RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. - Bjarne Knudsen; Jotun Hein (Bioinform., 1999)

Semi-automated update and cleanup of structural RNA alignment databases. - Jan Gorodkin; Christian Zwieb; Bjarne Knudsen (Bioinform., 2001)

SRPDB (Signal Recognition Particle Database). - Jan Gorodkin; Bjarne Knudsen; Christian Zwieb; Tore Samuelsson (Nucleic Acids Res., 2001)

tmRDB (tmRNA database). - Bjarne Knudsen; Jacek Wower; Christian Zwieb; Jan Gorodkin (Nucleic Acids Res., 2001)

Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree. - Bjarne Knudsen (WABI, 2003)

Pfold: RNA secondary structure prediction using stochastic context-free grammars. - Bjarne Knudsen; Jotun Hein (Nucleic Acids Res., 2003)

SRPDB: Signal Recognition Particle Database. - Magnus Alm Rosenblad; Jan Gorodkin; Bjarne Knudsen; Christian Zwieb; Tore Samuelsson (Nucleic Acids Res., 2003)

tmRDB (tmRNA database). - Christian Zwieb; Jan Gorodkin; Bjarne Knudsen; Jody Burks; Jacek Wower (Nucleic Acids Res., 2003)

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

Accurate and fast methods to estimate the population mutation rate from error prone sequences. - Bjarne Knudsen; Michael M. Miyamoto (BMC Bioinform., 2009)

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)

Handling design-level requirements across distributed teams: Developing a new feature for 12 Danish mobile banking apps. - Lars Bruun; Mikkel Bovbjerg Hansen; Jorgen Bondergaard Iversen; Jens Baek Jorgensen; Bjarne Knudsen (RE, 2014)

Variability Handling for Mobile Banking Apps on iOS and Android. - Jens Bæk Jørgensen; Bjarne Knudsen; Lennert Sloth; Johan Rugager Vase; Henrik Bærbak Christensen (WICSA, 2016)