The publications below are a collection of

  • Research Papers
  • Book Chapters
  • Application Notes
  • Poster Presentations
  • Conference Talks and Papers

Research Papers

The research papers contained in this section are organized by the year in which they were published. Do note that not all the papers below have been accepted for publication; but all have been submitted for peer-review. In the cases for which they have not yet been published, I’ve added a parenthetical describing its status:

  • In Press. The paper has been accepted, but no journal particulars are available yet.
  • Re-Submitted. The paper has been submitted for peer review to a journal. No revisions have been performed as per the request of the reviewers.
  • Submitted with Revisions. The paper was reviewed, and after addressing the reviewers comments, it has been re-submitted.

If you have any questions regarding any of the papers, please contact me, and I will do my best to respond in a timely manner.


  • Valdes C, Brennan M, Dobra A, Clarke B, Clarke J. Detecting Bacterial Genomes in a Metagenomic Sample Using NGS Reads. Statistics and Its Interface. Volume 8, Number 4. pp. 477-494.
  • A.Marranci, A.Tuccoli, E. Mercoledi, M. Vitiello, C. Valdes, F. Russo, M. Dal Monte, M. Pellegrini, E. Capobianco, N.Tsinoremas, L.Poliseno (2014) Identification of BRAF 3’UTR Isoforms in Melanoma. The Journal of Investigative Dermatology 135, no. 6 (June 2015): 1694–97. doi:10.1038/jid.2015.47.


  • Clarke B, Valdes C, Dobra A, Clarke J. A Bayes Testing Approach to Metagenomic Profiling in Bacteria. Statistics and Its Interface. Volume 8, Number 2, pp. 173-185. 2015.


  • Valdes, C; P, Seo; N, Tsinoremas; & J, Clarke, ‘Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays.’. Journal of clinical bioinformatics, 3, 2013, 8.


  • Gosnik, M; Khuri, S; Valdes, C; Jiang, Z; Tsinoremas, N. ‘GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation.’. in Advances in Bioinformatics, 2011. p. 271563.


  • Mathee, K, G Narasimhan, C Valdes, X Qiu, JM Matewish, M Koehrsen, et al., ‘Dynamics of Pseudomonas aeruginosa genome evolution.’. in Proceedings of the National Academy of Sciences of the United States of America, 105, 2008, 3100–3105.


  • G. Narasimhan, K. Mathee, C. Valdes, E. Zeng, R. Olavarietta, M. Doud, P. Godfrey, M. Koehrsen, A. Rokas, C. Yandava, R. Engels, C. Kodira, B. Birren, J. Galagan, S. Lory. ‘Comparative Genomics of the Pathogen Pseudomonas aeruginosa.’ Fifth Annual RECOMB Satellite Workshop on Comparative Genomics, September 16-18, 2007.

Book Chapters


  • Valdes, C; Capobianco, E. ‘Methods to detect transcribed pseudogenes: RNA-Seq discovery allows learning through features.’. Methods in Molecular Biology, Volume 1167, 2014, pp.157–183.