for Two-channel DNA and Protein Microarray Data; in: Stafford P., (ed): Methods in Microarray Normalization. Taylor and Francis Publications, 2008

  10. Yu Mi Han, Roberto Romero, Jung-Sun Kim, Adi L. Tarca, Sun Kwon Kim, Sorin Draghici, Juan Pedro Kusanovic, Francesca Gotsch, Pooja Mittal, Sonia Hassan, Chong Jai Kim. Region-Specific Gene Expression Profiling: Novel Evidence for Biological Heterogeneity of the Human Amnion. Biology of Reproduction, prepublished online August 6, 2008

  11. Jung-Sun Kim, Roberto Romero, Adi Laurentiu Tarca, Christopher LaJeunesse, Yu Mi Han, Mi Jeong Kim, Yeon Lim Suh, Sorin Draghici, Pooja Mittal, Francesca Gotsch, Juan Pedro Kusanovic, Sonia Hassan, and Chong Jai Kim. Gene expression profiling demonstrates a novel role for fetal fibrocytes and the umbilical vessels in human fetoplacental development. The Journal of Cellular and Molecular Medicine, 2008 Aug, 12 (4):1317-30

  12. Rhee, Seung Yon and Wood, Valerie and Dolinski, Kara and Draghici, Sorin. Use and misuse of the gene ontology annotations. Nature Reviews Genetics, July 2008, 9 (4) : 509-15 .

  13. Dimmer, Emily and Huntley, Rachael and Barrell, Daniel and Binns, David and Draghici, Sorin and Camon, Evelyn and Hubank, Mike and Talmud, Philippa and Apweiler, Rolf and Lovering, Ruth. The Gene Ontology: providing a Functional role in Proteomic studies. Practical Proteomics, 17 Jul 2008. (published Online)

  14. Johanne Holm Toft, Ingrid Alsos Lian, Adi Laurentiu Tarca, Offer Erez, Jimmy Espinoza, Irina Poliakova Eide, Line Bjorge, Chen Sue, Sorin Draghici, Roberto Romero, Rigmor Austgulen. Whole-genome microarray and targeted analysis of angiogenesis-regulating gene expression (ENG, FLT1, VEGF, PlGF) in placentas from pre-eclamptic and small-for-gestational-age pregnancies. The Journal of Maternal-Fetal and Neonatal Medicine, 2008. (Accepted for publication)

  15. Bogdan Done, Purvesh Khatri, Arina Done and Sorin Draghici. Predicting novel human Gene Ontology annotations using semantic analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, January-March 2010; 7(1):91-99

  16. Ho-Sheng Lin, Harvinder S. Talwar, Adi L. Tarca, Alexei Ionan, Madhumita Chatterjee, Bin Ye, Jerzy Wojciechowski, Saroj Mohapatra, Marc D. Basson, George H. Yoo, Brian eshek, Fulvio Lonardo, Chuan-Ju G. Pan, Adam J. Folbe, Sorin Draghici, Judith Abrams, and Michael A. Tainsky. Autoantibody Approach for Serum-Based Detection of Head and Neck Cancer. Cancer Epidemiol Biomarkers 2007 November;16(11): 2396-405.

  17. Sorin Draghici, Adi Laurentiu Tarca, Longfei Yu, Stephen Ethier, and Roberto Romero. KUTE-BASE: Storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours. Bioinformatics. November 17, 2007.

  18. Montenegro D, Romero R, Pineles BL, Tarca AL, Kim YM, Draghici S, Kusanovic JP, Kim JS, Erez O, Mazaki-Tovi S, Hassan S, Espinoza J, Kim CJ. Differential expression of microRNAs with progression of gestation and inflammation in the human chorioamniotic membranes. Am J Obstet Gynecol. 2007 Sep;197(3):289.e1-6.

  19. Hassan SS, Romero R, Tarca AL, Draghici S, Pineles B, Bugrim A, Khalek N, Camacho N, Mittal P, Yoon BH, Espinoza J, Kim CJ, Sorokin Y, Malone J Jr. Signature pathways identified from gene expression profiles in the human uterine cervix before and after spontaneous term parturition. Am J Obstet Gynecol. 2007 Sep;197(3):250.e1-7. .

  20. Sorin Draghici, Purvesh Khatri, Adi Laurentiu Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, and Roberto Romero. A systems biology approach for pathway level analysis. Genome Research, 17:1537-1545, 2007.

  21. Adi L. Tarca, Vincent J. Carey, Xue-wen Chen, Roberto Romero, Sorin Draghici. Machine Learning and its Applications to Biology. PLoS Computational Biology, 3(6): 953-963, June 2007.

