Evolutionary rate variation and RNA secondary structure prediction. - Bjarne Knudsen; Ebbe Sloth Andersen; Christian K. Damgaard; Jørgen Kjems; Jan Gorodkin (Comput. Biol. Chem., 2004)

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars. - Zsuzsanna Sükösd; Bjarne Knudsen; Morten Vaerum; Jørgen Kjems; Ebbe Sloth Andersen (BMC Bioinform., 2011)

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. - Zsuzsanna Sükösd; Bjarne Knudsen; Jørgen Kjems; Christian N. S. Pedersen (Bioinform., 2012)

Characterising RNA secondary structure space using information entropy. - Zsuzsanna Sükösd; Bjarne Knudsen; James W. J. Anderson; Ádám Novák; Jørgen Kjems; Christian N. S. Pedersen (BMC Bioinform., 2013)