Neural Networks and Cellular Automata Complexity. - Jan Gorodkin; Allan Sørensen; Ole Winther (Complex Syst., 1993)

A Quantitative Study Of Pruning By Optimal Brain Damage. - Jan Gorodkin; Lars Kai Hansen; Anders Krogh; Claus Svarer; Ole Winther (Int. J. Neural Syst., 1993)

Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. - Jan Gorodkin; Laurie J. Heyer; Gary D. Stormo (ISMB, 1997)

Displaying the information contents of structural RNA alignments: the structure logos. - Jan Gorodkin; Laurie J. Heyer; Søren Brunak; Gary D. Stormo (Comput. Appl. Biosci., 1997)

Orbits of Boolean Functions. - Jan Gorodkin (Discret. Appl. Math., 1997)

Universal Distribution of Saliencies for Pruning in Layered Neural Networks. - Jan Gorodkin; Lars Kai Hansen; Benny Lautrup; Sara A. Solla (Int. J. Neural Syst., 1997)

Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. - Jan Gorodkin; Ole Lund; Claus A. F. Andersen; Søren Brunak (ISMB, 1999)

MatrixPlot: visualizing sequence constraints. - Jan Gorodkin; Hans Henrik Stærfeldt; Ole Lund; Søren Brunak (Bioinform., 1999)

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

Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. - Jan Gorodkin; Bodil Søgaard; Hanne Bay; Hans Doll; Per Kølster; Søren Brunak (Comput. Chem., 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)

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)

Comparing two K-category assignments by a K-category correlation coefficient. - Jan Gorodkin (Comput. Biol. Chem., 2004)

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

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)

The tmRDB and SRPDB resources. - Ebbe Sloth Andersen; Magnus Alm Rosenblad; Niels Larsen; Jesper Cairo Westergaard; Jody Burks; Iwona K. Wower; Jacek Wower; Jan Gorodkin; Tore Samuelsson; Christian Zwieb (Nucleic Acids Res., 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)

Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. - Peter Menzel; Jan Gorodkin; Peter F. Stadler (GCB, 2009)

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)

Sequence assembly. - K. Scheibye-Alsing; Steve Hoffmann; A. Frankel; Peter Jensen; Peter F. Stadler; Y. Mang; Niels Tommerup; M. J. Gilchrist; A.-B. Nygård; Susanna Cirera; Claus B. Jørgensen; Merete Fredholm; et al. (Comput. Biol. Chem., 2009)

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. - Stefan E. Seemann; Andreas S. Richter; Jan Gorodkin; Rolf Backofen (Algorithms Mol. Biol., 2010)

Fast local fragment chaining using sum-of-pair gap costs. - Christian Otto; Steve Hoffmann; Jan Gorodkin; Peter F. Stadler (Algorithms Mol. Biol., 2011)

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. - Peter Menzel; Peter F. Stadler; Jan Gorodkin (Bioinform., 2011)

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. - Stefan E. Seemann; Andreas S. Richter; Tanja Gesell; Rolf Backofen; Jan Gorodkin (Bioinform., 2011)

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. - Stefan E. Seemann; Peter Menzel; Rolf Backofen; Jan Gorodkin (Nucleic Acids Res., 2011)

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. - Jan Gorodkin; Ivo L. Hofacker (PLoS Comput. Biol., 2011)

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. - David Langenberger; Sachin Pundhir; Claus Thorn Ekstrøm; Peter F. Stadler; Steve Hoffmann; Jan Gorodkin (Bioinform., 2012)

RILogo: visualizing RNA-RNA interactions. - Peter Menzel; Stefan E. Seemann; Jan Gorodkin (Bioinform., 2012)

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. - Anne Wenzel; Erdinç Akbasli; Jan Gorodkin (Bioinform., 2012)

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. - Larry Croft; Damian Szklarczyk; Lars Juhl Jensen; Jan Gorodkin (BMC Syst. Biol., 2012)

The RNAsnp web server: predicting SNP effects on local RNA secondary structure. - Radhakrishnan Sabarinathan; Hakim Tafer; Stefan E. Seemann; Ivo L. Hofacker; Peter F. Stadler; Jan Gorodkin (Nucleic Acids Res., 2013)

Searching for SNPs disrupting RNA secondary structures. - Jan Gorodkin (CMSR@ECCB, 2014)

In silico discovery of de novo structured RNAs in genomic and transcriptomic sequence. - Jan Gorodkin (IWBBIO, 2014)

Protein-driven inference of miRNA-disease associations. - Søren Mørk; Sune Pletscher-Frankild; Albert Pallejà Caro; Jan Gorodkin; Lars Juhl Jensen (Bioinform., 2014)

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)

RAIN: RNA-protein Association and Interaction Networks. - Alexander Junge; Jan C. Refsgaard; Christian Garde; Xiaoyong Pan; Alberto Santos; Ferhat Alkan; Christian Anthon; Christian von Mering; Christopher T. Workman; Lars Juhl Jensen; Jan Gorodkin (Database J. Biol. Databases Curation, 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)

TISSUES 2.0: an integrative web resource on mammalian tissue expression. - Oana Palasca; Alberto Santos; Christian Stolte; Jan Gorodkin; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2018)

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. - Xiaoyong Pan; Lars Juhl Jensen; Jan Gorodkin (Bioinform., 2019)

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)

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. - Blake A. Sweeney; Anton I. Petrov; Carlos Eduardo Ribas; Robert D. Finn; Alex Bateman; Maciej Szymanski; Wojciech M. Karlowski; Stefan E. Seemann; Jan Gorodkin; Jamie J. Cannone; Robin Ray Gutell; Simon Kay; et al. (Nucleic Acids Res., 2021)

CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design. - Christian Anthon; Giulia Ilaria Corsi; Jan Gorodkin (Bioinform., 2022)

Patent data-driven analysis of literature associations with changing innovation trends. - Adrian Sven Geissler; Jan Gorodkin; Stefan E. Seemann (Frontiers Res. Metrics Anal., 2024)