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Items: 1 to 50 of 111

1.

A splice-site variant in the lncRNA gene RP1-140A9.1 cosegregates in the large Volkmann cataract family.

Eiberg H, Mikkelsen AF, Bak M, Tommerup N, Lund AM, Wenzel A, Sabarinathan R, Gorodkin J, Bang-Berthelsen CH, Hansen L.

Mol Vis. 2019 Jan 20;25:1-11. eCollection 2019.

2.

Special Issue: Computational Analysis of RNA Structure and Function.

Gorodkin J.

Genes (Basel). 2019 Jan 16;10(1). pii: E55. doi: 10.3390/genes10010055.

3.

Identification and characterization of novel conserved RNA structures in Drosophila.

Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J.

BMC Genomics. 2018 Dec 11;19(1):899. doi: 10.1186/s12864-018-5234-4.

4.

Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures.

Sabarinathan R, Anthon C, Gorodkin J, Seemann SE.

Genes (Basel). 2018 Dec 4;9(12). pii: E604. doi: 10.3390/genes9120604.

5.

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.

Doncheva NT, Morris JH, Gorodkin J, Jensen LJ.

J Proteome Res. 2019 Feb 1;18(2):623-632. doi: 10.1021/acs.jproteome.8b00702. Epub 2018 Dec 5.

PMID:
30450911
6.

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

Pan X, Xiong K, Anthon C, Hyttel P, Freude KK, Jensen LJ, Gorodkin J.

Genes (Basel). 2018 Nov 6;9(11). pii: E536. doi: 10.3390/genes9110536.

7.

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

Palasca O, Santos A, Stolte C, Gorodkin J, Jensen LJ.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay028. No abstract available.

8.

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters.

Alkan F, Wenzel A, Anthon C, Havgaard JH, Gorodkin J.

Genome Biol. 2018 Oct 26;19(1):177. doi: 10.1186/s13059-018-1534-x.

9.

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.

Pan X, Jensen LJ, Gorodkin J.

Bioinformatics. 2019 May 1;35(9):1494-1502. doi: 10.1093/bioinformatics/bty859.

PMID:
30295698
10.

Warburg Effect Metabolism Drives Neoplasia in a Drosophila Genetic Model of Epithelial Cancer.

Eichenlaub T, Villadsen R, Freitas FCP, Andrejeva D, Aldana BI, Nguyen HT, Petersen OW, Gorodkin J, Herranz H, Cohen SM.

Curr Biol. 2018 Oct 22;28(20):3220-3228.e6. doi: 10.1016/j.cub.2018.08.035. Epub 2018 Oct 4.

11.

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates.

Pan X, Wenzel A, Jensen LJ, Gorodkin J.

PLoS One. 2018 Aug 24;13(8):e0202369. doi: 10.1371/journal.pone.0202369. eCollection 2018.

12.

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs.

Brogaard L, Larsen LE, Heegaard PMH, Anthon C, Gorodkin J, Dürrwald R, Skovgaard K.

PLoS One. 2018 Apr 20;13(4):e0194765. doi: 10.1371/journal.pone.0194765. eCollection 2018.

13.

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

Palasca O, Santos A, Stolte C, Gorodkin J, Jensen LJ.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay003. Erratum in: Database (Oxford). 2018 Jan 1;2018:.

14.

Comparative RNA Genomics.

Backofen R, Gorodkin J, Hofacker IL, Stadler PF.

Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14.

PMID:
29277874
15.

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.

Kato Y, Gorodkin J, Havgaard JH.

BMC Genomics. 2017 Dec 2;18(1):935. doi: 10.1186/s12864-017-4309-y.

16.

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. 2018 Jan 9;46(1):104-119. doi: 10.1093/nar/gkx938.

17.

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. doi: 10.1038/s41598-017-06200-4.

18.

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. doi: 10.1101/gr.208652.116. Epub 2017 May 9.

19.

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. doi: 10.1093/bioinformatics/btx114.

20.

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. doi: 10.1016/j.gene.2017.03.015. Epub 2017 Mar 16.

