Publication list - Publika - Scientific publications from Oslo University Hospital

Publications by Knut Dagestad Rand

9 publications found

Original articles

Kanduri C, Scheffer L, Pavlović M, Rand KD, Chernigovskaya M, Pirvandy O, Yaari G, Greiff V, Sandve GK (2022)
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods
Gigascience, 12
DOI 10.1093/gigascience/giad074, PubMed 37848619

Grytten I, Dagestad Rand K, Sandve GK (2022)
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
Genome Biol, 23 (1), 209
DOI 10.1186/s13059-022-02771-2, PubMed 36195962

Pavlović M, Scheffer L, Motwani K, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Haff IH, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML et al. (2021)
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Nat Mach Intell, 3 (11), 936-944
DOI 10.1038/s42256-021-00413-z, PubMed 37396030

Grytten I, Rand KD, Nederbragt AJ, Sandve GK (2020)
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
BMC Genomics, 21 (1), 282
DOI 10.1186/s12864-020-6685-y, PubMed 32252628

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019)
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
PLoS Comput Biol, 15 (2), e1006731
DOI 10.1371/journal.pcbi.1006731, PubMed 30779737

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

Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2017)
Coordinates and intervals in graph-based reference genomes
BMC Bioinformatics, 18 (1), 263
DOI 10.1186/s12859-017-1678-9, PubMed 28521770

Review articles

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