Welcome

I am a faculty member in the Department of Computer Engineering at Bogazici University, and co-director of TABI (Text Analytics and Bioinformatics) Lab. I'm also a member of the AILAB. My research interests include bioinformatics, text mining, and natural language processing.

Short Bio:

I joined the Department of Computer Engineering at Bogazici University in 2011. Prior to that I worked in the Faculty of Computer and Informatics at Istanbul Technical University between 2010-2011. I received my Ph.D. degree in Computer Science and Engineering from the University of Michigan, Ann Arbor, USA in 2010. I hold an M.S. degree and a B.S. degree in Computer Engineering from Bogazici University.

Curriculum Vitae

News:

  • Ilknur Karadeniz presented "BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes" at the BioNLP Open Shared Tasks Workshop co-located with EMNLP at Hong Kong in November 2019.
  • Hakime Ozturk successfully defended her PhD thesis entitled "Text-based Machine Learning for Modelling Drug-Target Interactions" in October 2019. She will start her new position as a researcher at DKFZ (German Cancer Research Center) in December 2019.
  • Our research group obtained Tubitak 1001 grant on Chemical Language Processing for Target-based Drug Design.
  • Arzucan Ozgur gave a talk on "Drug target binding affinity prediction" at the Symposium on Biological Databases and Data Analysis at Koc University in September 2019.
  • Utku Turk presented "Improving the Annotations in the Turkish Universal Dependency Treebank" at (UDW, SyntaxFest), at Paris in August, 2019.
  • Saziye Betul Ozates presented "Turkish Treebanking: Unifying and Constructing Efforts" at the Linguistic Annotation Workshop (LAW), co-located with ACL at Florence in August, 2019.
  • Arzucan Ozgur gave a talk entitled "Biyomedikal veri icin metin isleme tekniklerinin kullanimi" at Kuzeybatida Yapay Ogrenme Yaz Okulu at Koc University in July 2019.
  • Ilknur Karadeniz successfully defended her PhD thesis entitled "Ontology-based Entity Tagging and Normalization in the Biomedical Domain." in January 2019 and started a new position as assistant professor at the Computer Engineering Department of Isik University.