  22. Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi L. Tarca, Sorin Draghici. Onto-Tools: New Additions and Improvements in 2006. Nucleic Acids Research, 35, W206-W211, July 2007.

  23. BL Pineles, R Romero, D Montenegro, AL Tarca, YM Han, YM Kim, S Draghici, J Espinoza, JP Kusanovic, P Mittal, SS Hassan, and CJ Kim Distinct subsets of microRNAs are expressed differentially in the human placentas of patients with preeclampsia.. Am J Obstet Gynecol, 196(3) : 261.e1-6, March 2007.

  24. Michael A. Tainsky, Madhumita Chatterjee, Nancy K. Levin, Sorin Draghici, and Judith Abrams Multianalyte Tests for the Early Detection of Cancer: Speedbumps and Barriers. Biomarker Insights, 2 : 261-267, 2007 .

  25. Chatterjee M, Ionan A, Draghici S, Tainsky MA. Epitomics: global profiling of immune response to disease using protein microarrays. OMICS: A Journal of Integrative Biology, 10(4): 499-506, December 2006

  26. Sorin Draghici, Sivakumar Sellamuthu, Purvesh Khatri. Babel's tower revisited: a universal resource for cross-referencing across annotation databases. Bioinformatics, 22(23):2934-2939, December 2006.

  27. KL Streicher, ZQ Yang, S Draghici, SP Ethier. Transforming function of the LSM1 oncogene in human breast cancers with the 8p11-12 amplicon. Oncogene:1-11, August 2006

  28. Tarca AL, Romero R, Draghici S. Analysis of microarray experiments of gene expression profiling. American Journal of Obstetrics and Gynecology 195(2):373-388, August 2006

  29. Khatri P, Desai V, Tarca AL, Sellamuthu S, Wildman DE, Romero R, Draghici S. New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate . Nucleic Acids Research, 34, W626-W631, July 2006

  30. Chatterjee M, Draghici S, Tainsky MA. Immunotheranostics: Breaking tolerance in immunotherapy using tumor autoantigens identified on protein microarrays. Current Opinion in Drug Discovery & Development, 9(3): 380-385 May 2006.

  31. Sorin Draghici, Purvesh Khatri, Aron C. Eklund and Zoltan Szallasi. Reliability and reproducibility issues in DNA microarray measurements. Trends in Genetics, 22(2):101-109, February 2006.

  32. Madhumita Chatterjee, Saroj Mohapatra, Alexei Ionan, Gagandeep Bawa, Rouba Ali-Fehmi, Xiaoju Wang, James Nowak, Bin Ye, Fatimah A. Nahhas, Karen Lu, Steven S. Witkin, David Fishman, Adnan Munkarah, Robert Morris, Nancy K. Levin, Natalie N. Shirley, Gerard Tromp, Judith Abrams, Sorin Draghici, and Michael A. Tainsky. Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays. Cancer Research, 66(2): 1181-90, January 15, 2006.

  33. Stephen Krawetz, Sorin Draghici, Goodrich R, Zhandong Liu, G. Charles Ostermeier. In silico and wet-bench identification of nuclear matrix attachment regions. Methods in Molecular Medicine, 108: 439-58, 2005.

  34. Sorin Draghici, Madhumita Chatterjee and Michael Tainsky. Epitomics: serum screening for the early detection of cancer on microarrays complex panels of tumor antigens. Expert Review of Molecular Diagnostics, 5(5):735-743, September 2005.

  35. Sanjay N Rakhade, Bin Yao, Sharlin Ahmed, Eishi Asano, Thomas Lamar Beaumont, AK, Sorin Draghici, Raul Krauss, Harry Chugani, Sood S, Jeffery A Loeb. A Common Pattern of Persistent Gene Activation in Human Neocortical Epileptic Foci. Annals of Neurology 58(5):736-47, November 2005.

  36. Otto Muzik, Siamak Pourabdollah, Csaba Juhasz, Diane C. Chugani, James Janisse and Sorin Draghici. Application of an objective method for localizing bilateral cortical FDG PET abnormalities to guide the resection of epileptic foci. IEEE Transactions on Biomedical Engineering, 52(9): 1574-81, September 2005.

  37. Purvesh Khatri and Sorin Draghici. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics, 21(18):3587-95, September 2005.

  38. Purvesh Khatri, Bogdan Done, Archana Rao, Arina Done and Sorin Draghici.A semantic analysis of the annotations of the human genome. Bioinformatics, 21(16): 3416-3421, August 2005.

