About Me
Hi there, my name is Nikos. I’m a bioinformatician, studying how the human genome folds in 3D and how mutations alter it to promote tumor growth. I got my bachelors degree in Computer Science at the Aristotle University of Thessaloniki and later moved into bioinformatics where I acquired a master’s degree and a PhD by the University of Copenhagen.
As you have probably guessed, I spend most of my working hours behind a screen. I enjoy coding, whether it is to ask questions on data, troubleshoot, or create pipelines. These days, I write most of my code in bash and R.
Sometimes I write R packages and Shiny apps, like a chart to represent multiple observations (sinaplot, geom_sina) or a webserver to browse recurrent genomic structural variants across multiple tumor types (SVscape).
Experience
Senior Research Scientist
Novo Nordisk, Måløv, DK
Sep 2021 - Present
- Targrt assessment of genetics and human expression evidence during the early stages of drug-discovery.
- Identification of deregulated genes/pathways and biomarker discovery in Heart Failure, NASH, CKD and Type-2 Diabetes through RNA-seq and scRNA-seq assays of in vitro and in vivo disease models.
Postdoctoral researcher
BRIC, University of Copenhagen
Dec 2019 - Aug 2021
Research position at the Weischenfeldt Group with focus on:
- Causes and consequences of genomic structural variants
- Assembly of highly rearranged genomes
Teaching assistant
Department of Biology, University of Copenhagen
Feb 2017 - Apr 2017, Feb 2016 - Apr 2016
Workshops of a bioinformatics introductory course to:
Research assistant
Department of Biology, University of Copenhagen
Oct 2015 - Jun 2016
- Development of sinaplot, a novel visualization method for multi-class data
- Survival analyses on the TCGA patient cohort using gene-signature expression profiles
Student assistant
BRIC, University of Copenhagen
Nov 2012 - Feb 2015
Part-time position at the Bioinformatics Core Facility
- Setup and maintainance of local Galaxy servers
- System administration
Education
Ph.D. in Cancer Genomics
University of Copenhagen
2019
Thesis
Functional consequences of structural variants on the 3D architecture of cancer genomes
Advisor
Joachim Weischenfeldt
Secondment at the Aidenlab, Baylor College of Medicine, Houston TX
M.Sc. in Bioinformatics
University of Copenhagen
2015
Thesis
Identifying strong survival predictors in Acute Myeloid Leukemia using gene signatures
Advisors
Nicolas Rapin & Frederik Otzen Bagger
B.Sc. in Computer Science
Aristotle University of Thessaloniki
2011
Thesis
Audio restoration of folklore song recordings from Western Macedonia, Epirus and Thessaly
Advisor
Ioannis Pitas
Publications
2022
Somatic structural variant formation is guided by and influences genome architecture. Sidiropoulos et al. Genome Research. doi: 10.1101/gr.275790.121
2020
Pan-cancer analysis of whole genomes. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network 2020. Nature, 578, 82-93. doi: 10.1038/s41586-020-1969-6
Analyses of non-coding somatic drivers in 2,693 cancer whole genomes. Rheinbay et al. Nature, 578, 102-111. doi: 10.1038/s41586-020-1965-x
2019
The splicing factor RBM25 controls MYC activity in acute myeloid leukemia. Ge & Schuster et al. Nature Communications. 10, 172. doi: 10.1038/s41467-018-08076-y
2018
Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Gerhauser et al. Cancer Cell 34, 996-1011.e8. doi: 10.1016/j.ccell.2018.10.016
SinaPlot: An Enhanced Chart for Simple and Truthful Representation of Single Observations Over Multiple Classes. Sidiropoulos et al. Journal of Computational and Graphical Statistics, 27(3). doi: 10.1080/10618600.2017.1366914
2017
The whole-genome landscape of medulloblastoma subtypes. Northcott et al. Nature, 547(7663), 311-317. doi: 10.1038/nature22973
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Ecker et al. Genome Biology, 18(1). doi: 10.1186/s13059-017-1156-8
The whole-genome panorama of cancer drivers. Sabarinathan & Pich et al. bioRxiv. doi: 10.1101/190330
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes. Waszak et al. bioRxiv. doi: 10.1101/208330
2015
Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools. Kielpinski, Sidiropoulos & Vinther. Methods in Enzymology vol. 558. doi: 10.1016/bs.mie.2015.01.014