Browse by Person

Article

Wang, Xiaoliang and Harrison, Andrew (2022) Non-kin selection enhances complexity in cooperation: A unified quantitative law. Computational Biology and Chemistry, 101. p. 107782. DOI https://doi.org/10.1016/j.compbiolchem.2022.107782

Woldegiorgis, Samuel Tareke and Wu, Ti and Gao, Linghui and Huang, Yunxia and Zheng, Yingjie and Qiu, Fuxiang and Xu, Shichang and Tao, Huan and Harrison, Andrew and Liu, Wei and He, Huaqin (2022) Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics, and QTLs. Genes, 13 (8). p. 1353. DOI https://doi.org/10.3390/genes13081353

Wang, Xiaoliang and Harrison, Andrew and Chang, Yunlong and Liu, Jian (2022) Pinching arc plasmas by high-frequency alternating longitudinal magnetic field. Physics of Plasmas, 29 (7). 073506-073506. DOI https://doi.org/10.1063/5.0083796

Osuntoki, Itunu G and Harrison, Andrew and Dai, Hongsheng and Bao, Yanchun and Zabet, Nicolae Radu (2022) ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. Bioinformatics, 38 (14). btac387-btac387. DOI https://doi.org/10.1093/bioinformatics/btac387

Chathoth, Keerthi and Mikheeva, Liudmila and Crevel, Gilles and Wolfe, Jareth and Hunter, Ioni and Beckett-Doyle, Saskia and Cotterill, Sue and Dai, Hongsheng and Harrison, Andrew and Zabet, Nicolae (2022) The role of Insulators and transcription in 3D chromatin organisation of flies. Genome Research, 32 (4). pp. 682-698. DOI https://doi.org/10.1101/gr.275809.121 (In Press)

Hu, Xiaotian and Feng, Cong and Zhou, Yincong and Harrison, Andrew and Chen, Ming (2022) DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. Bioinformatics, 28 (3). pp. 694-702. DOI https://doi.org/10.1093/bioinformatics/btab737

Cannataro, Mario and Harrison, Andrew (2021) Bioinformatics helping to mitigate the impact of COVID-19 - Editorial. Briefings in Bioinformatics, 22 (2). pp. 613-615. DOI https://doi.org/10.1093/bib/bbab063

Tareke Woldegiorgis, Samuel and Wang, Shaobo and He, Yiruo and Xu, Zhenhua and Chen, Lijuan and Tao, Huan and Zhang, Yu and Zou, Yang and Harrison, Andrew and Zhang, Lina and Ai, Yufang and Liu, Wei and He, Huaqin (2019) Rice Stress-Resistant SNP Database. Rice, 12 (1). 97-. DOI https://doi.org/10.1186/s12284-019-0356-0

Chen, Ming and Harrison, Andrew and Shanahan, Hugh and Orlov, Yuriy (2017) Biological Big Bytes: Integrative Analysis of Large Biological Datasets. Journal of Integrative Bioinformatics, 14 (3). DOI https://doi.org/10.1515/jib-2017-0052

Li, Kuan and Xu, Chaoqun and Huang, Jian and Liu, Wei and Zhang, Lina and Wan, Weifeng and Tao, Huan and Li, Li and Lin, Shukai and Harrison, Andrew and He, Huaqin (2017) Prediction and identification of the effectors of heterotrimeric G proteins in rice (Oryza sativaL.). Briefings in Bioinformatics, 18 (2). pp. 270-278. DOI https://doi.org/10.1093/bib/bbw021

Wang, Jingjing and Meng, Xianwen and Yuan, Chunhui and Harrison, Andrew P and Chen, Ming (2016) The roles of cross-talk epigenetic patterns in<i>Arabidopsis thaliana</i>. Briefings in Functional Genomics, 15 (4). pp. 278-287. DOI https://doi.org/10.1093/bfgp/elv025

Alhaji, Baba B and Dai, Hongsheng and Hayashi, Yoshiko and Vinciotti, Veronica and Harrison, Andrew and Lausen, Berthold (2016) Bayesian analysis for mixtures of discrete distributions with a non-parametric component. Journal of Applied Statistics, 43 (8). pp. 1369-1385. DOI https://doi.org/10.1080/02664763.2015.1100594

Bai, Youhuang and Dai, Xiaozhuan and Harrison, Andrew and Johnston, Caroline and Chen, Ming (2016) Toward a next-generation atlas of RNA secondary structure. Briefings in Bioinformatics, 17 (1). pp. 63-77. DOI https://doi.org/10.1093/bib/bbv026

