Jan Gorodkin

According to our database, Jan Gorodkin authored at least 49 papers between 1993 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2022

CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design.

Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin

Bioinform., December, 2022

2021

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, 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

Nucleic Acids Res., 2021

2020

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

2019

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.

Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin

Bioinform., 2019

2018

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

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

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

CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment.

Daniel Sundfeld, Jakob Hull Havgaard, Jan Gorodkin, Alba Cristina Magalhaes Alves de Melo

Proceedings of the 25th Euromicro International Conference on Parallel, 2017

2016

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

2014

Protein-driven inference of miRNA-disease associations.

Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen

Bioinform., 2014

In silico discovery of de novo structured RNAs in genomic and transcriptomic sequence.

Jan Gorodkin

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

Searching for SNPs disrupting RNA secondary structures.

Jan Gorodkin

Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), 2014

2013

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

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

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.

Anne Wenzel, Erdinç Akbasli, Jan Gorodkin

Bioinform., 2012

RILogo: visualizing RNA-RNA interactions.

Peter Menzel, Stefan E. Seemann, Jan Gorodkin

Bioinform., 2012

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

2011

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs.

Jan Gorodkin, Ivo L. Hofacker

PLoS Comput. Biol., 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

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

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.

Peter Menzel, Peter F. Stadler, Jan Gorodkin

Bioinform., 2011

Fast local fragment chaining using sum-of-pair gap costs.

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler

Algorithms Mol. Biol., 2011

2010

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

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, Jan Gorodkin

Comput. Biol. Chem., 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

Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search.

Peter Menzel, Jan Gorodkin, Peter F. Stadler

Proceedings of the German Conference on Bioinformatics 2009, 2009

2007

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix.

Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin

PLoS Comput. Biol., 2007

Multiple structural alignment and clustering of RNA sequences.

Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin

Bioinform., 2007

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, 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

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

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

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

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

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

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

Comparing two K-category assignments by a K-category correlation coefficient.

Jan Gorodkin

Comput. Biol. Chem., 2004

2003

tmRDB (tmRNA database).

Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower

Nucleic Acids Res., 2003

SRPDB: Signal Recognition Particle Database.

Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson

Nucleic Acids Res., 2003

2001

tmRDB (tmRNA database).

Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin

Nucleic Acids Res., 2001

SRPDB (Signal Recognition Particle Database).

Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson

Nucleic Acids Res., 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

Semi-automated update and cleanup of structural RNA alignment databases.

Jan Gorodkin, Christian Zwieb, Bjarne Knudsen

Bioinform., 2001

1999

MatrixPlot: visualizing sequence constraints.

Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak

Bioinform., 1999

Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints.

Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

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

Orbits of Boolean Functions.

Jan Gorodkin

Discret. Appl. Math., 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

Finding Common Sequence and Structure Motifs in a Set of RNA Sequences.

Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

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

Neural Networks and Cellular Automata Complexity.

Jan Gorodkin, Allan Sørensen, Ole Winther

Complex Syst., 1993