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Jan Gorodkin
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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)
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