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G. Menschaert, X. Wang, AR. Jones, F. Ghali, D. Fenyö, et al. V. Olexiouk, B. Zhang, EW. Deutsch, T. Ternent, JA. Vizcaíno. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19(1),
JA. Vizcaíno, G. Mayer, SR. Perkins, H. Barsnes, M. Vaudel, et al. Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, J. Rappsilber, E. Netz, M. Walzer, O. Kohlbacher, A. Leitner, RJ. Chalkley, F. Ghali, S. Martínez-Bartolomé, EW. Deutsch, AR. Jones. (2017). The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 16(7), pp.1275-1285.
F. Ghali, AR. Jones (2016). Proteogenomics: Proteomics for Genome Annotation. In: Proteome Informatics. The Royal Society of Chemistry, pp.365-384.
F. Ghali, R. Krishna, S. Perkins, A. Collins, D. Xia, et al. J. Wastling, AR. Jones. (2014). ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards. PROTEOMICS. 14(23-24), pp.2731-2741.
F. Ghali, R. Krishna, P. Lukasse, S. Martínez-Bartolomé, F. Reisinger, et al. H. Hermjakob, JA. Vizcaíno, AR. Jones. (2013). Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML. Molecular & Cellular Proteomics. 12(11), pp.3026-3035.
A. Cristea, F. Ghali, M. Joy (2011). Social, Personalized Lifelong Learning Personalized Lifelong Learning Personalized Lifelong Learning. IGI,
F. Ghali, AI. Cristea (2009). Social reference model for adaptive web learning. In: International Conference on Web-Based Learning. Springer Berlin Heidelberg, pp.162-171.
G. Menschaert, X. Wang, AR. Jones, F. Ghali, D. Fenyö, et al. V. Olexiouk, B. Zhang, EW. Deutsch, T. Ternent, JA. Vizcaíno. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19(1),
JA. Vizcaíno, G. Mayer, SR. Perkins, H. Barsnes, M. Vaudel, et al. Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, J. Rappsilber, E. Netz, M. Walzer, O. Kohlbacher, A. Leitner, RJ. Chalkley, F. Ghali, S. Martínez-Bartolomé, EW. Deutsch, AR. Jones. (2017). The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 16(7), pp.1275-1285.
J. Fan, S. Saha, G. Barker, KJ. Heesom, F. Ghali, et al. AR. Jones, DA. Matthews, C. Bessant. (2015). Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*. Molecular & Cellular Proteomics. 14(11), pp.3087-3093.
B. Wen, C. Du, G. Li, F. Ghali, AR. Jones, et al. L. Käll, S. Xu, R. Zhou, Z. Ren, Q. Feng, X. Xu, J. Wang. (2015). IPeak: An open source tool to combine results from multiple MS/MS search engines. PROTEOMICS. 15(17), pp.2916-2920.
R. Krishna, D. Xia, S. Sanderson, A. Shanmugasundram, S. Vermont, et al. A. Bernal, G. Daniel‐Naguib, F. Ghali, BP. Brunk, DS. Roos, JM. Wastling, AR. Jones. (2015). A large‐scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum. PROTEOMICS. 15(15), pp.2618-2628.
F. Ghali, R. Krishna, S. Perkins, A. Collins, D. Xia, et al. J. Wastling, AR. Jones. (2014). ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards. PROTEOMICS. 14(23-24), pp.2731-2741.
SL. Seymour, T. Farrah, P. Binz, RJ. Chalkley, JS. Cottrell, et al. BC. Searle, DL. Tabb, JA. Vizcaíno, G. Prieto, J. Uszkoreit, M. Eisenacher, S. Martínez‐Bartolomé, F. Ghali, AR. Jones. (2014). A standardized framing for reporting protein identifications in mzIdentML 1.2. PROTEOMICS. 14(21-22), pp.2389-2399.
J. Griss, AR. Jones, T. Sachsenberg, M. Walzer, L. Gatto, et al. J. Hartler, GG. Thallinger, RM. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan, F. Reisinger, Q-W. Xu, N. del Toro, Y. Pérez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, JA. Vizcaíno, H. Hermjakob. (2014). The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience. Molecular & Cellular Proteomics. 13(10), pp.2765-2775.
F. Ghali, R. Krishna, P. Lukasse, S. Martínez-Bartolomé, F. Reisinger, et al. H. Hermjakob, JA. Vizcaíno, AR. Jones. (2013). Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML. Molecular & Cellular Proteomics. 12(11), pp.3026-3035.
