Gene finding with a hidden Markov model of genome structure and evolution. - Jakob Skou Pedersen; Jotun Hein (Bioinform., 2003)

The UCSC Genome Browser Database: update 2006. - Angela S. Hinrichs; Donna Karolchik; Robert Baertsch; Galt P. Barber; Gill Bejerano; Hiram Clawson; Mark Diekhans; Terrence S. Furey; Rachel A. Harte; Fan Hsu; Jennifer Hillman-Jackson; Robert M. Kuhn; et al. (Nucleic Acids Res., 2006)

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. - Jakob Skou Pedersen; Gill Bejerano; Adam C. Siepel; Kate R. Rosenbloom; Kerstin Lindblad-Toh; Eric S. Lander; Jim Kent; Webb Miller; David Haussler (PLoS Comput. Biol., 2006)

The UCSC genome browser database: update 2007. - Robert M. Kuhn; Donna Karolchik; Ann S. Zweig; Heather Trumbower; Daryl J. Thomas; Archana Thakkapallayil; Charles W. Sugnet; Mario Stanke; Kayla E. Smith; Adam C. Siepel; Kate R. Rosenbloom; Brooke L. Rhead; et al. (Nucleic Acids Res., 2007)

The UCSC Genome Browser Database: 2008 update. - Donna Karolchik; Robert M. Kuhn; Robert Baertsch; Galt P. Barber; Hiram Clawson; Mark Diekhans; Belinda Giardine; Rachel A. Harte; Angela S. Hinrichs; Fan Hsu; Kord M. Kober; Webb Miller; et al. (Nucleic Acids Res., 2008)

ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction. - Sudhakar Sahoo; Michal P. Switnicki; Jakob Skou Pedersen (Bioinform., 2016)

PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. - Michal P. Switnicki; Malene Juul; Tobias Madsen; Karina D. Sørensen; Jakob Skou Pedersen (Bioinform., 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)

Genomic basis for RNA alterations in cancer. - Claudia Calabrese; Natalie R. Davidson; Deniz Demircioglu; Nuno A. Fonseca; Yao He; André Kahles; Kjong-Van Lehmann; Fenglin Liu; Yuichi Shiraishi; Cameron M. Soulette; Lara Urban; Liliana Greger; et al. (Nat., 2020)

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)