Publications

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2017


Translational co-regulation of a ligand and inhibitor by a conserved RNA element
Zaucker A, Nagorska A, Kumari P, Hecker N, Wang Y, Huang S, Cooper L, Sivashanmugam L, VijayKumar S, Brosens J, Gorodkin J, Sampath K Nucleic Acids Res. 2017 Oct 20.
[ PubMed | Paper ]

Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J Sci Rep. 2017 Jul 18;7(1):5776.
[ PubMed | Paper ]

The identification and functional annotation of RNA structures conserved in vertebrates
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J Genome Res. 2017 Aug;27(8):1371-1383. Epub 2017 May 9.
[ PubMed | Paper | Dataresource | Supplement ]

Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia
Junge A, Zandi R, Havgaard JH, Gorodkin J, Cowland JB Gene. 2017 Jun 5;615:35-40. Epub 2017 Mar 16.
[ PubMed | Paper ]

RNAscClust : clustering RNA sequences using structure conservation and graph based motifs
Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R Bioinformatics. 2017 Jul 15;33(14):2089-2096.
[ PubMed | Paper | Software ]

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck A, Stadler PF, Hofacker IL, Gorodkin J Nucleic Acids Res. 2017 May 5;45(8):e60.
[ PubMed | Paper | Software ]

RAIN: RNA–protein Association and Interaction Networks
Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J Database (Oxford). 2017 Jan 10;2017. Print 2017.
[ PubMed | Paper | Webserver ]

Conference Papers


CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment
Sundfeld D, Havgaard JH, Gorodkin J, Melo AC M A d 2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) 2017, CPAPER
[ Paper ]

2016


Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model
Mentzel CM J, Alkan F, Keinicke H, Jacobsen MJ, Gorodkin J, Fredholm M, Cirera S PLoS One. 2016 Nov 30;11(11):e0167285. eCollection 2016.
[ PubMed | Paper ]

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA O, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M Sci Rep. 2016 Oct 7;6:34589.
[ PubMed | Paper ]

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo AC M A, Gorodkin J Bioinformatics. 2016 Apr 15;32(8):1238-40. Epub 2015 Dec 24.
[ PubMed | Paper | Webserver | Software ]

2015


Quality Assessment of Domesticated Animal Genome Assemblies
Seemann SE, Anthon C, Palasca O, Gorodkin J Bioinformatics and Biology Insights 2015, 9S4:BBI.S29333
[ Paper ]

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure
Theis C, Zirbel CL, zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J PLoS One. 2015 Oct 28;10(10):e0139900. eCollection 2015.
[ PubMed | Paper ]

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J Nucleic Acids Res. 2015 Dec 2;43(21):10168-79. Epub 2015 Oct 17.
[ PubMed | Paper ]

Optimizing RNA structures by sequence extensions using RNAcop
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. Epub 2015 Aug 17.
[ PubMed | Paper | Webserver | Software ]

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs
Mentzel CM J, Anthon C, Jacobsen MJ, Karlskov-Mortensen P, Bruun CS, Jørgensen CB, Gorodkin J, Cirera S, Fredholm M PLoS One. 2015 Jul 29;10(7):e0131650. eCollection 2015.
[ PubMed | Paper ]

Differential and coherent processing patterns from small RNAs
Pundhir S, Gorodkin J Sci Rep. 2015 Jul 13;5:12062.
[ PubMed | Paper | Software ]

Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers
Stewart JB, Alaei-Mahabadi B, Sabarinathan R, Samuelsson T, Gorodkin J, Gustafsson CM, Larsson E PLoS Genet. 2015 Jun 30;11(6):e1005333. eCollection 2015 Jun.
[ PubMed | Paper ]

Emerging applications of read profiles towards the functional annotation of the genome
Pundhir S, Poirazi P, Gorodkin J Front Genet. 2015 May 19;6:188. eCollection 2015.
[ PubMed | Paper ]

Transcriptomic landscape of lncRNAs in inflammatory bowel disease
Mirza AH, Berthelsen CH, Seemann SE, Pan X, Frederiksen KS, Vilien M, Gorodkin J, Pociot F Genome Med. 2015 May 13;7(1):39. eCollection 2015.
[ PubMed | Paper ]

