Dr Andrew Harrison

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Email
harry@essex.ac.uk -
Telephone
+44 (0) 1206 872964
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Location
STEM 5.10, Colchester Campus
Profile
Biography
I was originally an Astrophysicist, studying how stars formed. I developed an interest in whether life can be found on planets other than the Earth and so decided to broaden my knowledge by moving into the rapidly expanding field of bioinformatics. I am interested in applying mathematics and statistics towards all areas of scientific research. My research efforts are concentrated on the analysis of data-rich functional genomics experiments. These include microarrays and I collaborate with a number of biologists and medics.
Qualifications
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PhD in Astrophysics
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BSc in Physics with Astrophysics University of Manchester, (1991)
Appointments
University of Essex
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Senior Lecturer, Mathematical Sciences, University of Essex (1/10/2004 - present)
Research and professional activities
Research interests
Bioinformatics
Big data science
Teaching and supervision
Previous supervision

Degree subject: Statistics
Degree type: Doctor of Philosophy
Awarded date: 24/5/2016

Degree subject: Bioinformatics
Degree type: Doctor of Philosophy
Awarded date: 2/3/2016

Degree subject: Statistics
Degree type: Doctor of Philosophy
Awarded date: 8/10/2015

Degree subject: Mathematics
Degree type: Master of Science (by Dissertation)
Awarded date: 22/9/2014

Degree subject: Bioinformatics
Degree type: Doctor of Philosophy
Awarded date: 6/1/2012
Publications
Journal articles (58)
Li, K., Xu, C., Huang, J., Liu, W., Zhang, L., Wan, W., Tao, H., Li, L., Lin, S., Harrison, A. and He, H., (2017). Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativaL.). Briefings in Bioinformatics. 18 (2), bbw021-bbw021
Li, K., Xu, C., Huang, J., Liu, W., Zhang, L., Wan, W., Tao, H., Li, L., Lin, S., Harrison, AP. and He, H., (2017). Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativaL.). Briefings in Bioinformatics. 18 (2), 270-278
Bai, Y., Dai, X., Harrison, A., Johnston, C. and Chen, M., (2016). Toward a next-generation atlas of RNA secondary structure. Briefings in Bioinformatics. 17 (1), 63-77
Wang, J., Meng, X., Yuan, C., Harrison, AP. and Chen, M., (2016). The roles of cross-talk epigenetic patterns inArabidopsis thaliana. Briefings in Functional Genomics. 15 (4), 278-287
Alhaji, BB., Dai, H., Hayashi, Y., Vinciotti, V., Harrison, A. and Lausen, B., (2016). Bayesian analysis for mixtures of discrete distributions with a non-parametric component. Journal of Applied Statistics. 43 (8), 1369-1385
Corpas, M., Valdivia-Granda, W., Torres, N., Greshake, B., Coletta, A., Knaus, A., Harrison, AP., Cariaso, M., Moran, F., Nielsen, F., Swan, D., Weiss SolĂs, DY., Krawitz, P., Schacherer, F., Schols, P., Yang, H., Borry, P., Glusman, G. and Robinson, PN., (2015). Crowdsourced direct-to-consumer genomic analysis of a family quartet. BMC Genomics. 16 (1), 910-
Bai, Y., Dai, X., Harrison, AP. and Chen, M., (2015). RNA regulatory networks in animals and plants: a long noncoding RNA perspective. Briefings in Functional Genomics. 14 (2), 91-101
Lin, S., Song, Q., Tao, H., Wang, W., Wan, W., Huang, J., Xu, C., Chebii, V., Kitony, J., Que, S., Harrison, A. and He, H., (2015). Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites. Scientific Reports. 5 (1), 11940-
