S Draghici

Summary

Affiliation: Wayne State University
Country: USA

Publications

  1. pmc Recent additions and improvements to the Onto-Tools
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 33:W762-5. 2005
  2. pmc DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells
    Duccio Cavalieri
    Department of Pharmacology, University of Firenze, Firenze, Italy
    Immunome Res 6:10. 2010
  3. pmc NetPath: a public resource of curated signal transduction pathways
    Kumaran Kandasamy
    Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
    Genome Biol 11:R3. 2010
  4. pmc Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 31:3775-81. 2003
  5. ncbi request reprint Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202, USA
    Bioinformatics 19:1348-59. 2003
  6. pmc KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Bioinformatics 24:738-40. 2008
  7. pmc Ontological analysis of gene expression data: current tools, limitations, and open problems
    Purvesh Khatri
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Bioinformatics 21:3587-95. 2005
  8. ncbi request reprint Epitomics: serum screening for the early detection of cancer on microarrays using complex panels of tumor antigens
    Sorin Draghici
    Karmanos Cancer Institute Wayne State University, Program in Molecular Biology and Human Genetics, Department of Computer Science, Wayne State University, 5143 Cass Ave, Room 431 State Hall, Detroit, MI 48202, USA
    Expert Rev Mol Diagn 5:735-43. 2005
  9. pmc A systems biology approach for pathway level analysis
    Sorin Draghici
    Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48202, USA
    Genome Res 17:1537-45. 2007
  10. ncbi request reprint A neural network based artificial vision system for licence plate recognition
    S Draghici
    Dept of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Int J Neural Syst 8:113-26. 1997

