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Duke-NUS Centre for Computational Biology Faculty:

Owen John Llewellyn Rackham

Assistant Professor


Dr Rackham is an expert in the development of computational approaches for cell reprogramming and disease-gene association. His group works on ways to identify key regulators that can control cell fate in order to find novel routes for cell conversion, as well as identifying drug targets to develop new cell therapies and pharmacological treatments for human disease. He has extensive expertise in the analysis of high-throughput sequencing data, biological network analysis and statistics. He completed his PhD in complexity sciences in 2012, after which he became an MRC career development fellow at Imperial College London. In 2015 he moved to Duke-NUS Medical School as a senior research fellow and subsequently started his own group in 2016 focusing on data-driven tools for cell reprogramming and disease.

Dr Rackham has published 37 papers, has been cited over 3500 times and has an h-index of 19. His work has been the focus of patent applications, and he has founded a spin-out company Mogrify, which operates in both Australia and the UK. He is also an active member of several international consortium including the FANTOM consortium and the Human Cell Atlas.

My group is interested in what defines human cells and how their phenotype emerges from the complex interplay between the genome, transcriptome and environment. We develop methods that leverage the large volume of gene expression, epigenetic and interaction data that is being generated to develop biological hypotheses about how certain perturbations can influence the fate a cell. Our goal is to allow for the systematic identification of determinants of cell fate that can be used to further our understanding of cell biology, but also to develop new cell and gene therapies.

Publications in the last 5 years:
[1] Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen JL Rackham et al. An atlas of human long non-coding RNAs with accurate 5′ ends, Nature, 543:7644 199-204, 2017 JIF: 38

[2] Owen JL Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto. A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation, Genetics, 205:4 1443-1458, 2017 JIF: 6

[3] Kamaraj, Uma S; Gough, Julian; Polo, Jose M; Petretto, Enrico; OJL Rackham. Computational methods for direct cell conversion, Cell Cycle,1-12,2016,Taylor & Francis JIF: 4

[4] Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A Ramilowski, OJL Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair RR Forrest, Takeya Kasukawa, Hideya Kawaji Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals, Nucleic Acids Research,45,D1,D737-D743,2017,Oxford University Press JIF: 9

[5] Schafer, Sebastian; de Marvao, Antonio; Adami, Eleonora; Fiedler, Lorna R; Ng, Benjamin; Khin, Ester; OJL Rackham; van Heesch, Sebastiaan; Pua, Chee J; Kui, Miao; Titin-truncating variants affect heart function in disease cohorts and the general population, Nature Genetics,49,1,46-53,2017 JIF: 29

[6] OJL Rackham, J Firas, H Fang, ME Oates, M Holmes, A Knaupp, the FANTOM consortium, H Suzuki, C Nefzger, CO Daub, JW Shin, E Petretto, ARR Forrest, Y Hayashizaki, JM Polo, J Gough. A predictive computational framework for direct reprogramming between human cell types. Nature Genetics, 2016 (first and corresponding author) JIF: 29

[7] MR Johnson, K Shkura*, SR Langley*, A Delahaye-Duriez*, P Srivastava*, WD Hill*, OJL Rackham*, G Davies, SE Harris, A Moreno-Moral, M Rotival, D Speed, S Petrovski, A Katz, C Hayward, DJ Porteous, BH Smith, S Padmanabhan, LJ Hocking, JM Starr, DC Liewald, A Visconti, M Falchi, L Bottolo, T Rossetti, B Danis, M Mazzuferi, P Foerch, A Grote, C Helmstäedter, AJ Becker, RM Kaminski, IJ Deary, E Petretto. Systems Genetics Identifies a Convergent Gene Network for Cognitive Function and Neurodevelopmental Disease. Nature Neuroscience, 2015 (*joint second author) JIF: 16

[8] JJ Diaz-Montana*, OJL Rackham*, N Diaz-Diaz, E Petretto. Web-based Gene Pathogenicity Analysis (WGPA): A web platform to interpret gene pathogenicity from personal genome data. Bioinformatics, 2015 (*joint first author) JIF: 5

[9] V Linkeviciute, OJL Rackham, J Gough, ME Oates, H Fang. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie, 2015 (second author) JIF: 3

[10] OJL Rackham, P Dellaportas, E Petretto, L Bottolo. WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools. Bioinformatics, 2015 (first author) JIF: 5

[11] OJL Rackham, HA Shihab, MR Johnson, E Petretto. EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization. Nucleic Acids Research, 2015 (first author) JIF: 9

[12] ME Oates, J Stahlhacke, DV Vavoulis, B Smithers, OJL Rackham, AJ Sardar, J Zaucha, N Thurlby, H Fang, J Gough. The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Research, 2015 (contributing author) JIF: 9

[13] J Zaucha, J Stahlhacke, ME Oates, N Thurlby, OJL Rackham, H Fang, B Smithers, J Gough. A Proteome Quality Index. Environmental microbiology, 2015 (contributing author) JIF: 6

[14] TE Lewis, I Sillitoe, A Andreeva, TL Blundell, DWA Buchan, C Chothia, D Cozzetto, JM Dana, I Filippis, J Gough, DT Jones, LA Kelley, GJ Kleywegt, F Minneci, J Mistry, AG Murzin, B Ochoa-Montaño, ME Oates, M Punta, OJL Rackham, J Stahlhacke, MJE Sternberg, S Velankar, C Orengo. Genome3D: exploiting structure to help users understand their sequence.s Nucleic Acids Research, 2014 (contributing author) JIF: 9

[15] AJ Sardar, ME Oates, H Fang, ARR Forrest, H Kawaji, J Gough, OJL Rackham, The evolution of human cells in terms of protein innovation. Molecular biology and evolution, 2014 (corresponding author) JIF: 9

[16] FANTOM Consortium. A promoter-level mammalian expression atlas. Nature, 2014 (contributing author) JIF: 41

[17] FANTOM Consortium. An atlas of active enhancers across human cell types and tissues. Nature, 2014 (contributing author). JIF: 41

[18] Genome3D consortium. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Research, 2013 (contributing author) JIF: 9
Patents held (related or unrelated to the study) Cell Reprogramming – Application number: 2015905349. (Application filed in Australia)