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

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

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

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

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

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

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

RAIN: RNA-protein Association and Interaction Networks. - Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; Mering, Christian von; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan (Database J. Biol. Databases Curation, 2017)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The tmRDB and SRPDB resources. - Andersen, Ebbe Sloth; Rosenblad, Magnus Alm; Larsen, Niels; Westergaard, Jesper Cairo; Burks, Jody; Wower, Iwona K.; Wower, Jacek; Gorodkin, Jan; Samuelsson, Tore; Zwieb, Christian (Nucleic Acids Res., 2006)

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

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

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

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

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

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

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

Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. - Gorodkin, Jan; Søgaard, Bodil; Bay, Hanne; Doll, Hans; Kølster, Per; Brunak, Søren (Comput. Chem., 2001)

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

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

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

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

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

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

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

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

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

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