Mary Panahiazar

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Mary Panahiazar

Maryam Panahiazar(Mary)
updated: Post doctorate Research Associate at Mayo Clinic.

I have a Ph.D. in Bioinformatics and I am pursuing my second Ph.D. in Computer Science at the Ohio Center of Excellence in Knowledge-enabled Computing Kno.e.sis Center.


Ph.D Candidate, Computer Science and Engineering
Kno.e.sis Center, Wright State University

Ph.D, Bioinformatics
University of Georgia

MS.c, Computer Engineering
Sharif University of Technology


I am Research Assistant and PhD Candidate in Computer Science at the Ohio Center of Excellence in Knowledge-enabled Computing (Kno.e.sis). I joined the Knoesis Center in February 2011. I have a Ph.D. in Bioinformatics from the University of Georgia and M.Sc. in Computer Engineering from Sharif University of Technology.

Work Experiences

  • Kno.e.sis Center, Dayton, OH, USA
  • National Institute of Health (NIH), Bethesda, MD, USA
  • Center for Tropical and Emerging Global Disease(CTEGD), Athens, GA, USA
  • Mount Desert Island Laboratory, ME, USA
  • IBM / DPI company, Tehran, Iran
  • Iran Telecommunication Research Center (ITRC) /, Tehran, Iran

Research Interests

  • Semantic Integration using knowledge-based Information Extraction and Semantic Annotation, Algorithms and Semantic Web Techniques to resolve Ambiguity.
  • Machine Learning
  • Ontology Development.
  • Data Mining, Text Mining for Prediction and Decision Making.
  • Information Retrieval.
  • Image Processing and Annotation.
  • Retrieving Data from Different Data Sources such as Experimental Data and Results from Structural Data sets, Data from Scientific Literature and Academic Articles.
  • Make the Federated Queries through Different Data Sources for Knowledge Discovery.
  • Big Data Challenges and Opportunities.
  • User Modeling and Interactions.
  • Natural Language Processing.
  • Question Answering Systems.


  • PhylOnt, A Domain Specific Ontology in Phylogeny Analysis.

PhylOnt is in collaboration with University of Georgia
The specific objective of this research is to develop and deploy an ontology for phylogenetic analysis application and web services and down- stream use of phylogenetic trees in Scientific Literature and Standard files such as XML. This is a foundation to allow an integrated platform in phylogenetically based comparative analysis and data integration. PhylOnt is an extensible ontology, that describes the methods employed to estimate trees given a data matrix, models and programs used for phylogenetic analysis and descriptions of phylogenetic trees including branch-length information and support values. It also describes the provenance information for phylogenetics analysis data such as information about publications and studies related to phylogenetic analyses. To illustrate the utility of PhylOnt, I annotated scientific literature and files to support semantic search. Project Period : 2010 – 2012

  • PSE-Tcruzi, A novel ontology-driven semantic problem-solving environment (PSE) for T.cruzi Wiki Page.

PSE is in collaboration with the Center for Topical and Emerging Diseases (CTEGD) and the National Center for Biomedical Ontologies (NCBO)
It allows the dynamic integration of local and public data to answer biological questions at multiple levels of granularity. This data Included in the multimodal datasets will be the genomic data and the associated bioinformatics predictions, functional information from metabolic pathways, experimental data from mass spectrometry and microarray experiments, and textual information from Pubmed. Project Period : 2008 - 2012

  • SemHealth, Advancing Open mHealth with Semantic Web Technology.
  • MUDDIS, Multidimensional Semantic Integration Approach for Knowledge Discovery.

MUDDIS is in collaboration with National institute of health(NIH)
The driving principle in using multi-dimensional approach is to create effective domain specific knowledge discovery, based on gene annotation with the use of scientific and provenance information from different resources. Find the similarity between genes can be useful in different areas of life science and biomedical fields such as model organism research and drug discovery in human. We regroup genes based on their functional annotations, structural annotations, genes responsible for disorders and gene-drug interactions. The novelty of this work is to query through different data sources and make a collection of data for similarity calculation calculated in different levels of granularity. Data from literature, open public databases such as OMIM and gene-centered information at NCBI are used as individual resources for different feature of the gene. Each additional features increases the value of knowledge that can be explained within individual resources. Project Period : 2012 – Current

  • Kino, An Integrated Tools to Annotate and Search Documents such as Scientific Literature, Academic Articles and XML Files.

It is an integrated suite of tools that enables scientists to annotate web-based documents. Kino-Phylo consists of an NCBO integrated front-end that allows the convenient annotation and submission of web documents through a browser plugin, and an annotation aware back-end, capable of providing faceted search capabilities. Project Period : 2010 - 2012

Usually semantic annotation needs resources such Ontologies to map the concepts from resources to the target data set for annotation. In the process of annotation, extra information is added to resources, which connect a part of the data to corresponding concept in the ontology. The process of describing the publications with Ontology concepts helps to use the existing valuable information in publications for integration and reusability of published data. Project Period : 2011 - 2012

  • PhylAnt-X, Semantic Annotation of XML files with Meta Data.

