Sinan U. Umu

Sinan U. Umu

Postdoctoral Scientist

Cancer Registry of Norway

Biography

I am a postdoc at Cancer Registry of Norway, Oslo. My research interests include RNA sequencing, early detection of cancer (e.g. lung, colorectal) and RNA-RNA interactions.

I did my PhD (Biotechnology/Bioinformatics) at University of Canterbury, New Zealand. I was working on non-coding RNA interactions in prokaryotes. My PhD thesis focused on ncRNA-mRNA interactions in prokaryotic genomes (bacteria and archaea).

Interests

  • RNA biology
  • Cancer biomarkers
  • Non-coding RNAs
  • RNA-RNA interactions

Education

  • PhD in Biotechnology, 2016

    University of Canterbury, New Zealand

  • MSc in Bioinformatics, 2012

    Middle East Technical University, Turkiye

  • BSc in Physics, 2005

    Middle East Technical University, Turkiye

Experience

 
 
 
 
 

Postdoc

Cancer Registry of Norway (Kreftregisteret)

October 2016 – Present Oslo
  • Analysis of serum RNA profiles using RNA sequencing
  • Investigating prediagnostic serum samples for cancer footprints
  • Prediction of carcinogenesis using machine learning models
  • Developing bioinformatics pipelines using Snakemake
  • Variant calling in HPV genomes
  • Building AI models for miRNA prediction
  • Prediction of RNA-RNA interactions
 
 
 
 
 

PhD candidate

University of Canterbury

November 2012 – August 2016 Christchurch
  • Prokaryotic genome annotation
  • Non-coding RNA annotation
  • DNA (Illumina, Pacbio, Nanopore) and RNA sequencing (Illumina)
  • Prediction and benchmarking of RNA-RNA interactions
  • Investigation of prokaryotic RNA interactions
  • Building parallel programming interfaces
  • Modelling protein production in prokaryotes
  • Avoidance hypothesis
 
 
 
 
 

Research Assistant

Department of Chemistry, METU

August 2006 – October 2012 Ankara
  • Network security
  • Database management
  • Web servers maintenance
  • Linux server deployment

Skills

R-cran

(tidyverse syntax, ggplot, caret, Rmarkdown, shiny apps, functional programming, parallelization)

Python

(biopython, numpy, scipy, Snakemake, parallel python, pandas, flask)

Linux

(shell scripting, HPC systems)

Data Science

(Keras framework, h2o, SQL, machine learning)

Recent Publications

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A 10 year prediagnostic followup study shows that serum RNA signals are highly dynamic in lung carcinogenesis
TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity

Contact