Corpas, Manuel and Valdivia-Granda, Willy and Torres, Nazareth and Greshake, Bastian and Coletta, Alain and Knaus, Alexej and Harrison, Andrew P and Cariaso, Mike and Moran, Federico and Nielsen, Fiona and Swan, Daniel and Weiss Solís, David Y and Krawitz, Peter and Schacherer, Frank and Schols, Peter and Yang, Huangming and Borry, Pascal and Glusman, Gustavo and Robinson, Peter N (2015) Crowdsourced direct-to-consumer genomic analysis of a family quartet. BMC Genomics, 16 (1). 910-. DOI https://doi.org/10.1186/s12864-015-1973-7

Shanahan, H and 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, Shoukai and Song, Qi and Tao, Huan and Wang, Wei and Wan, Weifeng and Huang, Jian and Xu, Chaoqun and Chebii, Vivien and Kitony, Justine and Que, Shufu and Harrison, Andrew and He, Huaqin (2015) Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites. Scientific Reports, 5 (1). 11940-. DOI https://doi.org/10.1038/srep11940

Yuan, C and Wang, J and Harrison, AP and Meng, X and Chen, D and Chen, M (2015) Genome-wide view of natural antisense transcripts in Arabidopsis thaliana. DNA Research, 22 (3). pp. 233-243. DOI https://doi.org/10.1093/dnares/dsv008

Bai, Y and Dai, X and Harrison, AP and Chen, M (2015) RNA regulatory networks in animals and plants: a long noncoding RNA perspective. Briefings in Functional Genomics, 14 (2). pp. 91-101. DOI https://doi.org/10.1093/bfgp/elu017

Mahmoud, Osama and Harrison, Andrew and Perperoglou, Aris and Gul, Asma and Khan, Zardad and Metodiev, Metodi V and Lausen, Berthold (2014) A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. BMC Bioinformatics, 15 (1). 274-. DOI https://doi.org/10.1186/1471-2105-15-274

Shanahan, Hugh P and Owen, Anne M and Harrison, Andrew P (2014) Bioinformatics on the Cloud Computing Platform Azure. PLoS ONE, 9 (7). e102642-e102642. DOI https://doi.org/10.1371/journal.pone.0102642

Chen, Dijun and Fu, Liang-Yu and Zhang, Zhao and Li, Guoliang and Zhang, Hang and Jiang, Li and Harrison, Andrew P and Shanahan, Hugh P and Klukas, Christian and Zhang, Hong-Yu and Ruan, Yijun and Chen, Ling-Ling and Chen, Ming (2014) Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Research, 42 (5). pp. 3028-3043. DOI https://doi.org/10.1093/nar/gkt1294

Musa, Ibrahim K and Walker, Stuart D and Owen, Anne M and Harrison, Andrew P (2014) Self-service infrastructure container for data intensive application. Journal of Cloud Computing: Advances, Systems and Applications, 3 (1). p. 5. DOI https://doi.org/10.1186/2192-113x-3-5

Harrison, A and Binder, H and Buhot, A and Burden, CJ and Carlon, E and Gibas, C and Gamble, LJ and Halperin, A and Hooyberghs, J and Kreil, DP and Levicky, R and Noble, PA and Ott, A and Pettitt, BM and Tautz, D and Pozhitkov, AE (2013) Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research, 41 (5). pp. 2779-2796. DOI https://doi.org/10.1093/nar/gks1358

Upton, Graham JG and Harrison, Andrew P (2012) Motif effects in Affymetrix GeneChips seriously affect probe intensities. Nucleic Acids Research, 40 (19). pp. 9705-9716. DOI https://doi.org/10.1093/nar/gks717

Shanahan, Hugh P and Memon, Farhat N and Upton, Graham JG and Harrison, Andrew P (2012) Normalized Affymetrix expression data are biased by G-quadruplex formation. Nucleic Acids Research, 40 (8). pp. 3307-3315. DOI https://doi.org/10.1093/nar/gkr1230

Langdon, WB and Upton, GJG and 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). pp. 647-653. DOI https://doi.org/10.1109/tcbb.2008.108

Upton, Graham JG and Harrison, Andrew P (2010) The Detection of Blur in Affymetrix GeneChips. Statistical Applications in Genetics and Molecular Biology, 9 (1). Article37-. DOI https://doi.org/10.2202/1544-6115.1590

Memon, FN and Owen, AM and Sanchez-Graillet, O and 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-. DOI https://doi.org/10.1515/jib-2010-111

Rowsell, J and da Silva Camargo, R and Langdon, WB and Stalteri, MA and Harrison, AP (2010) Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. Journal of integrative bioinformatics, 7 (3). DOI https://doi.org/10.1515/jib-2010-137

Sanchez-Graillet, O and Stalteri, MA and Rowsell, J and Upton, GJG and Harrison, AP (2010) Using surveys of Affymetrix GeneChips to study antisense expression. Journal of integrative bioinformatics, 7 (2). pp. 1662-1668. DOI https://doi.org/10.1515/jib-2010-114

