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2024
1 Pavlović, Milena; al Hajj, Ghadi; Kanduri, Chakravarthi; Pensar, Johan; Wood, Mollie Elizabeth; Sollid, Ludvig Magne; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. Nature Machine Intelligence 2024 ;Volum 6.(1) s. 15-24
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2023
2 al Hajj, Ghadi; Pensar, Johan; Sandve, Geir Kjetil Ferkingstad.
DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation. PLOS ONE 2023 ;Volum 18.(4)
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3 Chlubnova, Marketa; Christophersen, Asbjørn Otto; Sandve, Geir Kjetil Ferkingstad; Lundin, Knut Erik Aslaksen; Jahnsen, Jørgen; Dahal-Koirala, Shiva; Sollid, Ludvig Magne.
Identification of gluten T cell epitopes driving celiac disease. Science Advances 2023 ;Volum 9.(4) s. 1-8
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4 Dæhlen, Morten; Sandve, Geir Kjetil Ferkingstad; Braa, Kristin.
KI-milliarden må brukes på en rettferdig grønn og digital omstilling. Khrono.no 2023
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5 Hsieh, Ping-Han; Lopes-Ramos, Camila Miranda; Zucknick, Manuela; Sandve, Geir Kjetil Ferkingstad; Glass, Kimberly; Kuijjer, Marieke.
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics 2023 ;Volum 39.(10) s. -
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6 Kalyanasundaram, Sumana; Lefol, Yohan Pierre; Gundersen, Sveinung; Rognes, Torbjørn; Alsøe, Lene; Nilsen, Hilde; Hovig, Eivind; Sandve, Geir Kjetil Ferkingstad; Domanska, Diana.
hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks. PLOS ONE 2023 ;Volum 18.(7) s. -
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7 Kanduri, Chakravarthi; Scheffer, Lonneke; Pavlović, Milena; Rand, Knut Dagestad; Chernigovskaia, Maria; Pirvandy, Oz; Yaari, Gur; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods. GigaScience 2023 ;Volum 12. s. 1-16
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8 Olstad, Emilie Willoch; Nordeng, Hedvig Marie Egeland; Sandve, Geir Kjetil Ferkingstad; Lyle, Robert; Gervin, Kristina.
Effects of prenatal exposure to (es)citalopram and maternal depression during pregnancy on DNA methylation and child neurodevelopment. Translational Psychiatry 2023 ;Volum 13.(1) s. -
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9 Sandve, Geir Kjetil Ferkingstad.
Deciphering how adaptive immune cells recognise pathogens: gathering suited data, defining appropriate assessments and incrementally improving machine learning methodology. 21st Swedish Bioinformatics Workshop; 2023-11-06 - 2023-11-06
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10 Sandve, Geir Kjetil Ferkingstad.
Hvorfor er maskinlæring viktig i medisin?. Lansering av dScience partnerprogram; 2023-03-06 - 2023-03-06
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11 Shakibfar, Saeed; Nyberg, Fredrik; Li, Huiqi; Zhao, Jing; Nordeng, Hedvig Marie Egeland; Sandve, Geir Kjetil Ferkingstad; Pavlović, Milena; Hajiebrahimi, Mohammadhossein; Andersen, Morten; Sessa, Maurizio.
Artificial intelligence-driven prediction of COVID-19-related hospitalization and death: a systematic review. Frontiers in Public Health 2023 ;Volum 11. s. -
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12 Shakibfar, Saeed; Zhao, Jing; Li, Huiqi; Nordeng, Hedvig Marie Egeland; Lupattelli, Angela; Pavlović, Milena; Sandve, Geir Kjetil Ferkingstad; Nyberg, Fredrik; Wettermark, Björn; Hajiebrahimi, Mohammadhossein; Andersen, Morten; Sessa, Maurizio.
Machine learning-driven development of a disease risk score for COVID-19 hospitalization and mortality: a Swedish and Norwegian register-based study. Frontiers in Public Health 2023 ;Volum 11. s. -
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13 Vu, Mai Ha; Akbar, Rahmad; Robert, Philippe; Sandve, Geir Kjetil Ferkingstad; Haug, Dag Trygve Truslew; Greiff, Victor.