  39. Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done and Sorin Draghici.Recent additions and improvements to the Onto-Tools. Nucleic Acids Research, 33(Web Server issue):W762-W765, July 2005.

  40. 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.

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

  42. 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.

  43. 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.

  44. 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, 10(3): 849-859, February 2004.

  45. 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.

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

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

  48. 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.

  49. 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.

  50. 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, Suppl: 36-44, March 2003.

  51. 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, Suppl:55-61, March 2003.

  52. 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, February 2003.

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

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

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

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

  57. Purvesh Khatri, Sorin Draghici, G. Charles Ostermeier, Stephen A. Krawetz - Profiling Gene Expression Using Onto-Express. Genomics, 79(2):266-270, February 2002.

  58. 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, May 2001.

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

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

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

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

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

figure for citaions

Peer-reviewed Conference Publication (top)

  1. Calin Voichita, Purvesh Khatri, Sorin Draghici: Identifying uncertainty regions in Support Vector Machines using geometric margin and convex hulls. Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on, 1-8 June 2008

  2. Purvesh Khatri, Sorin Draghici, Adi L. Tarca, Sonia S. Hassan, Roberto Romero. A system biology approach for the steady-state analysis of gene signaling networks. 12th Iberoamerican Congress on Pattern Recognition, CIARP 2007, Valparaiso, Chile. November 13-16, 2007.
  3. Bogdan Done, Purvesh Khatri, Arina Done, and Sorin Draghici. A semantic analysis of genome annotations using weighting schemes. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Honolulu, Hawaii,USA, April 1-5, 2007.

  4. Valmik Desai, Purvesh Khatri, Arina Done, Aviva Friedman, Michael Tainsky and Sorin Draghici. A novel bioinformatics technique for predicting condition-specific transcription factor binding sites. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, USA, November 14-15, 2005.

  5. Sorin Draghici, Purvesh Khatri, Yanhong Liu, Kitty J. Chase, Elizabeth A. Bode, David A. Kulesh, Leonard P Wasieloski, David A. Norwood, Jaques Reifman. Identification of genomic signatures for the design of assays for the detection and monitoring of the anthrax threats. In Pacific Symposium on Biocomputing (PSB), The Big Island of Hawaii, USA, Jan 4-8 2005.

  6. 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.

  7. 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, May 19-21 2003.

  8. 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.

  9. 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.

  10. 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.

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  21. 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.

  22. 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.

  23. 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.

  24. 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.

  25. 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 Sdchsisches Verlagshaus GmbH, ISBN 3-860050190-3.

  26. 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.

  27. 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).

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. Sorin Draghici - The Constraint Based Decomposition Training Architecture, Proceedings of World Congress on Neural Networks, WCNN94 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. Beyond classical statistics - A system biology approach for pathway level analysis - 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2006, Fortaleza, Brazil, August 6-10, 2006
  2. A system biology approach for pathway level analysis - Invited talk in the special interest group "Managing the Data Explosion in System Biology", Amereican Society for Cell Biology, San Diego, December, 2006.
  3. Tools and methods for the analysis of modern high throughput genomics experiments, Invited Talk in the 2nd annual NSF Plant Microarray Analysis Short Course, Boston, August 2-4, 2006.

  4. System Biology,Chips-to-Hits Boston, MA, September 2006.

  5. Invited Talk, Department of Computer Science, University of California, San Diego October 26 2005.

  6. Data Analysis of DNA Microarrays, 3 day course, University of Pisa, Pisa, Italy, July 13-15 2005.

  7. Data Analysis of DNA Microarrays, 2 day course, Northwestern University, Chicago, IL, May 5-6 2005.

  8. Data Analysis of DNA Microarrays, 2 day course, Bethesda, MD, March 3-4 2005.

  9. Gene Ontology: Current tools and Open Problems, Invited Talk, European Bioinformatics Institute(EBI), Cambridge University, Cambridge, United Kingdom, November 22 2004.

  10. Methods and Tools for Microarray Data Analysis, Keynote Presentation,Flanders Interuniversity Institute for Biotechnology,Leuven, Belgium, October 19 2004.

  11. Microarray Design and Analysis, Invited talk at the 4-th VIB Microarray Users Group Meeting, Leuven, Belgium, October 18 2004.

  12. 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.

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

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

  15. 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.

  16. 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.

  17. 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.

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

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

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

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

  22. 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.

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

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

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

  26. 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.

  27. 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.

  28. 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

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

  30. 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.

  31. 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.

  32. 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.

  33. 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.

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

  35. 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.

  36. 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.

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

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

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

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

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

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

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

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

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

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

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

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

  49. 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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