Memon, Farhat Naureen and Upton, Graham JG and Harrison, Andrew P (2010) A Comparative Study of the Impact of G‐Stack Probes on Various Affymetrix GeneChips of Mammalia. Journal of Nucleic Acids, 2010 (1). pp. 1-6. DOI https://doi.org/10.4061/2010/489736

Kheniche, A and Salhi, A and Harrison, A and Dowden, JM (2010) A Deterministic DNA Database Search. Advances in Experimental Medicine and Biology, 680. pp. 371-378. DOI https://doi.org/10.1007/978-1-4419-5913-3_42

Langdon, WB and Harrison, AP (2009) Evolving DNA motifs to predict GeneChip probe performance. Algorithms for Molecular Biology, 4 (1). 6-. DOI https://doi.org/10.1186/1748-7188-4-6

Langdon, WB and 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). pp. 259-277. DOI https://doi.org/10.1093/bib/bbp018

Upton, GJG and Sanchez-Graillet, O and Rowsell, J and Arteaga-Salas, JM and Graham, NS and Stalteri, MA and Memon, FN and May, ST and Harrison, AP (2009) On the causes of outliers in Affymetrix GeneChip data. Briefings in Functional Genomics and Proteomics, 8 (3). pp. 199-212. DOI https://doi.org/10.1093/bfgp/elp027

Upton, Graham JG and Langdon, William B and Harrison, Andrew P (2008) G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics, 9 (1). 613-. DOI https://doi.org/10.1186/1471-2164-9-613

Langdon, WB and Harrison, AP (2008) GP on SPMD parallel graphics hardware for mega Bioinformatics data mining. Soft Computing, 12 (12). pp. 1169-1183. DOI https://doi.org/10.1007/s00500-008-0296-x

Harrison, Andrew P and Rowsell, Joanna and Camargo, Renata da Silva and Langdon, William B and Stalteri, Maria and Upton, Graham JG and Arteaga-Salas, Jose M (2008) The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA. Biochemical Society Transactions, 36 (3). pp. 511-513. DOI https://doi.org/10.1042/bst0360511

Arteaga-Salas, Jose Manuel and Harrison, Andrew P and Upton, Graham JG (2008) Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information. Statistical Applications in Genetics and Molecular Biology, 7 (1). Article29-. DOI https://doi.org/10.2202/1544-6115.1383

Sanchez-Graillet, O and Rowsell, J and Langdon, WB and Stalteri, M and Arteaga-Salas, JM and 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). pp. 298-305. DOI https://doi.org/10.1515/jib-2008-98

Arteaga-Salas, JM and Zuzan, H and Langdon, WB and Upton, GJG and Harrison, AP (2008) An overview of image-processing methods for Affymetrix GeneChips. Briefings in Bioinformatics, 9 (1). pp. 25-33. DOI https://doi.org/10.1093/bib/bbm055

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). pp. 190-198. DOI https://doi.org/10.1016/s1672-0229(09)60007-3

Harrison, Andrew P and Johnston, Caroline E and Orengo, Christine A (2007) Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics, 8 (1). 195-. DOI https://doi.org/10.1186/1471-2105-8-195

Stalteri, Maria A and Harrison, Andrew P (2007) Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics, 8 (1). 13-. DOI https://doi.org/10.1186/1471-2105-8-13

Book Section

Harrison, Andrew and Shanahan, Hugh (2014) An Overview of Gene Regulation. In: Approaches in Integrative Bioinformatics. Springer Berlin Heidelberg, pp. 21-69. ISBN 9783642412806. Official URL: http://dx.doi.org/10.1007/978-3-642-41281-3_2

Monograph

Langdon, WB and Harrison, AP (2008) CES-483 Evolving Regular Expressions for GeneChip Probe Performance Prediction. UNSPECIFIED. CES-483, University of Essex, Colchester.

Conference or Workshop Item

Alhaji, Baba B and Dai, Hongsheng and Hayashi, Yoshiko and Vinciotti, Veronica and Harrison, Andrew and Lausen, Berthold (2016) Analysis of ChIP-seq Data Via Bayesian Finite Mixture Models with a Non-parametric Component. In: UNSPECIFIED, ? - ?.

Mahmoud, Osama and Harrison, Andrew and Gul, Asma and Khan, Zardad and Metodiev, Metodi V and Lausen, Berthold (2016) Minimizing Redundancy Among Genes Selected Based on the Overlapping Analysis. In: UNSPECIFIED, ? - ?.

Kheniche, A and Salhi, A and Harrison, A and Dowden, JM (2008) A deterministic algorithm for DNA sequence comparison. In: UNSPECIFIED, ? - ?.

Langdon, William B and Harrison, Andrew P (2008) Evolving Regular Expressions for GeneChip Probe Performance Prediction. In: UNSPECIFIED, ? - ?.