Iain Milne
Most research would be impossible without software, and my research is about providing intuitive, professional software applications – often with a strong visualization component – that underpin many sequencing, genotyping and analysis projects both within the institute and further afield. To this end, I lead the development of a range of extensively used programs with a worldwide install base of over 150,000 users. These programs use a combination of traditional desktop interfaces along with back-end components that rely heavily on our high-performance scientific computing cluster and infrastructure.
For more information on these applications, please visit the website for the Information and Computational Sciences group.
I also manage and maintain the Institute's Linux-based scientific-computing resources, including the HPC cluster and associated storage and network services. This resource provides almost 500 CPU cores of computing power to researchers at the James Hutton Institute, along with access to over 2 TB of memory and just shy of half a petabyte of storage.
Areas of Expertise
- Object oriented programming (Java, C#, C++).
- Software visualization.
- Interface design and programming.
- Web technologies/application programming (frontend and middleware).
- J2EE (web services, JDBC, JavaBeans, JavaMail, Servlets, JSP, JSF).
- Parallel programming and high-performance computing technologies.
- Network programming.
- Windows/Linux systems administration.
Bibliography
- Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology, 18, 1574-1587
- Raubach, S.; Kilian, B.; Dreher, K.; Amri, A.; Bassi, F.M.; Boukar, O.; Cook, D.; Cruickshank, A.; Fatokun, C.; El Haddad, N.; Humphries, A.; Jordan, D.; Kehel, Z.; Kumar, S.; Labarosa, S.J.; Nguyen, L.H.; Mace, E.; McCouch, S.; McNally, K.; Marshall, D.F.; Mikwa, E.O.; Milne, I.; Odeny, D.A.; Plazas, M.; Prohens, J.; Rieseberg, L.H.; Schafleitner, R.; Sharma, S.; Stephen, G.; Quang Tin, H.; Togola, A.; Warschefsky, E.; Werner, P.; Shaw, P. (2021) From bits to bites: advancement of the Germinate platform to support prebreeding informatics for crop wild relatives., Crop Science, 61, 1538-1566
- Sansaloni, C.; Franco, J.; Santos, B.; Percival-Alwyn, L.; Singh, S.; Petroli, C.; Campos, J.; Dreher, K.; Payne, T.; Marshall, D.; Kilian, B.; Milne, I.; Raubach, S.; Shaw, P.; Stephen, G.; Carling, J.; Saint Pierre, C.; Burgueño, J.; Crosa, J.; Li, H.; Guzman, C.; Kehel, Z.; Amri, A.; Kilian, A.; Wenzl, P.; Uauy, C.; Banziger, M.; Caccamo, M.; Pixley, K. (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints, Nature Communications, 11, art.4572
- Selby, P.; Abbeloos, R.; Backlund, J.E.; Basterrechea Salido, M.; Bauchet, G.; Benites-Alfaro, O.; Birkett, C.; Calaminos, V.C.; Carceller, P.; Cornut, G.; Costa, B.V.; Edwards, J.D.; Finkers, R.; Gao, S.Y.; Ghaffar, M.; Glaser, P.; Guignon, V.; Hok, P.; Kilian, A.; König, P; Lagare, J.E.B.; Lange, M.; Laporte, M.-A.; Larmande, P.; LeBauer, D.; Lyon, D.; Marshall, D.; Matthews, D.; Milne, I.; Mistry, N.; Morales, N.; Mueller, L.; Neveu, P.; Papoutsoglou, E.; Pearce, B.; Perez-Masias, I.; Pommier, C.; Ramirez-Gonzalez, R.H.; Rathore, A.; Raquel, A.M.; Raubach, S; Rife, T.; Robbins, K.; Rouard, R.; Sarma, C.; Scholz, U.; Selby, P.; Sempere, G.; Shaw, P.; Simon, R.; Soldevilla, N.; Stephen, G.; Sun, Q.; Tovar, C.; Uszynski, G.; Verouden, M. (2019) BrAPI - an Application Programming Interface for plant breeding applications., Bioinformatics, 35, 4147-4155.
- 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.
- Hackett, C.A.; Boskamp, B.; Vogogias, A.; Preedy, K.F.; Milne, I. (2017) TetraploidSNPMap: Software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data., Journal of Heredity, 108, 438-442.
- 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.
- Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
- 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.
- Baker, K.; Dhillon, T.; Colas, I.; Cook, N.; Milne, I.; Milne, L.; Bayer, M.; Flavell, A.J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance., Plant Journal, 84, 111-124.