JA. Medina‐Aunon, R. Krishna, F. Ghali, JP. Albar, AJ. Jones (2013). A guide for integration of proteomic data standards into laboratory workflows. PROTEOMICS. 13(3-4), pp.480-492.
F. Ghali, R. Krishna, P. Lukasse, S. Martinez-Bartolome, F. Reisinger, et al. H. Hermjakob, JA. Vizcaino, AR. Jones. (2013). A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator. Molecular & Cellular Proteomics. pp.mcp-O113.
D. Xia, F. Ghali, SJ. Gaskell, R. O'Cualain, PFG. Sims, et al. AR. Jones. (2012). Software for analysing ion mobility mass spectrometry data to improve peptide identification. PROTEOMICS. 12(12), pp.1912-1916.
F. Reisinger, R. Krishna, F. Ghali, D. Ríos, H. Hermjakob, et al. J. Antonio Vizcaíno, AR. Jones. (2012). jmz
S. Kluge, M. Hoffmann, D. Benndorf, E. Rapp, U. Reichl, et al. J. Merl, M. Ueffing, SM. Hauck, C. von Toerne, D. Xia, . others. (2012). Cell Biology. Proteomics. 12, pp.1893-2064.
AI. Cristea, F. Ghali (2011). Towards adaptation in e-learning 2.0. New Review of Hypermedia and Multimedia. 17(2), pp.199-238.
AI. Cristea, F. Ghali, M. Joy (2011). Social, personalized lifelong learning. E-infrastructures and technologies for lifelong learning: Next generation environments. pp.90-125.
F. Ghali, AR. Jones (2016). Proteogenomics: Proteomics for Genome Annotation. In: Proteome Informatics. The Royal Society of Chemistry, pp.365-384.
A. Cristea, F. Ghali, M. Joy (2011). Social, Personalized Lifelong Learning Personalized Lifelong Learning Personalized Lifelong Learning. IGI,
F. Ghali, AI. Cristea (2009). Authoring for e-learning 2.0: A case study. In: 2009 Ninth IEEE International Conference on Advanced Learning Technologies. IEEE, pp.170-174.
F. Ghali, AI. Cristea (2009). MOT 2.0: A Case Study on the Usefuleness of Social Modeling for Personalized E-Learning Systems. In: AIED. pp.333-340.
F. Ghali, AI. Cristea (2009). Social reference model for adaptive web learning. In: International Conference on Web-Based Learning. Springer Berlin Heidelberg, pp.162-171.
F. Ghali, AI. Cristea (2008). Interoperability between MOT and learning management systems: converting CAF to IMS QTI and IMS CP. In: International Conference on Adaptive Hypermedia and Adaptive Web-Based Systems. Springer Berlin Heidelberg, pp.296-299.
F. Ghali, AI. Cristea (2008). Evaluation of interoperability between MOT and regular learning management systems. In: European Conference on Technology Enhanced Learning. Springer Berlin Heidelberg, pp.104-109.
F. Ghali, AI. Cristea (2008). EVALUATION OF AUTHORING FOR ADAPTATION AND DELIVERY VIA LEARNING MANAGEMENT SYSTEMS. In: Proceedings of the 11th IASTED International Conference. pp.14-14.
F. Ghali, M. Sharp, AI. Cristea (2008). Folksonomies and ontologies in authoring of adaptive hypermedia. In: A3H: Sixth International Workshop on Authoring of Adaptive and Adaptable Hypermedia. pp.5-5.
T. Gross, F. Ghali, A. Cristea (2008). Communication and Collaboration Towards Problem Solving: Evaluation of PILS. In: 3rd European Conference on Technology Enhanced Learning EC-TEL 2008, IGACLE workshop. Maastricht, The Netherlands.
F. Ghali, AI. Cristea, C. Stewart, M. Hendrix (2008). Collaborative adaptation authoring and social annotation in MOT. In: A3H: Sixth International Workshop on Authoring of Adaptive and Adaptable Hypermedia. pp.54-54.
F. Ghali, AI. Cristea, C. Stewart (2008). My online teacher 2.0.
F. Ghali, J. Foss User Guide on the Concept Adaptation Model Tool. University of Warwick
T. Ternent, F. Ghali, D. Fenyo, AR. Jones, JA. Vizcaíno (2016). proBed: extension of the BED format for mapping peptides identified by mass spectrometry to a genome.