Linguistically inspired roadmap for building biologically reliable protein language models. Nature Machine Intelligence 2023 ;Volum 5.(5) s. 485-496
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14 Wæhler, Hallvard Austin; Labba, Nils-Anders Johannes; Paulsen, Ragnhild Elisabeth Heimtun; Sandve, Geir Kjetil Ferkingstad; Eskeland, Ragnhild.
ANDA: an open-source tool for automated image analysis of in vitro neuronal cells. BMC Neuroscience 2023 ;Volum 24.(1) s. 1-11
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2022
15 Akbar, Rahmad; Robert, Philippe Paul Auguste; Weber, Cédric R.; Widrich, Michael; Frank, Robert; Pavlovic, Milena; Scheffer, Lonneke; Chernigovskaia, Maria; Snapkow, Igor; Slabodkin, Andrei; Mehta, Brij Bhushan; Miho, Enkelejda; Lund-Johansen, Fridtjof; Andersen, Jan Terje; Hochreiter, Sepp; Haff, Ingrid Hobæk; Klambauer, Günter; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor.
In silico proof of principle of machine learning-based antibody design at unconstrained scale. mAbs 2022 ;Volum 14:e2031482.(1) s. 1-18
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16 Dahal-Koirala, Shiva; Balaban, Gabriel; Neumann, Ralf Stefan; Scheffer, Lonneke; Lundin, Knut; Greiff, Victor; Sollid, Ludvig Magne; Qiao, Shuo-Wang; Sandve, Geir Kjetil Ferkingstad.
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings in Bioinformatics 2022 ;Volum 23.(2) s. 1-14
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17 Dance, Amber; Sandve, Geir Kjetil Ferkingstad; Morris, Samantha; Saez-Rodriguez, Julio; Heyn, Holger; Levin, Joshua.
Which single-cell analysis tool is best? Scientists offer advice. Nature 2022
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18 Doeland, Elin Martine; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor.
Immunforsvaret har skjulte mønstre om sykdom og infeksjoner. Forskning.no 2022
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19 Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony; Sandve, Geir Kjetil Ferkingstad.
Method development for the identification of cis-regulatory signatures of cell types. Events Norwegian Bioinformatics Days 2022; 2022-09-28 - 2022-09-30
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20 Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony; Sandve, Geir Kjetil Ferkingstad.
Method development for the identification of cis-regulatory signatures of cell types. Nordic AI Meet 2022, Nordic Young Researchers Symposium; 2022-11-14 - 2022-11-15
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21 Ferenc, Katalin Terezia; Mathelier, Anthony; Hsieh, Ping-Han; Sandve, Geir Kjetil Ferkingstad.
Method development for the identification of cis-regulatory signatures of cell types. EMBL Partnership Conference; 2022-09-21 - 2022-09-23
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22 Grytten, Ivar; Rand, Knut Dagestad; Sandve, Geir Kjetil Ferkingstad.
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels. Genome Biology 2022 ;Volum 23.(1)
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23 Kanduri, Chakravarthi; Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Chernigovskaia, Maria; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. GigaScience 2022 ;Volum 11.(05)
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24 Minotto, Thomas; Haff, Ingrid Hobæk; Sandve, Geir Kjetil Ferkingstad.
Detecting statistical interactions in immune receptor datasets. I: Proceedings of the 36th International Workshop on Statistical Modelling. EUT Edizioni Università di Trieste 2022 ISBN 978-88-5511-309-0. s. 253-257
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25 Olstad, Emilie Willoch; Nordeng, Hedvig Marie Egeland; Sandve, Geir Kjetil Ferkingstad; Lyle, Robert; Gervin, Kristina.
Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures. Clinical Epigenetics 2022 ;Volum 14.(1) s. -
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26 Robert, Philippe Paul Auguste; Akbar, Rahmad; Frank, Robert; Pavlović, Milena; Widrich, Michael; Snapkov, Igor; Slabodkin, Andrei; Chernigovskaya, Maria; Scheffer, Lonneke; Smorodina, Eva; Rawat, Puneet; Mehta, Brij Bhushan; Vu, Mai Ha; Mathisen, Ingvild Frøberg; Prósz, Aurél; Abram, Krzysztof; Olar, Alex; Miho, Enkelejda; Haug, Dag Trygve Truslew; Lund-Johansen, Fridtjof; Hochreiter, Sepp; Haff, Ingrid Hobæk; Klambauer, Günter; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor.
Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction. Nature Computational Science 2022 ;Volum 2.(12) s. 845-865
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27 Rognes, Torbjørn; Scheffer, Lonneke; Greiff, Victor; Sandve, Geir Kjetil.
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinformatics 2022 ;Volum 38.(17) s. 4230-4232
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28 Sandve, Geir Kjetil Ferkingstad.
Are quick and dirty programming habits sufficient in science - and do we at all need to consider code quality in science education?. The bi-weekly ODD seminar series at CCSE; 2022-03-01 - 2022-03-01
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29 Sandve, Geir Kjetil Ferkingstad.
Det inspirerende og frustrerende ved at programmering er en kreativ prosess. Faglig-pedagogisk dag, Universitetet i Oslo; 2022-11-03 - 2022-11-03
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30 Sandve, Geir Kjetil Ferkingstad.
How the choice of programming language matters when learning programming - Python, Java, R and more. The bi-weekly ODD seminar series at CCSE; 2022-11-07 - 2022-11-07
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31 Sandve, Geir Kjetil Ferkingstad.
Kunstig intelligens viser oss hva immunforsvaret jobber med. Åpen dag, Universitet i Oslo; 2022-03-10 - 2022-03-10
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32 Sandve, Geir Kjetil Ferkingstad; Greiff, Victor.
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. Bioinformatics 2022 ;Volum 38.(21) s. 4994-4996
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33 Sandve, Geir Kjetil Ferkingstad; Greiff, Victor; Haff, Ingrid Hobæk; Vu, Mai Ha.
Deciphering the Immune System Through Linguistics-Inspired Statistical Machine Learning. dScience Lunch Seminar; 2022-09-15 - 2022-09-15
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34 Sandve, Geir Kjetil Ferkingstad; Pensar, Johan.
Machine Learning and Causality. dScience Breakfast Club; 2022-11-29 - 2022-11-29
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35 Weber, Cédric R.; Rubio, Teresa; Wang, Longlong; Zhang, Wei; Robert, Philippe Paul Auguste; Akbar, Rahmad; Snapkov, Igor; Wu, Jinghua; Kuijjer, Marieke; Tarazona, Sonia; Conesa, Ana; Sandve, Geir Kjetil Ferkingstad; Liu, Xiao; Reddy, Sai T.; Greiff, Victor.
Reference-based comparison of adaptive immune receptor repertoires. Cell Reports Methods 2022 ;Volum 2.(8)
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2021
36 Akbar, Rahmad; Robert, Philippe Paul Auguste; Pavlović, Milena; Jeliazkov, Jeliazko R.; Snapkov, Igor; Slabodkin, Andrei; Weber, Cédric R.; Scheffer, Lonneke; Miho, Enkelejda; Haff, Ingrid Hobæk; Haug, Dag Trygve Truslew; Lund-Johansen, Fridtjof; Safonova, Yana; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor.
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell reports 2021 ;Volum 34:108856.(11) s. 1-21
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37 Arnaout, Ramy A.; Luning Prak, Eline T.; Schwab, Nicholas; Rubelt, Florian; Greiff, Victor; Pavlović, Milena; Sandve, Geir Kjetil Ferkingstad; Snapkov, Igor; Arora, Rohit; Bashford-Rogers, Rachael; Breden, Felix; Bukhari, Syed Ahmad Chan; Corrie, Brian; Cowell, Lindsay G.; Efroni, Sol; Gooley, Christopher; Heiden, Jason Vander; Koguchi, Yoshinobu; Langerak, Ton; Soon Lim, Thean; Mariotti-Ferrandiz, Encarnita; Marquez, Susanna; Meysman, Pieter; Miho, Enkelejda; Motwani, Keshav; Nouri, Nima; Soto, Cinque; Stervbo, Ulrik; Trück, Johannes; van den Ham, Henk-Jan; Watson, Corey; Weber, Cédric R..
The Future of Blood Testing Is the Immunome. Frontiers in Immunology 2021 ;Volum 12:626793. s. 1-6
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38 Balaban, Gabriel; Grytten, Ivar; Rand, Knut Dagestad; Scheffer, Lonneke; Sandve, Geir Kjetil.
