Professor Hugh Shanahan

  1. 2020
  2. Published

    “Ethics When You Least Expect It”: A Modular Approach to Short Course Data Ethics Instruction

    Bezuidenhout, L., Quick, R. & Shanahan, H., 17 Feb 2020, In : Science and Engineering Ethics. p. 1-25 25 p.

    Research output: Contribution to journalArticle

  3. 2019
  4. Submitted

    Teaching FAIR

    Shanahan, H., 4 May 2019, (Submitted) In : Data Intelligence.

    Research output: Contribution to journalArticle

  5. Submitted

    9 Simple recommendations for teaching data skills

    Shanahan, H., 16 Apr 2019, (Submitted) In : Data Science Journal.

    Research output: Contribution to journalArticle

  6. Submitted

    Embedding Open Science practice into Data Science Training

    Shanahan, H., 1 Jan 2019, (Submitted).

    Research output: Contribution to conferencePoster

  7. 2018
  8. Published

    Transcriptomics: Quantifying Non-Uniform Read Distribution Using MapReduce

    Alnasir, J. & Shanahan, H., 27 Dec 2018, In : International Journal for the Foundations of Computer Science. 29, 8, 20 p.

    Research output: Contribution to journalArticle

  9. Published

    The application of Hadoop in structural bioinformatics

    Alnasir, J. & Shanahan, H., 20 Nov 2018, In : Briefings in Bioinformatics. p. 1-10 10 p., bby106.

    Research output: Contribution to journalArticle

  10. E-pub ahead of print

    Systems Metagenomics: Applying Systems Biology Thinking to Human Microbiome Analysis

    Radwan, G. S. & Shanahan, H., 24 Aug 2018, Computational Methods in Systems Biology - 16th International Conference, CMSB 2018, Proceedings. Springer-Verlag, Vol. 11095 LNBI. p. 318-321 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11095 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  11. Published

    Systems Metagenomics

    Shanahan, H. & Radwan, G., 15 Jul 2018.

    Research output: Contribution to conferencePoster

  12. Published
  13. Submitted

    “Ethics When You Least Expect It”: A Modular Approach to Data Ethics Instruction

    Shanahan, H., Bezuidenhout, L. & Quick, R., 2018, (Submitted).

    Research output: Contribution to conferencePaper

  14. 2017
  15. Published

    Biological Big Bytes: Integrative Analysis of Large Biological Datasets

    Shanahan, H., Chen, M., Harrison, A. & Orlov, Y., 13 Sep 2017, In : Journal of Integrative Bioinformatics. 14, 3, 2 p.

    Research output: Contribution to journalEditorial

  16. Published

    A Novel Method to Detect Bias in Short Read NGS Data

    Alnasir, J. & Shanahan, H., 2017, In : Journal of Integrative Bioinformatics. 14, 3, p. 1-9 9 p.

    Research output: Contribution to journalArticle

  17. 2016
  18. Published
  19. Published
  20. 2015
  21. Published

    Investigation into the annotation of protocol sequencing steps in the sequence read archive

    AlNasir, J. & Shanahan, H., 1 Dec 2015, In : GigaScience. 4, 1, p. 1-11 11 p.

    Research output: Contribution to journalArticle

  22. Published

    Teaching Data Science and Cloud Computing in Low and Middle Income Countries

    Shanahan, H., Harrison, A. & May, S., 23 Nov 2015, In : Advanced Techniques in Biology & Medicine. 3, 3, p. 1-5 5 p., 1000150.

    Research output: Contribution to journalArticle

  23. Published
  24. Published
  25. In preparation

    PDB-Hadoop: Parallelising Legacy applications on the Protein Databank using Apache Hadoop

    AlNasir, J. & Shanahan, H., 2015, (In preparation) In : Bioinformatics.

