Karolis Koncevičius

I use statistics to analyse large epigenomic datasets.
Laboratory of Epigenomic Studies, Institute of Biotechnology, Life Sciences Center, Vilnius, Lithuania.

karolis.koncevicius@gmail.com

software

R package matrixTests - fast hypothesis tests on rows and columns of matrices.
R package annmatrix - a matrix object with persistent row and column metadata.
R package basetheme - system for adding themes to base graphics plots.
Vim plugin vim-sendtowindow - operator to send text between adjacent windows.

Coauthor of R package inops - dozens of clever additional infix operators.
Coauthor of R package DiscoRhythm - methods for discovering rhythmicity in biological data.
Coauthor of R package trendecon - functions for obtaining long daily time series from Google trends.
Coauthor by courtesy of R package ridgeline - ridgeline density plots.

Contributions to R package evaluate - #96.

publications

2024 Aging Cell - Epigenetic age oscillates during the day.
2019 Genome Biology - Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease.
2018 Nature Communications - Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging.
2016 Nature Structural and Molecular Biology - Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.
2013 Nature Communications - DNA unmethylome profiling by covalent capture of CpG sites.
2012 Nature Structural and Molecular Biology - 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary.

2023 Plos One - Scikick: A sidekick for workflow clarity and reproducibility during extensive data analysis .
2020 Bioinformatics - DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity.
2014 IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2014) - The 10th annual mlsp competition: Third place.

talks

2020 LA R Users Group - Lesser Known Base R Features.

2021 poster at COINS conference - "Cytosine modifications exhibit circadian oscillations that are involved in epigenetic aging and complex disease".
2014 poster at IEEE MLSP conference - "The 10th annual mlsp competition: Third place".

teaching

2019-present - "Biomedical Data Analysis", faculty of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania.

2023 B.S. Rugilė Peleckytė - "Ensemble learning methods for the prediction of epigenetic age".
2022 B.S. Aušrinė Šveikauskaitė - "How the estimation of epigenetic age is influenced by environmental factors and human disease".
2021 B.S. Asta Kvedaraitė - "R package for visualizing results of various epigenome wide association studies".
2021 B.S. Simas Bijeikis - "Analysis of genomic regions exhibiting differential DNA modification between phenotypes".
2020 B.S. Ignas Račinskas - "Visualization and Comparison of Epigenetic Disease Profiles".
2020 B.S. Artūras Terasenka - Visualization and Comparison of Epigenetic Disease Profiles.

writing

2021 A half-hour to learn R
2020 R base plotting without wrappers

other

A collection of various notes about R.
Sparsely active on StackOverflow and CrossValidated.