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@article{ansari2016novel,
	Author = {Ansari, Sahar and Voichi\c{t}a, C\u{a}lin and Donato, Michele and Tagett, Rebecca and Dr\u{a}ghici, Sorin},
	Date-Added = {2016-04-14 16:25:41 +0000},
	Date-Modified = {2016-04-14 16:25:41 +0000},
	Doi = {10.1109/JPROC.2016.2531000},
	Journal = {Proceedings of the IEEE},
	Month = {March},
	Number = {99},
	Pages = {1--14},
	Publisher = {IEEE},
	Title = {A novel pathway analysis approach based on the unexplained disregulation of genes},
	Url = {http://dx.doi.org/10.1109/JPROC.2016.2531000},
	Volume = {PP},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/JPROC.2016.2531000}}

@inproceedings{DraghiciValmik:2005,
	Address = {San Diego, USA},
	Author = {Valmik Desai and Purvesh Khatri and Arina Done and Aviva Friedman and Michael Tainsky and Sorin Draghici},
	Booktitle = {Proc. of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology},
	Date-Added = {2013-03-11 19:04:08 +0000},
	Date-Modified = {2013-03-11 19:04:08 +0000},
	Month = {November 14-15},
	Title = {A novel bioinformatics technique for predicting condition-specific transcription factor binding sites},
	Year = {2005}}

@article{Khatri:2007,
	Author = {Khatri, Purvesh and Calin Voichita and Khalid Kattan and Nadeem Ansari and Avani Khatri and Constantin Georgescu and Adi Laurentiu Tarca and Sorin Dr{\v{a}}ghici},
	Date-Added = {2013-03-11 19:03:31 +0000},
	Date-Modified = {2013-03-11 19:03:31 +0000},
	Journal = {Nucleic Acids Research},
	Month = {July},
	Number = {Web Server issue},
	Title = {Onto-{T}ools: New Additions and Improvements in 2006},
	Volume = {37},
	Year = {2007}}

@article{DraghiciOC:2003,
	Author = {Sorin Dr\u{a}ghici and Purvesh Khatri and Abhik Shah and Michael Tainsky},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {BioTechniques},
	Month = {March},
	Pages = {55--61},
	Title = {Assessing the functional bias of commercial microarrays using the {Onto-Compare} database},
	Volume = {Microarrays and Cancer: Research and Applications},
	Year = {2003}}

@article{DraghiciOE2:2003,
	Author = {Sorin Dr\u{a}ghici and Purvesh Khatri and Rui P. Martins and G. Charles Ostermeier and Stephen A. Krawetz},
	Comment = {former DraghiciOE2:2002},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Genomics},
	Month = {February},
	Number = {2},
	Pages = {98--104},
	Title = {Global functional profiling of gene expression},
	Volume = {81},
	Year = {2003}}

@article{DraghiciOntologicalToolsReview:2005,
	Author = {Purvesh Khatri and Sorin Draghici},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Bioinformatics},
	Number = {18},
	Pages = {3587--3595},
	Title = {Ontological analysis of gene expression data: current tools, limitations, and open problems},
	Volume = {21},
	Year = {2005}}

