Career Profile

I am a PhD Student in bioinformatics with major in molecular biology. My points of interest are statistical modelling, genomics, and human genetics. I am passionate about storytelling, writing, and … sport.

Experiences

Ph.D. student - Data integration and epigenomics

2015 - Present
Bioinformatics and Omics Data Science Group, BIMSB, Berlin

My core research idea is to develop a computational model to associate regulatory regions and their target genes using data integration approaches:

  • Integrated various datasets (H3K4me1,H3K27ac, DNAme, DHS, HiC) and algorithms (elastic net, random forest, distance correlation and correlation)
  • in process of writing: reg2gene: Predicting enhancer - gene associations using ensemble learning approaches [publication and thesis]
  • Developed two R packages: reg2gene and myDNA
  • Started myDNA blog and developed myDNA Shiny App

Visiting scientist - Machine learning and polygenic risk scores

Spring 2015
MRC Human Genetics Unit, University of Edinburgh, Edinburgh

I focused on improving machine learning models to calculate polygenic risk score

  • Performed GWAS and analysis of exome datasets
  • Tested LASSO, ridge regression, random forest, CART calculation for polygenic risk scores for metabolic syndrome
  • Co-authored 1 publication

Researcher - Meta-analyses/sys reviews and infectious diseases

2013 - 2015
prepare-europe.eu, Medical Faculty, University of Split, Split

I supported epidemiological research of infectious diseases:

  • Published 2 systematic reviews and meta-analyses
  • Developed guidelines to improve research design of future association studies
  • Awarded with the New Voices in Global Health Award at the World Health Summit

Researcher - Data analysis and pop genetics in a Biobank facility

2012 - 2014
10,001 Dalmatians - Croatian National Biobank, University of Split

I assisted in establishing and managing the Croatian National Biobank:

  • Interviewed and phenotyped >500 participants
  • Participated in collection and processing of human tissues and other samples
  • Created and maintained filing system for storing records
  • Contributed to the development and maintenance of SOPs
  • Graduated with topic in population genetics: Genetic structure of the human population of Korčula island
  • Analyzed genotypes of thousand Croatian individual with R, STRUCTURE, ADMIXTURE, PLINK, and ADMIXTOOLS softwares.

Biospeleologist - fieldwork and phylogenetic analysis

2007 - 2012
University of Zagreb, University of Ljubljana
  • Collected samples and data in >100 speleological objects during multiple speleological expeditions in different EU countries
  • Reached the bottom of the deepest Croatian cave: Lukina Jama - Trojama (-1431m)
  • Awarded with The Rector’s Award for “Phylogenetic analysis of endemic bivalve Congeria kusceri Bole, 1962 (Dreissenidae, Bivalvia).”
  • Mastered problem solving skills in the wet lab environment: PCR, DNA isolation and sequencing, cell and bacterial culture manipulation…
  • Awarded with: The City of Zagreb Scholarship, University of Zagreb Scholarship for Top Students

Research during the high-school

2004 - 2014
5th Gymnasium

I have been actively engaged in the scientific research since 2004:

  • Conducted research projects:Mendel’s laws applied on the history of one dog family (2004), Human evolution: biology or math? (2005), Cariogram of some fish species (2006)
  • Developed strong analytical skills at the: Summer School of Biology (2004-2006) and Summer School of Science (2006)
  • Developed strong communication and presenting skills by giving talks at the: National Competitions, Faculty of Science (2005), Matrix Croatica (2004-2006)
  • Awarded with: 1st prize at the National Competition in Biology (2004), 2nd prize at the National Competition in Biology (2005 - 2006)

Projects

myDNA - R package for the analysis of direct-to-consumer (DTC) reported genotypes from companies such as myHeritage, 23andMe, ancestryDNA, etc.
climbersforclimbers - Web-site with chains of interviews with climbers - coming in January 2020
PREPARE - Platform for European Preparedness Against (Re-)emerging Epidemics

Publications

Host genetics and susceptibility to congenital and childhood cytomegalovirus infection: a systematic review.
Gelemanović, Andrea, Patarčić I,,et al.
Croatian medical journal 57.4 (2016): 321-330.
Directional dominance on stature and cognition in diverse human populations.
Joshi, Peter K.,…, Patarcic I,…,et al
Nature 523.7561 2015: 459-462.
The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis.
Patarčić I, Gelemanović A, Kirin M, Kolčić I, Baillie K, Rudan I, Campbell H, de Jong M, Polašek O
Scientific Reports 2015
Homozygous loss-of-function variants in European cosmopolitan and isolate populations
Kaiser V., …, Patarcic I, …, Wilson J.F.
Human molecular genetics (2015): ddv272

Conferences and talks

European Human Genetics Conference
Gothenburg, Sweden, 2019, TALK
FEBS Advanced Course 3rd Danube Conference on Epigenetics
Budapest, Hungary, 2018
EMBO Conference: Principles of Chromosomal Structure and Function
Heidelberg, Germany, 2018
CRG and BIMSB Retreat
Barcelona, Spain, 2017, TALK
European Human Genetics Conference
Copenhagen, Denmark, 2017
Bioinformatics Social Meeting
Berlin, Germany, 2016, TALK
EMBO Conference: From functional genomics to systems biology
Heidelberg, Germany, 2016
World Health Summit
Berlin, Germany, 2015
21st International Conference on Subterranean Biology
Košice, Slovakia, 2014
Scientific symposium: Special values of deep karst.
Krasno, Croatia, 2012
18th International Karstological School - Classical Karst
Postojna, Slovenia, 2010