A Deformable Template Model, with Special Reference to Elliptical Templates. - Asger Hobolth; Jan Pedersen 001; Eva Bjørn Vedel Jensen (J. Math. Imaging Vis., 2002)

Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates. - Ole F. Christensen; Asger Hobolth; Jens Ledet Jensen (J. Comput. Biol., 2005)

Applications of Hidden Markov Models for Characterization of Homologous DNA Sequences with a Common Gene. - Asger Hobolth; Jens Ledet Jensen (J. Comput. Biol., 2005)

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. - Paula Tataru; Asger Hobolth (BMC Bioinform., 2011)

Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley's K-Function or Runs of Homozygosity? - Svend V. Nielsen; Simon Simonsen; Asger Hobolth (WABI, 2016)

Significance evaluation in factor graphs. - Tobias Madsen; Asger Hobolth; Jens Ledet Jensen; Jakob Skou Pedersen (BMC Bioinform., 2017)

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments. - Morten Muhlig Nielsen; Paula Tataru; Tobias Madsen; Asger Hobolth; Jakob Skou Pedersen (Algorithms Mol. Biol., 2018)

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data. - Johanna Bertl; Qianyun Guo; Malene Juul; Søren Besenbacher; Morten Muhlig Nielsen; Henrik Hornshøj; Jakob Skou Pedersen; Asger Hobolth (BMC Bioinform., 2018)

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. - Malene Juul; Tobias Madsen; Qianyun Guo; Johanna Bertl; Asger Hobolth; Manolis Kellis; Jakob Skou Pedersen (Bioinform., 2019)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Graph-based algorithms for phase-type distributions. - Tobias Røikjer; Asger Hobolth; Kasper Munch (Stat. Comput., 2022)

A Sampling Algorithm to Compute the Set of Feasible Solutions for NonNegative Matrix Factorization with an Arbitrary Rank. - Ragnhild Laursen; Asger Hobolth (SIAM J. Matrix Anal. Appl., 2022)

PhaseTypeR: an R package for phase-type distributions in population genetics. - Iker Rivas-González; Lars Nørvang Andersen; Asger Hobolth (J. Open Source Softw., 2023)

Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization. - Marta Pelizzola; Ragnhild Laursen; Asger Hobolth (BMC Bioinform., 2023)

On the Relation Between Autoencoders and Non-negative Matrix Factorization, and Their Application for Mutational Signature Extraction. - Ida Egendal; Rasmus Froberg Brøndum; Marta Pelizzola; Asger Hobolth; Martin Bøgsted (CoRR, 2024)

On the Relation Between Linear Autoencoders and Non-Negative Matrix Factorization for Mutational Signature Extraction. - Ida Egendal; Rasmus Froberg Brøndum; Marta Pelizzola; Asger Hobolth; Martin Bøgsted (J. Comput. Biol., 2025)

Advanced posterior analyses of hidden Markov models: finite Markov chain imbedding and hybrid decoding. - Zenia Elise Damgaard Bæk; Moisès Coll Macià; Laurits Skov; Asger Hobolth (CoRR, 2025)