PdbMotif–a tool for the automatic identification and display of motifs in protein structures. - Mansoor A. S. Saqi; Roger A. Sayle (Comput. Appl. Biosci., 1994)

PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure. - Roger A. Sayle; Mansoor A. S. Saqi; M. Weir; Andrew Lyall (Comput. Appl. Biosci., 1995)

DSC: public domain protein secondary structure predication. - Ross D. King; Mansoor A. S. Saqi; Roger A. Sayle; Michael J. E. Sternberg (Comput. Appl. Biosci., 1997)

Protein analyst - a distributed object environment for protein sequence and structure analysis. - Mansoor A. S. Saqi; David L. Wild; M. J. Hartshorn (Bioinform., 1999)

Spectral clustering of protein sequences. - Alberto Paccanaro; Chakra Chennubhotla 001; James A. Casbon; Mansoor A. S. Saqi (IJCNN, 2003)

Analysis of superfamily specific profile-profile recognition accuracy. - James A. Casbon; Mansoor A. S. Saqi (BMC Bioinform., 2004)

S4: structure-based sequence alignments of SCOP superfamilies. - James A. Casbon; Mansoor A. S. Saqi (Nucleic Acids Res., 2005)

A high level interface to SCOP and ASTRAL implemented in Python. - James A. Casbon; Gavin E. Crooks; Mansoor A. S. Saqi (BMC Bioinform., 2006)

On single and multiple models of protein families for the detection of remote sequence relationships. - James A. Casbon; Mansoor A. S. Saqi (BMC Bioinform., 2006)

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. - Richard J. B. Dobson; Patricia B. Munroe; Mark J. Caulfield; Mansoor A. S. Saqi (BMC Bioinform., 2006)

Functional diversity within protein superfamilies. - James A. Casbon; Mansoor A. S. Saqi (J. Integr. Bioinform., 2006)

Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins. - Richard J. B. Dobson; Patricia B. Munroe; Charles A. Mein; Mark J. Caulfield; Mansoor A. S. Saqi (BIRD, 2008)

Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. - Artem Lysenko; Matthew Morritt Hindle; Jan Taubert; Mansoor A. S. Saqi; Christopher J. Rawlings (Briefings Bioinform., 2009)

Global sequence properties for superfamily prediction: a machine learning approach. - Richard J. B. Dobson; Patricia B. Munroe; Mark J. Caulfield; Mansoor A. S. Saqi (J. Integr. Bioinform., 2009)

An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching. - Mansoor A. S. Saqi; Richard J. B. Dobson; Preben Kraben; David A. Hodgson; David L. Wild (J. Integr. Bioinform., 2009)

Handling Missing Features with Boosting Algorithms for Protein-Protein Interaction Prediction. - Fabrizio Smeraldi; Michael Defoin-Platel; Mansoor A. S. Saqi (DILS, 2010)

AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations. - Michael Defoin-Platel; Matthew Morritt Hindle; Artem Lysenko; Stephen J. Powers; Dimah Z. Habash; Christopher J. Rawlings; Mansoor A. S. Saqi (BMC Bioinform., 2011)

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. - Artem Lysenko; Michael Defoin-Platel; Keywan Hassani-Pak; Jan Taubert; Charlie Hodgman; Christopher J. Rawlings; Mansoor A. S. Saqi (BMC Bioinform., 2011)

Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum. - Laura Bennett; Artem Lysenko; Lazaros G. Papageorgiou; Martin Urban; Kim E. Hammond-Kosack; Christopher J. Rawlings; Mansoor A. S. Saqi; Sophia Tsoka (CMSB, 2012)

Integrating Multiple Studies of Wheat Microarray Data to Identify Treatment-Specific Regulatory Networks. - Valeria Bo; Artem Lysenko; Mansoor A. S. Saqi; Dimah Z. Habash; Allan Tucker (IDA, 2013)

Protein interaction networks associated with cardiovascular disease and cancer: exploring the effect of bias on shared network properties. - Richard J. B. Dobson; Patricia B. Munroe; Mark J. Caulfield; Mansoor A. S. Saqi (Int. J. Data Min. Bioinform., 2014)

Representing and querying disease networks using graph databases. - Artem Lysenko; Irina A. Roznovat; Mansoor A. S. Saqi; Alexander Mazein; Christopher J. Rawlings; Charles Auffray (BioData Min., 2016)

STON: exploring biological pathways using the SBGN standard and graph databases. - Vasundra Touré; Alexander Mazein; Dagmar Waltemath; Irina Balaur; Mansoor A. S. Saqi; Ron Henkel; Johann Pellet; Charles Auffray (BMC Bioinform., 2016)

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. - Irina Balaur; Alexander Mazein; Mansoor A. S. Saqi; Artem Lysenko; Christopher J. Rawlings (Bioinform., 2017)

EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. - Irina Balaur; Mansoor A. S. Saqi; Ana Barat; Artem Lysenko; Alexander Mazein; Christopher J. Rawlings; Heather J. Ruskin; Charles Auffray (J. Comput. Biol., 2017)

A computational framework for complex disease stratification from multiple large-scale datasets. - Bertrand De Meulder; Diane Lefaudeux; Aruna T. Bansal; Alexander Mazein; Amphun Chaiboonchoe; Hassan Ahmed; Irina Balaur; Mansoor A. S. Saqi; Johann Pellet; Stéphane Ballereau; Nathanaël Lemonnier; Kai Sun 005; et al. (BMC Syst. Biol., 2018)

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. - Mansoor A. S. Saqi; Artem Lysenko; Yike Guo; Tatsuhiko Tsunoda; Charles Auffray (Briefings Bioinform., 2019)