Publications
Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi
COST Action CA21113
Mol Ther Nucleic Acids. 2023 Oct 29;34:102066. eCollection 2023 Dec 12
[ PubMed | Paper ]
Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function
Nagorska A, Zaucker A, Lambert F, Inman A, Toral-Perez S, Gorodkin J, Wan Y, Smutny M, Sampath K*
Development. 2023 Dec 1;150(23):dev201657. Epub 2023 Nov 30
[ PubMed | Paper ]
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease
Velissari R, Ilieva M, Dao J, Miller HE, Madsen JH, Gorodkin J, Aikawa M, Ishii H, Uchida S*
Brief Funct Genomics. 2023 Oct 3:elad044
[ PubMed | Paper ]
Alteration of microglial metabolism and inflammatory profile contributes to neurotoxicity in a hiPSC-derived microglia model of frontotemporal dementia 3
Haukedal H, Syshoj Lorenzen S, Winther Westi E, Corsi GI, Gadekar VP, McQuade A, Davtyan H, Doncheva NT, Schmid B, Chandrasekaran A, Seemann SE, Cirera S, Blurton-Jones M, Meyer M, Gorodkin J, Aldana BI, Freude K*
Brain Behav Immun. 2023 Oct;113:353-373. Epub 2023 Aug 3
[ PubMed | Paper ]
Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds
Bush K, Corsi GI, Yan AC, Haynes K, Layzer JM, Zhou JH, Llanga T, Gorodkin J, Sullenger BA*
Cell Chem Biol. 2023 Aug 17;30(8):879-892.e5. Epub 2023 Jun 29
[ PubMed | Paper ]
Letter to the editor: Testing on external independent datasets is necessary to corroborate machine learning model improvement
Corsi GI, Anthon C, Gorodkin J*
Bioinformatics. 2023 Jun 1;39(6):btad327
[ PubMed | Paper ]
Golgi fragmentation - One of the earliest organelle phenotypes in Alzheimer's disease neurons
Haukedal H, Corsi GI, Gadekar VP, Doncheva NT, Kedia S, de Haan N, Chandrasekaran A, Jensen P, Schionning P, Vallin S, Marlet FR, Poon A, Pires C, Agha FK, Wandall HH, Cirera S, Simonsen AH, Nielsen TT, Nielsen JE, Hyttel P, Muddashetty R, Aldana BI, Gorodkin J, Nair D, Meyer M, Larsen MR, Freude K*
Front Neurosci. 2023 Feb 16;17:1120086. eCollection 2023
[ PubMed | Paper ]
Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis
Yarani R*†, Palasca O†, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J, Pociot F*
Front Mol Biosci. 2023 Jan 5;9:1081176. eCollection 2022
[ PubMed | Paper ]
CRISPRi screen for enhancing heterologous alpha-amylase yield in Bacillus subtilis
Geissler AS, Fehler AO, Poulsen LD, Gonzalez-Tortuero E, Kallehauge TB, Alkan F, Anthon C, Seemann SE, Rasmussen MD, Breuner A, Hjort C, Vinther J, Gorodkin J*
J Ind Microbiol Biotechnol. 2023 Feb 17;50(1):kuac028
[ PubMed | Paper ]
The transcriptomic landscape of neurons carrying PSEN1 mutations reveals changes in extracellular matrix components and non-coding gene expression
Corsi GI†, Gadekar VP†, Haukedal H, Doncheva NT, Anthon C, Ambardar S, Palakodeti D, Hyttel P, Freude K, Seemann SE, Gorodkin J*
Neurobiol Dis. 2023 Mar;178:105980. Epub 2022 Dec 23
[ PubMed | Paper ]
RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols
Vegni J†, Sun Y†, Seemann SE, Zappaterra M, Davoli R, Dall'Olio S, Gorodkin J*, Zambonelli P*
Animals (Basel). 2023 Mar 28;13(7):1187
[ PubMed | Paper ]
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design
Anthon C, Corsi GI, Gorodkin J*
Bioinformatics. 2022 Dec 13;38(24):5437-5439
[ PubMed | Paper | Webserver ]
Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming
Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Handfield LF, Asenjo-Martinez A, Lisa-Vargas I, Seemann SE, Lee JTH, Patikas N, Kornum BR, Denham M, Hyttel P, Witter MP, Gorodkin J, Pers TH, Hemberg M, Khodosevich K, Hall VJ*
Front Cell Dev Biol. 2022 Aug 15;10:976549. eCollection 2022
[ PubMed | Paper ]
The Bacillaceae-1 RNA motif comprises two distinct classes
Gonzalez-Tortuero E, Anthon C, Havgaard JH, Geissler AS, Breuner A, Hjort C, Gorodkin J*, Seemann SE*
Gene. 2022 Oct 20;841:146756. Epub 2022 Jul 26
[ PubMed | Paper ]
Massively targeted evaluation of therapeutic CRISPR off-targets in cells
Pan X†, Qu K†, Yuan H†, Xiang X†, Anthon C†, Pashkova L, Liang X, Han P, Corsi GI, Xu F, Liu P, Zhong J, Zhou Y, Ma T, Jiang H, Liu J, Wang J, Jessen N, Bolund L, Yang H, Xu X, Church GM*, Gorodkin J*, Lin L*, Luo Y*
Nat Commun. 2022 Jul 13;13(1):4049
[ PubMed | Paper ]
The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production
Geissler AS, Poulsen LD, Doncheva NT, Anthon C, Seemann SE, Gonzalez-Tortuero E, Breuner A, Jensen LJ, Hjort C, Vinther J, Gorodkin J*
Front Microbiol. 2022 Aug 4;13:909493. eCollection 2022
[ PubMed | Paper | Dataresource ]
