Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. - Jakob Hull Havgaard; Rune B. Lyngsø; Gary D. Stormo; Jan Gorodkin (Bioinform., 2005)

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. - Jakob Hull Havgaard; Rune B. Lyngsø; Jan Gorodkin (Nucleic Acids Res., 2005)

MicroRNA sequence motifs reveal asymmetry between the stem arms. - Jan Gorodkin; Jakob Hull Havgaard; Milena Ensterö; Milena Sawera; Peter Jensen; M. Öhman; Merete Fredholm (Comput. Biol. Chem., 2006)

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. - Frank Panitz; Henrik Stengaard; Henrik Hornshøj; Jan Gorodkin; Jakob Hedegaard; Susanna Cirera; Bo Thomsen; Lone B. Madsen; Anette Høj; Rikke K. Vingborg; Bujie Zahn; Xuegang Wang; et al. (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Multiple structural alignment and clustering of RNA sequences. - Elfar Torarinsson; Jakob Hull Havgaard; Jan Gorodkin (Bioinform., 2007)

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix. - Jakob Hull Havgaard; Elfar Torarinsson; Jan Gorodkin (PLoS Comput. Biol., 2007)

Structural profiles of human miRNA families from pairwise clustering. - Bogumil Kaczkowski; Elfar Torarinsson; Kristin Reiche; Jakob Hull Havgaard; Peter F. Stadler; Jan Gorodkin (Bioinform., 2009)

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment. - Daniel Sundfeld; Jakob Hull Havgaard; Alba Cristina Magalhaes Alves de Melo; Jan Gorodkin (Bioinform., 2016)

CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment. - Daniel Sundfeld; Jakob Hull Havgaard; Jan Gorodkin; Alba Cristina Magalhaes Alves de Melo (PDP, 2017)

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. - Milad Miladi; Alexander Junge; Fabrizio Costa; Stefan E. Seemann; Jakob Hull Havgaard; Jan Gorodkin; Rolf Backofen (Bioinform., 2017)

Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities. - Daniel Sundfeld; George Teodoro; Jakob Hull Havgaard; Jan Gorodkin; Alba C. M. A. Melo (Concurr. Comput. Pract. Exp., 2020)