Novel Methodology for Predicting the Functional Effects of Genetic Variation

Research output

Research output per year 2015 2016 2017 2020

• 17 Article (Academic Journal)
• 1 Conference Contribution (Conference Proceeding)
• 1 Review article (Academic Journal)

Research output per year

Research output per year

Search results

• 2020

  A Novel Stratification Framework for Predicting Outcome in Patients with Prostate Cancer

  Campbell, I. C. G., Luca, B., Moulton, V., Ellis, C., Edwards, D. R., Cooper, R., Clark, J., Brewer, D. & Campbell, C., 20 Mar 2020, In: British Journal of Cancer.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  • Inpatient 100%
  • Prostate Cancer 100%
  • Malignant Neoplasm 40%
  • Biochemical Recurrence 40%
  • Patient 20%
  6 Citations (Scopus)

• CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome

  Rogers, M. F., Gaunt, T. R. & Campbell, C., 13 Apr 2020, In: Bioinformatics. btaa242.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Malignant Neoplasm 100%
  • Somatics 100%
  • Point Mutation 100%
  • Coding Region 57%
  • Germline 42%
  9 Citations (Scopus)

  89 Downloads (Pure)

• Prediction of driver variants in the cancer genome via machine learning methodologies

  Rogers, M. F., Gaunt, T. R. & Campbell, I. C. G., 22 Oct 2020, In: Briefings in Bioinformatics. (2020), 10 p., bbaa250.

  Research output: Contribution to journal › Review article (Academic Journal) › peer-review

  Open Access

  File

  • Learning 100%
  • Drive 100%
  • Cell Proliferation 100%
  • Sequencing 100%
  • Human Genome 100%
  7 Citations (Scopus)

  88 Downloads (Pure)
• 2018

  FATHMM-XF: accurate prediction of pathogenic point mutations via extended features

  Rogers, M., Shihab, H. A., Mort, M., Cooper, D. N., Gaunt, T. & Campbell, C., 1 Feb 2018, In: Bioinformatics. 34, 3, p. 511-513 3 p., btx536.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Point Mutation 100%
  • Mutation 50%
  • Coding 50%
  • Human Genome 50%
  194 Citations (Scopus)

  537 Downloads (Pure)
• 2017

  An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

  Ferlaino, M., Rogers, M. F., Shihab, H. A., Mort, M., Cooper, D. N., Gaunt, T. R. & Campbell, C., 6 Oct 2017, In: BMC Bioinformatics. 18, 1, 442.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Indel 100%
  • Coding Region 100%
  • Human Genome 100%
  • Coding 20%
  • Mutation 20%
  23 Citations (Scopus)

  325 Downloads (Pure)

• A Pathway-centric Approach to Rare Variant Association Analysis

  Richardson, T., Timpson, N., Campbell, C. & Gaunt, T., Jan 2017, In: European Journal of Human Genetics. 25, 1, p. 123-129 7 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Nested Gene 100%
  • Association 100%
  • Association Analysis 100%
  • Centric Approach 100%
  • Annotation 40%
  10 Citations (Scopus)

  305 Downloads (Pure)

• CScape: a tool for predicting oncogenic single-point mutations in the cancer genome

  Rogers, M., Shihab, H., Gaunt, T. & Campbell, C., 14 Sept 2017, In: Scientific Reports. 7, 1, 11 p., 11597.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Point Mutation 100%
  • Coding Region 100%
  • Malignant Neoplasm 100%
  • Tools 100%
  • Accuracy 50%
  34 Citations (Scopus)

  417 Downloads (Pure)

• GTB – An Online Genome Tolerance Browser

  Shihab, H., Rogers, M., Ferlaino, M., Campbell, C. & Gaunt, T., 6 Jan 2017, In: BMC Bioinformatics. 18, 20, 6 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Mutation 100%
  • Computer Model 100%
  • Single-Nucleotide Polymorphism 100%
  • Electric Potential 50%
  • Human Genome 50%
  4 Citations (Scopus)

  358 Downloads (Pure)

• HIPred: an integrative approach to predicting haploinsufficient genes

  Shihab, H., Rogers, M., Campbell, C. & Gaunt, T., 15 Jun 2017, In: Bioinformatics. 33, 12, p. 1751-1757 7 p., btx028.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Nested Gene 100%
  • Haploinsufficiency 66%
  • Learning 16%
  • Sequencing 16%
  • DNA 16%
  23 Citations (Scopus)

  392 Downloads (Pure)

• Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis

  Scott, H., Rogers, M. F., Scott, H. L., Campbell, C., Warburton, E. C. & Uney, J. B., 15 Jun 2017, In: Behavioural Brain Research. 328, p. 1-12 12 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Gene 100%
  • Perirhinal Cortex 100%
  • Gene Expression 100%
  • Transcriptomics 100%
  • Recognition Memory 100%
  5 Citations (Scopus)

