Geir Kjetil Sandve

According to our database, Geir Kjetil Sandve authored at least 45 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2024

Linguistics-based formalization of the antibody language as a basis for antibody language models.

Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff

Nat. Comput. Sci., June, 2024

Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics.

Milena Pavlovic, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve

Nat. Mac. Intell., 2024

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

Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer

CoRR, 2024

Predictability of antigen binding based on short motifs in the antibody CDRH3.

Lonneke Scheffer, Eric Emanuel Reber, Brij Bhushan Mehta, Milena Pavlovic, Maria Chernigovskaya, Eve Richardson, Rahmad Akbar, Fridtjof Lund-Johansen, Victor Greiff, Ingrid Hobæk Haff, Geir Kjetil Sandve

Briefings Bioinform., 2024

Incorporating probabilistic domain knowledge into deep multiple instance learning.

Ghadi S. Al Hajj, Aliaksandr Hubin, Chakravarthi Kanduri, Milena Pavlovic, Knut Dagestad Rand, Michael Widrich, Anne H. Schistad Solberg, Victor Greiff, Johan Pensar, Günter Klambauer, Geir Kjetil Sandve

Proceedings of the Forty-first International Conference on Machine Learning, 2024

2023

Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.

Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer

Bioinform., October, 2023

Linguistically inspired roadmap for building biologically reliable protein language models.

Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Victor Greiff, Dag Trygve Truslew Haug

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.

Geir Kjetil Sandve, Victor Greiff

Bioinform., October, 2022

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction.

Philippe A. Robert, Rahmad Akbar, Robert Frank, Milena Pavlovic, Michael Widrich, Igor Snapkov, Andrei Slabodkin, Maria Chernigovskaya, Lonneke Scheffer, Eva Smorodina, Puneet Rawat, Brij Bhushan Mehta, Mai Ha Vu, Ingvild Frøberg Mathisen, Aurél Prósz, Krzysztof Abram, Alex Olar, Enkelejda Miho, Dag Trygve Truslew Haug, Fridtjof Lund-Johansen, Sepp Hochreiter, Ingrid Hobæk Haff, Günter Klambauer, Geir Kjetil Sandve, Victor Greiff

Nat. Comput. Sci., 2022

ImmunoLingo: Linguistics-based formalization of the antibody language.

Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff

CoRR, 2022

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

Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Victor Greiff, Geir Kjetil Sandve, Dag Trygve Truslew Haug

CoRR, 2022

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

Ghadi S. Al Hajj, Johan Pensar, Geir Kjetil Sandve

CoRR, 2022

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

Milena Pavlovic, Ghadi S. Al Hajj, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve

CoRR, 2022

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

Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve

Bioinform., 2022

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

Shiva Dahal-Koirala, Gabriel Balaban, Ralf Stefan Neumann, Lonneke Scheffer, Knut Erik Aslaksen Lundin, Victor Greiff, Ludvig Magne Sollid, Shuo-Wang Qiao, Geir Kjetil Sandve

Briefings Bioinform., 2022

2021

Ten simple rules for quick and dirty scientific programming.

Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve

PLoS Comput. Biol., 2021

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires.

Milena Pavlovic, Lonneke Scheffer, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, Fabian L. M. Bernal, Alexandre Almeida Costa, Brian Corrie, Rahmad Akbar, Ghadi S. Al Hajj, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut D. Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig Magne Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve

Nat. Mach. Intell., 2021

2020

Hopfield Networks is All You Need.

Hubert Ramsauer, Bernhard Schäfl, Johannes Lehner, Philipp Seidl, Michael Widrich, Lukas Gruber, Markus Holzleitner, Milena Pavlovic, Geir Kjetil Sandve, Victor Greiff, David P. Kreil, Michael Kopp, Günter Klambauer, Johannes Brandstetter, Sepp Hochreiter

CoRR, 2020

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

Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes

BMC Bioinform., 2020

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

Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff

Bioinform., 2020

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

Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve

Briefings Bioinform., 2020

Modern Hopfield Networks and Attention for Immune Repertoire Classification.

