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DNORM: Disease name normalization study
NCBI Disease Corpus
Medical Concepts Relations Study
Click-words Study
PubMed Logs Study
SplicePort
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Rezarta Islamaj Doğan's Research Page

Rezarta Islamaj Doğan, PhD
Staff Scientist
NCBI, NLM, NIH
8600 Rockville Pike
Building 38A,6S-614E
Bethesda, MD 20894

Tel: (1) (301) 435 8769
Email: Rezarta.Islamaj AT nih.gov

PhD, Computer Science,
   University of Maryland at College Park, USA, 2007

Online CV
Research Interests:

  • Construction of linguistic resources to support biological text mining
  • Building tools that facilitate information retrieval and knowledge extraction from biomedical literature
  • Machine learning, data mining, feature generation

Selected Publications:

NCBI Disease Corpus: A Resource for Disease Name Recognition and Concept Normalization.
with Robert Leaman and Zhiyong Lu
J Biomed Inform 2014. PubMed-link

Author name disambiguation for PubMed
with Wanli Liu, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu andW. John Wilbur
Journal of the Association for Information Science and Technology 2014. JASIST-link

DNorm: disease name normalization with pairwise learning to rank.
with Robert Leaman and Zhiyong Lu
Bioinformatics 2013. PubMed-link

BioC: a minimalist approach to interoperability for biomedical text processing.
with Don Comeau, Paolo Ciccarese, Kevin Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Tom Wiegers, Cathy Wu, and John Wilbur.
DATABASE 2013. PubMed-link

Reports on the 2012 AAAI Fall Symposium series
with Yolanda Gil, Haym Hirsh, Narayanan Krishnan, Michael Lewis, Cetin Mericli, Parisa Rashidi, Victor Raskin, Samarth Swarup, Wei Sun, Julia Taylor and Lana Yeganova
AI Magazine Spring 2013. AI-digital

A context-blocks model for identifying clinical relationships in patient records
with Aurélie Névéol and Zhiyong Lu
BMC Bioinformatics 2011. BMC Bioinformatics-link

Click-words: Learning to Predict Document Keywords from a User Perspective
with Zhiyong Lu
Bioinformatics 2010. Article in PubMed Central

Extracting Rx Information from Clinical Narrative
with James G. Mork, Olivier Bodenreider, Dina Demner-Fushman, François-Michel Lang, Zhiyong Lu,
Aurélie Névéol, Lee Peters, Sonya E. Shooshan and Alan R. Aronson
JAMIA 2010. JAMIA-link to fulltext

Understanding PubMed® user search behavior through log analysis
with G. Craig Murray, Aurélie Névéol, and Zhiyong Lu
Database, 2009. Article in PubMed Central

Features Generated for Computational Splice-Site Prediction Correspond
to Functional Elements

with Lise Getoor, W. John Wilbur and Stephen M. Mount
BMC Bioinformatics, 2007. Article in PubMed Central

SplicePort: An Interactive Splice-Site Analysis Tool
with Lise Getoor, W. John Wilbur and Stephen M. Mount
Nucleic Acids Research, 2007.Article in PubMed Central

A Feature Generation Algorithm with Applications to Biological Sequence Classification
with Lise Getoor and W. John Wilbur
Chapter in Computational Methods of Feature Selection, Huan Liu and Hiroshi Motoda editors, 2007. SPRINGER-link

Structural footprinting in protein structure comparison: The impact of structural fragments.
with Elena Zotenko, W. John Wilbur, Diane P. O'Leary and Teresa M. Przytycka
BMC Structural Biology, 2007.Article in PubMed Central

All Publications

Revised: May14, 2012.


New:

ISMB 2014 Highlights talk on BioC

Program

Talk


BIOC:

Interoperability for Biomedical Text Processing

BioC.SourceForge.Net


CORPORA

BioC-PMC Full Text Corpus
Paper and Data


Abbreviation definitions in biomedical literature
Paper and Data


NCBI Disease Corpus
Paper and Data


Past Events:

BioCreative IV Workshop Proceedings


Information Retrieval and Knowledge Discovery in Biomedical Text at AAAI Fall Symposia 2012 Proceedings


Machine Learning for Biomedical Literature Analysis and Text Retrieval at ICMLA 2011 Journal of Biomedical Semantics Issue


BMC Bioinformatics Supplement on Machine Learning for Biomedical Text Analysis BMC Bioinformatics issue