- 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.
- Shaw, P.D.; Graham, M.; Kennedy, J.; Milne, I.; Marshall, D.F. (2014) Helium: visualization of large scale plant pedigrees., BMC Bioinformatics, 15, Article No. 259.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
- 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.
- Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
- 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.
- Bayer, M.; Liu, H.; Marshall, D.F.; Russell, J.; Hedley, P.E.; Milne, I.; Stephen G.; Waugh, R.; (2011) A GBS data processing pipeline for barley., StatSeq Meeting on Genotyping by Sequencing. Wageningen, Netherlands, 3-4 November 2011 (Talk).
- 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.
- Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
- 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.
- Moragues, M.; Comadran, J.; Waugh, R.; Milne, I.; Flavell, A.J.; Russell, J.R. (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data., Theoretical and Applied Genetics, 120, 1525-1534.
- 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.
- Milne, I.; Lindner, D.; Bayer, M.M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops., Bioinformatics, 25, 126-127.
- Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
- Russell, J.R.; Moragues, M.; Dawson, I.K.; Waugh, R.; Marshall, D.F.; Milne, I.; Grando, S.; Tondelli, A.; Cattivelli, L.; Hubner, S.; Fridman, E.; Flavell, A.J. (2009) Genetic diversity analysis of wild and landrace barleys using the BODA1 Illumina genotyping platform., 19th International Triticeae Mapping Initiative - 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August - 4 September 2009 (Talk).
- Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis - new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
- Hackett, C.A.; Milne, I.; Bradshaw, J.E.; Luo, Z.W. (2007) TetraploidMap for Windows: Linkage map construction and QTL mapping in autotetraploid species., Journal of Heredity, 98, 727-729.
- Husmeier, D.; Wright, F.; Milne, I. (2005) Detecting interspecific recombination with a pruned probabilistic divergence measure., Bioinformatics, 21, 1797-1806.
- Milne, I.; Rowe, G. (2004) OGRE: Three-dimensional program visualization for novice programmers., Education and Information Technologies, 9, 219-237.
- Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology, 18, 1574-1587
- Raubach, S.; Kilian, B.; Dreher, K.; Amri, A.; Bassi, F.M.; Boukar, O.; Cook, D.; Cruickshank, A.; Fatokun, C.; El Haddad, N.; Humphries, A.; Jordan, D.; Kehel, Z.; Kumar, S.; Labarosa, S.J.; Nguyen, L.H.; Mace, E.; McCouch, S.; McNally, K.; Marshall, D.F.; Mikwa, E.O.; Milne, I.; Odeny, D.A.; Plazas, M.; Prohens, J.; Rieseberg, L.H.; Schafleitner, R.; Sharma, S.; Stephen, G.; Quang Tin, H.; Togola, A.; Warschefsky, E.; Werner, P.; Shaw, P. (2021) From bits to bites: advancement of the Germinate platform to support prebreeding informatics for crop wild relatives., Crop Science, 61, 1538-1566
- Sansaloni, C.; Franco, J.; Santos, B.; Percival-Alwyn, L.; Singh, S.; Petroli, C.; Campos, J.; Dreher, K.; Payne, T.; Marshall, D.; Kilian, B.; Milne, I.; Raubach, S.; Shaw, P.; Stephen, G.; Carling, J.; Saint Pierre, C.; Burgueño, J.; Crosa, J.; Li, H.; Guzman, C.; Kehel, Z.; Amri, A.; Kilian, A.; Wenzl, P.; Uauy, C.; Banziger, M.; Caccamo, M.; Pixley, K. (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints, Nature Communications, 11, art.4572
- Selby, P.; Abbeloos, R.; Backlund, J.E.; Basterrechea Salido, M.; Bauchet, G.; Benites-Alfaro, O.; Birkett, C.; Calaminos, V.C.; Carceller, P.; Cornut, G.; Costa, B.V.; Edwards, J.D.; Finkers, R.; Gao, S.Y.; Ghaffar, M.; Glaser, P.; Guignon, V.; Hok, P.; Kilian, A.; König, P; Lagare, J.E.B.; Lange, M.; Laporte, M.-A.; Larmande, P.; LeBauer, D.; Lyon, D.; Marshall, D.; Matthews, D.; Milne, I.; Mistry, N.; Morales, N.; Mueller, L.; Neveu, P.; Papoutsoglou, E.; Pearce, B.; Perez-Masias, I.; Pommier, C.; Ramirez-Gonzalez, R.H.; Rathore, A.; Raquel, A.M.; Raubach, S; Rife, T.; Robbins, K.; Rouard, R.; Sarma, C.; Scholz, U.; Selby, P.; Sempere, G.; Shaw, P.; Simon, R.; Soldevilla, N.; Stephen, G.; Sun, Q.; Tovar, C.; Uszynski, G.; Verouden, M. (2019) BrAPI - an Application Programming Interface for plant breeding applications., Bioinformatics, 35, 4147-4155.
