Owen J. L. Rackham

firefox I am an enthusiastic research scientist whose main interests are in the application of mathematics and complex systems thinking to big data problems. My current research is focused on the application of machine learning and graph theory in the field of regenerative medicine. The current era of biology is having to deal with vast quantities of data and I feel that its the role of computer scientists and bioinformaticians to work in unison with biologists to get the most out of this data in a efficient and meaningful way. I am currently working with the RIKEN omics sciences centre in Japan on identifying transcription factors for directed re-programming of cells, focusing on gaining a network level understanding the regulation involved in this process. We hope to one day be able to create any human cell type from any other as this would have huge medical implications. Our work is being supported by a JSPS short term award which will enable me to work in Japan for a period of 4 months at the beginning of 2011.

As well as my academic work two colleagues and myself have embarked on a company called emergent analytics. This is a venture that aims to take the lessons from bioinformatics (the original big data field) and apply it to the rapidily advancing area of data science. Many important lessons have already been learnt about dealing with large data including pattern identification, network construction and time series analysis. We hope to make the tools developed over the last 20 years of research available to the business community.


Academic History

Post Doctoral Researcher
Predicting the transcription factors that facilitate cell reprogramming University of Bristol (2012-04-10)

Ph.D. in Complexity Sciences
PhD Title: Understanding and controlling the multiscale dynamics of the cell University of Bristol (2008-07-13)

Awarded (Merit):
Complexity Sciences MRes University of Bristol (2008-07-12)

Awarded (Distinction):
Natural Computation MSc Birmingham University (2007-09-01)

Awarded (first class with honours):
Computer Science BSc Exeter University (2005-07-12)


Awarded (outreach award):
STEM University Department of the Year STEM Ambassadors (South-West Region) (2012-09-26)

Awarded (4 month fellowship):
JSPS Short Term Award JSPS (value: approx £15K) (2010-09-08)

Awarded (travel fellowship):
Roberts Fund Travel Award Roberts Trust (value: £500) (2010-06-10)

Appointed as:
NOISEmaker EPSRC (2010-04-22)

Awarded (1 year EPSRC scholarship):
EPRSC masters scholarship EPSRC (2006-09-01)

Journal Articles

Adam Sardar, Matt Oates, Hai Fang, Alistair R.R. Forrest, Hideya Kawaji, David Morais, The FANTOM Consortium, Julian Gough, Owen J.L. Rackham.
The Evolution of cell type in terms of protein innovation Molecular Biology and Evolution (2013-05-29)

Owen. J. L. Rackham, Hai Fang, Jay Shin, Alistair Forrest, Julian Gough
Mogrify: Defining Factors For Direct Reprogramming Between All Cell Types under review (2013-05-29)

Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada,cIlka Hoof,Jette Bornholdt,Mette Boyd,Yun Chen,Xiaobei Zhao,Christian Schmidl,Takahiro Suzuki,Evgenia Ntini,Erik Arner,Eivind Valen,Kang Li,Lucia Schwarzfischer,Dagmar Glatz,Johanna Raithel,Berit Lilje,Nicolas Rapin,Frederik Otzen Bagger,Mette Jĝrgensen,Peter Refsing Andersen,Nicolas Bertin,Owen Rackham,A. Maxwell Burroughs,J. Kenneth Baillie, Yuri Ishizu,Yuri Shimizu,Erina Furuhata,Shiori Maeda,Yutaka Negishi,Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann,Masayoshi Itoh,Hideya Kawaji,Naoto Kondo,Jun Kawai,Andreas Lennartsson,Carsten O. Daub,Peter Heutink,David A. Hume,Torben Heick Jensen,Harukazu Suzuki,Yoshihide Hayashizaki,Ferenc Müller,The FANTOM Consortium,Alistair R. R. Forrest,Piero Carninci,Michael Rehli & Albin Sandelin
An atlas of active enhancers across human cell types and tissues Nature (2013-05-29)

Alistair R.R. Forrest, Hideya Kawaji, Michael Rehlil, J. Kenneth Baillie, Michiel J.L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio...(author list shortened for convenience) Owen J. L. Rackham and FANTOM Consortium (middle author)
A promoter level mammalian expression atlas Nature (2013-05-29)

