2012
Sequence and expression analysis of gaps in human chromosome 20.
Minocherhomji S, Seemann S, Mang Y, El-Schich Z, Bak M, Hansen C, Papadopoulos N, Josefsen K, Nielsen H, Gorodkin J, Tommerup N, Silahtaroglu A
Nucleic Acids Res. 2012, in press.
[ PubMed | Paper ]
Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila.
Andersen KL, Nielsen H
Nucleic Acids Res. 40:1267-81, 2012
[ PubMed | Paper ]
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
Langenberger D, Pundhir S, Ekstrom CT, Stadler PF, Hoffmann S, Gorodkin J
Bioinformatics. 28:17-24, 2012
[ PubMed | Paper | Software ]
RNA Folding with Soft Constraints: Reconciliation of Probing Data and Thermodynamic Secondary Structure Prediction
Washietl S, Hofacker I, Stadler P, Kellis M
Accepted 28. Dec 2011 NAR-02501-R-2011
[ Paper ]
2011
From structure prediction to genomic screens for novel non-coding RNAs.
Gorodkin J, Hofacker IL
PLoS Comput Biol. 7:e1002100, 2011
[ PubMed | Paper ]
Fast local fragment chaining using sum-of-pair gap costs.
Otto C, Hoffmann S, Gorodkin J, Stadler PF
Algorithms Mol Biol. 6:4, 2011
[ PubMed | Paper | Software ]
In silico evolution of early metabolism.
Ullrich A, Rohrschneider M, Scheuermann G, Stadler PF, Flamm C
Artif Life. 17:87-108, 2011
[ PubMed | Paper ]
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.
Seemann SE, Menzel P, Backofen R, Gorodkin J
Nucleic Acids Res. 39:W107-11, 2011
[ PubMed | Paper | Webserver ]
Proteinortho: detection of (co-)orthologs in large-scale analysis.
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ
BMC Bioinformatics. 12:124, 2011
[ PubMed | Paper ]
A folding algorithm for extended RNA secondary structures
zu Siederdissen CH, Bernhart SH, Stadler PF, Hofacker IL
Bioinformatics. 27:i129, 2011
[ Paper ]
Corpus callosum abnormalities, intellectual disability, speech impairment, and autism in patients with haploinsufficiency of ARID1B.
Halgren C, Kjaergaard S, Bak M, Hansen C, El-Schich Z, Anderson C, Henriksen K, Hjalgrim H, Kirchhoff M, Bijlsma E, Nielsen M, den Hollander N, Ruivenkamp C, Isidor B, Le Caignec C, Zannolli R, Mucciolo M, Renieri A, Mari F, Anderlid BM, Andrieux J, Dieux A, Tommerup N, Bache I
Clin Genet. 2011 Jul 29. doi: 10.1111/j.1399-0004.2011.01755.x.
[ PubMed | Paper ]
Topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME
Bioinformatics. 27:1076-85, 2011
[ PubMed | Paper ]
Traces of post-transcriptional RNA modifications in deep sequencing data.
Findeiss S, Langenberger D, Stadler PF, Hoffmann S
Biol Chem. 392:305-13, 2011
[ PubMed | Paper ]
Global microRNA analysis of the NCI-60 cancer cell panel.
Sokilde R, Kaczkowski B, Podolska A, Cirera S, Gorodkin J, Moller S, Litman T
Mol Cancer Ther. 10:375-84, 2011
[ PubMed | Paper ]
Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes.
Bang-Berthelsen CH, Pedersen L, Floyel T, Hagedorn PH, Gylvin T, Pociot F
BMC Genomics. 12:97, 2011
[ PubMed | Paper ]
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.
Menzel P, Stadler PF, Gorodkin J
Bioinformatics. 27:317-25, 2011
[ PubMed | Paper | Webserver | Software ]
Genome browsers.
Torarinsson E
Methods Mol Biol. 703:53-65, 2011
[ PubMed | Paper ]
PLEXY: efficient target prediction for box C/D snoRNAs.
Kehr S, Bartschat S, Stadler PF, Tafer H
Bioinformatics. 27:279-80, 2011
[ PubMed | Paper ]
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J
Bioinformatics. 27:211-9, 2011
[ PubMed | Paper | Webserver ]
2010
High glucose suppresses human islet insulin biosynthesis by inducing miR-133a leading to decreased polypyrimidine tract binding protein-expression.
Fred RG, Bang-Berthelsen CH, Mandrup-Poulsen T, Grunnet LG, Welsh N
PLoS One. 5:e10843, 2010
[ PubMed | Paper ]
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.
Seemann SE, Richter AS, Gorodkin J, Backofen R
Algorithms Mol Biol. 5:22, 2010
[ PubMed | Paper ]
A study of alternative splicing in the pig.
Nygard AB, Cirera S, Gilchrist MJ, Gorodkin J, Jorgensen CB, Fredholm M
BMC Res Notes. 3:123, 2010
[ PubMed | Paper ]
De novo prediction of structured RNAs from genomic sequences.
Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL
Trends Biotechnol. 28:9-19, 2010
[ PubMed | Paper | Sup ]
Evolutionary Genomics of MicroRNAs and Their Relatives.
Tanzer A, Riester M, Hertel J, Bermudez-Santana CI, Gorodkin J, Hofacker IL, Stadler PF
In Gustavo Caetano-Anolles, editor, Evolutionary Genomics. Wiley
[ Paper | Abstract ]
Before 2010
Structural profiles of human miRNA families from pairwise clustering.
Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J
Bioinformatics. 25:291-4, 2009
[ PubMed | Paper | Sup ]
Sequence assembly.
Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygard AB, Cirera S, Jorgensen CB, Fredholm M, Gorodkin J
Comput Biol Chem. 33:121-36, 2009
[ PubMed | Paper | Sup ]
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
Anandam P, Torarinsson E, Ruzzo WL
Bioinformatics. 25:668-9, 2009
[ PubMed | Paper | Sup ]
454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides.
Zagrobelny M, Scheibye-Alsing K, Jensen NB, Moller BL, Gorodkin J, Bak S
BMC Genomics. 10:574, 2009
[ PubMed | Paper ]
The tedious task of finding homologous noncoding RNA genes.
Menzel P, Gorodkin J, Stadler PF
RNA. 15:2075-82, 2009
[ PubMed | Paper | Sup ]
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search.
Menzel P, Gorodkin J, Stadler PF
Lecture Notes in Informatics: Proceedings of the German Conference on Bioinformatics. 212-220, 2009
[ Paper | Abstract ]
WAR: Webserver for aligning structural RNAs.
Torarinsson E, Lindgreen S
Nucleic Acids Res. 36:W79-84, 2008
[ PubMed | Paper | Webserver ]
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.
Seemann SE, Gorodkin J, Backofen R
Nucleic Acids Res. 36:6355-62, 2008
[ PubMed | Paper | Sup ]
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J
Genome Res. 18:242-51, 2008
[ PubMed | Paper | Sup ]
SNP-finding in pig mitochondrial ESTs.
Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J
Anim Genet. 39:193-5, 2008
[ PubMed | Paper ]
Detection of RNA structures in porcine EST data and related mammals.
Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J
BMC Genomics. 8:316, 2007
[ PubMed | Paper |Sup1 Sup2 ]
Semiautomated improvement of RNA alignments.
Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J
RNA. 13:1850-9, 2007
[ PubMed | Paper | Software | Sup ]
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
Panitz F, Stengaard H, Hornshoj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Hoj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C
Bioinformatics. 23:i387-91, 2007
[ PubMed | Paper ]
Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences.
Karlskov-Mortensen P, Hu ZL, Gorodkin J, Reecy JM, Fredholm M
Anim Genet. 38:401-5, 2007
[ PubMed | Paper | Sup ]
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.
Havgaard JH, Torarinsson E, Gorodkin J
PLoS Comput Biol. 3:1896-908, 2007
[ PubMed | Paper | Software | Sup ]
EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues.
Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J
BMC Genomics. 8:367, 2007
[ PubMed | Paper |Sup1 Sup2 Sup3 ]
Principles and limitations of computational microRNA gene and target finding.
Lindow M, Gorodkin J
DNA Cell Biol. 26:339-51, 2007
[ PubMed | Paper | Sup ]
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.
Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jorgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshoj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M
Genome Biol. 8:R45, 2007
[ PubMed | Paper |Sup1 Sup2 Sup3 Sup4 ]
Multiple structural alignment and clustering of RNA sequences.
Torarinsson E, Havgaard JH, Gorodkin J
Bioinformatics. 23:926-32, 2007
[ PubMed | Paper ]
MicroRNA sequence motifs reveal asymmetry between the stem arms.
Gorodkin J, Havgaard JH, Enstero M, Sawera M, Jensen P, Ohman M, Fredholm M
Comput Biol Chem. 30:249-54, 2006
[ PubMed | Paper | Sup ]
Linkage mapping of gene-associated SNPs to pig chromosome 11.
Sawera M, Cirera S, Jorgensen CB, Gorodkin J, Fredholm M
Anim Genet. 37:199-204, 2006
[ PubMed | Paper ]
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.
Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J
Genome Res. 16:885-9, 2006
[ PubMed | Paper |Sup1 Sup2 ]
The tmRDB and SRPDB resources.
Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C
Nucleic Acids Res. 34:D163-8, 2006
[ PubMed | Paper ]
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.
Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L
BMC Genomics. 6:70, 2005
[ PubMed | Paper |Sup1 Sup2 ]
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J
Bioinformatics. 21:1815-24, 2005
[ PubMed | Paper ]
Mapping and expression studies of the mir17-92 cluster on pig chromosome 11.
Sawera M, Gorodkin J, Cirera S, Fredholm M
Mamm Genome. 16:594-8, 2005
[ PubMed | Paper ]
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.