Profiling of Ribose Methylations in RNA by High-Throughput Sequencing
Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H Angew Chem Int Ed Engl. 2015 Jan 7;54(2):451-5. Epub 2014 Nov 21.
[ PubMed | Paper ]

Popular Science


Emerging tools for RNA structure analysis in polymorphic data
Sabarinathan R, Seemann SE, Gorodkin J Biozoom 2:3, 2015
[ Paper ]

2014


Structured RNAs and synteny regions in the pig genome
Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J BMC Genomics. 2014 Jun 10;15:459.
[ PubMed | Paper ]

Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project
Pundhir S, Hannibal TD, Bang-Berthelsen CH, Wegener AK, Pociot F, Holmberg D, Gorodkin J Gene. 2014 Jul 15;545(1):80-7. Epub 2014 May 3.
[ PubMed | Paper ]

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J PLoS One. 2014 Jan 8;9(1):e82699. eCollection 2014.
[ PubMed | Paper ]

Protein-driven inference of miRNA-disease associations
Mork S, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen L J Bioinformatics. 2014 Feb 1;30(3):392-7. Epub 2013 Nov 21.
[ PubMed | Paper | Software | Dataresource ]

Books, Book Chapters


Computational Approaches for Predicting Mutation Effects on RNA Structure
Sabarinathan R, Gorodkin J In Comprehensive Biomedical Physics. Anders Brahme, Vol 6. 111, Amsterdam: Elsevier, 2014
[ Chapter ]

De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences
Ruzzo WL, Gorodkin J In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods Mol Biol. 2014;1097:303-18.
[ PubMed | Chapter ]

RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments
Havgaard JH, Gorodkin J In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods Mol Biol. 2014;1097:275-90.
[ PubMed | Chapter ]

Concepts and Introduction to RNA Bioinformatics
Gorodkin J, Hofacker IL, Ruzzo WL In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods Mol Biol. 2014;1097:1-31.
[ PubMed | Chapter ]

2013


Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
Alquezar-Planas DE, Mourier T, Bruhn CA W, Hansen AJ, Vitcetz SN, Mørk S, Gorodkin J, Nielsen HA, Guo Y, Sethuraman A, Paxinos EE, Shan T, Delwart EL, Nielsen LP Sci Rep. 2013;3:2468.
[ PubMed | Paper ]

The RNAsnp web server: predicting SNP effects on local RNA secondary structure
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9. Epub 2013 Apr 29.
[ PubMed | Paper | Webserver | Software ]

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J Hum Mutat. 2013 Apr;34(4):546-56.
[ PubMed | Paper | Software ]

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
Theis C, Honer zu Siederdissen C, Hofacker I L, Gorodkin J Nucleic Acids Res. 2013 Dec;41(22):9999-10009. Epub 2013 Sep 4.
[ PubMed | Paper | Software ]

MicroRNA discovery by similarity search to a database of RNA-seq profiles
Pundhir S, Gorodkin J Front Genet. 2013 Jul 11;4:133. eCollection 2013.
[ PubMed | Paper | Webserver ]

2012


Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Podolska A, Anthon C, Bak M, Tommerup N, Skovgaard K, Heegaard PM, Gorodkin J, Cirera S, Fredholm M BMC Genomics. 2012 Sep 6;13:459.
[ PubMed | Paper ]

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain
Seemann SE, Sunkin SM, Hawrylycz MJ, Ruzzo WL, Gorodkin J BMC Genomics. 2012 May 31;13:214.
[ PubMed | Paper ]

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 Aug;40(14):6660-72. Epub 2012 Apr 17.
[ PubMed | Paper ]

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J Bioinformatics. 2012 Jan 1;28(1):17-24. Epub 2011 Nov 3.
[ PubMed | Paper | Software ]

