Doctoral Thesis with Honors at ecSeq

Posted on September 07, 2022

University Leipzig

Adam Nunn successfully defended his doctoral thesis on September 5, 2022

On Monday, our PhD student Adam Nunn successfully defended his thesis at the Faculty of Mathematics & Computer Science of the Leipzig University.

The referees all agreed in their decisions: "Summa cum laude" (Passed with highest honors)

Adam has achieved incredible things in the last four years. He has managed the complete server infrastructure of the Marie Skłodowska-Curie Innovative Training Network EpiDiverse, was the main contact person for all 15 PhD students of the project when it came to bioinformatics questions and assembled a new genome in cooperation with University of Minnesota. He also designed, created and maintained several methylation pipelines, which were used by all PhD students for their research.

And here's the thing: He did all of this in parallel to his PhD work.

His PhD thesis was on detecting DNA variants in Bisulfite-Seq data. For this, Adam chose an incredibly simple and clever approach that allowed him to outperform all the tools already on the market. The best inventions don't always have to be the most complicated. Simplicity is where true innovation lies.

During his time as a graduate student, Adam published six papers and was first author on four of these:

  • Nunn A, Otto C, Fasold M, Stadler PF, Langenberger D: 'Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches', BMC Genomics 23, Article number: 477 (2022)

  • Nunn A, Rodríguez-Arévalo I, Tandukar Z, Frels K, Contreras-Garrido A, Carbonell-Bejerano P, Zhang P, Ramos-Cruz D, Jandrasits K, Lanz C, Brusa A, Mirouze M, Dorn K, Galbraith D, Jarvis BA, Sedbrook JC, Wyse DL, Otto C, Langenberger D, Stadler PF, Weigel D, Marks MD, Anderson JA, Becker C, Chopra R: 'Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates', Plant Biotechnol J., 20(5):944-963 (2022)

  • Gawehns F, Postuma M, van Antro M, Nunn A, Sepers B, Fatma S, van Gurp TP, Wagemaker NCAM, Mateman AC, Milanovic-Ivanovic S, Groβe I, van Oers K, Vergeer P, Verhoeven KJF: 'epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing', Mol Ecol Resour, 22(5):2087-2104 (2022)

  • Nunn A, Can SN, Otto C, Fasold M, Díez Rodríguez B, Fernández-Pozo N, Rensing SA, Stadler PF, Langenberger D: 'EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics', NAR Genomics and Bioinformatics, 3(4), lqab106 (2021)

  • Can SN, Nunn A, Galanti D, Langenberger D, Becker C, Volmer K, Heer K, Opgenoorth L, Fernandez-Pozo N, Rensing SA: 'The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline.', Epigenomes, 5(2):12 (2021)

  • Nunn A, Otto C, Stadler PF, Langenberger D: 'Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis', Briefings in Bioinformatics, Volume 22, Issue 5 (2021)

Dr. Adam Nunn

Adam Nunn started with a BSc in Biological Sciences from University of Portsmouth and a double MSc in Bioinformatics and Biology from Lund University, Sweden. Between the bachelor's and the master's degree, he worked for four years as a lead research scientist for a UK-based company where he focused on developing biological alternatives to chemical pesticides. In 2017 he joined ecSeq Bioinformatics GmbH for his PhD studies. His work is fully funded by the Marie Skłodowska-Curie Innovative Training Network EpiDiverse and in cooperation with Prof. Peter F. Stadler, holder of the bioinformatics chair at Leipzig University. On September 5, 2022, he successfully defended his doctoral thesis at the University of Leipzig. His work was evaluated with a "Summa cum laude" and he will be entitled to use the title "Dr. rer. nat" in the future.

Dr. Adam Nunn
Dr. Adam Nunn
Dr. Adam Nunn
Dr. Adam Nunn
Dr. Adam Nunn
Dr. Adam Nunn

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