Nikos Sidiropoulos

3D genomics, data-viz, analog cameras and volleyball

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:

  • Pairwise & multiple alignment
  • Phylogenies
  • RNA-seq analysis
  • Use of MEGA and Galaxy

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