Analyses of pig genomes provide insight into porcine demography and evolution
Groenen MA M, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens H, Li S, Larkin DM, Kim H, Frantz LA F, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi S, Chow W, Clark RC, Clee C, Crooijmans RP M A, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du Z, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG R, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu Z, Humphray SJ, Hunt T, Hornshøj H, Jeon J, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim J, Kim K, Kim T, Larson G, Lee K, Lee K, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Truong Nguyen D, Ni P, Oh S, Onteru S, Panitz F, Park E, Park H, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB Nature. 2012 Nov 15;491(7424):393-8.
[ PubMed | Paper | Dataresource ]

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbaşli E, Gorodkin J Bioinformatics. 2012 Nov 1;28(21):2738-46. Epub 2012 Aug 24.
[ PubMed | Paper | Software ]

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs
Croft L, Szklarczyk D, Jensen L, Gorodkin J BMC Syst Biol. 2012 Jul 23;6:90.
[ PubMed | Paper | Dataresource ]

RILogo: visualizing RNA–RNA interactions
Menzel P, Seemann SE, Gorodkin J Bioinformatics. 2012 Oct 1;28(19):2523-6. Epub 2012 Jul 23.
[ PubMed | Paper | Webserver | Software ]

Books, Book Chapters


Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM
Havgaard J, Kaur S, Gorodkin J Curr Protoc Bioinformatics. 2012 Sep;Chapter 12:Unit12.11.
[ PubMed | Chapter ]

2011


From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Gorodkin J, Hofacker IL PLoS Comput Biol. 2011 Aug;7(8):e1002100. Epub 2011 Aug 4.
[ PubMed | Paper ]

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
Seemann S E, Menzel P, Backofen R, Gorodkin J Nucleic Acids Res. 2011 Jul;39(Web Server issue):W107-11. Epub 2011 May 23.
[ PubMed | Paper | Webserver ]

Fast local fragment chaining using sum-of-pair gap costs
Otto C, Hoffmann S, Gorodkin J, Stadler PF Algorithms Mol Biol. 2011 Mar 18;6:4.
[ PubMed | Paper | Software ]

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. 2011 Mar;10(3):375-84. Epub 2011 Jan 20.
[ PubMed | Paper ]

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Menzel P, Stadler PF, Gorodkin J Bioinformatics. 2011 Feb 1;27(3):317-25. Epub 2010 Dec 1.
[ PubMed | Paper | Webserver | Software ]

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J Bioinformatics. 2011 Jan 15;27(2):211-9. Epub 2010 Nov 18.
[ PubMed | Paper | Webserver | Software ]

2010


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. 2010 May 21;5:22.
[ PubMed | Paper ]

A study of alternative splicing in the pig
Nygard A, Cirera S, Gilchrist MJ, Gorodkin J, Jørgensen CB, Fredholm M BMC Res Notes. 2010 May 5;3:123.
[ PubMed | Paper | Dataresource ]

De novo prediction of structured RNAs from genomic sequences
Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL Trends Biotechnol. 2010 Jan;28(1):9-19. Epub 2009 Nov 26.
[ PubMed | Paper | Dataresource | Sup ]

Books, Book Chapters


Evolutionary Genomics of MicroRNAs and Their Relatives
Tanzer A, Riester M, Hertel J, Bermudez-Santana CI, Gorodkin J, Hofacker IL, Stadler PF In Evolutionary Genomics and Systems Biology. Gustavo Caetano-Anolles (Ed.), Wiley-Blackwell, Hoboken NJ, 2010, pp. 295-327.
[ Paper | Abstract ]

2009


454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides
Zagrobelny M, Scheibye-Alsing K, Jensen N, Møller B, Gorodkin J, Bak S BMC Genomics. 2009 Dec 2;10:574.
[ PubMed | Paper ]

The tedious task of finding homologous noncoding RNA genes
Menzel P, Gorodkin J, Stadler P F RNA. 2009 Dec;15(12):2075-82. Epub 2009 Oct 27.
[ PubMed | Paper | Dataresource | Sup ]

Sequence assembly
Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler P, Mang Y, Tommerup N, Gilchrist M, Nygård A, Cirera S, Jørgensen C, Fredholm M, Gorodkin J Comput Biol Chem. 2009 Apr;33(2):121-36. Epub 2008 Dec 6.
[ PubMed | Paper | Dataresource | Sup ]