Hai Fang, Matt Oates, Ralph Pethica, Jenny Greenwood, Adam Sardar, Owen J.L. Rackham, Alexandros Stamatakis, David A. de Lima Morais & Julian Gough
A daily-updated tree of (sequenced) life as a reference for genome research Scientific Reports (2013-05-15)

Lewis, T. E., Sillitoe, I., Andreeva, A., Blundell, T. L., Buchan, D. W. A., Chothia, C., Cuff, A, Dana, J. Filippis,I, Gough,J. Hunter,S. Jones,D. Kelley,L. Kleywegt,G. Minneci,F. Mitchell,A. Murzin, A. Ochoa-Montano, B. Owen J. L. Rackham, Smith,J. Sternberg, M. Velankar, S. Yeats, C. Orengo, C
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. NAR (2013-01-10)

Edward Gasson, Mark SIddall, Daniel J. Lunt, Owen J. L. Rackham, Caroline H. Lear, David Pollard
Exploring uncertainties in the relationship between temperature and sea level over the past 50 million years Reviews of Geophysics (2012-01-19)

David de Lima Morais, Hai Fang, Owen J L Rackham, Derek Wilson, Ralph Pethica, Cyrus Chothia, Julian Gough.
SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic acids research (2010-10-21)

Owen J.L. Rackham, Martin Madera, Craig T. Armstrong, Thomas L. Vincent, Derek N. Woolfson and Julian Gough
The Evolution and Structure Prediction of Coiled Coils Across All Genomes. Journal of Molecular Biology (2010-08-10)

Owen J.L. Rackham, Tsaneva-Atanasova K, Ganesh A and Mellor JR
A Ca2+-based computational model for NMDA receptor-dependent synaptic plasticity at individual post-synaptic spines in the hippocampus Frontiers in Synaptic Neuroscience (2010-06-21)

Conference Proceedings

Rackham O.J.L Yao X.
The multi-ant ACO algorithm for the winter road salting problem UK Workshop on Computational Intelligence 2007 (2007-07-01)

Invited talks

Rackham O.J.L
Spiricoil : The next step in studying evolution and structure prediction of coiled coils International Workshop on Coiled-coils, Collegen and Co-proteins (2009-10-06)

Poster presentation

Owen J.L. Rackham, Martin Madera, Craig T. Armstrong, Thomas L. Vincent, Derek N. Woolfson and Julian Gough
Spiricoil: Online resource for coiled-coil prediction International Workshop on Coiled-coils, Collegen and Co-proteins (2009-11-06)

Owen J.L. Rackham, Martin Madera, Craig T. Armstrong, Thomas L. Vincent, Derek N. Woolfson and Julian Gough
Coiled coil genome annotation: prediction, structure, and evolutionary Past ISMB (2009-06-27)

Schools/Conferences Attended

Conference attended:
Systems Biology: Networks Wellcome Trust, Hinxton (2010-08-11)

Conference attended:
Statistical modelling and inference for networks (Statworks) Bristol (2010-06-28)

Summer school attended:
Statistical Inference in Computational Biology Edinburgh e-Science Institute (2010-06-14)

Summer school attended:
RNAs: structure, function and therapy Lipari school (2009-06-13)

Conference attended:
Regional Meeting on Mathematics, Computation and Biology Bristol (2009-06-02)

Winter school attended:
UK-Japan Winter School - Complexity and Dynamics Bath (2009-01-08)

Conference attended:
Regional Meeting on Mathematics, Computation and Biology HP labs, Bristol (2008-06-24)

Conference attended:
From Molecules to Human Societies Imperial College London (2008-05-07)

Training course attended:
HECTOR: Intro to MPI Hector

Training course attended:
Team building EPSRC


Module assistant:
Databases Bristol University (2010-01-01)

Helpdesk Advisor:
Predictive Life Sciences Mathematical Helpdesk Bristol University (2009-09-01)

Module Coordinator:
Advanced research skills Bristol University

Public Engagement / Media

Press coverage Bristol Evening Post (2010-08-09)

Press coverage Bath Chronicle (2010-08-07)

Science Area Compere / Exhibitor Greenman Music Festival (2010-07-20)

Science busking training EPRSC (2010-07-05)

Exhibitor for NOISE Cheltenham Science Festival (2010-06-09)

Media traing EPRSC

Advanced media training EPSRC

Reviewer PLoS Computational Biology

Reviewer Biomolecular concepts