Research Grants

Collaborators

Detail Information

Publications52

  1. pmc Recent additions and improvements to the Onto-Tools
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 33:W762-5. 2005
    ..Pathway-Express is a new tool that helps the users find the most interesting pathways for their input list of genes. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html...
  2. pmc DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells
    Duccio Cavalieri
    Department of Pharmacology, University of Firenze, Firenze, Italy
    Immunome Res 6:10. 2010
    ..Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs)...
  3. pmc NetPath: a public resource of curated signal transduction pathways
    Kumaran Kandasamy
    Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
    Genome Biol 11:R3. 2010
    ..We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches...
  4. pmc Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 31:3775-81. 2003
    ..All tools above are seamlessly integrated. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html...
  5. ncbi request reprint Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202, USA
    Bioinformatics 19:1348-59. 2003
    ..Two common methods for gene selection are: (a) selection by fold difference (at least n fold variation) and (b) selection by altered ratio (at least n standard deviations away from the mean ratio)...
  6. pmc KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Bioinformatics 24:738-40. 2008
    ..However in BASE, like in most other microarray data repositories, the experiment annotation and raw data uploading can be very timeconsuming, especially for large microarray experiments...
  7. pmc Ontological analysis of gene expression data: current tools, limitations, and open problems
    Purvesh Khatri
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Bioinformatics 21:3587-95. 2005
    ..We propose these as challenges for the next generation of secondary data analysis tools...
  8. ncbi request reprint Epitomics: serum screening for the early detection of cancer on microarrays using complex panels of tumor antigens
    Sorin Draghici
    Karmanos Cancer Institute Wayne State University, Program in Molecular Biology and Human Genetics, Department of Computer Science, Wayne State University, 5143 Cass Ave, Room 431 State Hall, Detroit, MI 48202, USA
    Expert Rev Mol Diagn 5:735-43. 2005
    ..This technology of global epitope/antigen profiling is referred to as 'epitomics'...
  9. pmc A systems biology approach for pathway level analysis
    Sorin Draghici
    Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48202, USA
    Genome Res 17:1537-45. 2007
    ..This analysis method has been implemented as a Web-based tool, Pathway-Express, freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu)...
  10. ncbi request reprint A neural network based artificial vision system for licence plate recognition
    S Draghici
    Dept of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Int J Neural Syst 8:113-26. 1997
    ....
  11. ncbi request reprint The constraint based decomposition (CBD) training architecture
    S Draghici
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Neural Netw 14:527-50. 2001
    ..CBD provides the second best average accuracy on the problems tested as well as the best reliability (the lowest standard deviation)...
  12. ncbi request reprint Global functional profiling of gene expression
    Sorin Draghici
    Department of Computer Science, Wayne State University, 5143 Cass Avenue, Detroit, MI 48202, USA
    Genomics 81:98-104. 2003
    ..OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms...
  13. ncbi request reprint Predicting HIV drug resistance with neural networks
    Sorin Draghici
    Department of Computer Science, 431 State Hall, Wayne State University, Detroit, MI 48202, USA
    Bioinformatics 19:98-107. 2003
    ..The ability to predict the drug resistance of HIV protease mutants may be useful in developing more effective and longer lasting treatment regimens...
  14. ncbi request reprint Statistical intelligence: effective analysis of high-density microarray data
    Sorin Draghici
    431 State Hall, Dept of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Drug Discov Today 7:S55-63. 2002
    ..This review focuses on the methods currently available for the selection of such genes. Fold change, unusual ratio, univariate testing with correction for multiple experiments, ANOVA and noise sampling methods are reviewed and compared...
  15. ncbi request reprint On the capabilities of neural networks using limited precision weights
    Sorin Draghici
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    Neural Netw 15:395-414. 2002
    ..The approach presented is also discussed in the context of the VC-complexity...
  16. pmc Onto-Tools: new additions and improvements in 2006
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 35:W206-11. 2007
    ..The Onto-Tools are freely available at http://vortex.cs.wayne.edu/projects.htm...
  17. ncbi request reprint Assessing the functional bias of commercial microarrays using the onto-compare database
    Sorin Draghici
    Department of Computer Science, Wayne State University, Detroit, MI, USA
    Biotechniques . 2003
    ..At the same time, processes such as cell cycle control, oncogenesis, and negative control of cell proliferation are better represented on the BD Biosciences Clontech Atlas Select human apoptosis array...
  18. pmc A semantic analysis of the annotations of the human genome
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Bioinformatics 21:3416-21. 2005
    ..We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database...
  19. pmc Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 32:W449-56. 2004
    ..OE, OC and OD now have an integrated GO browser that allows the user to customize the level of abstraction for each GO category. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html...
  20. ncbi request reprint Mining HIV dynamics using independent component analysis
    Sorin Draghici
    Department of Computer Science, Wayne State University, IA, USA
    Bioinformatics 19:981-6. 2003
    ..Moreover, the incorporation of the actual laboratory data sets into the analysis phase offers a powerful advantage when compared with other mathematical procedures that consider the general behavior of HIV dynamics...
  21. pmc New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate
    Purvesh Khatri
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 34:W626-31. 2006
    ..Currently, Onto-Translate allows arbitrary mappings between 28 types of IDs for 53 organisms. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html...