Structural profiles of human miRNA families from pairwise clustering
Kaczkowski B, Torarinsson E, Reiche K, Havgaard J H, Stadler P F, Gorodkin J Bioinformatics. 2009 Feb 1;25(3):291-4. Epub 2008 Dec 4.
[ PubMed | Paper | Dataresource | Sup ]

Conference Papers


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 ]

2008


Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
Seemann SE, Gorodkin J, Backofen R Nucleic Acids Res. 2008 Nov;36(20):6355-62. Epub 2008 Oct 4.
[ PubMed | Paper | Sup ]

SNP-finding in pig mitochondrial ESTs
Scheibye-Alsing K, Cirera S, Gilchrist M J, Fredholm M, Gorodkin J Anim Genet. 2008 Apr;39(2):193-5. Epub 2008 Feb 6.
[ PubMed | Paper ]

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
Torarinsson E, Yao Z, Wiklund E D, Bramsen J B, Hansen C, Kjems J, Tommerup N, Ruzzo W L, Gorodkin J Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.
[ PubMed | Paper | Dataresource | Sup ]

2007


Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Havgaard JH, Torarinsson E, Gorodkin J PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20.
[ 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. 2007 Oct 11;8:367.
[ PubMed | Paper |Sup1 Sup2 Sup3 ]

Detection of RNA structures in porcine EST data and related mammals
Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J BMC Genomics. 2007 Sep 10;8:316.
[ PubMed | Paper |Sup1 Sup2 ]

Semiautomated improvement of RNA alignments
Andersen E S, Lind-Thomsen A, Knudsen B, Kristensen S E, Havgaard J H, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J RNA. 2007 Nov;13(11):1850-9. Epub 2007 Sep 5.
[ 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 L B, Hoj A, Vingborg R K, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen C B, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen B J, Havgaard J H, Brunak S, Fredholm M, Bendixen C Bioinformatics. 2007 Jul 1;23(13):i387-91.
[ PubMed | Paper ]

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences
Karlskov-Mortensen P, Hu Z L, Gorodkin J, Reecy J M, Fredholm M Anim Genet. 2007 Aug;38(4):401-5. Epub 2007 Jun 9.
[ PubMed | Paper | Sup ]

Principles and Limitations of Computational MicroRNA Gene and Target Finding
Lindow M, Gorodkin J DNA Cell Biol. 2007 May;26(5):339-51.
[ 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, Jørgensen 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, Stærfeldt H, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M Genome Biol. 2007;8(4):R45.
[ PubMed | Paper | Dataresource |Sup1 Sup2 Sup3 Sup4 ]

Multiple structural alignment and clustering of RNA sequences
Torarinsson E, Havgaard J H, Gorodkin J Bioinformatics. 2007 Apr 15;23(8):926-32. Epub 2007 Feb 25.
[ PubMed | Paper ]

2006


MicroRNA sequence motifs reveal asymmetry between the stem arms
Gorodkin J, Havgaard J, Ensterö M, Sawera M, Jensen P, Öhman M, Fredholm M Comput Biol Chem. 2006 Aug;30(4):249-54. Epub 2006 Jun 22.
[ PubMed | Paper | Sup ]

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. 2006 Jul;16(7):885-9. Epub 2006 Jun 2.
[ PubMed | Paper | Dataresource |Sup1 Sup2 ]

Linkage mapping of gene-associated SNPs to pig chromosome 11
Sawera M, Cirera S, Jorgensen C B, Gorodkin J, Fredholm M Anim Genet. 2006 Jun;37(3):199-204.
[ PubMed | Paper ]

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. 2006 Jan 1;34(Database issue):D163-8.
[ PubMed | Paper ]

2005


Mapping and expression studies of the mir17-92 cluster on pig Chromosome 11
Sawera M, Gorodkin J, Cirera S, Fredholm M Mamm Genome. 2005 Aug;16(8):594-8. Epub 2005 Sep 14.
[ PubMed | Paper ]

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, Jørgensen CB, Cirera S, Gorodkin J, Faraut T, Yerle M, Fredholm M Genomics. 2005 Oct;86(4):405-13.
[ PubMed | Paper ]

