Jan Gorodkin

52 papers A 2C 1Journal 45Unranked 4
YearRankTypeTitle / Venue / Authors
2024 J jnl
Patent data-driven analysis of literature associations with changing innovation trends.
Frontiers Res. Metrics Anal.
Adrian Sven Geissler, Jan Gorodkin, Stefan E. Seemann
2023 J jnl
Letter to the editor: Testing on external independent datasets is necessary to corroborate machine learning model improvement.
Bioinform.
Giulia Ilaria Corsi, Christian Anthon, Jan Gorodkin
2022 J jnl
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design.
Bioinform.
Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin
2021 J jnl
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
Nucleic Acids Res.
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
2020 J jnl
Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities.
Concurr. Comput. Pract. Exp.
Daniel Sundfeld, George Teodoro, Jakob Hull Havgaard, Jan Gorodkin, Alba C. M. A. Melo
2019 J jnl
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.
Bioinform.
Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin
2018 J jnl
TISSUES 2.0: an integrative web resource on mammalian tissue expression.
Database J. Biol. Databases Curation
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
2018 J jnl
TISSUES 2.0: an integrative web resource on mammalian tissue expression.
Database J. Biol. Databases Curation
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
2017 C conf
CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment.
PDP
Daniel Sundfeld, Jakob Hull Havgaard, Jan Gorodkin, Alba Cristina Magalhaes Alves de Melo
2017 J jnl
RAIN: RNA-protein Association and Interaction Networks.
Database J. Biol. Databases Curation
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
2017 J jnl
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Bioinform.
Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen
2016 J jnl
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
Bioinform.
Daniel Sundfeld, Jakob Hull Havgaard, Alba Cristina Magalhaes Alves de Melo, Jan Gorodkin
2014 — conf
In silico discovery of de novo structured RNAs in genomic and transcriptomic sequence.
IWBBIO
Jan Gorodkin
2014 J jnl
Protein-driven inference of miRNA-disease associations.
Bioinform.
Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen
2014 — conf
Searching for SNPs disrupting RNA secondary structures.
CMSR@ECCB
Jan Gorodkin
2013 J jnl
The RNAsnp web server: predicting SNP effects on local RNA secondary structure.
Nucleic Acids Res.
Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
2012 J jnl
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.
BMC Syst. Biol.
Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin
2012 J jnl
RILogo: visualizing RNA-RNA interactions.
Bioinform.
Peter Menzel, Stefan E. Seemann, Jan Gorodkin
2012 J jnl
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.
Bioinform.
Anne Wenzel, Erdinç Akbasli, Jan Gorodkin
2012 J jnl
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
Bioinform.
David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin
2011 J jnl
Fast local fragment chaining using sum-of-pair gap costs.
Algorithms Mol. Biol.
Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
2011 J jnl
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs.
PLoS Comput. Biol.
Jan Gorodkin, Ivo L. Hofacker
2011 J jnl
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Bioinform.
Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin
2011 J jnl
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.
Nucleic Acids Res.
Stefan E. Seemann, Peter Menzel, Rolf Backofen, Jan Gorodkin
2011 J jnl
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.
Bioinform.
Peter Menzel, Peter F. Stadler, Jan Gorodkin
2010 J jnl
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.
Algorithms Mol. Biol.
Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen
2009 — conf
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search.
GCB
Peter Menzel, Jan Gorodkin, Peter F. Stadler
2009 J jnl
Sequence assembly.
Comput. Biol. Chem.
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
2009 J jnl
Structural profiles of human miRNA families from pairwise clustering.
Bioinform.
Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin
2007 J jnl
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix.
PLoS Comput. Biol.
Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin
2007 J jnl
Multiple structural alignment and clustering of RNA sequences.
Bioinform.
Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin
2007 — conf
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
ISMB/ECCB (Supplement of Bioinformatics)
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
2006 J jnl
MicroRNA sequence motifs reveal asymmetry between the stem arms.
Comput. Biol. Chem.
Jan Gorodkin, Jakob Hull Havgaard, Milena Ensterö, Milena Sawera, Peter Jensen, M. Öhman, Merete Fredholm
2006 J jnl
The tmRDB and SRPDB resources.
Nucleic Acids Res.
Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, Christian Zwieb
2005 J jnl
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Bioinform.
Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin
2005 J jnl
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.
Nucleic Acids Res.
Jakob Hull Havgaard, Rune B. Lyngsø, Jan Gorodkin
2004 J jnl
Comparing two K-category assignments by a K-category correlation coefficient.
Comput. Biol. Chem.
Jan Gorodkin
2004 J jnl
Evolutionary rate variation and RNA secondary structure prediction.
Comput. Biol. Chem.
Bjarne Knudsen, Ebbe Sloth Andersen, Christian K. Damgaard, Jørgen Kjems, Jan Gorodkin
2003 J jnl
SRPDB: Signal Recognition Particle Database.
Nucleic Acids Res.
Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson
2003 J jnl
tmRDB (tmRNA database).
Nucleic Acids Res.
Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower
2001 J jnl
Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks.
Comput. Chem.
Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak
2001 J jnl
SRPDB (Signal Recognition Particle Database).
Nucleic Acids Res.
Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson
2001 J jnl
Semi-automated update and cleanup of structural RNA alignment databases.
Bioinform.
Jan Gorodkin, Christian Zwieb, Bjarne Knudsen
2001 J jnl
tmRDB (tmRNA database).
Nucleic Acids Res.
Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin
1999 J jnl
MatrixPlot: visualizing sequence constraints.
Bioinform.
Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak
1999 A conf
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints.
ISMB
Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak
1997 J jnl
Displaying the information contents of structural RNA alignments: the structure logos.
Comput. Appl. Biosci.
Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo
1997 A conf
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences.
ISMB
Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo
1997 J jnl
Orbits of Boolean Functions.
Discret. Appl. Math.
Jan Gorodkin
1997 J jnl
Universal Distribution of Saliencies for Pruning in Layered Neural Networks.
Int. J. Neural Syst.
Jan Gorodkin, Lars Kai Hansen, Benny Lautrup, Sara A. Solla
1993 J jnl
A Quantitative Study Of Pruning By Optimal Brain Damage.
Int. J. Neural Syst.
Jan Gorodkin, Lars Kai Hansen, Anders Krogh, Claus Svarer, Ole Winther
1993 J jnl
Neural Networks and Cellular Automata Complexity.
Complex Syst.
Jan Gorodkin, Allan Sørensen, Ole Winther