Yuan, C., Wang, J., Harrison, AP., Meng, X., Chen, D. and Chen, M., (2015). Genome-wide view of natural antisense transcripts in Arabidopsis thaliana. DNA Research. 22 (3), 233-243
Shanahan, H., Harrison, AP. and Tobias May, S., (2015). Teaching Data Science and Cloud Computing in Low and Middle Income Countries. Advanced Techniques in Biology & Medicine. 03 (03)
Lin, S., Song, Q., Tao, H., Wang, W., Wan, W., Huang, J., Xu, C., Chebii, V., Kitony, J., Que, S., Harrison, AP. and He, H., (2015). Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites. Scientific Reports. 5, creators-Harrison=3AAndrew_P=3A=3A
Shanahan, HP., Owen, AM. and Harrison, AP., (2014). Bioinformatics on the Cloud Computing Platform Azure. PLoS ONE. 9 (7), e102642-e102642
Mahmoud, O., Harrison, A., Perperoglou, A., Gul, A., Khan, Z., Metodiev, MV. and Lausen, B., (2014). A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. BMC Bioinformatics. 15 (1), 274-
Musa, IK., Walker, SD., Owen, AM. and Harrison, AP., (2014). Self-service infrastructure container for data intensive application. Journal of Cloud Computing: Advances, Systems and Applications. 3 (1), 5-5
Chen, D., Fu, L-Y., Zhang, Z., Li, G., Zhang, H., Jiang, L., Harrison, AP., Shanahan, HP., Klukas, C., Zhang, H-Y., Ruan, Y., Chen, L-L. and Chen, M., (2014). Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Research. 42 (5), 3028-3043
Peddada, SD., Shanahan, HP., Owen, AM. and Harrison, AP., (2014). Bioinformatics on the Cloud Computing Platform Azure. PloS One. 9 (7), creators-Harrison=3AAndrew_P=3A=3A
Musa, IK., Walker, S., Owen, AM. and Harrison, AP., (2014). Self-service infrastructure container for data intensive application. Journal of Cloud Computing: Advances, Systems and Applications. 3 (1), creators-Walker=3AStuart=3A=3A
Mahmoud, O., Harrison, AP., Perperoglou, A., Gul, A., Khan, Z., Metodiev, M. and Lausen, B., (2014). A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. BMC Bioinformatics. 15 (1), creators-Lausen=3ABerthold=3A=3A
Harrison, A., Binder, H., Buhot, A., Burden, CJ., Carlon, E., Gibas, C., Gamble, LJ., Halperin, A., Hooyberghs, J., Kreil, DP., Levicky, R., Noble, PA., Ott, A., Pettitt, BM., Tautz, D. and Pozhitkov, AE., (2013). Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research. 41 (5), 2779-2796
Shanahan, HP., Memon, FN., Upton, GJG. and Harrison, AP., (2012). Normalized Affymetrix expression data are biased by G-quadruplex formation. Nucleic Acids Research. 40 (8), 3307-3315
Rizig, MA., McQuillin, A., Ng, A., Robinson, M., Harrison, A., Zvelebil, M., Hunt, SP. and Gurling, HM., (2012). A gene expression and systems pathway analysis of the effects of clozapine compared to haloperidol in the mouse brain implicates susceptibility genes for schizophrenia. Journal of Psychopharmacology. 26 (9), 1218-1230
Upton, GJG. and Harrison, AP., (2012). Motif effects in Affymetrix GeneChips seriously affect probe intensities. Nucleic Acids Research. 40 (19), 9705-9716
Upton, GJG. and Harrison, AP., (2010). The Detection of Blur in Affymetrix GeneChips. Statistical Applications in Genetics and Molecular Biology. 9 (1), Article37-
Langdon, WB., Upton, GJG., da Silva Camargo, R. and Harrison, AP., (2010). A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7 (4), 647-653
Memon, FN., Owen, AM., Sanchez-Graillet, O., Upton, GJG. and Harrison, AP., (2010). Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.. Journal of integrative bioinformatics. 7 (2), 111-
Sanchez-Graillet, O., Stalteri, MA., Rowsell, J., Upton, GJG. and Harrison, AP., (2010). Using surveys of Affymetrix GeneChips to study antisense expression.. Journal of integrative bioinformatics. 7 (2), 1662-1668