Michael Widrich, Bernhard Schäfl, Milena Pavlovic, Hubert Ramsauer, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer

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.

Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve

PLoS Comput. Biol., 2019

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

Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve

Bioinform., 2019

2018

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve

Nucleic Acids Res., 2018

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.

Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve

BMC Bioinform., 2018

2017

Coordinates and intervals in graph-based reference genomes.

Knut D. Rand, Ivar Grytten, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve

BMC Bioinform., 2017

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

Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander Johan Nederbragt

BMC Bioinform., 2017

The rainfall plot: its motivation, characteristics and pitfalls.

Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve

BMC Bioinform., 2017

2016

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

Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Cech, Geir Kjetil Sandve

Bioinform., 2016

In the loop: promoter-enhancer interactions and bioinformatics.

Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland

Briefings Bioinform., 2016

2014

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

Doug James, Nancy Wilkins-Diehr, Victoria Stodden, Dirk Colbry, Carlos Rosales, Mark R. Fahey, Justin Shi, Rafael Ferreira da Silva, Kyo Lee, Ralph Roskies, Laurence Loewe, Susan Lindsey, Rob Kooper, Lorena A. Barba, David H. Bailey, Jonathan M. Borwein, Óscar Corcho, Ewa Deelman, Michael C. Dietze, Benjamin Gilbert, Jan Harkes, Seth Keele, Praveen Kumar, Jong Lee, Erika Linke, Richard Marciano, Luigi Marini, Chris Mattmann, Dave Mattson, Kenton McHenry, Robert T. McLay, Sheila Miguez, Barbara S. Minsker, María S. Pérez-Hernández, Dan Ryan, Mats Rynge, Idafen Santana-Pérez, Mahadev Satyanarayanan, Gloriana St. Clair, Keith Webster, Eivind Hovig, Daniel S. Katz, Sophie Kay, Geir Kjetil Sandve, David Skinner, Gabrielle Allen, John Cazes, Kym Won Cho, Jim Fonseca, Lorraine J. Hwang, Lars Koesterke, Pragnesh Patel, Line Pouchard, Edward Seidel, Isuru Suriarachchi

CoRR, 2014

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

Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig

Bioinform., 2014

2013

Ten Simple Rules for Reproducible Computational Research.

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig

PLoS Comput. Biol., 2013

The Genomic HyperBrowser: an analysis web server for genome-scale data.

Geir Kjetil Sandve, Sveinung Gundersen, Morten Johansen, Ingrid Kristine Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck, Kai Trengereid, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Matús Kalas, Tonje Lien, Morten Rye, Arnoldo Frigessi, Eivind Hovig

Nucleic Acids Res., 2013

2011

Identifying elemental genomic track types and representing them uniformly.

Sveinung Gundersen, Matús Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve

BMC Bioinform., 2011

Sequential Monte Carlo multiple testing.

Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård

Bioinform., 2011

2008

Potentials and limitations of motif-based binding site prediction in DNA.

Geir Kjetil Ferkingstad Sandve

PhD thesis, 2008

Compo: composite motif discovery using discrete models.

Geir Kjetil Sandve, Osman Abul, Finn Drabløs

BMC Bioinform., 2008

Assessment of composite motif discovery methods.

Kjetil Klepper, Geir Kjetil Sandve, Osman Abul, Jostein Johansen, Finn Drabløs

BMC Bioinform., 2008

BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes.

Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Improved benchmarks for computational motif discovery.

Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs

BMC Bioinform., 2007

False Discovery Rates in Identifying Functional DNA Motifs.

Osman Abul, Geir Kjetil Sandve, Finn Drabløs

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Accelerating Motif Discovery: Motif Matching on Parallel Hardware.

Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005

Generalized Composite Motif Discovery.

Geir Kjetil Sandve, Finn Drabløs

Proceedings of the Knowledge-Based Intelligent Information and Engineering Systems, 2005