Jan Gorodkin

David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin: deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics 28(1): 17-24 (2012)

Peter Menzel, Stefan E. Seemann, Jan Gorodkin: RILogo: visualizing RNA-RNA interactions. Bioinformatics 28(19): 2523-2526 (2012)

Anne Wenzel, Erdinç Akbasli, Jan Gorodkin: RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinformatics 28(21): 2738-2746 (2012)

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler: Fast local fragment chaining using sum-of-pair gap costs. Algorithms for Molecular Biology 6: 4 (2011)

Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin: PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics 27(2): 211-219 (2011)

Peter Menzel, Peter F. Stadler, Jan Gorodkin: maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics 27(3): 317-325 (2011)

Stefan E. Seemann, Peter Menzel, Rolf Backofen, Jan Gorodkin: The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. Nucleic Acids Research 39(Web-Server-Issue): 107-111 (2011)

Jan Gorodkin, Ivo L. Hofacker: From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Computational Biology 7(8) (2011)

Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen: Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms for Molecular Biology 5: 22 (2010)

Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin: Structural profiles of human miRNA families from pairwise clustering. Bioinformatics 25(3): 291-294 (2009)

K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin: Sequence assembly. Computational Biology and Chemistry 33(2): 121-136 (2009)

Peter Menzel, Jan Gorodkin, Peter F. Stadler: Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB 2009: 211-220

Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin: Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23(8): 926-932 (2007)

Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin: Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix. PLoS Computational Biology 3(10) (2007)

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, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. ISMB/ECCB (Supplement of Bioinformatics) 2007: 387-391

Jan Gorodkin, Jakob Hull Havgaard, Milena Ensterö, Milena Sawera, Peter Jensen, M. Öhman, Merete Fredholm: MicroRNA sequence motifs reveal asymmetry between the stem arms. Computational Biology and Chemistry 30(4): 249-254 (2006)

Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, Christian Zwieb: The tmRDB and SRPDB resources. Nucleic Acids Research 34(Database-Issue): 163-168 (2006)

Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21(9): 1815-1824 (2005)

Jakob Hull Havgaard, Rune B. Lyngsø, Jan Gorodkin: The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Research 33(Web-Server-Issue): 650-653 (2005)

Bjarne Knudsen, Ebbe Sloth Andersen, Christian K. Damgaard, Jørgen Kjems, Jan Gorodkin: Evolutionary rate variation and RNA secondary structure prediction. Computational Biology and Chemistry 28(3): 219-226 (2004)

Jan Gorodkin: Comparing two K-category assignments by a K-category correlation coefficient. Computational Biology and Chemistry 28(5-6): 367-374 (2004)

Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson: SRPDB: Signal Recognition Particle Database. Nucleic Acids Research 31(1): 363-364 (2003)

Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower: tmRDB (tmRNA database). Nucleic Acids Research 31(1): 446-447 (2003)

Jan Gorodkin, Christian Zwieb, Bjarne Knudsen: Semi-automated update and cleanup of structural RNA alignment databases. Bioinformatics 17(7): 642-645 (2001)

Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak: Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. Computers & Chemistry 25(3): 301-307 (2001)

Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson: SRPDB (Signal Recognition Particle Database). Nucleic Acids Research 29(1): 169-170 (2001)

Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin: tmRDB (tmRNA database). Nucleic Acids Research 29(1): 171-172 (2001)

Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak: MatrixPlot: visualizing sequence constraints. Bioinformatics 15(9): 769-770 (1999)

Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak: Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB 1999: 95-105

Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo: Displaying the information contents of structural RNA alignments: the structure logos. Computer Applications in the Biosciences 13(6): 583-586 (1997)

Jan Gorodkin: Orbits of Boolean Functions. Discrete Applied Mathematics 75(3): 269-275 (1997)

Jan Gorodkin, Lars Kai Hansen, Benny Lautrup, Sara A. Solla: Universal Distribution of Saliencies for Pruning in Layered Neural Networks. Int. J. Neural Syst. 8(5-6): 489-498 (1997)

Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo: Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB 1997: 120-123

Jan Gorodkin, Lars Kai Hansen, Anders Krogh, Claus Svarer, Ole Winther: A Quantitative Study Of Pruning By Optimal Brain Damage. Int. J. Neural Syst. 4(2): 159-169 (1993)