  487 Downloads (Pure)

• Unsupervised network analysis of the plastic supraoptic nucleus transcriptome predicts caprin2 regulatory interactions

  Loh, S. Y., Jahans-Price, T., Greenwood, M. P., Greenwood, M., Hoe, S. Z., Konopacka, A., Campbell, C., Murphy, D. & Hindmarch, C. C. T., Nov 2017, In: eNeuro. 4, 6, 13 p., e0243-17.2017.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Transcriptome 100%
  • Supraoptic Nucleus 100%
  • Nested Gene 50%
  • Rat 50%
  • Gene 50%
  4 Citations (Scopus)

  285 Downloads (Pure)
• 2016

  A protein domain and family based approach to rare variant association analysis

  Richardson, T., Shihab, H., Rivas, M. A., McCarthy, M. I., Campbell, C., Timpson, N. & Gaunt, T., 29 Apr 2016, In: PLoS ONE. 11, 4, 12 p., e0153803.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Association 100%
  • Protein Family 100%
  • Nested Gene 37%
  • Gene 37%
  • Lipid 12%
  4 Citations (Scopus)

  301 Downloads (Pure)

• Collapsed Methylation Quantitative Trait Loci analysis for Low Frequency and Rare variants

  Richardson, T., Shihab, H., Hemani, G., Zheng, J., Hannon, E., Mill, J., Carnero-Montoro, E., Bell, J. T., Lyttleton, O., McArdle, W., Ring, S., Rodriguez, S., Campbell, C., Davey Smith, G., Relton, C., Timpson, N. & Gaunt, T., 1 Oct 2016, In: Human Molecular Genetics. 25, 19, p. 4339-4349 11 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Methylation 100%
  • Quantitative Trait Locus 100%
  • Association 75%
  • DNA Methylation 50%
  • Time 25%
  9 Citations (Scopus)

  423 Downloads (Pure)

• Incorporating non-coding annotations into rare variant analysis

  Richardson, T., Campbell, C., Timpson, N. & Gaunt, T., 29 Apr 2016, In: PLoS ONE. 11, 4, 15 p.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Coding 100%
  • Filtration 100%
  • Association 30%
  • Bioinformatics 30%
  • Nested Gene 20%
  7 Citations (Scopus)

  300 Downloads (Pure)

• RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways

  Jiang, L., Hindmarch, C. C. T., Rogers, M., Campbell, C., Waterfall, C., Coghill, J., Mathieson, P. W. & Welsh, G. I., 24 Oct 2016, In: Scientific Reports. 6, 11 p., 35671.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Immunity 100%
  • Glucocorticoid 100%
  • Gene 100%
  • Podocyte 100%
  • RNA Sequence 100%
  20 Citations (Scopus)

  325 Downloads (Pure)

• Texture analysis in gel electrophoresis images using an integrative kernel-based approach

  Fernandez-Lozano, C., Seoane, J. A. A., Gestal, M., Gaunt, T. R., Dorado, J., Pazos, A. & Campbell, I. C. G., 13 Jan 2016, In: Scientific Reports. 6, 13 p., 19256.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Approach 100%
  • Image 100%
  • Texture 100%
  • Gel 100%
  • Electrophoresis 100%
  14 Citations (Scopus)

  344 Downloads (Pure)
• 2015

  An Integrative Approach to Predicting the Functional Effects of Non-Coding and Coding Sequence Variation

  Shihab, H. A., Rogers, M. F., Gough, J. J. T., Mort, M., Cooper, D. N., Day, I. N. M., Gaunt, T. R. & Campbell, I. C. G., 15 May 2015, In: Bioinformatics. 31, 10, p. 1536–1543

  Research output: Contribution to journal › Article (Academic Journal) › peer-review
  381 Citations (Scopus)

• iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

  Rivers, C. A., Idris, J., Scott, H. L., Rogers, M. F., Lee, Y-B., Gaunt, J. R., Phylactou, L., Curk, T., Campbell, I. C. G., Ule, J., Norman, M. R. & Uney, J. B., 22 Dec 2015, In: BMC Biology. 13, 1, 15 p., 111.

  Research output: Contribution to journal › Article (Academic Journal) › peer-review

  Open Access

  File

  • Exon 100%
  • RNA Processing 100%
  • Coding 80%
  • Nested Gene 60%
  • Isoform 60%
  17 Citations (Scopus)

  379 Downloads (Pure)

• Sequential data selection for predicting the pathogenic effects of sequence variation

  Rogers, M. F., Campbell, C., Shihab, H. A., Gaunt, T. R., Mort, M. & Cooper, D. N., 16 Dec 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers (IEEE), p. 639-644 6 p. 7359759

  Research output: Chapter in Book/Report/Conference proceeding › Conference Contribution (Conference Proceeding)

  Open Access

  File

  • Data Source 100%
  • Learning 71%
  • Multiple Kernel Learning 57%
  • Models 57%
  • Weight 57%
  4 Citations (Scopus)

  368 Downloads (Pure)