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 ]