  22. pmc Autoantibody approach for serum-based detection of head and neck cancer
    Ho Sheng Lin
    Department of Surgery, John D Dingell VA Medical Center, Wayne State University, Detroit, Michigan 48201, USA
    Cancer Epidemiol Biomarkers Prev 16:2396-405. 2007
    ....
  23. pmc Characterization of the myometrial transcriptome and biological pathways of spontaneous human labor at term
    Pooja Mittal
    Perinatology Research Branch, NICHD NIH DHHS, Bethesda, Maryland, USA
    J Perinat Med 38:617-43. 2010
    ..to characterize the transcriptome of human myometrium during spontaneous labor at term...
  24. pmc Signature pathways identified from gene expression profiles in the human uterine cervix before and after spontaneous term parturition
    Sonia S Hassan
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
    Am J Obstet Gynecol 197:250.e1-7. 2007
    ..This study aimed to discover "signature pathways" that characterize biologic processes, based on genes differentially expressed in the uterine cervix before and after spontaneous labor...
  25. pmc Predicting novel human gene ontology annotations using semantic analysis
    Bogdan Done
    Department of Computer Science, Wayne State University, 5143 Cass Ave, Detroit, MI 48202, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:91-9. 2010
    ..For the remaining 10 percent, we did not find any relevant publications to confirm or contradict the predictions. The n2tn weighting scheme also outperformed the simple binary scheme used in our previous approach...
  26. doi request reprint The transcriptome of cervical ripening in human pregnancy before the onset of labor at term: identification of novel molecular functions involved in this process
    Sonia S Hassan
    Department of Obstetrics and Gynecology, Wayne State University Hutzel Women s Hospital, Detroit, MI 48201, USA
    J Matern Fetal Neonatal Med 22:1183-93. 2009
    ..The aim of this study was to identify changes in the cervical transcriptome in the human uterine cervix as a function of ripening before the onset of labor...
  27. pmc Babel's tower revisited: a universal resource for cross-referencing across annotation databases
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Bioinformatics 22:2934-9. 2006
    ..Navigating between various such name spaces by mapping IDs from one database to another is a very important issue which is not properly addressed at the moment...
  28. ncbi request reprint MicroRNA expression profiling of the human uterine cervix after term labor and delivery
    Sonia S Hassan
    Department of Obstetrics and Gynecology, Wayne State University Hutzel Hospital, Detroit, MI, USA
    Am J Obstet Gynecol 202:80.e1-8. 2010
    ..MicroRNAs (miRNAs) are noncoding RNAs involved in posttranscriptional regulation of target genes. The objective of this study was to determine the miRNA expression profile of the human uterine cervix after spontaneous term labor (TL)...
  29. pmc Application of an objective method for localizing bilateral cortical FDG PET abnormalities to guide the resection of epileptic foci
    Otto Muzik
    Department of Pediatrics and Radiology, Children s Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI 48201, USA
    IEEE Trans Biomed Eng 52:1574-81. 2005
    ..The accuracy of this approach with respect to invasive subdural electroencephalography (EEG) data was assessed in a group of children with neocortical epilepsy...
  30. pmc Reliability and reproducibility issues in DNA microarray measurements
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Trends Genet 22:101-9. 2006
    ..The main problems seem to be the sub-optimal design or choice of probes and some incorrect probe annotations. Well-designed data-analysis approaches can rectify some of these problems...
  31. pmc Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells
    Bin Yao
    Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
    BMC Bioinformatics 5:99. 2004
    ....
  32. pmc Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays
    Madhumita Chatterjee
    Program in Molecular Biology and Human Genetics, Barbara Ann Karmanos Cancer Institute, Wayne State University, 110 East Warren, Detroit, MI 48201, USA
    Cancer Res 66:1181-90. 2006
    ..Further work with larger panels of antigens should provide a comprehensive set of markers with sufficient sensitivity and specificity suitable for clinical testing in high-risk populations...
  33. pmc A novel signaling pathway impact analysis
    Adi Laurentiu Tarca
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Bioinformatics 25:75-82. 2009
    ..Both approaches treat the pathways as simple sets of genes, disregarding the complex gene interactions that these pathways are built to describe...
  34. pmc Developing classifiers for the detection of cancer using multi-analytes
    Adi Laurentiu Tarca
    Department of Computer Science, Wayne State University, Detroit, MI, USA
    Methods Mol Biol 520:259-72. 2009
    ..This chapter describes the principles of the classifier development and underlines the most common pitfalls. A simulated dataset is used to illustrate the main concepts involved in supervised classification...
  35. ncbi request reprint Immunotheranostics: breaking tolerance in immunotherapy using tumor autoantigens identified on protein microarrays
    Madhumita Chatterjee
    Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Program in Molecular Biology and Human Genetics, Detroit, MI 48201, USA
    Curr Opin Drug Discov Devel 9:380-5. 2006
    ....
  36. ncbi request reprint Gene expression profiles predict survival and progression of pleural mesothelioma
    Harvey I Pass
    Thoracic Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
    Clin Cancer Res 10:849-59. 2004
    ..We hypothesized that gene expression profiles could predict time to progression and survival in surgically cytoreduced pleural mesothelioma of all stages...
  37. ncbi request reprint Profiling gene expression using onto-express
    Purvesh Khatri
    Department of Computer Science, Wayne State University School of Medicine, Detroit, MI, 48201, USA
    Genomics 79:266-70. 2002
    ..The profiles created by Onto-Express fundamentally increase the value of gene expression analyses by facilitating the translation of quantitative value sets to records that contain biological implications...
  38. ncbi request reprint Applications and challenges of DNA microarray technology in military medical research
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Mil Med 169:654-9. 2004
