Geir Kjetil Sandve

46 papers A* 2B 1C 2Journal 40Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Attribution assignment for deep-generative sequence models enables interpretability analysis using positive-only data. CoRR Robert Frank, Michael Widrich, Rahmad Akbar, Günter Klambauer, Geir Kjetil Sandve, Philippe A. Robert, Victor Greiff
2024	J	`jnl`	CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. CoRR Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer
2024	J	`jnl`	Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. Nat. Mac. Intell. Milena Pavlovic, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve
2024	A*	`conf`	Incorporating probabilistic domain knowledge into deep multiple instance learning. ICML 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
2024	J	`jnl`	Linguistics-based formalization of the antibody language as a basis for antibody language models. Nat. Comput. Sci. Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff
2024	J	`jnl`	Predictability of antigen binding based on short motifs in the antibody CDRH3. Briefings Bioinform. 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
2023	J	`jnl`	Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinform. Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
2023	J	`jnl`	Linguistically inspired roadmap for building biologically reliable protein language models. Nat. Mac. Intell. Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Victor Greiff, Dag Trygve Truslew Haug
2022	J	`jnl`	Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. Bioinform. Geir Kjetil Sandve, Victor Greiff
2022	J	`jnl`	Advancing protein language models with linguistics: a roadmap for improved interpretability. CoRR Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Victor Greiff, Geir Kjetil Sandve, Dag Trygve Truslew Haug
2022	J	`jnl`	CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinform. Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve
2022	J	`jnl`	DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation. CoRR Ghadi S. Al Hajj, Johan Pensar, Geir Kjetil Sandve
2022	J	`jnl`	ImmunoLingo: Linguistics-based formalization of the antibody language. CoRR Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff
2022	J	`jnl`	Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics. CoRR Milena Pavlovic, Ghadi S. Al Hajj, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve
2022	J	`jnl`	TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings Bioinform. 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
2022	J	`jnl`	Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. Nat. Comput. Sci. 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
2021	J	`jnl`	Ten simple rules for quick and dirty scientific programming. PLoS Comput. Biol. Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve
2021	J	`jnl`	The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 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
2020	J	`jnl`	Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings Bioinform. Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve
2020	J	`jnl`	Hopfield Networks is All You Need. CoRR 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
2020	A*	`conf`	Modern Hopfield Networks and Attention for Immune Repertoire Classification. NeurIPS Michael Widrich, Bernhard Schäfl, Milena Pavlovic, Hubert Ramsauer, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer
2020	J	`jnl`	Modern Hopfield Networks and Attention for Immune Repertoire Classification. CoRR Michael Widrich, Bernhard Schäfl, Hubert Ramsauer, Milena Pavlovic, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer
2020	J	`jnl`	NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinform. Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes
2020	J	`jnl`	immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinform. Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff
2019	J	`jnl`	Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinform. Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve
2019	J	`jnl`	Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput. Biol. Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve
2018	J	`jnl`	Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res. 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
2018	J	`jnl`	Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinform. Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve
2017	J	`jnl`	Coordinates and intervals in graph-based reference genomes. BMC Bioinform. Knut D. Rand, Ivar Grytten, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve
2017	J	`jnl`	NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinform. Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander Johan Nederbragt
2017	J	`jnl`	The rainfall plot: its motivation, characteristics and pitfalls. BMC Bioinform. Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve
2016	J	`jnl`	Galaxy Portal: interacting with the galaxy platform through mobile devices. Bioinform. Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Cech, Geir Kjetil Sandve
2016	J	`jnl`	In the loop: promoter-enhancer interactions and bioinformatics. Briefings Bioinform. Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland
2014	J	`jnl`	HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinform. Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig
2014	J	`jnl`	Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE. CoRR 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
2013	J	`jnl`	Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig
2013	J	`jnl`	The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res. 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
2011	J	`jnl`	Identifying elemental genomic track types and representing them uniformly. BMC Bioinform. Sveinung Gundersen, Matús Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve
2011	J	`jnl`	Sequential Monte Carlo multiple testing. Bioinform. Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård
2008	J	`jnl`	Assessment of composite motif discovery methods. BMC Bioinform. Kjetil Klepper, Geir Kjetil Sandve, Osman Abul, Jostein Johansen, Finn Drabløs
2008	B	`conf`	BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. RECOMB Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing
2008	J	`jnl`	Compo: composite motif discovery using discrete models. BMC Bioinform. Geir Kjetil Sandve, Osman Abul, Finn Drabløs
2007	C	`conf`	False Discovery Rates in Identifying Functional DNA Motifs. BIBE Osman Abul, Geir Kjetil Sandve, Finn Drabløs
2007	J	`jnl`	Improved benchmarks for computational motif discovery. BMC Bioinform. Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs
2006	C	`conf`	Accelerating Motif Discovery: Motif Matching on Parallel Hardware. WABI Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs
2005	—	`conf`	Generalized Composite Motif Discovery. KES (3) Geir Kjetil Sandve, Finn Drabløs