AK
Anders Krogh
AlgorithmsMarkov ChainsModels, MolecularSoftwarebioinformaticsModels, GeneticModels, StatisticalGenome, BacterialNeural Networks, ComputerGenome
On Valency
published · living versionsW_yaar2ca2·v1 · currentpublished
BEND 2.0: Benchmarking the Capabilities Needed to Design DNA
with Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli, Panagiotis Antoniadis +4
1 version
Preprints & journals
137 papers in the corpus · 1993–2026A deep generative decoder predicts microRNA expression from bulk and single-cell mRNA profiles10.64898/2026.05.29.727918v2 · Zamani, F., Rasmussen, A. M., Schuster, V. et al.2026 · 0 citationsbioRxiv
How to Use Quantum Computers for Biomolecular Free Energies.42001298 · Günther, Jakob, Weymuth, Thomas, Bensberg, Moritz et al.2026 · 5 citationsJournal of chemical theory and computation. 2026;22(9):4329-4345
Enhancing Generative Decoders with Stochastic Training on Biomedical Data with Missingness10.64898/2025.12.01.690409v1 · Shen, X., Bjerregaard, A., Li, Y. et al.2025 · 0 citationsbioRxiv
What Do Single-Cell Models Already Know About Perturbations?41465115 · Bjerregaard, Andreas, Prada-Luengo, Iñigo, Das, Vivek et al.2025 · 1 citationGenes. 2025;16(12)
Development, implementation, and validation of an open-source Federated Learning platform to accelerate innovation and boost personalized medicine in rare and ultra-rare hematological diseases: an initiative by GenoMed4All Consortium10.1101/2025.08.07.25333044v1 · Asti, G., Apellaniz, P., Carota, L. et al.2025 · 2 citationsmedRxiv
Machine Learning-Enhanced Calculation of Quantum-Classical Binding Free Energies.40762518 · Bensberg, Moritz, Eckhoff, Marco, Thomasen, F Emil et al.2025 · 10 citationsJournal of chemical theory and computation. 2025;21(16):8182-8198
Hierarchical Quantum Embedding by Machine Learning for Large Molecular Assemblies.40729449 · Bensberg, Moritz, Eckhoff, Marco, Husistein, Raphael T et al.2026 · 7 citationsJournal of chemical theory and computation. 2025;21(15):7662-7674
Riemannian Generative Decoder2506.19133v3 · Andreas Bjerregaard, S\oren Hauberg, Anders Krogh2025 · 0 citationsTransactions on Machine Learning Research, 2026. ISSN 2835-8856. https://openreview.net/forum?id=vuPMXg1FDT
Foundation models of protein sequences: A brief overview.39983412 · Bjerregaard, Andreas, Groth, Peter Mørch, Hauberg, Søren et al.2025 · 16 citationsCurrent opinion in structural biology. 2025;91:103004
multiDGD: A versatile deep generative model for multi-omics data.39567490 · Schuster, Viktoria, Dann, Emma, Krogh, Anders et al.2024 · 37 citationsNature communications. 2024;15(1):10031
MOSAIC: An Artificial Intelligence-Based Framework for Multimodal Analysis, Classification, and Personalized Prognostic Assessment in Rare Cancers.38875514 · D'Amico, Saverio, Dall'Olio, Lorenzo, Rollo, Cesare et al.2024 · 24 citationsJCO clinical cancer informatics. 2024;8:e2400008
A primer on synthetic health data2401.17653v2 · Jennifer A Bartell, Sander Boisen Valentin, Anders Krogh et al.2024 · 3 citationsarXiv
N-of-one differential gene expression without control samples using a deep generative model.37974217 · Prada-Luengo, Iñigo, Schuster, Viktoria, Liang, Yuhu et al.2023 · 6 citationsGenome biology. 2023;24(1):263
The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data.37572301 · Schuster, Viktoria, Krogh, Anders2023 · 8 citationsBioinformatics (Oxford, England). 2023;39(9)
Synthetic Data Generation by Artificial Intelligence to Accelerate Research and Precision Medicine in Hematology.37390377 · D'Amico, Saverio, Dall'Olio, Daniele, Sala, Claudia et al.2023 · 96 citationsJCO clinical cancer informatics. 2023;7:e2300021
Context dependent prediction in DNA sequence using neural networks.36157058 · Grønbæk, Christian, Liang, Yuhu, Elliott, Desmond et al.2023 · 1 citationPeerJ. 2022;10:e13666
Correction to: Context dependency of nucleotide probabilities and variants in human DNA.35538429 · Liang, Yuhu, Grønbæk, Christian, Fariselli, Piero et al.2022 · 1 citationBMC genomics. 2022;23(1):356
DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks10.1101/2022.04.08.487609v1 · Hallgren, J., Tsirigos, K., Damgaard Pedersen, M. et al.2022 · 1,521 citationsbioRxiv
Context dependency of nucleotide probabilities and variants in human DNA.35100973 · Liang, Yuhu, Grønbæk, Christian, Fariselli, Piero et al.2022 · 12 citationsBMC genomics. 2022;23(1):87
A Manifold Learning Perspective on Representation Learning: Learning Decoder and Representations without an Encoder.34828101 · Schuster, Viktoria, Krogh, Anders2021 · 1 citationEntropy (Basel, Switzerland). 2021;23(11)
High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers.33176066 · Terkelsen, Thilde, Pernemalm, Maria, Gromov, Pavel et al.2021 · 48 citationsMolecular oncology. 2021;15(2):429-461
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.32633756 · Tovo, Anna, Menzel, Peter, Krogh, Anders et al.2020 · 33 citationsNucleic acids research. 2020;48(16):e93
Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration.32605588 · Terkelsen, Thilde, Russo, Francesco, Gromov, Pavel et al.2020 · 39 citationsBreast cancer research : BCR. 2020;22(1):73
CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data.32176694 · Terkelsen, Thilde, Krogh, Anders, Papaleo, Elena2020 · 13 citationsPLoS computational biology. 2020;16(3):e1007665
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads.31830908 · Prada-Luengo, Iñigo, Krogh, Anders, Maretty, Lasse et al.2020 · 156 citationsBMC bioinformatics. 2019;20(1):663
Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.30290141 · Liu, Siyang, Huang, Shujia, Chen, Fang et al.2019 · 279 citationsCell. 2018;175(2):347-359.e14
Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny.10.1101/407692v1 · Cappellini, E., Welker, F., Pandolfi, L. et al.2018 · 20 citationsbioRxiv
Accurate genotyping across variant classes and lengths using variant graphs.29915429 · Sibbesen, Jonas Andreas, Maretty, Lasse, Danish Pan-Genome Consortium et al.2019 · 91 citationsNature genetics. 2018;50(7):1054-1059
Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches.29163426 · Elcheninov, Alexander G, Menzel, Peter, Gudbergsdottir, Soley R et al.2020 · 31 citationsFrontiers in microbiology. 2017;8:2140
Erratum.29044400 · Fox, Keith A A, Gersh, Bernard J, Traore, Sory et al.2019 · 3 citationsEuropean heart journal. Quality of care & clinical outcomes. 2017;3(4):328
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.28746312 · Maretty, Lasse, Jensen, Jacob Malte, Petersen, Bent et al.2017 · 153 citationsNature. 2017;548(7665):87-91
Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.28410363 · Plass, Mireya, Rasmussen, Simon H, Krogh, Anders2017 · 51 citationsPLoS computational biology. 2017;13(4):e1005460
RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine.27213950 · Hougaard Pedersen, Sara, Maretty, Lasse, Ramachandran, Roshni et al.2017 · 8 citationsPloS one. 2016;11(5):e0155039
Fast and sensitive taxonomic classification for metagenomics with Kaiju.27071849 · Menzel, Peter, Ng, Kim Lee, Krogh, Anders2016 · 2,124 citationsNature communications. 2016;7:11257
Highly accessible AU-rich regions in 3′ untranslated regions are hotspots for binding of proteins and miRNAs10.1101/042986v3 · Mireya Plass, Simon H Rasmussen, Anders Krogh2016 · 0 citationsbioRxiv
Transcriptome dynamics of the microRNA inhibition response.26861627 · Wen, Jiayu, Leucci, Eleonora, Vendramin, Roberto et al.2019 · 1 citationNucleic acids research. 2016;44(9):4486
Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.26705468 · Liu, Siyang, Huang, Shujia, Rao, Junhua et al.2016 · 22 citationsGigaScience. 2015;4:64
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs.26439881 · Gudbergsdóttir, Sóley Ruth, Menzel, Peter, Krogh, Anders et al.2016 · 53 citationsEnvironmental microbiology. 2016;18(3):863-74
Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.26264976 · Fang, Xiaodong, Nevo, Eviatar, Han, Lijuan et al.2016 · 7 citationsNature communications. 2015;6:8051
Transcriptome dynamics of the microRNA inhibition response.26089393 · Wen, Jiayu, Leucci, Eleonora, Vendramin, Roberto et al.2015 · 6 citationsNucleic acids research. 2015;43(13):6207-21
Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.26054396 · Hansen, Heidi Theil, Rasmussen, Simon Horskjær, Adolph, Sidsel Kramshøj et al.2016 · 40 citationsGenome biology. 2015;16:123
De novo assembly of a haplotype-resolved human genome.26006006 · Cao, Hongzhi, Wu, Honglong, Luo, Ruibang et al.2016 · 66 citationsNature biotechnology. 2015;33(6):617-22
SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.25805860 · Poulsen, Line Dahl, Kielpinski, Lukasz Jan, Salama, Sofie R et al.2015 · 53 citationsRNA (New York, N.Y.). 2015;21(5):1042-52
Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin.25885340 · Vikeså, Jonas, Møller, Anne Kirstine H, Kaczkowski, Bogumil et al.2016 · 47 citationsBMC cancer. 2015;15:151
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.25712554 · Menzel, Peter, Gudbergsdóttir, Sóley Ruth, Rike, Anne Gunn et al.2016 · 119 citationsMicrobial ecology. 2015;70(2):411-24
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.25597990 · Besenbacher, Søren, Liu, Siyang, Izarzugaza, José M G et al.2015 · 172 citationsNature communications. 2015;6:5969
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology.25671094 · Cao, Hongzhi, Hastie, Alex R, Cao, Dandan et al.2015 · 161 citationsGigaScience. 2014;3(1):34
SNPest: a probabilistic graphical model for estimating genotypes.25294605 · Lindgreen, Stinus, Krogh, Anders, Pedersen, Jakob Skou2015 · 5 citationsBMC research notes. 2014;7:698
Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes.25176646 · Fang, Xiaodong, Seim, Inge, Huang, Zhiyong et al.2015 · 196 citationsCell reports. 2014;8(5):1354-64
Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.24892994 · Fang, Xiaodong, Nevo, Eviatar, Han, Lijuan et al.2015 · 138 citationsNature communications. 2014;5:3966
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