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2020 – today
- 2022
[j43]Christian Anthon
, Giulia Ilaria Corsi, Jan Gorodkin:
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design. Bioinform. 38(24): 5437-5439 (2022)- 2021
- [j42]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): D212-D220 (2021) - 2020
- [j41]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)
2010 – 2019
- 2019
- [j40]Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin:
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinform. 35(9): 1494-1502 (2019) - 2018
- [j39]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: bay003 (2018) - [j38]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: bay028 (2018) - 2017
- [j37]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: baw167 (2017) - [j36]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): 2089-2096 (2017) - [c7]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: 295-302 - 2016
- [j35]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): 1238-1240 (2016) - 2014
- [j34]Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen:
Protein-driven inference of miRNA-disease associations. Bioinform. 30(3): 392-397 (2014) - [c6]Jan Gorodkin:
Searching for SNPs disrupting RNA secondary structures. CMSR@ECCB 2014: 65-66 - [c5]Jan Gorodkin:
In silico discovery of de novo structured RNAs in genomic and transcriptomic sequence. IWBBIO 2014: 285 - 2013
- [j33]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): 475-479 (2013) - 2012
- [j32]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): 17-24 (2012) - [j31]Peter Menzel, Stefan E. Seemann, Jan Gorodkin:
RILogo: visualizing RNA-RNA interactions. Bioinform. 28(19): 2523-2526 (2012) - [j30]Anne Wenzel, Erdinç Akbasli, Jan Gorodkin:
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinform. 28(21): 2738-2746 (2012) - [j29]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: 90 (2012) - 2011
- [j28]Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler:
Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol. Biol. 6: 4 (2011) - [j27]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): 211-219 (2011) - [j26]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): 317-325 (2011) - [j25]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): 107-111 (2011) - [j24]Jan Gorodkin, Ivo L. Hofacker:
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Comput. Biol. 7(8) (2011) - 2010
- [j23]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: 22 (2010)
2000 – 2009
- 2009
- [j22]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): 291-294 (2009) - [j21]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): 121-136 (2009) - [c4]Peter Menzel, Jan Gorodkin, Peter F. Stadler:
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB 2009: 211-220 - 2007
- [j20]Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin:
Multiple structural alignment and clustering of RNA sequences. Bioinform. 23(8): 926-932 (2007) - [j19]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) - [c3]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 - 2006
- [j18]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): 249-254 (2006) - [j17]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): 163-168 (2006) - 2005
- [j16]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): 1815-1824 (2005) - [j15]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): 650-653 (2005) - 2004
- [j14]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): 219-226 (2004) - [j13]Jan Gorodkin:
Comparing two K-category assignments by a K-category correlation coefficient. Comput. Biol. Chem. 28(5-6): 367-374 (2004) - 2003
- [j12]Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson:
SRPDB: Signal Recognition Particle Database. Nucleic Acids Res. 31(1): 363-364 (2003) - [j11]Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower:
tmRDB (tmRNA database). Nucleic Acids Res. 31(1): 446-447 (2003) - 2001
- [j10]Jan Gorodkin, Christian Zwieb, Bjarne Knudsen:
Semi-automated update and cleanup of structural RNA alignment databases. Bioinform. 17(7): 642-645 (2001) - [j9]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): 301-307 (2001) - [j8]Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson:
SRPDB (Signal Recognition Particle Database). Nucleic Acids Res. 29(1): 169-170 (2001) - [j7]Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin:
tmRDB (tmRNA database). Nucleic Acids Res. 29(1): 171-172 (2001)
1990 – 1999
- 1999
- [j6]Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak:
MatrixPlot: visualizing sequence constraints. Bioinform. 15(9): 769-770 (1999) - [c2]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 - 1997
- [j5]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): 583-586 (1997) - [j4]Jan Gorodkin:
Orbits of Boolean Functions. Discret. Appl. Math. 75(3): 269-275 (1997) - [j3]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) - [c1]Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo:
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB 1997: 120-123 - 1993
- [j2]Jan Gorodkin, Allan Sørensen, Ole Winther:
Neural Networks and Cellular Automata Complexity. Complex Syst. 7(1) (1993) - [j1]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)
Coauthor Index
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