- 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.
- Hackett, C.A.; Boskamp, B.; Vogogias, A.; Preedy, K.F.; Milne, I. (2017) TetraploidSNPMap: Software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data., Journal of Heredity, 108, 438-442.
- 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.
- Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
- Baker, K.; Dhillon, T.; Colas, I.; Cook, N.; Milne, I.; Milne, L.; Bayer, M.; Flavell, A.J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance., Plant Journal, 84, 111-124.
- 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.
- Shaw, P.D.; Graham, M.; Kennedy, J.; Milne, I.; Marshall, D.F. (2014) Helium: visualization of large scale plant pedigrees., BMC Bioinformatics, 15, Article No. 259.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
- 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.
- Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
- 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.
- Moragues, M.; Comadran, J.; Waugh, R.; Milne, I.; Flavell, A.J.; Russell, J.R. (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data., Theoretical and Applied Genetics, 120, 1525-1534.
- Milne, I.; Lindner, D.; Bayer, M.M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops., Bioinformatics, 25, 126-127.
- Hackett, C.A.; Milne, I.; Bradshaw, J.E.; Luo, Z.W. (2007) TetraploidMap for Windows: Linkage map construction and QTL mapping in autotetraploid species., Journal of Heredity, 98, 727-729.
- Husmeier, D.; Wright, F.; Milne, I. (2005) Detecting interspecific recombination with a pruned probabilistic divergence measure., Bioinformatics, 21, 1797-1806.
- Milne, I.; Rowe, G. (2004) OGRE: Three-dimensional program visualization for novice programmers., Education and Information Technologies, 9, 219-237.
- Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D.; McGuire, G. (2004) TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments., Bioinformatics, 20, 1806-1807.
- Milne, I.; Rowe, G. (2002) Difficulties in learning and teaching programme - views of students and tutors., Education and Information Technologies, 7, 55-66.
- 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.
- 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.
- Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
- Bayer, M.; Liu, H.; Marshall, D.F.; Russell, J.; Hedley, P.E.; Milne, I.; Stephen G.; Waugh, R.; (2011) A GBS data processing pipeline for barley., StatSeq Meeting on Genotyping by Sequencing. Wageningen, Netherlands, 3-4 November 2011 (Talk).
- Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
- Russell, J.R.; Moragues, M.; Dawson, I.K.; Waugh, R.; Marshall, D.F.; Milne, I.; Grando, S.; Tondelli, A.; Cattivelli, L.; Hubner, S.; Fridman, E.; Flavell, A.J. (2009) Genetic diversity analysis of wild and landrace barleys using the BODA1 Illumina genotyping platform., 19th International Triticeae Mapping Initiative - 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August - 4 September 2009 (Talk).
- Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis - new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
- Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D. (2004) TOPALi - Software for detecting recombinants in DNA multiple alignments., Plant and Animal Genome Conference (PAG) XII Proceedings, San Diego, California, 10-12 January 2004.
- Parkes, S.M.; Martin, I.; Milne, I. (1999) Lunar surface simulation-modelling for vision-guided lunar landers., DASI '99. Lisbon, 369-374.
- Shaw, P.; Raubach, S.; Macaulay, M.; Schreiber, M.; Milne, I.; Bayer, M.; Kilian, B. (2023) Going for BOLD Supporting the Biodiversity for Opportunities, Livelihoods and Development Project with Germinate and GridScore, Plant and Animal Genome 30, 13-18 January 2023. San Diego, USA & Online.
- Baker, K.; Bayer, M.; Cook, N.; Dreissig, S.; Dhillon, T.; Russell, J.; Hedley, P.; Morris, J.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The peri-centromeric heterochromatin of barley is a permissive environment for gene diversity, expression and evolution., Plant and Animal Genome XXII, San Diego, California, USA, 12-16 January 2014.
