Publications 2023

Kalyanasundaram S, Lefol Y, Gundersen S, Rognes T, Alsøe L, Nilsen HL, Hovig E, Sandve GK, Domanska D (2023)
hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks
PLoS One, 18 (7), e0286330
DOI 10.1371/journal.pone.0286330, PubMed 37467208

Lefol Y, Korfage T, Mjelle R, Prebensen C, Lüders T, Müller B, Krokan H, Sarno A, Alsøe L, CONSORTIUM LEMONAID, Berdal JE, Sætrom P, Nilsen H, Domanska D (2023)
TiSA: TimeSeriesAnalysis-a pipeline for the analysis of longitudinal transcriptomics data
NAR Genom Bioinform, 5 (1), lqad020
DOI 10.1093/nargab/lqad020, PubMed 36879899

Publications 2022

Domanska D, Majid U, Karlsen VT, Merok MA, Beitnes AR, Yaqub S, Bækkevold ES, Jahnsen FL (2022)
Single-cell transcriptomic analysis of human colonic macrophages reveals niche-specific subsets
J Exp Med, 219 (3)
DOI 10.1084/jem.20211846, PubMed 35139155

Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2022)
MirGeneDB 2.1: toward a complete sampling of all major animal phyla
Nucleic Acids Res, 50 (D1), D204-D210
DOI 10.1093/nar/gkab1101, PubMed 34850127

Høye E, Fromm B, Böttger PHM, Domanska D, Torgunrud A, Lund-Andersen C, Abrahamsen TW, Fretland ÅA, Dagenborg VJ, Lorenz S, Edwin B, Hovig E, Flatmark K (2022)
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer
NAR Cancer, 4 (1), zcab051
DOI 10.1093/narcan/zcab051, PubMed 35047825

Umu SU, Rapp Vander-Elst K, Karlsen VT, Chouliara M, Bækkevold ES, Jahnsen FL, Domanska D (2022)
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
Gigascience, 12
DOI 10.1093/gigascience/giad091, PubMed 37889009

Yadav A, Verhaegen S, Filis P, Domanska D, Lyle R, Sundaram AYM, Leithaug M, Østby GC, Aleksandersen M, Berntsen HF, Zimmer KE, Fowler PA, Paulsen RE, Ropstad E (2022)
Exposure to a human relevant mixture of persistent organic pollutants or to perfluorooctane sulfonic acid alone dysregulates the developing cerebellum of chicken embryo
Environ Int, 166, 107379
DOI 10.1016/j.envint.2022.107379, PubMed 35792514

Publications 2021

Bengtsen M, Winje IM, Eftestøl E, Landskron J, Sun C, Nygård K, Domanska D, Millay DP, Meza-Zepeda LA, Gundersen K (2021)
Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle
PLoS Genet, 17 (11), e1009907
DOI 10.1371/journal.pgen.1009907, PubMed 34752468

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Noia JMD (2021)
Erratum: The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 3 (1), zcaa045
DOI 10.1093/narcan/zcaa045, PubMed 34316697

Publications 2020

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2020)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res, 48 (D1), D132-D141
DOI 10.1093/nar/gkz885, PubMed 31598695

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2020)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res, 48 (D1), D1172
DOI 10.1093/nar/gkz1016, PubMed 31642479

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM (2020)
The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 2 (3), zcaa019
DOI 10.1093/narcan/zcaa019, PubMed 33554121

Salvatore S, Dagestad Rand K, Grytten I, Ferkingstad E, Domanska D, Holden L, Gheorghe M, Mathelier A, Glad I, Kjetil Sandve G (2020)
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis
Brief Bioinform, 21 (5), 1523-1530
DOI 10.1093/bib/bbz083, PubMed 31624847

Publications 2018

Domanska D, Kanduri C, Simovski B, Sandve GK (2018)
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis
BMC Bioinformatics, 19 (1), 481
DOI 10.1186/s12859-018-2438-1, PubMed 30547739

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK (2018)
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Nucleic Acids Res, 46 (W1), W186-W193
DOI 10.1093/nar/gky474, PubMed 29873782

Publications 2017

Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H (2017)
Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1
Sci Rep, 7 (1), 7199
DOI 10.1038/s41598-017-07314-5, PubMed 28775312

Domanska D, Vodák D, Lund-Andersen C, Salvatore S, Hovig E, Sandve GK (2017)
The rainfall plot: its motivation, characteristics and pitfalls
BMC Bioinformatics, 18 (1), 264
DOI 10.1186/s12859-017-1679-8, PubMed 28521741

Kanduri C, Domanska D, Hovig E, Sandve GK (2017)
Genome build information is an essential part of genomic track files
Genome Biol, 18 (1), 175
DOI 10.1186/s13059-017-1312-1, PubMed 28911336

Salvatore S, Domanska D, Wood M, Nordeng H, Sandve GK (2017)
Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy
PLoS One, 12 (12), e0190101
DOI 10.1371/journal.pone.0190101, PubMed 29284043

Simovski B, Vodák D, Gundersen S, Domanska D, Azab A, Holden L, Holden M, Grytten I, Rand K, Drabløs F, Johansen M, Mora A, Lund-Andersen C, Fromm B, Eskeland R, Gabrielsen OS, Ferkingstad E, Nakken S, Bengtsen M, Nederbragt AJ, Thorarensen HS, Akse JA, Glad I, Hovig E, Sandve GK (2017)
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
Gigascience, 6 (7), 1-12
DOI 10.1093/gigascience/gix032, PubMed 28459977

Publications 2016

Azab A, Domanska D (2016)
Software Provisioning Inside a Secure Environment as Docker Containers using STROLL File-system
IEEE ACM INT SYMP, 674-683
DOI 10.1109/CCGrid.2016.106

Domanska D, Lukasik S (2016)
Handling high-dimensional data in air pollution forecasting tasks
Ecol. Inform., 34, 70-91
DOI 10.1016/j.ecoinf.2016.04.007