José Carlos Clemente Litrán Ph.D. student (3rd year) Japan Advanced Institute for Science and Technology Genetic Knowledge Systems Laboratory [conferences]

Contact Information

Graduate School of Knowledge Science
Japan Advanced Institute of Science and Technology (JAIST)
1-1 Asahidai, Nomi-shi
Ishikawa 923-1292 JAPAN

clemente at-sign jaist dot ac dot jp

Research Interests

My research is focused on the development of computational and statistical methods for biology. More specifically, I am interested in:
• Phylogenetics & Metabolic Pathways
  
• NLP in Scientific Documents
  
• Biomedical Ontologies
  

Publications: Phylogenetics/Metabolic Pathways

• José C. Clemente and Kenji Satou and Gabriel Valiente.
  Phylogenetic Reconstruction from Non-Genomic Data
  Bioinformatics 23(2):e110-e115, 2007.
  

• José C. Clemente.
  Pathway Alignment through Context Similarity
  JAIST Research Report, KS-RR-2007-001, January 2007.
  

• José C. Clemente and Kenji Satou and Gabriel Valiente.
  Findind Conserved and Non-Conserved Reactions Using a Metabolic Pathway Alignment Algorithm
  Genome Informatics 17(2):46-56. Universal Academy Press, Tokyo. December 2006
  [paper] [sup. material]

• Jaume Casanovas and José C. Clemente and Joe Miró-Julià and Francesc Roselló and Kenji Satou and Gabriel Valiente.
  Fuzzy Clustering improves Phylogenetic Relationships Reconstruction from Metabolic Pathways
  In Proc. 11th Int. Conf. Information Processing and Management of Uncertainty in Knowledge-Based Systems, Editions EDK, pp. 2807-2814, Paris, France. July 2006.
  [paper]

• José C. Clemente and Kenji Satou and Gabriel Valiente.
  Reconstruction of Phylogenetic Relationships from Metabolic Pathways based on the Enzyme Hierarchy and the Gene Ontology
  Genome Informatics 16(2):45-55. Universal Academy Press, Tokyo. December 2005
  [paper]

Publications: NLP

• José C. Clemente and Kentaro Torisawa and Kenji Satou.
  Improving the Identification of Non-Anaphoric it using Support Vector Machines
  In Proc. of the Intl. Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 2004), Geneva, Switzerland. August 2004.
  [paper]

• José C. Clemente and Kentaro Torisawa and Kenji Satou.
  Comparison of Phrase Indexing for Biomedical and Newswire Documents
  In Proc. of IFSR 2005, Kobe, Japan. November 2005 [non-refeered].
  [paper]

Publications: Transcriptional Regulatory Rules

• Tho Hoan Pham and José C. Clemente and Kenji Satou and Tu Bao Ho.
  Computational Discovery of Transcriptional Regulatory Rules
  Bioinformatics, 21(supl. 2):ii101-ii107, September 2005. Oxford University Press.
  

• Tho Hoan Pham and José C. Clemente and Kenji Satou and Tu Bao Ho.
  Rule Evaluation Heuristics for Knowledge Discovery
  In Proc. of Knowledge Discovery and Data Management in Biomedical Science (KDDMBS 2005), pp. 29-44, Hanoi, Vietnam. May 2005.
  

Publications: Others

• José C. Clemente and Xavier Défago and Kenji Satou.
  Asynchronous peer-to-peer communication for failure resilient distributed genetic algorithms.
  In Proc. of the 15th IASTED Intl. Conf. on Parallel and Distributed Computing and Systems (PDCS 2003), pp. 769-773, Marina del Rey CA, USA. November 2003.
  [paper]

Master Thesis

• José C. Clemente.
  Resolution of Pleonastic it in Biological and Medical Documents.
  Japan Advanced Institute of Science and Technology, School of Knowledge Science, March 2004.
  (full thesis available on request)
  [abstract]

Seminars

• JAIST Natural Language Group
  
• Protein-protein Interaction