- Shaw, P.D.; Kennedy, J.; Graham, M.; Milne, I.; Marshall, D.F. (2014) Evaluation of Helium: Visualization of large scale plant pedigrees., BiVi (Biological Visualization) 1st Annual Meeting, Edinburgh Napier University, Edinburgh, 16-17 December 2014.
- Stephen, G.; Milne, I.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., VizBi 2014, 2nd EMBO Conference on Visualizing Biological Data, EML-Heidelberg, Germany, 5-7 March 2014.
- Milne, I.; Stephen, G.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., International Plant and Animal Genome XXII, San Diego, CA, USA, 11-15 January 2014.
- Shaw, P.D.; Raubach, S.; Milne, I.; Stephen, G.; Wenzl, P.; Hearne, S.; Singh,; Marshall, D.F. (2014) Germinate: Wheat and maize databases for the Seeds of Discovery Project., International Plant and Animal Genome XXII Conference, San Diego, California, 11-15 January 2014.
- Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
- Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
- Shaw, P.; Thomas, B.; Ramsay, L.; Waugh, R.; Comadran, J.; Stephen, G.; Milne, I.; Graham, M.; Kennedy, J.; Marshall, D. (2013) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0974.
- Milne, I.; Stephen, G.; Bayer, M.; Cardle, L.; Shaw, P.; Marshall, D. (2013) Optimisation of SNP and alternative splicing discovery using the Tablet NGS viewer., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0971.
- Wenzl, P.; Baum, M.; Bonnett, D.; Braun, H.; Brennan, P.; Buckler, E.S.; Byurgeno, J.; Chen, C.; Christen, J.A.; Cibrian, A.; Cortes Cruz, M.; Gamboa, S.C.; Costich, D.; Crossa, J.; de la Cruz Larios, L.; Duveiller, E.; Edmeades, G.; El-Bouhssini, M.; Banda, A.E.; Lopez, P.; Franco, J.; Davila, G.F.; Castillo, G.G.; Lopez, J.H.G.; Montiel, N.; Ceniceros, F.; Hearne, S.; Casillas, J.; Muela, V.; Moreno, J.; Killan, A.; Li, H.; Lopes, M.; Mahuku, G.; Juarez, F.; Marshall, D.; Milne, I. et al. (2013) Seeds of discovery: unlocking the genetic potential of maize and wheat genetic resources., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0768.
- Shaw, P.; Kennedy J.; Milne, I.; Graham, M.; Marshall, D.F. (2012) Using a mathematical graph framework for visualization of inheritance patterns in commercial plant pedigrees., BioVis - 2nd IEEE Symposium on Biological Data Visualisation. Seattle, USA, 14-15 October 2012 (Poster).
- Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2011) Germinate 2 - Storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
- Shaw, P.; Kennedy, J.; Graham, M.; Milne, I.; Marshall, D.F. (2011) Visualizing genetic transmission patterns in plant pedigrees., BioVis 2011, 1st IEEE Symposium on Biological Data Visialization, Providence, Rhode Island, 23-24 October 2011. (Poster)
- Marshall, D.F.; Milne, I.; Bayer, M.; Shaw, P.; Cardle, L.; Stephen, G.; Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Russell, J.R.; Flavell, A.J.; Waugh, R. (2010) What you see is what you get: SCRI visualization tools for SNP discovery, genotype analysis and comparative mapping., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
- Marshall, D.F.; Milne, I.; Bayer, M.; Shaw, P.; Cardle, L.; Stephen, G.; Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Russell, J.R.; Flavell, A.J.; Waugh, R. (2010) Tablet, flapjack and strudel; SCRI visualization tools to support SNP discovery, genotype analysis and comparative mapping., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Poster).
- Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2010) Germinate 2 - storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
- Milne, I.; Bayer, M.M.; Shaw, P.; Cardle, L.; Marshall, D.F. (2009) Flapjack - a high performance application for graphical genotyping., Plant & Animal Genome XVII, San Diego, California, USA, 10-14 January 2009 (Abstract).
- Milne, I.; Lindner, D.; Wright, F. (2007) TOPAi v2: Extended multiple sequence alignment analysis software using web services and cluster computing., ISMB 2007, Vienna, 21-25 July 2007 (Poster).
- Milne, I.; Wright, F. (2004) A simple algorithm to automatically detect recombinants in DNA/RNA sequence alignments., ISMB/ECCB 2004. Glasgow, 31 July - 4 August 2004. (Poster).