    Research output: Contribution to journalArticle

  26. 2014
  27. Published

    Bioinformatics on the cloud computing platform Azure

    Shanahan, H., Harrison, A. & Owen, A. M., 22 Jul 2014, In : PLoS ONE. 9, 7, p. e102642

    Research output: Contribution to journalArticle

  28. 2013
  29. E-pub ahead of print

    Dissecting the chromatin interactome of microRNA genes

    Chen, D., Fu, L-Y., Zhang, Z., Yu, G., Zhang, H., Jiang, L., Harrison, A., Shanahan, H., Klukas, C., Zhang, H-Y., Ruan, Y., Chen, LI-LI. & Chen, M., 20 Dec 2013, In : Nucleic Acids Research.

    Research output: Contribution to journalArticle

  30. Published

    Jasmonate controls leaf growth by repressing cell proliferation and the onset of endoreduplication while maintaining a potential stand-by mode

    Noir, S., Bömer, M., Takahashi, N., Ishida, T., Tsui, T-L., Balbi, V., Shanahan, H., Sugimoto, K. & Devoto, A., Apr 2013, In : Plant physiology. 161, 4, p. 1930-1951

    Research output: Contribution to journalArticle

  31. Forthcoming

    An Overview of Gene Regulation

    Shanahan, H. & Harrison, A., 2013, (Accepted/In press) Approaches to Integrative Bioinformatics. Chen, MI. & Hofstaedt, R. (eds.). Springer, p. 21-69

    Research output: Chapter in Book/Report/Conference proceedingChapter

  32. 2012
  33. Published

    Normalized Affymetrix expression data are biased by G-quadruplex formation

    Shanahan, H. P., Memon, F. N., Upton, G. J. G. & Harrison, A. P., 1 Apr 2012, In : Nucleic Acids Research. 40, 8, p. 3307-3315 9 p.

    Research output: Contribution to journalArticle

  34. In preparation

    modCDF - modifying CDF's for microarrays using sequence similarity

    Shanahan, H., Harrison, A., Upton, G. & Memon, F., 2012, (In preparation) In : Bioinformatics. 2 p.

    Research output: Contribution to journalArticle

  35. 2011
  36. Published

    A novel high-throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutation

    Wang, X., Roig-Villanova, I., Khan, S., Shanahan, H., Quail, P. H., Martinez-Garcia, J. F. & Devlin, P. F., 2011, In : Journal of Experimental Botany. 62, 8, p. 2973-2987 15 p.

    Research output: Contribution to journalArticle

  37. 2010
  38. Published

    The identification of Transcription Factor Binding Sites using string kernels

    Shanahan, H., 10 Sep 2010.

    Research output: Contribution to conferenceOther

  39. 2009
  40. Published

    Regulatory processes underscoring the light control of shoot meristem activity and leaf initiation

    Lopez Juez, E., Dillon, E., Magyar, Z., Khan, S., Hazeldine, S., Murray, J. A., Beemster, G. T., Bogre, L. & Shanahan, H., Jun 2009, p. S205-S205. 1 p.

    Research output: Contribution to conferenceAbstract

  41. Published
  42. Published

    Can we improve on the identification of transcription factor binding sites?

    Shanahan, H. P., 2009, p. 39-40. 2 p.

    Research output: Contribution to conferenceOther

  43. Published

    How many extant pinniped species remain to be descibed ?

    Shanahan, H., Woodley, M. & M., N., 2009, In : Historical Biology. 20, 4, p. 225-235

    Research output: Contribution to journalArticle

  44. 2008
  45. Published

    Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis

    López-Juez, E., Dillon, E., Magyar, Z., Khan, S., Hazeldine, S., de Jager, S. M., Murray, J. A., Beemster, G. T., Bögre, L. & Shanahan, H., Apr 2008, In : Plant Cell. 20, 4, p. 947-968 22 p.

    Research output: Contribution to journalArticle

  46. Published
  47. 2005
  48. Published

    HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

    Ferrer-Costa, C., Shanahan, H. P., Jones, S. & Thornton, J. M., 15 Sep 2005, In : Bioinformatics. 21, 18, p. 3679-3680 2 p.

    Research output: Contribution to journalArticle

  49. Published

    Amino acid architecture and the distribution of polar atoms on the surfaces of proteins

    Shanahan, H. P. & Thornton, J. M., 15 Aug 2005, In : BIOPOLYMERS. 78, 6, p. 318-328 11 p.

