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ORCIDGeir Kjetil Sandve
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2020 – today
- 2024
[j30]Milena Pavlovic
, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve:
Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. Nat. Mac. Intell. 6(1): 15-24 (2024)- [j29]Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff:
Linguistics-based formalization of the antibody language as a basis for antibody language models. Nat. Comput. Sci. 4(6): 412-422 (2024) - [c6]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:
Incorporating probabilistic domain knowledge into deep multiple instance learning. ICML 2024 - [i8]Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer:
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. CoRR abs/2405.18655 (2024) - 2023
- [j28]Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer:
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinform. 39(10) (2023) - [j27]Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Victor Greiff, Dag Trygve Truslew Haug:
Linguistically inspired roadmap for building biologically reliable protein language models. Nat. Mac. Intell. 5(5): 485-496 (2023) - 2022
- [j26]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:
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings Bioinform. 23(2) (2022) - [j25]Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve:
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinform. 38(17): 4230-4232 (2022) - [j24]Geir Kjetil Sandve, Victor Greiff:
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. Bioinform. 38(21): 4994-4996 (2022) - [j23]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:
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. Nat. Comput. Sci. 2(12): 845-865 (2022) - [i7]Milena Pavlovic, Ghadi S. Al Hajj, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve:
Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics. CoRR abs/2204.09291 (2022) - [i6]Ghadi S. Al Hajj, Johan Pensar, Geir Kjetil Sandve:
DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation. CoRR abs/2205.11234 (2022) - [i5]Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Victor Greiff, Geir Kjetil Sandve, Dag Trygve Truslew Haug:
Advancing protein language models with linguistics: a roadmap for improved interpretability. CoRR abs/2207.00982 (2022) - [i4]Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff:
ImmunoLingo: Linguistics-based formalization of the antibody language. CoRR abs/2209.12635 (2022) - 2021
- [j22]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:
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3(11): 936-944 (2021) - [j21]Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve:
Ten simple rules for quick and dirty scientific programming. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j20]Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve:
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings Bioinform. 21(5): 1523-1530 (2020) - [j19]Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff:
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinform. 36(11): 3594-3596 (2020) - [j18]Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes:
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinform. 21(1): 66 (2020) - [c5]Michael Widrich, Bernhard Schäfl, Milena Pavlovic, Hubert Ramsauer, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer:
Modern Hopfield Networks and Attention for Immune Repertoire Classification. NeurIPS 2020 - [i3]Michael Widrich, Bernhard Schäfl, Hubert Ramsauer, Milena Pavlovic, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer:
Modern Hopfield Networks and Attention for Immune Repertoire Classification. CoRR abs/2007.13505 (2020) - [i2]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:
Hopfield Networks is All You Need. CoRR abs/2008.02217 (2020)
2010 – 2019
- 2019
- [j17]Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve:
Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinform. 35(9): 1615-1624 (2019) - [j16]Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve:
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput. Biol. 15(2) (2019) - 2018
- [j15]Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve:
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinform. 19(1): 481:1-481:9 (2018) - [j14]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:
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res. 46(Webserver-Issue): W186-W193 (2018) - 2017
- [j13]Knut D. Rand, Ivar Grytten, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve:
Coordinates and intervals in graph-based reference genomes. BMC Bioinform. 18(1): 263:1-263:8 (2017) - [j12]Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve:
The rainfall plot: its motivation, characteristics and pitfalls. BMC Bioinform. 18(1): 264:1-264:11 (2017) - [j11]Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander Johan Nederbragt:
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinform. 18(1): 338 (2017) - 2016
- [j10]Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland:
In the loop: promoter-enhancer interactions and bioinformatics. Briefings Bioinform. 17(6): 980-995 (2016) - [j9]Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Cech, Geir Kjetil Sandve:
Galaxy Portal: interacting with the galaxy platform through mobile devices. Bioinform. 32(11): 1743-1745 (2016) - 2014
- [j8]Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig:
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinform. 30(11): 1620-1622 (2014) - [i1]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:
Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE. CoRR abs/1412.5557 (2014) - 2013
- [j7]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:
The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res. 41(Webserver-Issue): 133-141 (2013) - [j6]Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig:
Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. 9(10) (2013) - 2011
- [j5]Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård:
Sequential Monte Carlo multiple testing. Bioinform. 27(23): 3235-3241 (2011) - [j4]Sveinung Gundersen, Matús Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve:
Identifying elemental genomic track types and representing them uniformly. BMC Bioinform. 12: 494 (2011)
2000 – 2009
- 2008
- [b1]Geir Kjetil Ferkingstad Sandve:
Potentials and limitations of motif-based binding site prediction in DNA. Norwegian University of Science and Technology, Trondheim, Norway, 2008 - [j3]Kjetil Klepper, Geir Kjetil Sandve, Osman Abul, Jostein Johansen, Finn Drabløs:
Assessment of composite motif discovery methods. BMC Bioinform. 9 (2008) - [j2]Geir Kjetil Sandve, Osman Abul, Finn Drabløs:
Compo: composite motif discovery using discrete models. BMC Bioinform. 9 (2008) - [c4]Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing:
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. RECOMB 2008: 66-81 - 2007
- [j1]Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs:
Improved benchmarks for computational motif discovery. BMC Bioinform. 8 (2007) - [c3]Osman Abul, Geir Kjetil Sandve, Finn Drabløs:
False Discovery Rates in Identifying Functional DNA Motifs. BIBE 2007: 387-394 - 2006
- [c2]Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs:
Accelerating Motif Discovery: Motif Matching on Parallel Hardware. WABI 2006: 197-206 - 2005
- [c1]Geir Kjetil Sandve, Finn Drabløs:
Generalized Composite Motif Discovery. KES (3) 2005: 763-769
Coauthor Index
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