Geir Kjetil Sandve

Orcid: 0000-0002-4959-1409

According to our database1, Geir Kjetil Sandve authored at least 42 papers between 2005 and 2024.

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Bibliography

2024
Linguistics-based formalization of the antibody language as a basis for antibody language models.
Nat. Comput. Sci., June, 2024

CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data.
CoRR, 2024

2023
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.
Bioinform., October, 2023

Linguistically inspired roadmap for building biologically reliable protein language models.
Nat. Mac. Intell., May, 2023

2022
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking.
Bioinform., October, 2022

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction.
Nat. Comput. Sci., 2022

ImmunoLingo: Linguistics-based formalization of the antibody language.
CoRR, 2022

Advancing protein language models with linguistics: a roadmap for improved interpretability.
CoRR, 2022

DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation.
CoRR, 2022

Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics.
CoRR, 2022

CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching.
Bioinform., 2022

TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences.
Briefings Bioinform., 2022

2021
Ten simple rules for quick and dirty scientific programming.
PLoS Comput. Biol., 2021

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.
Nat. Mach. Intell., 2021

2020
Hopfield Networks is All You Need.
CoRR, 2020

NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.
BMC Bioinform., 2020

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.
Bioinform., 2020

Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis.
Briefings Bioinform., 2020

Modern Hopfield Networks and Attention for Immune Repertoire Classification.
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

2019
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.
PLoS Comput. Biol., 2019

Colocalization analyses of genomic elements: approaches, recommendations and challenges.
Bioinform., 2019

2018
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.
Nucleic Acids Res., 2018

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.
BMC Bioinform., 2018

2017
Coordinates and intervals in graph-based reference genomes.
BMC Bioinform., 2017

NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.
BMC Bioinform., 2017

The rainfall plot: its motivation, characteristics and pitfalls.
BMC Bioinform., 2017

2016
Galaxy Portal: interacting with the galaxy platform through mobile devices.
Bioinform., 2016

In the loop: promoter-enhancer interactions and bioinformatics.
Briefings Bioinform., 2016

2014
Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE.
CoRR, 2014

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.
Bioinform., 2014

2013
Ten Simple Rules for Reproducible Computational Research.
PLoS Comput. Biol., 2013

The Genomic HyperBrowser: an analysis web server for genome-scale data.
Nucleic Acids Res., 2013

2011
Identifying elemental genomic track types and representing them uniformly.
BMC Bioinform., 2011

Sequential Monte Carlo multiple testing.
Bioinform., 2011

2008
Potentials and limitations of motif-based binding site prediction in DNA.
PhD thesis, 2008

Compo: composite motif discovery using discrete models.
BMC Bioinform., 2008

Assessment of composite motif discovery methods.
BMC Bioinform., 2008

BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes.
Proceedings of the Research in Computational Molecular Biology, 2008

2007
Improved benchmarks for computational motif discovery.
BMC Bioinform., 2007

False Discovery Rates in Identifying Functional DNA Motifs.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Accelerating Motif Discovery: Motif Matching on Parallel Hardware.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005
Generalized Composite Motif Discovery.
Proceedings of the Knowledge-Based Intelligent Information and Engineering Systems, 2005


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