Jan Gorodkin

Publication Activity (10 Years)

Years Active: 1993-2022
Publications (10 Years): 10

Top Topics

Expression Profiles

Multiple Alignment

Secondary Structure

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Publications

Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design. Bioinform. 38 (24) (2022)
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, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49 (Database-Issue) (2021)
Daniel Sundfeld, George Teodoro, Jakob Hull Havgaard, Jan Gorodkin, Alba C. M. A. Melo
Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities. Concurr. Comput. Pract. Exp. 32 (10) (2020)
Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinform. 35 (9) (2019)
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
TISSUES 2.0: an integrative web resource on mammalian tissue expression. Database J. Biol. Databases Curation 2018 (2018)
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
TISSUES 2.0: an integrative web resource on mammalian tissue expression. Database J. Biol. Databases Curation 2018 (2018)
Daniel Sundfeld, Jakob Hull Havgaard, Jan Gorodkin, Alba Cristina Magalhaes Alves de Melo
CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment. PDP (2017)
Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinform. 33 (14) (2017)
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
RAIN: RNA-protein Association and Interaction Networks. Database J. Biol. Databases Curation 2017 (2017)
Daniel Sundfeld, Jakob Hull Havgaard, Alba Cristina Magalhaes Alves de Melo, Jan Gorodkin
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment. Bioinform. 32 (8) (2016)
Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen
Protein-driven inference of miRNA-disease associations. Bioinform. 30 (3) (2014)
Jan Gorodkin
In silico discovery of de novo structured RNAs in genomic and transcriptomic sequence. IWBBIO (2014)
Jan Gorodkin
Searching for SNPs disrupting RNA secondary structures. CMSR@ECCB (2014)
Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
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. Bioinform. 28 (1) (2012)
Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. BMC Syst. Biol. 6 (2012)
Peter Menzel, Stefan E. Seemann, Jan Gorodkin
RILogo: visualizing RNA-RNA interactions. Bioinform. 28 (19) (2012)
Anne Wenzel, Erdinç Akbasli, Jan Gorodkin
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinform. 28 (21) (2012)
Jan Gorodkin, Ivo L. Hofacker
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Comput. Biol. 7 (8) (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 Res. 39 (Web-Server-Issue) (2011)
Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol. Biol. 6 (2011)
Peter Menzel, Peter F. Stadler, Jan Gorodkin
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinform. 27 (3) (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. Bioinform. 27 (2) (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 Mol. Biol. 5 (2010)
Peter Menzel, Jan Gorodkin, Peter F. Stadler
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB (2009)
Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin
Structural profiles of human miRNA families from pairwise clustering. Bioinform. 25 (3) (2009)
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, Jan Gorodkin
Sequence assembly. Comput. Biol. Chem. 33 (2) (2009)
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)
Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin
Multiple structural alignment and clustering of RNA sequences. Bioinform. 23 (8) (2007)
Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix. PLoS Comput. Biol. 3 (10) (2007)
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 Res. 34 (Database-Issue) (2006)
Jan Gorodkin, Jakob Hull Havgaard, Milena Ensterö, Milena Sawera, Peter Jensen, M. Öhman, Merete Fredholm
MicroRNA sequence motifs reveal asymmetry between the stem arms. Comput. Biol. Chem. 30 (4) (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%. Bioinform. 21 (9) (2005)
Jakob Hull Havgaard, Rune B. Lyngsø, Jan Gorodkin
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Jan Gorodkin
Comparing two K-category assignments by a K-category correlation coefficient. Comput. Biol. Chem. 28 (5-6) (2004)
Bjarne Knudsen, Ebbe Sloth Andersen, Christian K. Damgaard, Jørgen Kjems, Jan Gorodkin
Evolutionary rate variation and RNA secondary structure prediction. Comput. Biol. Chem. 28 (3) (2004)
Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson
SRPDB: Signal Recognition Particle Database. Nucleic Acids Res. 31 (1) (2003)
Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower
tmRDB (tmRNA database). Nucleic Acids Res. 31 (1) (2003)
Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson
SRPDB (Signal Recognition Particle Database). Nucleic Acids Res. 29 (1) (2001)
Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin
tmRDB (tmRNA database). Nucleic Acids Res. 29 (1) (2001)
Jan Gorodkin, Christian Zwieb, Bjarne Knudsen
Semi-automated update and cleanup of structural RNA alignment databases. Bioinform. 17 (7) (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. Comput. Chem. 25 (3) (2001)
Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak
MatrixPlot: visualizing sequence constraints. Bioinform. 15 (9) (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)
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) (1997)
Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB (1997)
Jan Gorodkin
Orbits of Boolean Functions. Discret. Appl. Math. 75 (3) (1997)
Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo
Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13 (6) (1997)
Jan Gorodkin, A. Sørensen, Ole Winther
Neural Networks and Cellular Automata Complexity. Complex Syst. 7 (1) (1993)
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) (1993)