Select Publications

Journal articles

Tombor LS; John D; Glaser SF; Luxán G; Forte E; Furtado M; Rosenthal N; Baumgarten N; Schulz MH; Wittig J; Rogg EM; Manavski Y; Fischer A; Muhly-Reinholz M; Klee K; Looso M; Selignow C; Acker T; Bibli SI; Fleming I; Patrick R; Harvey RP; Abplanalp WT; Dimmeler S, 2021, 'Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction', Nature Communications, vol. 12, pp. 681, http://dx.doi.org/10.1038/s41467-021-20905-1

Janbandhu V; Tallapragada V; Patrick R; Li Y; Abeygunawardena D; Humphreys DT; Martin EMMA; Ward AO; Contreras O; Farbehi N; Yao E; Du J; Dunwoodie SL; Bursac N; Harvey RP, 2021, 'Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction.', Cell Stem Cell, http://dx.doi.org/10.1016/j.stem.2021.10.009

Patrick R; Humphreys DT; Janbandhu V; Oshlack A; Ho JWK; Harvey RP; Lo KK, 2020, 'Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data', Genome Biology, vol. 21, pp. 167, http://dx.doi.org/10.1186/s13059-020-02071-7

Vidal R; Wagner JUG; Braeuning C; Fischer C; Patrick R; Tombor L; Muhly-Reinholz M; John D; Kliem M; Conrad T; Guimarães-Camboa N; Harvey R; Dimmeler S; Sauer S, 2019, 'Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart', JCI Insight, vol. 4, http://dx.doi.org/10.1172/jci.insight.131092

Combes AN; Phipson B; Lawlor KT; Dorison A; Patrick R; Zappia L; Harvey RP; Oshlack A; Little MH, 2019, 'Erratum: Correction: Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk (doi:10.1242/dev.178673) (Development (Cambridge, England) (2019) 146 12 PII: dev182162)', Development (Cambridge, England), vol. 146, http://dx.doi.org/10.1242/dev.182162

Combes AN; Phipson B; Lawlor KT; Dorison A; Patrick R; Zappia L; Harvey RP; Oshlack A; Little MH, 2019, 'Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk', Development (Cambridge), vol. 146, http://dx.doi.org/10.1242/DEV.178673

Farbehi N; Patrick R; Dorison A; Xaymardan M; Janbandhu V; Wystub-Lis K; Ho JWK; Nordon RE; Harvey RP, 2019, 'Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury', eLife, vol. 8, http://dx.doi.org/10.7554/eLife.43882

Kabir MH; Patrick R; Ho JWK; O'Connor MD, 2018, 'Identification of active signaling pathways by integrating gene expression and protein interaction data', BMC Systems Biology, vol. 12, http://dx.doi.org/10.1186/s12918-018-0655-x

Farbehi N; Patrick R; Xaymardan M; Harvey R; Nordon R, 2018, 'Large-scale, single cell RNA sequencing defines novel cellular subsets required for cardiac repair', Cytotherapy, vol. 20, pp. S14 - S14, http://dx.doi.org/10.1016/j.jcyt.2018.02.024

Patrick R; Kobe B; Lê Cao KA; Bodén M, 2017, 'PhosphoPICK-SNP: Quantifying the effect of amino acid variants on protein phosphorylation', Bioinformatics, vol. 33, pp. 1773 - 1781, http://dx.doi.org/10.1093/bioinformatics/btx072

Zamir L; Singh R; Nathan E; Patrick R; Yifa O; Yahalom-Ronen Y; Arraf AA; Schultheiss TM; Suo S; Han JDJ; Peng G; Jing N; Wang Y; Palpant N; Tam PPL; Harvey RP; Tzahor E, 2017, 'Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta', eLife, vol. 6, http://dx.doi.org/10.7554/eLife.20994

Patrick R; Horin C; Kobe B; Cao KAL; Bodén M, 2016, 'Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence', Biochimica et Biophysica Acta - Proteins and Proteomics, vol. 1864, pp. 1599 - 1608, http://dx.doi.org/10.1016/j.bbapap.2016.08.001

Patrick R; Le Cao KA; Kobe B; Boden M, 2015, 'PhosphoPICK: Modelling cellular context to map kinase-substrate phosphorylation events', Bioinformatics, vol. 31, pp. 382 - 389, http://dx.doi.org/10.1093/bioinformatics/btu663

Mehdi AM; Patrick R; Bailey TL; Boden M, 2014, 'Predicting the dynamics of protein abundance', Molecular and Cellular Proteomics, vol. 13, pp. 1330 - 1340, http://dx.doi.org/10.1074/mcp.M113.033076

Patrick R; Cao KAL; Davis M; Kobe B; Bodén M, 2012, 'Mapping the stabilome: A novel computational method for classifying metabolic protein stability', BMC Systems Biology, vol. 6, http://dx.doi.org/10.1186/1752-0509-6-60

Asli NS; Xaymardan M; Patrick R; Farbehi N; Cornwell J; Forte E; Waardenberg AJ; Janbandhu V; Kesteven S; Chandrakanthan V; Malinowska H; Reinhard H; Schofield P; Christ D; Ahmed I; Bouveret R; Srivastava S; Mishra RK; Dhawan J; Chong JJH; Nordon R; Macdonald P; Graham RM; Feneley M; Harvey RP, 'PDGFRα signaling in cardiac fibroblasts modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair', , http://dx.doi.org/10.1101/225979

Working Papers

Patrick R; Humphreys D; Janbandhu V; Oshlack A; Ho JWK; Harvey R; Lo K, 2019, Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data, http://dx.doi.org10.1101/867309

Preprints

Patrick R; Horin C; Kobe B; Lê Cao K-A; Bodén M, Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence, http://dx.doi.org/10.1101/043679


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