Publications

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2017


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.
[ PubMed | Paper ]

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


SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization
Damas ND, Marcatti M, Côme C, Christensen LL, Nielsen MM, Baumgartner R, Gylling HM, Maglieri G, Rundsten CF, Seemann SE, Rapin N, Thézenas S, Vang S, Ørntoft T, Andersen CL, Pedersen JS, Lund AH Nat Commun. 2016 Dec 22;7:13875.
[ PubMed | Paper ]

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 ]

GLP-1 induces barrier protective expression in Brunner’s glands and regulates colonic inflammation
Bang-Berthelsen CH, Holm TL Pyke C, Simonsen L, Sokilde R, Pociot F, Heller S, Folkersen L, Kvist PH, Jakerott M, Fleckner J, Villen M, Knudsen LB, Heding A, Frederiksen KS Inflammatory Bowel Diseases, Accepted
[ 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 ]

MicroRNAs as regulators of beta-cell function and dysfunction
Osmai M, Osmai Y, Bang-Berthelsen CH, Pallesen EM H, Vestergaard AL, Novotny GW, Pociot F, Mandrup-Poulsen T Diabetes Metab Res Rev. 2016 May;32(4):334-49. Epub 2015 Nov 11.
[ PubMed | Paper ]

2015


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. eCollection 2015.
[ PubMed | 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


Wet-lab tested microRNA assays for qPCR studies with SYBR(R) Green and DNA primers in pig tissues
Mentzel CM, Skovgaard K, Cordoba S, Herrera Uribe J, Busk PK, Cirera S Microrna. 2014;3(3):174-88.
[ PubMed | Paper | Sup ]

Circulating MicroRNAs in Plasma of Hepatitis B e Antigen Positive Children Reveal Liver-Specific Target Genes
Winther TN, Jacobsen KS, Mirza AH, Heiberg IL, Bang-Berthelsen CH, Pociot F, Hogh B Int J Hepatol. 2014;2014:791045. Epub 2014 Dec 17.
[ PubMed | Paper ]

miRNA profiles in cerebrospinal fluid from patients with central hypersomnias
Holm A, Bang-Berthelsen CH, Knudsen S, Modvig S, Kornum BR, Gammeltoft S, Jennum PJ J Neurol Sci. 2014 Dec 15;347(1-2):199-204. Epub 2014 Oct 2.
[ PubMed | Paper ]

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 ]

Genetic versus Non-Genetic Regulation of miR-103, miR-143 and miR-483-3p Expression in Adipose Tissue and Their Metabolic Implications—A Twin Study
Bork-Jensen J, Thuesen A, Bang-Bertelsen C, Grunnet L, Pociot F, Beck-Nielsen H, Ozanne S, Poulsen P, Vaag A Genes (Basel). 2014 Jul 9;5(3):508-17.
[ 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 ]

miRNA profiles in plasma from patients with sleep disorders reveal dysregulation of miRNAs in narcolepsy and other central hypersomnias
Holm A, Bang-Berthelsen CH, Knudsen S, Kornum BR, Modvig S, Jennum P, Gammeltoft S SLEEP, E-pub
[ Paper ]

Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference
Lopes M, Kutlu B, Miani M, Bang-Berthelsen CH, Størling J, Pociot F, Goodman N, Hood L, Welsh N, Bontempi G, Eizirik DL Genomics. 2014 Apr;103(4):264-75. Epub 2014 Jan 24.
[ 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 ]

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods
Methods in Molecular Biology 2014, GENERIC
[ Book ]

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


LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF, Reiche K, Backofen R Algorithms Mol Biol. 2013 Apr 20;8:14. eCollection 2013.
[ PubMed | Paper ]

Widespread purifying selection on RNA structure in mammals
Smith MA, Gesell T, Stadler PF, Mattick JS Nucleic Acids Res. 2013 Sep;41(17):8220-36. Epub 2013 Jul 11.
[ PubMed | Paper ]

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
Lorenz R, Bernhart SH, Qin J, Siederdissen CHz, Tanzer A, Amman F, Hofacker IL, Stadler PF IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):832-44.
[ PubMed | Paper ]

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
Lange SJ, Alkhnbashi OS, Rose D, Will S, Backofen R Nucleic Acids Res. 2013 Sep;41(17):8034-44. Epub 2013 Jul 17.
[ PubMed | Paper ]