Annotation the XML file with concepts from Ontologies will be useful to make the XML files more understandable with the agent of the web for searching, integrating and re-usability. Users do not always know the structure of an ontology ’s con- tent or how to use the ontology to do the annotation themselves. In my approach, I over- come this limitation by showing the all possible Ontologies from NCBO for a selected concept during the annotation process. Project Period : 2011 - 2012

  • Telqas, A Telecommunication Literature Question Answering

System Benefits from a Text Categorization Mechanism

  • DAMEP, Data Mining for Exchange Prediction


  • Data integration in life science, Semantic Web Health Care and Life Sciences (HCLS) 2012, MIT, USA, Aug 27 - 30, 2012
  • Building a semantic foundation for phyloinformatics, Taxonomic Database Working Group(TDWG) 2011


Journal, Conference and Workshop Publications

  • Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach

Maryam Panahiazar, Amit P Sheth, Ajith Ranabahu, Rutger A Vos and Jim Leebens-Mack BMC Medical Genomics 2013, 6(Suppl 3):S5 doi:10.1186/1755-8794-6-S3-S5 impact factor 3.47

  • PhylOnt : A Domain-Specic Ontology for Phylogeny Analysis

Maryam Panahiazar, Ajith Ranabahu, Vahid Taslimi, Hima Yalamanchili, Arlin Stoltzfus, Jim Leebens-Mack, and Amit Sheth. IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012, 52: 1, 106-116 lower than 20% acceptance rate

  • Semantic Technology and Translational Genomic Research

Maryam Panahiazar, Amit Sheth, Ajith Ranabahu and Jim Leebens-Mack 2012 AMIA Summit on Translational Bioinformatics,arch 19, 2012 - March 21, 2012, San Francisco, CA, TBI, 2012, 176

  • Using Semantic Technologies for Phylogeny

Maryam Panahiazar, Jim Leebens-Mack, Ajith Ranabahu and Amit Sheth. 2012 AMIA Summit on Translational Bioinformatics,arch 19, 2012 - March 21, 2012, San Francisco, CA, TBI, 2012, 175

  • Building a Foundation to Enable Semantic Technologies for phylogenetically based Comparitive Analysis

Maryam Panahiazar, Rutger A Vos, Enrico Pntell, Todd Vision, Jim Leebens-Mack, 2011 Informatics for Phylogenetics, Evolution, and Biodiversity, iEvoBio 2011 , Oklahoma, USA, June 21 - 22, 2011

  • Web Service Composition using Service Suggestions

R Wang, C Guttula, Maryam Panahiazar, J Miller, et al, 2011 IEEE International Conference on Web Services- ICWS, Washington DC, July 2011 lower than 20% acceptance rate

  • Semantic Annotation and Search for resources in the next GenerationWeb with SA-REST SA-REST for Service Annotation

Ajith Ranabahu, Amit Sheth, Maryam Panahiazar, Sanjaya Wijeratne, W3C Workshop on Data and Services Integration, 2011

  • Kino: A Generic Document Management System for Biologists Using SA-REST and Faceted Search

Ajith Ranabahu, Parikh Priti, Maryam Panahiazar, Amit Sheth, Flora Logan-Klumpler, 2011 IEEE Fifth International Conference on Semantic Computing, 2011 lower than 20% acceptance rate

  • Aligning the Parasite Experiment Ontology and the Ontology for Biomedical Investigations Using

AgreementMaker Valerie Cross, Priti Parikh, Maryam Panahiazar, ICBO: Internationla Conference on Biomedical Ontology, 2011. 2-8 lower than 20% acceptance rate

  • A hybrid approache for semi-automatic ontology development with knowledge extraction from focused textual documents.

Saeed Mohammadloo, Maryam Panahiazar, Bahadorreza Ofoght, and Kambiz Badie,In proceeding of the 10th Annual CSI(Computer Society of Iran)Computer Conference, Tehran, Ir. 2005

  • A Survey of Intelligent Agents for User Modeling on the WEB and Modeling the User Behavior in Question Answering System

Maryam Panahiazar, Jafar Habibi, Maryam Karimzadegan,11th Annual Conference of Computer Society of Iran, 2006


  • Semantic Web Services Approaches

Springer Link

Pending Publications

  • MUDIDS,A Multi Dimensional Integrative Approach to Comparing Gene for Knowledge Discovery

Maryam Panahiazar, Olivier Bodenreider, Bastien Rance, Amit P. Sheth, Jim Leebens Mack, Journal of Biomedical Semantics,2013

Professional Activities

Member of

  • Member of the Semantic Web Health Care and Life Sciences (HCLS)
  • Member of the IEEE
  • Member of the W3C
  • Member of the AAAS/Science

Journal Reviewer

  • IEEE Transactions on Services Computing, 2012
  • International Journal on Semantic Web and Information Systems

Session Chair

Program committee member for the following upcoming conferences

Selected Courses

Computer Science

*Advanced Database
*Advance Topic in Semantic Web, Data Mining and Text Mining
*Advanced Software Engineering
*Advanced Computer Architecture
*Image Processing
*Advance Graphics 
*Decision Support System
*Computer Performance Evaluation
*Modeling and Computer Network
*Database System 2
*Distributed Systems
*Computational Mathematics 

Bioinformatics and Statistics

*Advanced Gene Analysis
*Algorithm for Computational Biology
*Advanced Topic in Molecular Genetics
*Genomics and Bioinformatics
*Biology for Quantitative scientist
*Application in Genomics Analysis
*Bioinformatics Application
*Statistic Analysis
*Bioinformatics Statistics 1
*Bioinformatics Statistics 2

Other Interests

*Zoomba Dancing
*listening Music, playing tar and citar
*Sky Diving

Contact Information

  • Email: <mary> at knoesis dot org
  • About me:My Interest
  • LinkedIn: Mary Panahiazar
  • Skype: maryam.panahiazar
  • Yahoo: marypanahiazar
  • Office Address: Knoesis Center, 376 Joshi Research Center, Wright State University, 3640 Colonel Glenn Hwy., Fairborn, Ohio 45435-0001
  • Phone: +1(207)478-2545