    Research output: Contribution to journalArticle

  50. 2004
  51. Published

    An examination of the conservation of surface patch polarity for proteins

    Shanahan, H. P. & Thornton, J. M., 22 Sep 2004, In : Bioinformatics. 20, 14, p. 2197-2204 8 p.

    Research output: Contribution to journalArticle

  52. Published

    Identifying DNA-binding proteins using structural motifs and the electrostatic potential

    Shanahan, H. P., Garcia, M. A., Jones, S. & Thornton, J. M., 2004, In : Nucleic Acids Research. 32, 16, p. 4732-4741 10 p.

    Research output: Contribution to journalArticle

  53. 2003
  54. Published

    Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

    Jones, S., Shanahan, H. P., Berman, H. M. & Thornton, J. M., 15 Dec 2003, In : Nucleic Acids Research. 31, 24, p. 7189-7198 10 p.

    Research output: Contribution to journalArticle

  55. Published

    Light hadron spectroscopy with two flavors of dynamical quarks on the lattice (vol 65, art no 054505, 2002)

    Khan, A. A., Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Mar 2003, In : Physical Review D . 67, 5, p. - 6 p.

    Research output: Contribution to journalArticle

  56. Published

    Light hadron spectrum and quark masses from quenched lattice QCD

    Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A. & Yoshie, T., 1 Feb 2003, In : Physical Review D . 67, 3, p. - 46 p.

    Research output: Contribution to journalArticle

  57. Published

    Erratum: Dynamical quark effects on light quark masses (vol 85, pg 4674, 2000)

    Khan, A. A., Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 17 Jan 2003, In : Physical Review Letters. 90, 2, p. - 2 p.

    Research output: Contribution to journalArticle

  58. 2002
  59. Published

    Light hadron spectroscopy with two flavors of dynamical quarks on the lattice

    Khan, A. A., Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Mar 2002, In : Physical Review D . 65, 5, p. - 50 p.

    Research output: Contribution to journalArticle

  60. 2001
  61. Published

    Kaon B parameter from quenched domain-wall QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K. I., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Dec 2001, In : Physical Review D . 6411, 11, p. - 21 p.

    Research output: Contribution to journalArticle

  62. Published

    Topological susceptibility in lattice QCD with two flavors of dynamical quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Dec 2001, In : Physical Review D . 6411, 11, p. - 10 p.

    Research output: Contribution to journalArticle

  63. Published

    Hybrid quarkonia with dynamical sea quarks

    Manke, T., Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Nov 2001, In : Physical Review D . 6409, 9, p. - 4 p.

    Research output: Contribution to journalArticle

  64. Published

    Equation of state in finite-temperature QCD with two flavors of improved Wilson quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K. I., Okamoto, M., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A. & Yoshie, T., 1 Oct 2001, In : Physical Review D . 6407, 7, p. art. no.-074510 17 p.

    Research output: Contribution to journalArticle

  65. Published

    B meson decay constants from two-flavor lattice QCD with nonrelativistic heavy quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A. & Yoshie, T., 1 Sep 2001, In : Physical Review D . 6405, 5, p. - 24 p.

    Research output: Contribution to journalArticle

  66. Published

    Decay constants of B and D mesons from improved relativistic lattice QCD with two flavors of sea quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Aug 2001, In : Physical Review D . 6403, 3, p. - 17 p.

    Research output: Contribution to journalArticle

  67. Published

    Chiral properties of domain-wall quarks in quenched QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K. I., Noaki, J., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A. & 2 others, Yoshie, T. & CP-PACS Collaboration, 1 Jun 2001, In : Physical Review D . 6311, 11, p. - 19 p.

    Research output: Contribution to journalArticle

  68. Published

    Calculation of K -> pi matrix elements in quenched domain-wall QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K. I., Noaki, J., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & 1 others, CP-PACS collaboration, Mar 2001, In : Nuclear Physics B - Proceedings Supplements. 94, p. 283-286 4 p.

    Research output: Contribution to journalArticle

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