Fabio Gori PhD Student of Machine Learning Group Intelligent Systems Section Institute for Computing and Information Sciences (ICIS) Faculty of Science Radboud University Nijmegen Research Publications Tools and Programs Contacts Other

Research

Current Research Activities

I am working on Machine Learning for Metagenomics Data Analysis.
My supervisor is Elena Marchiori; my co-promoters are Mike Jetten (Microbiology Department - Radboud University Nijmegen) and Tom Heskes. From September 2010 to May 2011, I was in charge of Machine Learning group weekly colloquium.

Research Interests

1. Machine Learning for Metagenomics Data Analysis
2. Constrained Optimization Theory and Image Space analysis

Publications

Journal Papers

• Fabio Gori, Susannah G.  Tringe, Gianluigi Folino, Sacha A. F. T.  van Hijum, Huub J. M.  Op den Camp, Mike S. M. Jetten, and Elena Marchiori.
  Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.
  BMC Genomics, volume 14, page 7. 2013. doi:10.1186/1471-2164-14-7 Open Access article


• Fabio Gori, Susannah G. Tringe, Boran Kartal, Elena Marchiori and Mike S. M. Jetten.
  The metagenomic basis of anammox metabolism in Candidatus ‘Brocadia fulgida’.
  Biochemical Society Transaction, volume 39, issue 6, pages 1799-1804. 2011. doi:10.1042/BST20110707 Article


• Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, and Elena Marchiori.
  MTR: Taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.
  Bioinformatics, volume 27, issue 2, pages 196-203. Oxford Journals, 2011. Open Access article, Code

Conference Papers

• Fabio Gori, Dimitrios Mavroeidis, Mike S. M. Jetten, and Elena Marchiori.
  Genomic signatures for metagenomic data analysis: exploiting the reverse complementarity of tetranucleotides.
  5th IEEE International Conference on Systems Biology (ISB 2011). Accepted Manuscript, Online Supplementary Material


• Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, and Elena Marchiori.
  Evidence-based clustering of reads and taxonomic analysis of metagenomic data.
  In Pattern Recognition in Bioinformatics, 4th IAPR International Conference, PRIB 2009, Sheffield, UK, September 7-9, 2009. Proceedings, volume 5780 of Lecture Notes in Computer Science, pages 102-112. Springer, 2009. Download PDF


• Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, and Elena Marchiori.
  Clustering metagenome short reads using weighted proteins.
  In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 7th European Conference, EvoBIO 2009, Tübingen, Germany, April 15-17, 2009, Proceedings, volume 5483 of Lecture Notes in Computer Science, pages 152-163. Springer, 2009. Download PDF, Code
  

Tools and Programs

• Greedy Set Cover Problem (SCP) algorithm for MATLAB MATLAB Central page
• MTR: Bioinformatics 2010 Paper, Code
• GWproxy: EvoBIO 2009 Paper, Code

Contacts

Other

Machine Learning Group Colloquium

Machine Learning Group Colloquium - Aug/Dec 2011

Machine Learning Group Colloquium - Jan/Jul 2011

Machine Learning Group Colloquium - 2010