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Havgaard J H, Lyngso R B, Gorodkin J Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3.
[ PubMed | Paper | Webserver | Software | Sup ]

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson R, Schierup MH, Jørgensen FG, Gorodkin J, Panitz F, Stærfeldt H, Christensen OF, Mailund T, Hornshøj 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. 2005 May 10;6:70.
[ PubMed | Paper | Dataresource |Sup1 Sup2 ]

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Havgaard J H, Lyngso R B, Stormo G D, Gorodkin J Bioinformatics. 2005 May 1;21(9):1815-24. Epub 2005 Jan 18.
[ PubMed | Paper ]

2004


Comparing two K-category assignments by a K-category correlation coefficient
Gorodkin J Comput Biol Chem. 2004 Dec;28(5-6):367-74.
[ PubMed | Paper | Webserver | Software ]

Evolutionary rate variation and RNA secondary structure prediction
Knudsen B, Andersen E, Damgaard C, Kjems J, Gorodkin J Comput Biol Chem. 2004 Jul;28(3):219-26.
[ PubMed | Paper ]

RNA interactions in the 5' region of the HIV-1 genome
Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J J Mol Biol. 2004 Feb 13;336(2):369-79.
[ PubMed | Paper ]

2003


tmRDB (tmRNA database)
Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J Nucleic Acids Res. 2003 Jan 1;31(1):446-7.
[ PubMed | Paper | Database ]

SRPDB: Signal Recognition Particle Database
Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res. 2003 Jan 1;31(1):363-4.
[ PubMed | Paper | Database ]

2001


A mini-greedy algorithm for faster structural RNA stem-loop search
Gorodkin J, Lyngso RB, Stormo GD Genome Inform. 2001;12:184-93.
[ PubMed | Paper ]

Semi-automated update and cleanup of structural RNA alignment databases
Gorodkin J, Zwieb C, Knudsen B Bioinformatics. 2001 Jul;17(7):642-5.
[ PubMed | Paper | Webserver | Software ]

Discovering common stem-loop motifs in unaligned RNA sequences
Gorodkin J, Stricklin SL, Stormo GD Nucleic Acids Res. 2001 May 15;29(10):2135-44.
[ 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. 2001 May;25(3):301-7.
[ PubMed | Paper ]

tmRDB (tmRNA database)
Knudsen B, Wower J, Zwieb C, Gorodkin J Nucleic Acids Res. 2001 Jan 1;29(1):171-2.
[ PubMed | Paper ]

SRPDB (Signal Recognition Particle Database)
Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res. 2001 Jan 1;29(1):169-70.
[ PubMed | Paper ]

1999


MatrixPlot: visualizing sequence constraints
Gorodkin J, Staerfeldt HH, Lund O, Brunak S Bioinformatics. 1999 Sep;15(9):769-70.
[ PubMed | Paper | Webserver | Software ]

Conference Papers


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 ]

1998


Computational applications of DNA structural scales
Baldi P, Chauvin Y, Brunak S, Gorodkin J, Pedersen AG Proc Int Conf Intell Syst Mol Biol. 1998;6:35-42.
[ PubMed | Paper ]

1997


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. 1997 Nov;10(11):1241-8.
[ 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. 1997 Dec;13(6):583-6.
[ PubMed | Paper | Webserver ]

Finding the most significant common sequence and structure motifs in a set of RNA sequences
Gorodkin J, Heyer LJ, Stormo GD Nucleic Acids Res. 1997 Sep 15;25(18):3724-32.
[ PubMed | Paper ]

Orbits of Boolean functions
Gorodkin J Discrete Applied Mathematics 75, 269-275, 1997
[ Paper | Abstract ]

Conference Papers


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. 1997;5:120-3.
[ PubMed | Paper ]

1993


A quantitative study of pruning by optimal brain damage
Gorodkin J, Hansen LK, Krogh A, Svarer C, Winther O Int J Neural Syst. 1993 Jun;4(2):159-69.
[ PubMed | Paper ]

Neural Networks and Cellular Automata Complexity
Gorodkin J, Sorensen A, Winther O Complex Systems 7, 1-23, 1993
[ Paper | Abstract ]