    ..This discussion contains material that would be useful for making programmatic recommendations that team strategic research investments and emerging technologies with U.S. Army Medical Research and Materiel Command resources...
  39. pmc Transforming function of the LSM1 oncogene in human breast cancers with the 8p11-12 amplicon
    K L Streicher
    Breast Cancer Program, Karmanos Cancer Institute, Detroit, MI 48201, USA
    Oncogene 26:2104-14. 2007
    ..Future work will continue to characterize these important changes to achieve a more complete understanding of the mechanism of hLsm1's effect on cancer progression...
  40. ncbi request reprint A common pattern of persistent gene activation in human neocortical epileptic foci
    Sanjay N Rakhade
    Center for Molecular Medicine and Genetics, Detroit, MI 48201, USA
    Ann Neurol 58:736-47. 2005
    ....
  41. pmc Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
    Nucleic Acids Res 31:3257-66. 2003
    ..These results provide the first evidence that nuclear matrix association dynamically mediates the looping of the beta-globin locus to achieve transcriptional control...
  42. ncbi request reprint Epitomics: global profiling of immune response to disease using protein microarrays
    Madhumita Chatterjee
    Program in Molecular Biology and Human Genetics, Barbara Ann Karmanos Cancer Institute Wayne State University, Detroit, Michigan, USA
    OMICS 10:499-506. 2006
    ..The immune system is the ultimate biosensor, superior to anything a human could create and ready to be exploited for biotechnology and biomedicine...
  43. ncbi request reprint Epigenetic silencing of multiple interferon pathway genes after cellular immortalization
    Olga I Kulaeva
    Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 110 Warren Ave, Detroit, MI 48201, USA
    Oncogene 22:4118-27. 2003
    ..This work indicates that gene silencing may be associated with an early event in carcinogenesis, cellular immortalization...
  44. pmc Mitochondrial manganese superoxide dismutase mRNA expression in human chorioamniotic membranes and its association with labor, inflammation, and infection
    Nandor Gabor Than
    Perinatology Research Branch, NICHD, NIH, DHHS, Detroit, Michigan 48201, USA
    J Matern Fetal Neonatal Med 22:1000-13. 2009
    ..Therefore, the aim of this study was to determine the differences in Mn SOD mRNA expression in the fetal membranes in patients with term and preterm labor (PTL) as well as in acute chorioamnionitis...
  45. pmc Differential expression pattern of genes encoding for anti-microbial peptides in the fetal membranes of patients with spontaneous preterm labor and intact membranes and those with preterm prelabor rupture of the membranes
    Offer Erez
    Perinatology Research Branch, NICHD, NIH, DHHS, Detroit, Michigan, USA
    J Matern Fetal Neonatal Med 22:1103-15. 2009
    ....
  46. pmc Analysis of microarray experiments of gene expression profiling
    Adi L Tarca
    Perinatology Research Branch, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    Am J Obstet Gynecol 195:373-88. 2006
    ..This article is intended to assist clinicians in appraising the quality of the scientific evidence now reported in the obstetric and gynecologic literature...
  47. ncbi request reprint Gene expression databases and data mining
    Pascale Anderle
    ISREC, Lausanne, Switzerland
    Biotechniques . 2003
    ..Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement...
  48. pmc Differential expression of microRNAs with progression of gestation and inflammation in the human chorioamniotic membranes
    Daniel Montenegro
    Perinatology Research Branch, National Institute of Child Health and Human Development National Institutes of Health Department of Health and Human Services, Bethesda, MD, USA
    Am J Obstet Gynecol 197:289.e1-6. 2007
    ..The aim of this study was to identify differential expression of microRNAs (miRNAs) in chorioamniotic membranes with advancing gestation, labor, and inflammation...
  49. ncbi request reprint Use and misuse of the gene ontology annotations
    Seung Yon Rhee
    Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, California 94305, USA
    Nat Rev Genet 9:509-15. 2008
    ..Here we describe key aspects of GO, which, when overlooked, can cause erroneous results, and address how these pitfalls can be avoided...
  50. doi request reprint 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
    Johanne Holm Toft
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    J Matern Fetal Neonatal Med 21:267-73. 2008
    ..In addition, a targeted analysis of angiogenesis-regulating gene expression was performed...
  51. pmc Gene expression profiling demonstrates a novel role for foetal fibrocytes and the umbilical vessels in human fetoplacental development
    Jung Sun Kim
    Perinatology Research Branch, NICHD NIH DHHS, Bethesda, MD, USA
    J Cell Mol Med 12:1317-30. 2008
    ..This study reports fibrocytes in the human umbilical cord and placenta for the first time, and a novel role for both circulating foetal cells and the umbilical vessels in placental development, which is deranged in IUGR...
  52. ncbi request reprint Distinct subsets of microRNAs are expressed differentially in the human placentas of patients with preeclampsia
    Beth L Pineles
    Perinatology Research Branch, National Institute of Child Health and Human Development National Institutes of Health Department of Health and Human Services, Bethesda, MD, USA
    Am J Obstet Gynecol 196:261.e1-6. 2007
    ..MicroRNAs (miRNAs) are critical posttranscriptional regulators of gene expression. This study was performed to determine whether preeclampsia and SGA are associated with alterations in placental miRNA expression...

Research Grants5

  1. Novel methods for the analysis of gene signaling pathways with applications in ob
    Sorin Draghici; Fiscal Year: 2010
    ..g. DNA microarrays, protein microarrays, metabolomics, etc.) are used. ..
  2. Infrastructure equipment for gene expression analysis
    Sorin Draghici; Fiscal Year: 2003
    ..Furthermore, the system may be expanded in the future, to accommodate new investigators at a cost that is very feasible. ..
  3. Novel Algorithms & Organisms for Onto-Tools
    Sorin Draghici; Fiscal Year: 2006
    ..The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well. ..
  4. Novel algorithms and organisms for Onto-Tools
    Sorin Draghici; Fiscal Year: 2007
    ..The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well. ..
  5. Novel Algorithms & Organisms for Onto-Tools
    Sorin Draghici; Fiscal Year: 2005
    ..The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well. ..