Ten simple rules for quick and dirty scientific programming. PLoS Computational Biology 2021 ;Volum 17:e1008549.(3) s. 1-15
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39 Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Neumann, Ralf Stefan; Christophersen, Asbjørn; Lundin, Knut E. A.; Sandve, Geir Kjetil; Qiao, Shuo-Wang; Sollid, Ludvig M..
Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs. Frontiers in Immunology 2021 ;Volum 12:639672. s. 1-13
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40 Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires. bioRxiv 2021
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41 Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
One billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction. bioRxiv 2021
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42 Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. bioRxiv 2021
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43 Kanduri, Chakravarthi; Sandve, Geir Kjetil Ferkingstad; Hovig, Eivind; De, Subhajyoti; Layer, Ryan.
Editorial: Genomic Colocalization and Enrichment Analyses. Frontiers in Genetics 2021 ;Volum 11.
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44 Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina Maria; Sandve, Geir Kjetil; Eskeland, Ragnhild; Gabrielsen, Odd Stokke.
Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. Scientific Reports 2021 ;Volum 11.(9008) s. -
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45 Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Kanduri, Chakravarthi; Kompova, Radmila; Vazov, Nikolay Aleksandrov; Waagan, Knut; Bernal, Fabian Leonardo Martinez; Costa, Alexandre Almeida; Corrie, Brian; Akbar, Rahmad; Al Hajj, Ghadi S.; Balaban, Gabriel; Brusko, Todd M.; Chernigovskaia, Mariia; Christley, Scott; Cowell, Lindsay G.; Frank, Robert; Grytten, Ivar; Gundersen, Sveinung; Haff, Ingrid Hobæk; Hovig, Eivind; Hsieh, Ping-Han; Klambauer, Günter; Kuijjer, Marieke L.; Lund-Andersen, Christin; Martini, Antonio; Minotto, Thomas; Pensar, Johan; Rand, Knut Dagestad; Riccardi, Enrico; Robert, Philippe Paul Auguste; Rocha, Artur; Slabodkin, Andrei; Snapkov, Igor; Sollid, Ludvig Magne; Titov, Dmytro; Weber, Cédric R.; Widrich, Michael; Yaari, Gur; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad.
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence 2021 ;Volum 3.(11) s. 936-944
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46 Sandve, Geir Kjetil Ferkingstad.
ImmuneML and the case for domain-tailored machine learning platforms. NORA Webinars; 2021-08-27 - 2021-08-27
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47 Slabodkin, Andrei; Chernigovskaia, Maria; Mikocziova, Ivana; Akbar, Rahmad; Scheffer, Lonneke; Pavlović, Milena; Bashour, Habib; Snapkov, Igor; Mehta, Brij Bhushan; Weber, Cédric R.; Gutierrez-Marcos, Jose; Sollid, Ludvig Magne; Haff, Ingrid Hobæk; Sandve, Geir Kjetil Ferkingstad; Robert, Philippe Paul Auguste; Greiff, Victor.
Individualized VDJ recombination predisposes the available Ig sequence space. Genome Research 2021 ;Volum 31.(12) s. 2209-2225
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48 Yao, Ying; Wyrozemski, Lukasz Adam; Lundin, Knut; Sandve, Geir Kjetil Ferkingstad; Qiao, Shuo Wang.
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. PLOS ONE 2021 ;Volum 16:e0258029.(10) s. 1-17
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49 Yao, Ying; Zia, Asima; Neumann, Ralf Stefan; Pavlović, Milena; Balaban, Gabriel; Lundin, Knut Erik Aslaksen; Sandve, Geir Kjetil; Qiao, Shuo Wang.
T cell receptor repertoire as a potential diagnostic marker for celiac disease. Clinical Immunology 2021 ;Volum 222:108621. s. 1-7
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2020
50 du Pré, Fleur; Blazevski, Jana; Dewan, Alisa Elinsdatter; Stamnæs, Jorunn; Kanduri, Srinivasa Kalyana Chakravarthi; Sandve, Geir Kjetil; Johannesen, Marie Kongshaug; Lindstad, Christian Borgen; Hnida, Kathrin; Fugger, Lars; Melino, Gerry; Qiao, Shuo-Wang; Sollid, Ludvig Magne.
B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2. Journal of Experimental Medicine (JEM) 2020 ;Volum 217:e20190860..(2) s. 1-14
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