New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. - Purvesh Khatri; Valmik Desai; Adi L. Tarca; Sivakumar Sellamuthu; Derek E. Wildman; Roberto Romero; Sorin Draghici (Nucleic Acids Res., 2006)

A System Biology Approach for the Steady-State Analysis of Gene Signaling Networks. - Purvesh Khatri; Sorin Draghici; Adi L. Tarca; Sonia S. Hassan; Roberto Romero (CIARP, 2007)

Onto-Tools: new additions and improvements in 2006. - Purvesh Khatri; Calin Voichita; Khalid Kattan; Nadeem Ansari; Avani Khatri; Constantin Georgescu; Adi L. Tarca; Sorin Draghici (Nucleic Acids Res., 2007)

Machine Learning and Its Applications to Biology. - Adi L. Tarca; Vincent J. Carey; Xue-wen Chen 001; Roberto Romero; Sorin Draghici (PLoS Comput. Biol., 2007)

KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours. - Sorin Draghici; Adi L. Tarca; Longfei Yu; Stephen Ethier; Roberto Romero (Bioinform., 2008)

A novel signaling pathway impact analysis. - Adi L. Tarca; Sorin Draghici; Purvesh Khatri; Sonia S. Hassan; Pooja Mittal; Jung-Sun Kim; Chong Jai Kim; Juan Pedro Kusanovic; Roberto Romero (Bioinform., 2009)

Down-weighting overlapping genes improves gene set analysis. - Adi L. Tarca; Sorin Draghici; Gaurav Bhatti; Roberto Romero (BMC Bioinform., 2012)

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. - Adi L. Tarca; Mario Lauria; Michael Unger; Erhan Bilal; Stéphanie Boué; Kushal Kumar Dey; Julia Hoeng; Heinz Koeppl; Florian Martin 002; Pablo Meyer 001; Preetam Nandy; Raquel Norel; et al. (Bioinform., 2013)

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. - Adel Dayarian; Roberto Romero; Zhiming Wang; Michael Biehl; Erhan Bilal; Sahand Hormoz; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Gyan Bhanot; Feng Luo 001; Adi L. Tarca (Bioinform., 2015)

Inter-species pathway perturbation prediction via data-driven detection of functional homology. - Christoph Hafemeister; Roberto Romero; Erhan Bilal; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Richard Bonneau; Adi L. Tarca (Bioinform., 2015)