Publications: Pfaff, Abigail

Journal Article

Savage, A.L.ORCID: 0000-0002-2231-9800, Iacoangeli, A., Schumann, G.G., Rubio-Roldan, A., Garcia-Perez, J.L., Al Khleifat, A., Kõks, S., Bubb, V.J., Al-Chalabi, A. and Quinn, J.P. (2022) Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene, 843 . Art. 146799.

Fröhlich, A., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Kõks, S. and Quinn, J.P. (2022) Characterisation of the Function of a SINE-VNTR-Alu Retrotransposon to Modulate Isoform Expression at the MAPT Locus. Frontiers in Molecular Neuroscience, 15 . Art. 815695.

Rothzerg, E., Pfaff, A.L.ORCID: 0000-0002-2231-9800 and Kõks, S. (2022) Innovative approaches for treatment of osteosarcoma. Experimental Biology and Medicine .

Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Quinn, J.P. and Kõks, S. (2022) Locus specific reduction of L1 expression in the cortices of individuals with amyotrophic lateral sclerosis. Molecular Brain, 15 (1). Art. 25.

Kõks, S., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V. J. and Quinn, J.P. (2022) Longitudinal intronic RNA-Seq analysis of Parkinson’s disease patients reveals disease-specific nascent transcription. Experimental Biology and Medicine .

Pfaff, A.L.ORCID: 0000-0002-2231-9800, Singleton, L.M. and Kõks, S. (2022) Mechanisms of disease-associated SINE-VNTR-Alus. Experimental Biology and Medicine .

Müller-Nedebock, A.C., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Pienaar, I.S., Kõks, S., van der Westhuizen, F.H., Elson, J.L. and Bardien, S. (2022) Mitochondrial DNA variation in Parkinson’s disease: Analysis of “out-of-place” population variants as a risk factor. Frontiers in Aging Neuroscience, 14 . Art. 921412.

Kõks, S., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Singleton, L.M., Bubb, V.J. and Quinn, J.P. (2022) Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson’s disease. Experimental Biology and Medicine .

Marshall, J.N.G., Fröhlich, A., Li, L., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Middlehurst, B., Spargo, T.P., Iacoangeli, A., Lang, B., Al-Chalabi, A., Kõks, S., Bubb, V.J. and Quinn, J.P. (2022) A polymorphic transcriptional regulatory domain in the amyotrophic lateral sclerosis risk gene CFAP410 correlates with differential isoform expression. Frontiers in Molecular Neuroscience, 15 . Art. 954928.

Kõks, G., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Quinn, J.P. and Kõks, S. (2021) At the dawn of the transcriptomic medicine. Experimental Biology and Medicine, 246 (3). pp. 286-292.

Kõks, S., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J. and Quinn, J.P. (2021) Expression quantitative trait loci (eQTLs) associated with retrotransposons demonstrate their modulatory effect on the transcriptome. International Journal of Molecular Sciences, 22 (12). Article 6319.

Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Quinn, J.P. and Kõks, S. (2021) Reference SVA insertion polymorphisms are associated with Parkinson’s disease progression and differential gene expression. npj Parkinson's Disease, 7 . Article 44.

Bakeberg, M.C., Gorecki, A.M., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Hoes, M.E., Kõks, S., Akkari, P.A., Mastaglia, F.L. and Anderton, R.S. (2021) TOMM40 ‘523’ poly-T repeat length is a determinant of longitudinal cognitive decline in Parkinson’s disease. npj Parkinson's Disease, 7 . Article 56.

Bakeberg, M.C., Hoes, M.E., Gorecki, A.M., Theunissen, F., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Kenna, J.E., Plunkett, K., Kõks, S., Akkari, P.A., Mastaglia, F.L. and Anderton, R.S. (2021) The TOMM40 ‘523’ polymorphism in disease risk and age of symptom onset in two independent cohorts of Parkinson’s disease. Scientific Reports, 11 . Article 6363.

Kõks, S., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J. and Quinn, J.P. (2021) Transcript variants of genes involved in neurodegeneration are differentially regulated by the APOE and MAPT haplotypes. Genes, 12 (3). Article 423.

Marshall, J.N., Lopez, A.I., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Kõks, S., Quinn, J.P. and Bubb, V.J. (2021) Variable number tandem repeats – Their emerging role in sickness and health. Experimental Biology and Medicine, 246 (12). pp. 1368-1376.

Pytte, J., Flynn, L.L., Anderton, R.S., Mastaglia, F.L., Theunissen, F., James, I., Pfaff, A.ORCID: 0000-0002-2231-9800, Kõks, S., Saunders, A.M., Bedlack, R., Burns, D.K., Lutz, M.W., Siddique, N., Siddique, T., Roses, A.D. and Akkari, P.A. (2020) Disease-modifying effects of an SCAF4 structural variant in a predominantly SOD1 ALS cohort. Neurology Genetics, 6 (4). e470.