Flagella disruption in Bacillus subtilis increases amylase production yield
Fehler AO, Kallehauge TB*, Geissler AS, Gonzalez-Tortuero E, Seemann SE, Gorodkin J, Vinther J*
Microb Cell Fact. 2022 Jul 2;21(1):131
[ PubMed | Paper ]
Differentially Expressed miRNAs in Ulcerative Colitis and Crohn's Disease
Yarani R*, Shojaeian A, Palasca O, Doncheva NT, Jensen LJ, Gorodkin J, Pociot F*
Front Immunol. 2022 Jun 6;13:865777. eCollection 2022
[ PubMed | Paper ]
CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context
Corsi GI, Qu K, Alkan F, Pan X, Luo Y*, Gorodkin J*
Nat Commun. 2022 May 30;13(1):3006
[ PubMed | Paper ]
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?
Seemann SE*, Mirza AH, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Workman CT, Pociot F, Tommerup N, Gorodkin J, Ruzzo WL
Nucleic Acids Res. 2022 Mar 21;50(5):2452-2463
[ PubMed | Paper ]
CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells
Corsi GI, Gadekar VP, Gorodkin J*, Seemann SE*
Nucleic Acids Res. 2022 Feb 28;50(4):e20
[ PubMed | Paper | Software ]
Astrocytic reactivity triggered by defective autophagy and metabolic failure causes neurotoxicity in frontotemporal dementia type 3
Chandrasekaran A, Dittlau KS, Corsi GI, Haukedal H, Doncheva NT, Ramakrishna S, Ambardar S, Salcedo C, Schmidt SI, Zhang Y, Cirera S, Pihl M, Schmid B, Nielsen TT, Nielsen JE, Kolko M, Kobolak J, Dinnyes A, Hyttel P, Palakodeti D, Gorodkin J, Muddashetty RS, Meyer M, Aldana BI, Freude KK*
Stem Cell Reports. 2021 Nov 9;16(11):2736-2751. Epub 2021 Oct 21
[ PubMed | Paper ]
A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA
Mohammadniaei M*, Zhang M, Ashley J, Christensen UB, Friis-Hansen LJ, Gregersen R, Lisby JG, Benfield TL, Nielsen FE, Henning Rasmussen J, Pedersen EB, Olinger ACR, Kolding LT, Naseri M, Zheng T, Wang W, Gorodkin J, Sun Y*
Nat Commun. 2021 Aug 24;12(1):5089
[ PubMed | Paper ]
Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning
Xiang X†, Corsi GI†, Anthon C†, Qu K†, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J*, Luo Y*
Nat Commun. 2021 May 28;12(1):3238
[ PubMed | Paper | Webserver | Software ]
Development of the Entorhinal Cortex Occurs via Parallel Lamination During Neurogenesis
Liu Y†, Bergmann T†, Mori Y, Peralvo Vidal JM, Pihl M, Vasistha NA, Thomsen PD, Seemann SE, Gorodkin J, Hyttel P, Khodosevich K, Witter MP, Hall VJ*
Front Neuroanat. 2021 May 5;15:663667. eCollection 2021
[ PubMed | Paper ]
Human pathways in animal models: possibilities and limitations
Doncheva NT*, Palasca O, Yarani R, Litman T, Anthon C, Groenen MAM, Stadler PF, Pociot F, Jensen LJ*, Gorodkin J*
Nucleic Acids Res. 2021 Feb 26;49(4):1859-1871
[ PubMed | Paper ]
Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Varela-Martinez E, Corsi GI, Anthon C, Gorodkin J*, Jugo BM*
Sci Rep. 2021 Jan 11;11(1):427
[ PubMed | Paper ]
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
RNAcentral Consortium
Nucleic Acids Res. 2021 Jan 8;49(D1):D212-D220
[ PubMed | Paper ]
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
Geissler AS, Anthon C, Alkan F, Gonzalez-Tortuero E, Poulsen LD, Kallehauge TB, Breuner A, Seemann SE, Vinther J, Gorodkin J*
Microb Genom. 2021 Feb;7(2):000524
[ PubMed | Paper | Dataresource ]
Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a
Creutzburg SCA, Wu WY, Mohanraju P, Swartjes T, Alkan F, Gorodkin J, Staals RHJ, van der Oost J*
Nucleic Acids Res. 2020 Apr 6;48(6):3228-3243
[ PubMed | Paper ]
Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities
Sundfeld D*, Teodoro G, Havgaard JH, Gorodkin J, Melo AC M A
Concurrency Computat Pract Exper. 2020; 32:e5468
[ Paper ]
Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Jacobsen MJ, Havgaard JH, Anthon C, Mentzel CMJ, Cirera S, Krogh PM, Pundhir S, Karlskov-Mortensen P, Bruun CS, Lesnik P, Guerin M, Gorodkin J, Jorgensen CB, Fredholm M*, Barres R*
Front Genet. 2019 Dec 17;10:1268. eCollection 2019
[ PubMed | Paper ]
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
[ PubMed | Paper ]
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. Epub 2018 Dec 5
[ PubMed | Paper | Software ]
RNAcentral: a hub of information for non-coding RNA sequences
The RNAcentral Consortium
Nucleic Acids Res. 2019 Jan 8;47(D1):D221-D229
[ PubMed | Paper | Dataresource ]
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
[ PubMed | Paper | Software ]
Editorials
Special Issue: Computational Analysis of RNA Structure and Function
Gorodkin J*
Genes (Basel). 2019 Jan 16;10(1):55