Havgaard JH, Lyngso RB, Gorodkin J
Nucleic Acids Res. 33:W650-3, 2005
[ PubMed | Paper | Webserver | Software | Sup ]
A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: identification of synteny breakpoints.
Lahbib-Mansais Y, Karlskov-Mortensen P, Mompart F, Milan D, Jorgensen CB, Cirera S, Gorodkin J, Faraut T, Yerle M, Fredholm M
Genomics. 86:405-13, 2005
[ PubMed | Paper ]
Evolutionary rate variation and RNA secondary structure prediction.
Knudsen B, Andersen ES, Damgaard C, Kjems J, Gorodkin J
Comput Biol Chem. 28:219-26, 2004
[ PubMed | Paper ]
Comparing two K-category assignments by a K-category correlation coefficient.
Gorodkin J
Comput Biol Chem. 28(5-6):367-74, 2004
[ PubMed | Paper | Webserver | Software ]
RNA interactions in the 5' region of the HIV-1 genome.
Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J
J Mol Biol. 336:369-79, 2004
[ PubMed | Paper ]
tmRDB (tmRNA database).
Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
Nucleic Acids Res. 31:446-7, 2003
[ PubMed | Paper | Database ]
SRPDB: Signal Recognition Particle Database.
Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
Nucleic Acids Res. 31:363-4, 2003
[ PubMed | Paper | Database ]
Semi-automated update and cleanup of structural RNA alignment databases.
Gorodkin J, Zwieb C, Knudsen B
Bioinformatics. 17:642-5, 2001
[ PubMed | Paper | Webserver | Software ]
A mini-greedy algorithm for faster structural RNA stem-loop search.
Gorodkin J, Lyngso RB, Stormo GD
Genome Inform. 12:184-93, 2001
[ PubMed | Paper ]
Discovering common stem-loop motifs in unaligned RNA sequences.
Gorodkin J, Stricklin SL, Stormo GD
Nucleic Acids Res. 29:2135-44, 2001
[ PubMed | Paper ]
Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks.
Gorodkin J, Sogaard B, Bay H, Doll H, Kolster P, Brunak S
Comput Chem. 25:301-7, 2001
[ PubMed | Paper ]
SRPDB (Signal Recognition Particle Database).
Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
Nucleic Acids Res. 29:169-70, 2001
[ PubMed | Paper ]
tmRDB (tmRNA database).
Knudsen B, Wower J, Zwieb C, Gorodkin J
Nucleic Acids Res. 29:171-2, 2001
[ PubMed | Paper ]
Using sequence motifs for enhanced neural network prediction of protein distance constraints.
Gorodkin J, Lund O, Andersen CA, Brunak S
Proc Int Conf Intell Syst Mol Biol. 1999:95-105.
[ PubMed | Paper ]
MatrixPlot: visualizing sequence constraints.
Gorodkin J, Staerfeldt HH, Lund O, Brunak S
Bioinformatics. 15:769-70, 1999
[ PubMed | Paper | Webserver | Software ]
Computational applications of DNA structural scales.
Baldi P, Chauvin Y, Brunak S, Gorodkin J, Pedersen AG
Proc Int Conf Intell Syst Mol Biol. 6:35-42, 1998
[ PubMed | Paper ]
Finding the most significant common sequence and structure motifs in a set of RNA sequences.
Gorodkin J, Heyer LJ, Stormo GD
Nucleic Acids Res. 25:3724-32, 1997
[ PubMed | Paper ]
Universal distribution of saliencies for pruning in layered neural networks.
Gorodkin J, Hansen LK, Lautrup B, Solla SA
Int J Neural Syst. 1997 Oct-Dec;8(5-6):489-98.
[ PubMed | Paper ]
Protein distance constraints predicted by neural networks and probability density functions.
Lund O, Frimand K, Gorodkin J, Bohr H, Bohr J, Hansen J, Brunak S
Protein Eng. 10:1241-8, 1997
[ PubMed | Paper | Oldserver ]
Displaying the information contents of structural RNA alignments: the structure logos.
Gorodkin J, Heyer LJ, Brunak S, Stormo GD
Comput Appl Biosci. 13:583-6, 1997
[ PubMed | Paper | Webserver ]
Finding common sequence and structure motifs in a set of RNA sequences.
Gorodkin J, Heyer LJ, Stormo GD
Proc Int Conf Intell Syst Mol Biol. 5:120-3, 1997
[ PubMed | Paper ]
Orbits of Boolean functions.
Gorodkin J
Discrete Applied Mathematics 75, 269-275
[ Paper | Abstract ]
Neural Networks and Cellular Automata Complexity.
Gorodkin J, Sorensen A, Winther O
Complex Systems 7, 1-23
[ Paper | Abstract ]
A quantitative study of pruning by optimal brain damage.
Gorodkin J, Hansen LK, Krogh A, Svarer C, Winther O
Int J Neural Syst. 4:159-69, 1993
[ PubMed | Paper ]