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Author Details

Geir Kjetil Sandve
University of Oslo
2006
76
23
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36696493Identification of gluten T cell epitopes driving celiac disease.Sci Adv2023
37802917Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.Bioinformatics2023
37875799ANDA: an open-source tool for automated image analysis of in vitro neuronal cells.BMC Neurosci2023
37058511DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation.PLoS One2023
37147306Effects of prenatal exposure to (es)citalopram and maternal depression during pregnancy on DNA methylation and child neurodevelopment.Transl Psychiatry2023
37408750Artificial intelligence-driven prediction of COVID-19-related hospitalization and death: a systematic review.Front Public Health2023
37467208hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks.PLoS One2023
37162841ANDA: An open-source tool for automated image analysis of neuronal differentiation.bioRxiv2023
35062022TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences.Brief Bioinform2022
37848619simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods.Gigascience2022
35377271In silico proof of principle of machine learning-based antibody design at unconstrained scale.MAbs2022
35765087Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures.Clin Epigenetics2022
35639633Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification.Gigascience2022
35852318CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching.Bioinformatics2022
36046619Reference-based comparison of adaptive immune receptor repertoires.Cell Rep Methods2022
36073940Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking.Bioinformatics2022
36195962KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.Genome Biol2022
33197618T cell receptor repertoire as a potential diagnostic marker for celiac disease.Clin Immunol2021
33574832Editorial: Genomic Colocalization and Enrichment Analyses.Front Genet2021
33903675Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB.Sci Rep2021
33927715Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs.Front Immunol2021
33730590A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.Cell Rep2021
33705383Ten simple rules for quick and dirty scientific programming.PLoS Comput Biol2021
34815307Individualized VDJ recombination predisposes the available Ig sequence space.Genome Res2021
34618841Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq.PLoS One2021
31624847Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis.Brief Bioinform2020
32085722NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.BMC Bioinformatics2020
31727780B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2.J Exp Med2020
32094913Author Correction: Human somatic cell mutagenesis creates genetically tractable sarcomas.Nat Genet2020
32154832immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.Bioinformatics2020
32252628Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods.BMC Genomics2020
30307532Colocalization analyses of genomic elements: approaches, recommendations and challenges.Bioinformatics2019
31839965Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production.United European Gastroenterol J2019
31251803A map of direct TF-DNA interactions in the human genome.Nucleic Acids Res2019
30779737Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.PLoS Comput Biol2019
30517703A map of direct TF-DNA interactions in the human genome.Nucleic Acids Res2019
29757191Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease.J Clin Invest2018
29873782Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.Nucleic Acids Res2018
30547739Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.BMC Bioinformatics2018
30517183Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments.PLoS One2018
28521741The rainfall plot: its motivation, characteristics and pitfalls.BMC Bioinformatics2017
28459977GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.Gigascience2017
29284043Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy.PLoS One2017
28600290High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease.J Immunol2017
28701187NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.BMC Bioinformatics2017
28911336Genome build information is an essential part of genomic track files.Genome Biol2017
28775312Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1.Sci Rep2017
28521770Coordinates and intervals in graph-based reference genomes.BMC Bioinformatics2017
26819474Galaxy Portal: interacting with the galaxy platform through mobile devices.Bioinformatics2016
26586731In the loop: promoter-enhancer interactions and bioinformatics.Brief Bioinform2016
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Collaborators

Eivind Hovig
Center for Bioinformatics, University of Oslo
Co-authored papers 19
Finn Drabl??s
NTNU - Norwegian University of Science and Technology
Co-authored papers 11
Sveinung Gundersen
Center for Bioinformatics, University of Oslo
Co-authored papers 10
Chakravarthi Kanduri
University of Oslo
Co-authored papers 9
Diana Domanska
University of Oslo
Co-authored papers 9
Ingrid K Glad
University of Oslo
Co-authored papers 8
Egil Ferkingstad
Co-authored papers 7
Marit Holden
University of Mainz
Co-authored papers 4
Boris Simovski
University of Oslo
Co-authored papers 4
Arnoldo Frigessi
University of Oslo
Co-authored papers 4
Anthony Mathelier
University of Oslo
Co-authored papers 3
Morten Beck Rye
St. Olavs Hospital, Trondheim University Hospital
Co-authored papers 3
Mat???? Kala??
University of Bergen
Co-authored papers 2
Christoph Bock
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 2
Daniel Vod??k
Institute for Cancer Research, Oslo University Hospital
Co-authored papers 2
Ryan M Layer
Boulder and BioFrontiers Institute, University of Colorado Boulder
Co-authored papers 2
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 1
Sigve Nakken
University of Oslo
Co-authored papers 1
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 1
Michael A Langston
University of Tennessee
Co-authored papers 1
James Taylor
Johns Hopkins University
Co-authored papers 1
Paul D Waterhouse
Princess Margaret Cancer Centre/University Health Network
Co-authored papers 1
Pirashaanthy Tharmapalan
Princess Margaret Cancer Centre, University Health Network, University of Toronto
Co-authored papers 1
Fred Nyberg
University of Gothenburg
Co-authored papers 1
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 1
Marco Salvetti
Co-authored papers 1
Andrey A Mironov
Lomonosov Moscow State University
Co-authored papers 1
Alexander V Favorov
Johns Hopkins School of Medicine
Co-authored papers 1
Camila M Lopes-Ramos
Harvard T. H. Chan School of Public Health
Co-authored papers 1
Jeliazko R Jeliazkov
Co-authored papers 1
Release 1.2