[ PubMed | Paper ]
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
[ PubMed | Paper | Dataresource ]
Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures
Sabarinathan R, Anthon C, Gorodkin J, Seemann SE*
Genes (Basel). 2018 Dec 4;9(12):604
[ PubMed | Paper | Software ]
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):536
[ PubMed | Paper | Webserver ]
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. Epub 2018 Oct 4
[ PubMed | Paper ]
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
[ PubMed | Paper | Webserver | Software ]
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. eCollection 2018
[ PubMed | Paper | Dataresource ]
IFN-lambda 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, Durrwald R, Skovgaard K
PLoS One. 2018 Apr 20;13(4):e0194765. eCollection 2018
[ PubMed | Paper ]
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:bay003
[ PubMed | Paper | Dataresource ]
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
[ PubMed | Paper ]
Books, Book Chapters
Comparative RNA Genomics
Backofen R, Gorodkin J, Hofacker IL, Stadler PF*
Comparative RNA Genomics In Comparative Genomics. Setubal JC, Stoye J, Stadler PF (Ed.), Methods Mol Biol. 2018;1704:363-400
[ PubMed | Chapter ]
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 ]
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 AF, 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:baw167. Print 2017
[ PubMed | Paper | Webserver ]
Conference Papers
CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment
Sundfeld D, Havgaard JH, Gorodkin J, De Melo AC*
2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) 2017, CPAPER
[ Paper ]
Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Gottingen 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. eCollection 2016
[ PubMed | Paper ]
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Holzer M, Krahling 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
[ PubMed | Paper ]
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. Epub 2015 Dec 24
[ PubMed | Paper | Webserver | Software ]
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
Sukosd 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, Anthon C, Jacobsen MJ, Karlskov-Mortensen P, Bruun CS, Jorgensen 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 ]
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(1):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 AM, 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 LJ*
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*
Computational Approaches for Predicting Mutation Effects on RNA Structure 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*
De novo discovery of structured ncRNA motifs in genomic sequences 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*
RNA structural alignments, part I: Sankoff-based approaches for structural alignments 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*
Concepts and introduction to RNA bioinformatics In RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods Mol Biol. 2014;1097:1-31
[ PubMed | Chapter ]
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, Mork 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 IL, 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 ]
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*, Ekstrom 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*, 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, Hornshoj 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
[ PubMed | Paper | Dataresource ]
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbasli E, Gorodkin J*
Bioinformatics. 2012 Nov 1;28(21):2738-46. Epub 2012 Aug 24
[ PubMed | Paper | Software ]
Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM
Havgaard J, Kaur S, Gorodkin J*
Curr Protoc Bioinformatics. 2012 Sep;Chapter 12:12.11.1-12.11.15
[ PubMed | Chapter ]
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs
Croft L, Szklarczyk D, Jensen LJ, 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 ]
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 SE, 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 ]
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 AB, Cirera S, Gilchrist MJ, Gorodkin J, Jorgensen 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*
Evolutionary Genomics of MicroRNAs and Their Relatives In Evolutionary Genomics and Systems Biology. Gustavo Caetano-Anolles (Ed.), Wiley-Blackwell, Hoboken NJ, 2010, pp. 295-327
[ Paper | Abstract ]