Kheniche, A., Salhi, A., Harrison, A. and Dowden, JM., (2010). A Deterministic DNA Database Search. Advances in Experimental Medicine and Biology. 680, 371-378
Rowsell, J., da Silva Camargo, R., Langdon, WB., Stalteri, MA. and Harrison, AP., (2010). Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.. Journal of integrative bioinformatics. 7 (3), 512-513
Memon, FN., Upton, GJG. and Harrison, AP., (2010). A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia. Journal of Nucleic Acids. 2010, 1-6
Memon, FN., Owen, AM., Sanchez-Graillet, O., Upton, GJG. and Harrison, AP., (2010). Identifying the impact of G-Quadruplexes on Affymetrix 3' Arrays using Cloud Computing. Journal of Integrative Bioinformatics. 7(2) (111)
Rowsell, J., Camargo, RDS., Langdon, WB., Stalteri, MA. and Harrison, AP., (2010). Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips. Journal of Integrative Bioinformatics. 7(3) (137)
Sanchez-Graillet, O., Stalteri, MA., Rowsell, J., Upton, GJG. and Harrison, AP., (2010). Using surveys of Affymetrix GeneChips to study antisense expression. Journal of integrative bioinformatics. 7(2) (114)
Upton, GJG. and Harrison, AP., (2010). The detection of blur in affymetrix GeneChips.. Statistical applications in genetics and molecular biology. 9 (1), creators-Harrison=3AAndrew_P=3A=3A
Langdon, WB., Upton, GJG. and Harrison, AP., (2009). Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips. Briefings in Bioinformatics. 10 (3), 259-277
Langdon, WB. and Harrison, AP., (2009). Evolving DNA motifs to predict GeneChip probe performance. Algorithms for Molecular Biology. 4 (1), 6-
Upton, GJG., Sanchez-Graillet, O., Rowsell, J., Arteaga-Salas, JM., Graham, NS., Stalteri, MA., Memon, FN., May, ST. and Harrison, AP., (2009). On the causes of outliers in Affymetrix GeneChip data. Briefings in Functional Genomics and Proteomics. 8 (3), 199-212
Harrison, AP., Rowsell, J., Camargo, RDS., Langdon, WB., Stalteri, M., Upton, GJG. and Arteaga-Salas, JM., (2008). The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA. Biochemical Society Transactions. 36 (3), 511-513
Langdon, WB. and Harrison, AP., (2008). GP on SPMD parallel graphics hardware for mega Bioinformatics data mining. Soft Computing. 12 (12), 1169-1183
Arteaga-Salas, JM., Harrison, AP. and Upton, GJG., (2008). Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information. Statistical Applications in Genetics and Molecular Biology. 7 (1), Article29-
Chen, M. and Harrison, AP., (2008). In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops. Genomics, Proteomics & Bioinformatics. 6 (3-4), 190-198
Upton, GJG., Langdon, WB. and Harrison, AP., (2008). G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics. 9 (1), 613-613
Arteaga-Salas, JM., Zuzan, H., Langdon, WB., Upton, GJG. and Harrison, AP., (2008). An overview of image-processing methods for Affymetrix GeneChips. Briefings in Bioinformatics. 9 (1), 25-33
Sanchez-Graillet, O., Rowsell, J., Langdon, WB., Stalteri, M., Arteaga-Salas, JM., Upton, GJG. and Harrison, AP., (2008). Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips.. Journal of integrative bioinformatics. 5 (2), 298-305
Upton, GJG., Langdon, WB. and Harrison, AP., (2008). G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics. 9 (1), creators-Harrison=3AAndrew_P=3A=3A
Harrison, AP., Rowsell, J., Camargo, RDS., Langdon, WB., Stalteri, M., Upton, GJG. and Arteaga-Salas, JM., (2008). The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA. Biochemical Society Transactions. 36 (Part 3), 511-513
