Publications

  Authors:   Year:   Free text: 

2017


Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J Scientific Reports 2017, 7(1)
[ 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 Research 2017, 27(8):1371-1383
[ 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, 615:35-40
[ 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, 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) 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 2017, 2017:baw167
[ 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 Nature Communications 2016, 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, 11(11):e0167285
[ 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 Scientific Reports 2016, 6(1)
[ 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 ]

Quality Assessment of Domesticated Animal Genome Assemblies
Seemann S, Anthon C, Palasca O, Gorodkin J Bioinformatics and Biology Insights 2015:Suppl. 4 49-58
[ Paper ]

2015


Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo AC M A, Gorodkin J Bioinformatics 2015, 32(8):1238-1240
[ PubMed | Paper | Webserver | Software ]

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, 10(10):e0139900
[ 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) 43 (21): 10168-10179
[ PubMed | Paper ]

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/Metabolism Research and Reviews 2015, 32(4):334-349
[ 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 Research 2015, 43(17):8135-8145
[ 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, 10(7):e0131650
[ PubMed | Paper ]

Differential and coherent processing patterns from small RNAs
Pundhir S, Gorodkin J Scientific Reports 2015, 5(1)
[ 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 Genetics 2015, 11(6):e1005333
[ PubMed | Paper ]

Emerging applications of read profiles towards the functional annotation of the genome
Pundhir S, Poirazi P, Gorodkin J Frontiers in Genetics 2015, 6
[ 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 Medicine 2015, 7(1)
[ 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. 3:174-88, 2014
[ 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 International Journal of Hepatology 2014, 2014:1-10
[ 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 Journal of the Neurological Sciences 2014, 347(1-2):199-204
[ 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 Angewandte Chemie International Edition 2015, 54(2):451
[ 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, 15(1):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 2014, 5(3):508-517
[ 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, 545(1):80-87
[ 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, 103(4):264-275
[ 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, 9(1):e82699
[ PubMed | Paper ]

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 ]

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 for Molecular Biology 2013, 8(1):14
[ PubMed | Paper ]

Widespread purifying selection on RNA structure in mammals
Smith MA, Gesell T, Stadler PF, Mattick JS Nucleic Acids Research 2013, 41(17):8220-8236
[ 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 Transactions on Computational Biology and Bioinformatics 2013, 10(4):832-844
[ 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 Research 2013, 41(17):8034-8044
[ PubMed | Paper ]

MicroRNAs in the Hypothalamus
Meister B, Herzer S, Silahtaroglu A Neuroendocrinology 2013, 98(4):243-253
[ 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, 8(11):e80384
[ 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 Scientific Reports 2013, 3(1)
[ PubMed | Paper ]

The RNAsnp web server: predicting SNP effects on local RNA secondary structure
Sabarinathan R, Tafer H, Seemann S E, Hofacker I L, Stadler P F, Gorodkin J Nucleic Acids Research 2013, 41(W1):W475-W479
[ 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
[ 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 human mutation 2013, 34(4): 546
[ PubMed | Paper | Software ]

Protein-driven inference of miRNA-disease associations
Mork S, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen L J Bioinformatics 2013, 30(3):392-397
[ PubMed | Paper | Software | Dataresource ]

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 Research 2013, 41(22):9999-10009
[ PubMed | Paper | Software ]

MicroRNA discovery by similarity search to a database of RNA-seq profiles
Pundhir S, Gorodkin J Frontiers in Genetics 2013, 4
[ PubMed | Paper | Webserver ]

Books, Book Chapters


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 in Molecular Biology 2013, GENERIC:303-318
[ 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 in Molecular Biology 2013, GENERIC:275-290
[ 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 in Molecular Biology 2013, GENERIC:1-31
[ PubMed | Chapter ]

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 European Journal of Human Genetics 2012, 20(12):1315-1319
[ 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, 13(1):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 Experimental Diabetes Research 2012, 2012:1-7
[ 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, 13(1):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 Research 2012, 40(14):6660-6672
[ 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 Research 2012, 40(10):4261-4272
[ 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, 491(7424):393-398
[ PubMed | Paper | Dataresource ]

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbaşli E, Gorodkin J Bioinformatics 2012, 28(21):2738-2746
[ 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 Systems Biology 2012, 6(1):90
[ PubMed | Paper | Dataresource ]

RILogo: visualizing RNA–RNA interactions
Menzel P, Seemann SE, Gorodkin J Bioinformatics 2012, 28(19):2523-2526
[ PubMed | Paper | Webserver | Software ]

Books, Book Chapters


Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM
Havgaard J, Kaur S, Gorodkin J Current Protocols in Bioinformatics 2012, CHAP
[ PubMed | Chapter ]

2011


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 Clinical Genetics 2011, 82(3):248-255
[ 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 2011, 28(1):17-24
[ PubMed | Paper | Software ]

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Gorodkin J, Hofacker IL PLoS Computational Biology 2011, 7(8):e1002100
[ 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 Research 2011, 39(suppl):W107-W111
[ 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, 12(1):124
[ PubMed | Paper ]

Fast local fragment chaining using sum-of-pair gap costs
Otto C, Hoffmann S, Gorodkin J, Stadler PF Algorithms for Molecular Biology 2011, 6(1):4
[ PubMed | Paper | Software ]

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

Traces of post-transcriptional RNA modifications in deep sequencing data
Findeiß S, Langenberger D, Stadler PF, Hoffmann S Biological Chemistry 2011, 392(4)
[ PubMed | Paper ]

Topology and prediction of RNA pseudoknots
Reidys CM, Huang FW D, Andersen JE, Penner RC, Stadler PF, Nebel ME Bioinformatics 2011, 27(8):1076-1085
[ 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, 12(1)
[ 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 Molecular Cancer Therapeutics 2011, 10(3):375-384
[ PubMed | Paper ]

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila
Andersen KL, Nielsen H Nucleic Acids Research 2011, 40(3):1267-1281
[ 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, 27(13):i129-i136
[ PubMed | Paper ]

2010


PLEXY: efficient target prediction for box C/D snoRNAs
Kehr S, Bartschat S, Stadler PF, Tafer H Bioinformatics 2010, 27(2):279-280
[ PubMed | Paper ]

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Menzel P, Stadler PF, Gorodkin J Bioinformatics 2010, 27(3):317-325
[ 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 2010, 27(2):211-219
[ PubMed | Paper | Webserver | Software ]

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, 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 for Molecular Biology 2010, 5(1):22
[ PubMed | Paper ]

A study of alternative splicing in the pig
Nygard A, Cirera S, Gilchrist MJ, Gorodkin J, Jørgensen CB, Fredholm M BMC Research Notes 2010, 3(1):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 in Biotechnology 2010, 28(1):9-19
[ PubMed | Paper | Dataresource | Sup ]

Books, Book Chapters


Genome Browsers
Torarinsson E In RNA. Nielsen H, RNA 2010, GENERIC:53-65
[ PubMed | Paper ]

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 ]