PMID:
28322996
21.

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.

Nucleic Acids Res. 2017 May 5;45(8):e60. doi: 10.1093/nar/gkw1325.

22.

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. doi: 10.1093/database/baw167. Print 2017. Erratum in: Database (Oxford). 2017 Jan 1;2017(1):.

23.

Corrigendum: 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, 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. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

24.

Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model.

Mentzel CM, Alkan F, Keinicke H, Jacobsen MJ, Gorodkin J, Fredholm M, Cirera S.

PLoS One. 2016 Nov 30;11(11):e0167285. doi: 10.1371/journal.pone.0167285. eCollection 2016.

25.

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, 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. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

26.

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.

Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J.

Bioinformatics. 2016 Apr 15;32(8):1238-40. doi: 10.1093/bioinformatics/btv748. Epub 2015 Dec 24.

27.

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. doi: 10.1371/journal.pone.0139900. eCollection 2015.

28.

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. doi: 10.1093/nar/gkv1039. Epub 2015 Oct 17.

29.

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. doi: 10.1093/nar/gkv813. Epub 2015 Aug 17.

30.

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs.

Mentzel CM, 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. doi: 10.1371/journal.pone.0131650. eCollection 2015.

31.

Differential and coherent processing patterns from small RNAs.

Pundhir S, Gorodkin J.

Sci Rep. 2015 Jul 13;5:12062. doi: 10.1038/srep12062.

32.

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. doi: 10.1371/journal.pgen.1005333. eCollection 2015 Jun.

33.

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. doi: 10.3389/fgene.2015.00188. eCollection 2015. Review.

34.

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. doi: 10.1186/s13073-015-0162-2. eCollection 2015.

35.

Quality Assessment of Domesticated Animal Genome Assemblies.

Seemann SE, Anthon C, Palasca O, Gorodkin J.

Bioinform Biol Insights. 2016 Jun 6;9(Suppl 4):49-58. doi: 10.4137/BBI.S29333. eCollection 2015.

36.

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. doi: 10.1002/anie.201408362. Epub 2014 Nov 21.

PMID:
25417815
37.

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. doi: 10.1186/1471-2164-15-459.

38.

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 AM, Pociot F, Holmberg D, Gorodkin J.

Gene. 2014 Jul 15;545(1):80-7. doi: 10.1016/j.gene.2014.05.004. Epub 2014 May 3.

PMID:
24797614
39.

De novo discovery of structured ncRNA motifs in genomic sequences.

Ruzzo WL, Gorodkin J.

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15. Review.

PMID:
24639166
40.

RNA structural alignments, part I: Sankoff-based approaches for structural alignments.

Havgaard JH, Gorodkin J.

Methods Mol Biol. 2014;1097:275-90. doi: 10.1007/978-1-62703-709-9_13.

PMID:
24639164
41.

Concepts and introduction to RNA bioinformatics.

Gorodkin J, Hofacker IL, Ruzzo WL.

Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1. Review.

PMID:
24639152
42.

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. doi: 10.1371/journal.pone.0082699. eCollection 2014.

43.

Protein-driven inference of miRNA-disease associations.

Mørk S, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen LJ.

Bioinformatics. 2014 Feb 1;30(3):392-7. doi: 10.1093/bioinformatics/btt677. Epub 2013 Nov 21.

44.

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795. Epub 2013 Sep 4.

45.

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing.

Alquezar-Planas DE, Mourier T, Bruhn CA, 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. doi: 10.1038/srep02468.

46.

MicroRNA discovery by similarity search to a database of RNA-seq profiles.

Pundhir S, Gorodkin J.

Front Genet. 2013 Jul 11;4:133. doi: 10.3389/fgene.2013.00133. eCollection 2013.

47.

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. doi: 10.1093/nar/gkt291. Epub 2013 Apr 29.

48.

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. doi: 10.1002/humu.22273. Erratum in: Hum Mutat. 2013 Jun;34(6):925.

49.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, 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 SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, 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, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, 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. doi: 10.1038/nature11622.

50.

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. doi: 10.1186/1471-2164-13-459.

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