Harrison, AP., Johnston, CE. and Orengo, CA., (2007). Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics. 8 (1), 195-
Stalteri, MA. and Harrison, AP., (2007). Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics. 8 (1), 13-
Redfern, OC., Harrison, A., Dallman, T., Pearl, FMG. and Orengo, CA., (2007). CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures. PLoS Computational Biology. 3 (11), e232-e232
Harrison, AP., Johnston, CE. and Orengo, CA., (2007). Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics. 8 (1), creators-Harrison=3AAndrew_P=3A=3A
Stalteri, MA. and Harrison, AP., (2007). Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics. 8 (1), creators-Harrison=3AAndrew_P=3A=3A
Stalteri, M. and Harrison, A., (2006). Comparisons of Annotation Predictions for Affymetrix GeneChips??. Applied Bioinformatics. 5 (4), 237-248
Myers, RE., Gale, CV., Harrison, A., Takeuchi, Y. and Kellam, P., (2005). A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics. 21 (17), 3535-3540
Pearl, F., (2004). The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research. 33 (Database issue), D247-D251
Harrison, A., Pearl, F., Sillitoe, I., Slidel, T., Mott, R., Thornton, J. and Orengo, C., (2003). Recognizing the fold of a protein structure. Bioinformatics. 19 (14), 1748-1759
Pearl, FMG., (2003). The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Research. 31 (1), 452-455
Harrison, A., Pearl, F., Mott, R., Thornton, J. and Orengo, C., (2002). Quantifying the Similarities within Fold Space. Journal of Molecular Biology. 323 (5), 909-926
Pearl, FMG., (2001). A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Research. 29 (1), 223-227
Pearl, FMG., (2000). Assigning genomic sequences to CATH. Nucleic Acids Research. 28 (1), 277-282
Book chapters (1)
Harrison, A. and Shanahan, H., (2014). An Overview of Gene Regulation. In: Approaches in Integrative Bioinformatics. Springer Berlin Heidelberg. 21- 69. 9783642412806
Conferences (7)
Mahmoud, O., Harrison, A., Gul, A., Khan, Z., Metodiev, MV. and Lausen, B., (2016). Minimizing Redundancy Among Genes Selected Based on the Overlapping Overlapping Analysis
Alhaji, BB., Dai, H., Hayashi, Y., Vinciotti, V., Harrison, A. and Lausen, B., (2016). Analysis of ChIP-seq Data Via Bayesian Finite Mixture Models with a Non-parametric Component
Khuhro, ZUA. and Harrison, AP., (2010). A set of tolerance values for identifying shared motifs in RNA tertiary structures
Langdon, WB., Rowsell, J. and Harrison, AP., (2009). Creating regular expressions as mRNA motifs with GP to predict human exon splitting
Langdon, WB. and Harrison, AP., (2008). Evolving Regular Expressions for GeneChip Probe Performance Prediction
Kheniche, A., Salhi, A., Harrison, A. and Dowden, JM., (2008). A deterministic algorithm for DNA sequence comparison
Orengo, CA., Bray, JE., Buchan, DWA., Harrison, A., Lee, D., Pearl, FMG., Sillitoe, I., Todd, AE. and Thornton, JM., (2002). The CATH protein family database: A resource for structural and functional annotation of genomes
Reports and Papers (1)
Langdon, WB. and Harrison, AP., (2008). CES-483 Evolving Regular Expressions for GeneChip Probe Performance Prediction
Grants and funding
2011
Development of Bioinformatics Research...
British Council
Virtual Multidisciplinary EnviroNments using Cloud Infrastructures (Venus-C)
Royal Holloway & Bedford New College
2010
Chips, Computers & Crops SS10-015
Medical Research Council
2009
Chips, crops and computers
Biotechnology & Biology Science Res.Council
2008
China Partnering Award
Biotechnology & Biology Science Res.Council