Savage, A.L.ORCID: 0000-0002-2231-9800, Lopez, A.I., Iacoangeli, A., Bubb, V.J., Smith, B., Troakes, C., Alahmady, N., Kõks, S., Schumann, G.G., Al-Chalabi, A. and Quinn, J.P. (2020) Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis. Molecular Brain, 13 . Article 154.

Pfaff, A.ORCID: 0000-0002-2231-9800, Bubb, V., Quinn, J. and Kõks, S. (2020) Polymorphic reference SVAs are associated with Parkinson's disease progression markers and differential gene expression in the PPMI cohort. Parkinsonism & Related Disorders, 79 (Supp. 1). e30.

Gorecki, A.M., Bakeberg, M.C., Theunissen, F., Kenna, J.E., Hoes, M.E., Pfaff, A.L.ORCID: 0000-0002-2231-9800, Akkari, P.A., Dunlop, S.A., Kõks, S., Mastaglia, F.L. and Anderton, R.S. (2020) Single nucleotide polymorphisms associated with gut homeostasis influence risk and age-at-onset of Parkinson's disease. Frontiers in Aging Neuroscience, 12 . Article 603849.

Pfaff, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Quinn, J.P. and Kõks, S. (2020) An increased burden of highly active retrotransposition competent L1s is associated with Parkinson’s disease risk and progression in the PPMI cohort. International Journal of Molecular Sciences, 21 (18). Article 6562.

Quinn, J.P., Savage, A.L.ORCID: 0000-0002-2231-9800 and Bubb, V.J (2019) Non-coding genetic variation shaping mental health. Current Opinion in Psychology, 27 . pp. 18-24.

Savage, A.L.ORCID: 0000-0002-2231-9800, Schumann, G.G., Breen, G., Bubb, V.J., Al-Chalabi, A. and Quinn, J.P. (2019) Retrotransposons in the development and progression of amyotrophic lateral sclerosis. Journal of Neurology, Neurosurgery & Psychiatry, 90 (3). pp. 284-293.

Gianfrancesco, O., Geary, B., Savage, A.L.ORCID: 0000-0002-2231-9800, Billingsley, K.J., Bubb, V.J. and Quinn, J.P. (2019) The role of SINE-VNTR-Alu (SVA) retrotransposons in shaping the human genome. International Journal of Molecular Sciences, 20 (23). Article 5977.

Vasieva, O., Cetiner, S., Savage, A.ORCID: 0000-0002-2231-9800, Schumann, G.G., Bubb, V.J. and Quinn, J.P. (2017) Potential impact of primate-specific SVA retrotransposons during the evolution of human cognitive function. Trends in Evolutionary Biology, 6 (1). Article 6514.

Vohhodina, J., Barros, E.M., Savage, A.L.ORCID: 0000-0002-2231-9800, Liberante, F.G., Manti, L., Bankhead, P., Cosgrove, N., Madden, A.F., Harkin, D.P. and Savage, K.I. (2017) The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Nucleic Acids Research, 45 (22). pp. 12816-12833.

Warburton, A., Savage, A.L.ORCID: 0000-0002-2231-9800, Myers, P., Peeney, D., Bubb, V.J. and Quinn, J.P. (2015) Molecular signatures of mood stabilisers highlight the role of the transcription factor REST/NRSF. Journal of Affective Disorders, 172 . pp. 63-73.

Wilm, T.P., Savage, A.L.ORCID: 0000-0002-2231-9800, Khursheed, K., Shatunov, A., Morrison, K.E., Shaw, P.J., Shaw, C.E., Smith, B., Breen, G., Al-Chalabi, A., Moss, D., Bubb, V.J. and Quinn, J.P. (2014) An evaluation of a SVA retrotransposon in the FUS promoter as a transcriptional regulator and its association to ALS. PLoS ONE, 9 (3). e90833.

Savage, A.L.ORCID: 0000-0002-2231-9800, Bubb, V.J., Breen, G. and Quinn, J.P. (2013) Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. BMC Evolutionary Biology, 13 . Article Number: 101.

Quinn, J.P., Warburton, A., Myers, P., Savage, A.L.ORCID: 0000-0002-2231-9800 and Bubb, V.J. (2013) Polymorphic variation as a driver of differential neuropeptide gene expression. Neuropeptides, 47 (6). pp. 395-400.

Conference Item

Jones, L.H., Marney, L.D., Quinn, J.P., Bubb, V.J., Kõks, S. and Pfaff, A.L.ORCID: 0000-0002-2231-9800 (2021) Identification of molecular markers that correlate with the progression of Parkinson’s Disease. In: BNA 2021 5th Festival of Neuroscience, 12 - 15 April 2021, Virtual.

Book Chapter

Kõks, S., Singleton, L.M., Quinn, J.P., Bubb, V.J. and Pfaff, A.L.ORCID: 0000-0002-2231-9800 (2022) Analysis of the retrotransposon SINE-VNTR-Alu (SVA) polymorphisms in the genetics and pathophysiology of complex diseases. In: Proukakis, C., (ed.) Genomic Structural Variants in Nervous System Disorders. Humana Press, pp. 63-77.