@article{DraghiciOntoTranslate:2006,
	Abstract = {Motivation: Annotation databases are widely used as public repositories
	of biological knowledge. However, most of these resources have been
	developed by independent groups which used different designs and
	different identifiers for the same biological entities. As we show
	in this article, incoherent name spaces between various databases
	represent a serious impediment to using the existing annotations
	at their full potential. 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. Results: We have developed
	a web-based resource, Onto-Translate (OT), which effectively addresses
	this problem. OT is able to map onto each other different types of
	biological entities from the following annotation databases: Swiss-Prot,
	TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept,
	IMAGE, RefSeq, UniGene, OMIM, PDB, Eukaryotic Promoter Database,
	HUGO Gene Nomenclature Committee and NetAffx. Currently, OT is able
	to perform 462 types of mappings between 29 different types of IDs
	from 17 databases concerning 53 organisms. Among these, over 300
	types of translations and 15 types of IDs are not currently supported
	by any other tool or resource. On average, OT is able to correctly
	map between 96 and 99% of the biological entities provided as input.
	In terms of speed, sets of [~]20 000 IDs can be translated in <30
	s, in most cases. Availability: OT is a part of Onto-Tools, which
	is freely available at http://vortex.cs.wayne.edu/Projects.html Contact:
	sorin@wayne.edu},
	Author = {Draghici, Sorin and Sellamuthu, Sivakumar and Khatri, Purvesh},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Doi = {10.1093/bioinformatics/btl372},
	Eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/23/2934.pdf},
	Journal = {Bioinformatics},
	Number = {23},
	Pages = {2934-2939},
	Title = {Babel's tower revisited: a universal resource for cross-referencing across annotation databases},
	Url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/23/2934},
	Volume = {22},
	Year = {2006},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/23/2934},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btl372}}

@article{DraghiciOT:2003,
	Author = {Sorin Dr\u{a}ghici and Purvesh Khatri and Pratik Bhavsar and Abhik Shah and Stephen A. Krawetz and Michael A. Tainsky},
	Comment = {formerly DraghiciOntoTools:2003},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Nucleic Acids Research},
	Month = {July},
	Number = {13},
	Pages = {3775--81},
	Title = {Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate},
	Volume = {31},
	Year = {2003}}

@article{DraghiciOT:2004,
	Author = {Purvesh Khatri and Pratik Bhavsar and Gagandeep Bawa and Sorin Dr\u{a}ghici},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Nucleic Acids Research},
	Month = {Jul},
	Pages = {W449-56},
	Title = {Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments},
	Volume = {32},
	Year = {2004}}

@article{DraghiciOT:2005,
	Author = {Purvesh Khatri and Sivakumar Sellamuthu and Pooja Malhotra and Kashyap Amin and Arina Done and Sorin Dr\u{a}ghici},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Nucleic Acids Research},
	Month = {Jul},
	Number = {Web server issue},
	Title = {{Recent additions and improvements to the Onto-Tools}},
	Volume = {33},
	Year = {2005}}

@article{DraghiciOT:2006,
	Abstract = {The Onto-Tools suite is composed of an annotation database and eight
	complementary, web-accessible data mining tools: Onto-Express, Onto-Compare,
	Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express
	and nsSNPCounter. Promoter-Express is a new tool added to the Onto-Tools
	ensemble that facilitates the identification of transcription factor
	binding sites active in specific conditions. nsSNPCounter is another
	new tool that allows computation and analysis of synonymous and non-synonymous
	codon substitutions for studying evolutionary rates of protein coding
	genes. Onto-Translate has also been enhanced to expand its scope
	and accuracy by fully utilizing the capabilities of the Onto-Tools
	database. 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.},
	Author = {Purvesh Khatri and Valmik Desai and Adi Laurentiu Tarca and Sivakumar Sellamuthu and Derek E. Wildman and Roberto Romero and Sorin Draghici},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Nucleic Acids Research},
	Keywords = {Binding Sites *Databases, Genetic Evolution, Molecular Internet *Polymorphism, Single Nucleotide *Promoter Regions (Genetics) Proteins/*genetics Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. *Software Systems Integration Transcription Factors/*metabolism User-Computer Interface},
	Pages = {W626-31},
	Title = {New {Onto-Tools}: {Promoter-Express}, {nsSNPCounter}, and {Onto-Translate}},
	Volume = {34},
	Year = {2006}}

@article{DraghiciPE:2007,
	Author = {Draghici, Sorin and Khatri, Purvesh and Tarca, Adi Laurentiu and Amin, Kashayp and Done, Arina and Voichita, Calin and Georgescu, Constantin and Romero, Roberto},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:29 +0000},
	Journal = {Genome Research},
	Number = {10},
	Pages = {1537-1545},
	Title = {A systems biology approach for pathway level analysis},
	Volume = {17},
	Year = {2007}}

