People

Dr Andrew Harrison

Senior Lecturer

Department of Mathematical Sciences

Email
harry@essex.ac.uk
Telephone

+44 (0) 1206 872964
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

PhD in Astrophysics
BSc in Physics with Astrophysics University of Manchester, (1991)

Appointments

University of Essex

Senior Lecturer, Mathematical Sciences, University of Essex (1/10/2004 - present)

Research and professional activities

Research interests

Bioinformatics

Open to supervise

Big data science

Open to supervise

Teaching and supervision

Current supervision

Najlaa Tarik Jassim Jassim

Degree subject: Statistics
Degree type: Doctor of Philosophy

Itunu Godwin Osuntoki

Degree subject: Bio-Statistics
Degree type: Doctor of Philosophy

Liudmila Mikheeva

Degree subject: Statistics
Degree type: Doctor of Philosophy

Previous supervision

Baba Bukar Alhaji Bukar

Thesis title: Bayesian Analysis for Mixtures of Discrete Distributions with a Non-Parametric Component
Degree subject: Statistics
Degree type: Doctor of Philosophy
Awarded date: 24/5/2016

Anne Margaret Owen

Thesis title: Wide Scale Analysis of Transcriptomics Data Using Cloud Computing Methods
Degree subject: Bioinformatics
Degree type: Doctor of Philosophy
Awarded date: 2/3/2016

Osama Fathy Abdelhaleem Mahmoud

Thesis title: Improving Statistical Learning Within Functional Genomic Experiments By Means of Feature Selection
Degree subject: Statistics
Degree type: Doctor of Philosophy
Awarded date: 8/10/2015

James Christopher Waumsley

Thesis title: An Analysis of Various Heuristic Approaches for Satisfying Routing Requests in Networks
Degree subject: Mathematics
Degree type: Master of Science (by Dissertation)
Awarded date: 22/9/2014

Farhat Naureen Memon

Thesis title: Study of the Effects Caused By the G-Quadruplex Structures on High-Throughput Nucleic Acid Measurements
Degree subject: Bioinformatics
Degree type: Doctor of Philosophy
Awarded date: 6/1/2012

Publications

Journal articles (59)

Ma, S., Song, Q., Tao, H., Harrison, A., Wang, S., Liu, W., Lin, S., Zhang, Z., Ai, Y. and He, H., (2019). Prediction of protein–protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). Briefings in Bioinformatics. 20 (2), 448-456

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 Solís, 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., 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

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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

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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