Data integration, analysis of integrated biological networks and disease stratification.

Dr Mansoor Saqi is Head of Translational Bioinformatics at the Biomedical Research Centre at Guys and St Thomas’s and Kings College London.  He has held positions at the Data Sciences Institute, Imperial College London, and at the CNRS (EISBM, Lyon). Previous to that he was a Principal Investigator in Bioinformatics at the Centre for Computational and Systems Biology at Rothamsted Research, UK, and before that he was a Senior Lecturer in Bioinformatics at Barts and The London School of Medicine. His research interests include data integration, analysis of integrated biological networks and disease stratification. He was co-organiser of Machine Learning in Medicine and Healthcare workshop at the Knowledge Discovery and Data Mining conference, KDD 2018, and a member of the Program Committee for ISMB/ECCB 2019 bioinformatics conference, Basel.

Selected Publications 

Emam I, Elyasigomari V, Matthews A, Pavlidis S, Rocca-Serra P, Guitton F, Verbeeck D, Grainger L, Borgogni E, Del Giudice G, Saqi M, Houston P, Guo Y. PlatformTM, a standards-based data custodianship platform for translational medicine research. Sci Data. 2019 Aug 13;6(1):149.

Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps:community-driven comprehensive representation of disease mechanisms. NPJ Syst Biol Appl. 2018 Jun 2;4:21.

De Meulder B, Lefaudeux D, Bansal AT, Mazein A, Chaiboonchoe A, Ahmed H, Balaur I, Saqi M, Pellet J, Ballereau S, Lemonnier N, Sun K, Pandis I, Yang X, Batuwitage M, Kretsos K, van Eyll J, Bedding A, Davison T, Dodson P, Larminie C, Postle A, Corfield J, Djukanovic R, Chung KF, Adcock IM, Guo YK, Sterk PJ, Manta A, Rowe A, Baribaud F, Auffray C; U-BIOPRED Study Group and the eTRIKS Consortium. A computational framework for complex disease stratification from multiple large-scale datasets. BMC Syst Biol. 2018 May 29;12(1):60.

Saqi M, Lysenko A, Guo YK, Tsunoda T, Auffray C. Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. Brief Bioinform. 2019 Mar 25;20(2):609-623.

Balaur I, Mazein A, Saqi M, Lysenko A, Rawlings CJ, Auffray C. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinformatics. 2017 Apr 1;33(7):1096-1098.

Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C. STON: exploring biological pathways using the SBGN standard and graph databases. BMC Bioinformatics. 2016 Dec 5;17(1):494. PubMed PMID: 27919219; PubMed Central PMCID: PMC5139139.

Balaur I, Saqi M, Barat A, Lysenko A, Mazein A, Rawlings CJ, Ruskin HJ, Auffray C. EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. J Comput Biol. 2017 Oct;24(10):969-980.

Lysenko A, Roznovăţ IA, Saqi M, Mazein A, Rawlings CJ, Auffray C. Representing and querying disease networks using graph databases. BioData Min. 2016 Jul 25;9:23.

Saqi M, Pellet J, Roznovat I, Mazein A, Ballereau S, De Meulder B, Auffray C. Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness. Methods Mol Biol. 2016;1386:43-60.

Rudd JJ, Kanyuka K, Hassani-Pak K, Derbyshire M, Andongabo A, Devonshire J, Lysenko A, Saqi M, Desai NM, Powers SJ, Hooper J, Ambroso L, Bharti A, Farmer A, Hammond-Kosack KE, Dietrich RA, Courbot M. Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. Plant Physiol. 2015 Mar;167(3):1158-85.

Habash DZ, Baudo M, Hindle M, Powers SJ, Defoin-Platel M, Mitchell R, Saqi M, Rawlings C, Latiri K, Araus JL, Abdulkader A, Tuberosa R, Lawlor DW, Nachit MM. Systems responses to progressive water stress in durum wheat. PLoS One. 2014 Sep 29;9(9):e108431.

Dobson RJ, Munroe PB, Caulfield MJ, Saqi MA. Protein interaction networks associated with cardiovascular disease and cancer: exploring the effect of bias on shared network properties. Int J Data Min Bioinform. 2014;9(4):339-57. PubMed PMID: 25757244.

Lysenko A, Urban M, Bennett L, Tsoka S, Janowska-Sejda E, Rawlings CJ, Hammond-Kosack KE, Saqi M. Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum. PLoS One. 2013 Jul 4;8(7):e67926.

Lysenko A, Defoin-Platel M, Hassani-Pak K, Taubert J, Hodgman C, Rawlings CJ, Saqi M. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics. 2011 May 25;12:203.