@article{Khatri:2002,
	Author = {Purvesh Khatri and Sorin Draghici and G. Charles Ostermeier and Stephen A. Krawetz},
	Comment = {formerly also known as DraghiciGenomics:2002},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Genomics},
	Month = {February},
	Number = {2},
	Pages = {266-270},
	Title = {Profiling Gene Expression Using {Onto-Express}},
	Volume = {79},
	Year = {2002}}

@article{Khatri:2004,
	Author = {Khatri, Purvesh and Bhavsar, Pratik and Bawa, Gagandeepsing and Draghici, Sorin},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Nucleic Acids Research},
	Note = {Suppl. 2},
	Pages = {W449-W456},
	Title = {Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments},
	Volume = {32},
	Year = {2004}}

@article{Khatri:2005a,
	Author = {Khatri, P. and Draghici, S.},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Bioinformatics},
	Number = {18},
	Pages = {3587-3595},
	Title = {Ontological analysis of gene expression data: current tools, limitations, and open problems},
	Volume = {21},
	Year = {2005}}

@article{Khatri:2005b,
	Author = {Khatri, P. and Sellamuthu, S. and Malhotra, P. and Amin, K. and Done, A. and Draghici, S.},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Nucleic Acids Research},
	Note = {Suppl. S},
	Pages = {W762-W765},
	Title = {Recent additions and improvements to the Onto-Tools},
	Volume = {33},
	Year = {2005}}

@article{Khatri:2005c,
	Author = {Khatri, P. and Sellamuthu, S. and Malhotra, P. and Amin, K. and Done, A. and Draghici, S.},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Nucleic Acids Research},
	Note = {Suppl. 2},
	Pages = {W762-W765},
	Title = {Recent additions and improvements to the Onto-Tools},
	Volume = {33},
	Year = {2005}}

@article{Khatri:2006,
	Author = {Khatri, Purvesh and Desai, Valmik and Tarca, Adi Laurentiu and Sellamuthu, Sivakumar and Wildman, Derek E. and Romero, Roberto and Draghici, Sorin},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Journal = {Nucleic Acids Research},
	Pages = {W626-W631},
	Title = {New {Onto-Tools}: {Promoter-Express}, {nsSNPCounter} and {Onto-Translate}},
	Volume = {34},
	Year = {2006}}

@inproceedings{Khatri:2007a,
	Address = {Valparaiso, Chile},
	Author = {Khatri, Purvesh and Draghici, Sorin and Tarca, Adi Laurentiu and Hassan, Sonia S. and Roberto Romero},
	Booktitle = {12th Iberoamerican Congress on Pattern Recognition},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:30 +0000},
	Month = {November 13-16},
	Title = {A system biology approach for the steady-state analysis of gene signaling networks},
	Year = {2007}}

@article{TarcaSPIA:2009,
	Author = {Adi Laurentiu Tarca and Sorin Draghici and Purvesh Khatri and Sonia S. Hassan and Pooja Mittal and Jung-sun Kim and Chong Jai Kim and Juan Pedro Kusanovic and Roberto Romero},
	Date-Added = {2013-03-07 16:17:28 +0000},
	Date-Modified = {2013-03-07 16:17:32 +0000},
	Journal = {Bioinformatics},
	Number = {1},
	Pages = {75-82},
	Title = {A Novel Signaling Pathway Impact Analysis ({SPIA})},
	Volume = {25},
	Year = {2009}}

@article{Voichita:2012,
	Author = {Calin Voichita and Michele Donato and Sorin Draghici},
	Journal = {Proceedings of the International Conference on Machine Learning Applications ({ICMLA})},
	Location = {Boca Raton, FL, USA},
	Month = dec,
	Title = {{Incorporating gene significance in the impact analysis of signaling pathways}},
	Year = {2012}}
