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Gordon Stephen

Staff picture: Gordon Stephen
Information and Computational Sciences
Information and Computational Sciences
Bioinformaticist
Gordon.Stephen@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

I am a software developer who graduated with a 1st Class BSc (Hons) in Applied Computing from the University of Dundee. Since joining the Institute in the summer of 2009 I have been working on software tools for the visualization of biological data.

Current research interests

Currently my research focuses on the design and development of software tools – primarily visualization programs – including: Tablet for next generation sequencing data, Flapjack for graphical genotyping and CurlyWhirly for viewing 3D graphs with a particular focus on the outputs of principal coordinates analysis.

Past research

  • April 2011 – present: Bioinformatics Software Developer, Information and Computational Sciences – James Hutton Institute.
  • August 2009 – April 2011: Java Programmer, Genetics Programme – (SCRI) Scottish Crop Research Institute.

Bibliography

  • Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Caprez, A.; Batut, B.; Haudgaard, M.; Cokelaer, T.; Beauchamp, K.A.; Pedersen, B.S.; Hoogstrate, Y.; Bretaudeau, A.; Ryan, D.; Le Corguillé, G.; Yusuf, D.; Luna-Valero, S.; Kirchner, R.; Brinda, K.; Wollmann, T.; Raden, M.; Pantano, L.; Soranzo, N.; van Heeringen, S.J.; Charlop-Powers, Z.; Unneberg, P.; de Smet, M.; Martin, M.; Von Kuster, G.; Antao, T.; Miladi, M.; Brueffer, C.; Thornton, K.; van den Beek, M.; Maticzka, D.; Blank, C.; Will, S.; Gravouil, K.; Wolff, J.; Holtgrewe, M.; Fallmann, J.; Piro, V.C.; Shlyakhter, I.; Yousif, A.; Mabon, P.; Zhang, X-O.; Cabral, J.; Shen, W.; Thomas, C.; Brown, J.; Enns, E.; de Hollander, M.; Boekel, J.; Kelleher, J.; Bouvier, D.; Turaga, N.; de Ruiter, J.R.; Choudhary, S.; Harding, N.; Kratz, A.; Fang, Z.; Kleinkauf, R.; Timm, H.; Khan, A.; Cock, P.J.A.; Seiler, E.; Nguyen, H.; Brislawn, C.; Stovner, E.B.; Johnson, J.E.; Hägglund, E.; Ewels, P.; Chambers, M.; Pruesse, E.; Guimera, R.V.; Ye, S.; Dunn, W.A.; Parsons, L.; Cornwell, M.; Reynolds, A.; Bargull, M.; Grassi, E.; Koppstein, D.; Patro, R.; Wohlers, I.; Stoler, N.; Blankenberg, D.; He, G.; Freeberg, M.; Farouini, R.; Junge, A.; Bogema, D.R.; Singh, S.; Cumbo, F.; Larson, D.E.; Wang, L.; Workentine, M.L.; Devisetty, U.K.; Laurent, S.; Garnier, X.; Agren, R.; Roger, P.; Eppley, J.M.; Li, W.; Rausch, R.; Chande, A.T.; Taylor, J.; Stöcker, B.K.; Milne, I.; Wright, P.R.; Taranto, A.P.; Chicco, D.; Abdennur, N.; Sennblad, B.; Baaijens, J.A.; Gopez, M.; Enache, O.M.; Pinello, L.; Srivastava, A.; de Bruijn, I.; Kensche, P.R.; Blin, K.; Pirola, Y.; Preussner, J.; Knudsen, M.; Bendall, M.L.; rai, V.; Gonnella, G.; Stahl, C.; Miles, A.; Waters, N.R.; Hiltemann, S.; Boursin, Y.; Perez-Riverol, Y.; Schmeier, S.; Clarke, E.; Arvai, K.; Jung, M.; Stephen, G.; Domenico, T.; seiler, J.; Rasche, E.; Kornobis, E.; Beisser, D.; Rahmann, S.; Mikheyev, A.S.; Tran, C.; Capellades, J.; Moskalenko, O.; Schröder, C.; Dirmeier, S.; Webster, T.H.; Salatino, A.E.; Urgese, G.; Köster, J., (2018) Bioconda: A sustainable and comprehensive software distribution for the life sciences., Nature Methods, 15, 475-476.
  • Baker, K.; Stephen, G.; Strachan, S.; Armstrong, M.; Hein, I., (2018) BLASTmap: A Shiny-based application to visualize BLAST results as interactive heat maps and a tool to design gene-specific baits for bespoke target enrichment sequencing., In: Ma, W. & Wolpert, T. (eds.). Plant Pathogenic Fungi and Oomyctes. Methods in Molecular Biology, Humana Press, New York, Volume 1848, pp199-206.
  • Shaw, P.D.; Raubach, S.; Hearne, S.J.; Dreher, K.; Bryan, G.; McKenzie, G.; Milne, I.; Stephen, G.; Marshall, D.F., (2017) Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives., Crop Science, 57, 1259-1273.
  • Milne, I.; Bayer, M.; Stephen, G.; Cardle, L.; Marshall, D., (2016) Tablet: visualizing next-generation sequence assemblies and mappings., In: Edwards, D. (ed.). Plant Bioinformatics: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, New York, 14, pp253-268.
  • Ribeiro, A.; Golicz, A.; Hackett, C.A.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J.; Bayer, M., (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryotic genome., BMC Bioinformatics, 16, Article No.382.
  • Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F., (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
  • Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F., (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
  • Milne, I.; Shaw, P.J.; Stephen, G.; Bayer, M.M.; Cardle, L.; Thomas, W.T.B.; Flavell, A.J.; Marshall, D.F., (2010) Flapjack - graphical genotype visualization., Bioinformatics, 26, 3133-3134.
  • Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F., (2010) Tablet - next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F., (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.

  • Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Caprez, A.; Batut, B.; Haudgaard, M.; Cokelaer, T.; Beauchamp, K.A.; Pedersen, B.S.; Hoogstrate, Y.; Bretaudeau, A.; Ryan, D.; Le Corguillé, G.; Yusuf, D.; Luna-Valero, S.; Kirchner, R.; Brinda, K.; Wollmann, T.; Raden, M.; Pantano, L.; Soranzo, N.; van Heeringen, S.J.; Charlop-Powers, Z.; Unneberg, P.; de Smet, M.; Martin, M.; Von Kuster, G.; Antao, T.; Miladi, M.; Brueffer, C.; Thornton, K.; van den Beek, M.; Maticzka, D.; Blank, C.; Will, S.; Gravouil, K.; Wolff, J.; Holtgrewe, M.; Fallmann, J.; Piro, V.C.; Shlyakhter, I.; Yousif, A.; Mabon, P.; Zhang, X-O.; Cabral, J.; Shen, W.; Thomas, C.; Brown, J.; Enns, E.; de Hollander, M.; Boekel, J.; Kelleher, J.; Bouvier, D.; Turaga, N.; de Ruiter, J.R.; Choudhary, S.; Harding, N.; Kratz, A.; Fang, Z.; Kleinkauf, R.; Timm, H.; Khan, A.; Cock, P.J.A.; Seiler, E.; Nguyen, H.; Brislawn, C.; Stovner, E.B.; Johnson, J.E.; Hägglund, E.; Ewels, P.; Chambers, M.; Pruesse, E.; Guimera, R.V.; Ye, S.; Dunn, W.A.; Parsons, L.; Cornwell, M.; Reynolds, A.; Bargull, M.; Grassi, E.; Koppstein, D.; Patro, R.; Wohlers, I.; Stoler, N.; Blankenberg, D.; He, G.; Freeberg, M.; Farouini, R.; Junge, A.; Bogema, D.R.; Singh, S.; Cumbo, F.; Larson, D.E.; Wang, L.; Workentine, M.L.; Devisetty, U.K.; Laurent, S.; Garnier, X.; Agren, R.; Roger, P.; Eppley, J.M.; Li, W.; Rausch, R.; Chande, A.T.; Taylor, J.; Stöcker, B.K.; Milne, I.; Wright, P.R.; Taranto, A.P.; Chicco, D.; Abdennur, N.; Sennblad, B.; Baaijens, J.A.; Gopez, M.; Enache, O.M.; Pinello, L.; Srivastava, A.; de Bruijn, I.; Kensche, P.R.; Blin, K.; Pirola, Y.; Preussner, J.; Knudsen, M.; Bendall, M.L.; rai, V.; Gonnella, G.; Stahl, C.; Miles, A.; Waters, N.R.; Hiltemann, S.; Boursin, Y.; Perez-Riverol, Y.; Schmeier, S.; Clarke, E.; Arvai, K.; Jung, M.; Stephen, G.; Domenico, T.; seiler, J.; Rasche, E.; Kornobis, E.; Beisser, D.; Rahmann, S.; Mikheyev, A.S.; Tran, C.; Capellades, J.; Moskalenko, O.; Schröder, C.; Dirmeier, S.; Webster, T.H.; Salatino, A.E.; Urgese, G.; Köster, J., (2018) Bioconda: A sustainable and comprehensive software distribution for the life sciences., Nature Methods, 15, 475-476.
  • Shaw, P.D.; Raubach, S.; Hearne, S.J.; Dreher, K.; Bryan, G.; McKenzie, G.; Milne, I.; Stephen, G.; Marshall, D.F., (2017) Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives., Crop Science, 57, 1259-1273.
  • Ribeiro, A.; Golicz, A.; Hackett, C.A.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J.; Bayer, M., (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryotic genome., BMC Bioinformatics, 16, Article No.382.
  • Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F., (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
  • Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F., (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
  • Milne, I.; Shaw, P.J.; Stephen, G.; Bayer, M.M.; Cardle, L.; Thomas, W.T.B.; Flavell, A.J.; Marshall, D.F., (2010) Flapjack - graphical genotype visualization., Bioinformatics, 26, 3133-3134.
  • Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F., (2010) Tablet - next generation sequence assembly visualization., Bioinformatics, 26, 401-402.

  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F., (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.

Printed from /staff/gordon-stephen on 12/12/18 04:28:53 PM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.