MicroRNAs in the Hypothalamus
Meister B, Herzer S, Silahtaroglu A Neuroendocrinology. 2013;98(4):243-53. Epub 2013 Sep 21.
[ PubMed | Paper ]

Hepatitis B Surface Antigen Quantity Positively Correlates with Plasma Levels of microRNAs Differentially Expressed in Immunological Phases of Chronic Hepatitis B in Children
Winther TN, Heiberg IL, Bang-Berthelsen CH, Pociot F, Hogh B PLoS One. 2013 Nov 11;8(11):e80384. eCollection 2013.
[ PubMed | Paper ]

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 ]

Differential Plasma MicroRNA Profiles in HBeAg Positive and HBeAg Negative Children with Chronic Hepatitis B
Winther TN, Bang-Berthelsen CH, Heiberg IL, Pociot F, Hogh B PLoS One. 2013;8(3):e58236. Epub 2013 Mar 4.
[ PubMed | Paper ]

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


Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity
Halgren C, Bache I, Bak M, Myatt MW, Anderson CM, Brøndum-Nielsen K, Tommerup N Eur J Hum Genet. 2012 Dec;20(12):1315-9. Epub 2012 May 23.
[ PubMed | Paper ]

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 ]

Circulating Levels of MicroRNA from Children with Newly Diagnosed Type 1 Diabetes and Healthy Controls: Evidence That miR-25 Associates to Residual Beta-Cell Function and Glycaemic Control during Disease Progression
Nielsen LB, Wang C, Sørensen K, Bang-Berthelsen CH, Hansen L, Andersen MM, Hougaard P, Juul A, Zhang C, Pociot F, Mortensen HB Exp Diabetes Res. 2012;2012:896362. Epub 2012 Jul 5.
[ 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 ]

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
Washietl S, Hofacker IL, Stadler PF, Kellis M Nucleic Acids Res. 2012 May;40(10):4261-72. Epub 2012 Jan 28.
[ PubMed | 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 B, Andrieux J, Dieux A, Tommerup N, Bache I Clin Genet. 2012 Sep;82(3):248-55. Epub 2011 Aug 24.
[ 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 ]

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila
Andersen KL, Nielsen H Nucleic Acids Res. 2012 Feb;40(3):1267-81. Epub 2011 Oct 3.
[ PubMed | Paper ]

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 ]

Proteinortho: Detection of (Co-)orthologs in large-scale analysis
Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF, Prohaska SJ BMC Bioinformatics. 2011 Apr 28;12:124.
[ PubMed | Paper ]

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 ]

In Silico Evolution of Early Metabolism
Ullrich A, Rohrschneider M, Scheuermann G, Stadler PF, Flamm C Artif Life. 2011 Spring;17(2):87-108. Epub 2011 Mar 3.
[ PubMed | Paper ]

Traces of post-transcriptional RNA modifications in deep sequencing data
Findeiß S, Langenberger D, Stadler PF, Hoffmann S Biol Chem. 2011 Apr;392(4):305-13. Epub 2011 Feb 24.
[ PubMed | Paper ]

Topology and prediction of RNA pseudoknots
Reidys CM, Huang FW D, Andersen JE, Penner RC, Stadler PF, Nebel ME Bioinformatics. 2011 Apr 15;27(8):1076-85. Epub 2011 Feb 17.
[ 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, Fløyel T, Hagedorn PH, Gylvin T, Pociot F BMC Genomics. 2011 Feb 4;12:97.
[ 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. 2011 Mar;10(3):375-84. Epub 2011 Jan 20.
[ PubMed | Paper ]

A folding algorithm for extended RNA secondary structures
zu Siederdissen C H, Bernhart S H, Stadler P F, Hofacker I L Bioinformatics. 2011 Jul 1;27(13):i129-36.
[ PubMed | Paper ]

PLEXY: efficient target prediction for box C/D snoRNAs
Kehr S, Bartschat S, Stadler PF, Tafer H Bioinformatics. 2011 Jan 15;27(2):279-80. Epub 2010 Nov 13.
[ 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 ]

Books, Book Chapters


Genome Browsers
Torarinsson E In RNA. Nielsen H, Methods Mol Biol. 2011;703:53-65.
[ PubMed | Paper ]

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. 2010 May 26;5(5):e10843.
[ 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. 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 ]