Publications

2023


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 ]

Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum

Corsi GI, Tichkule S, Sannella AR, Vatta P, Asnicar F, Segata N, Jex AR, van Oosterhout C*, Caccio SM Mol Ecol. 2023 May;32(10):2633-2645. Epub 2022 Jun 16
[ 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 ]

2022


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 ]

2021


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 ]

Modelling Nonalcoholic Steatohepatitis In Vivo-A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model

Skat-Rordam J†, Ipsen DH†, Seemann SE, Latta M, Lykkesfeldt J, Tveden-Nyborg P* Biomedicines. 2021 Sep 10;9(9):1198
[ 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 ]

The canine activated platelet secretome (CAPS): A translational model of thrombin-evoked platelet activation response

Cremer SE*, Catalfamo JL, Goggs R, Seemann SE, Kristensen AT, Szklanna PB, Maguire PB, Brooks MB Res Pract Thromb Haemost. 2020 Dec 3;5(1):55-68. eCollection 2021 Jan
[ 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 ]

2020


Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Ashwood C, Bittremieux W, Deutsch EW, Doncheva NT, Dorfer V, Gabriels R, Gorshkov V, Gupta S, Jones AR, Käll L, Kopczynski D, Lane L, Lautenbacher L, Legeay M, Locard-Paulet M, Mesuere B, Perez-Riverol Y, Netz E, Pfeuffer J, Sachsenberg T, Salz R, Samaras P, Schiebenhoefer H, Schmidt T, Schwämmle V, Soggiu A, Uszkoreit J, Van Den Bossche T, Van Puyvelde B, Van Strien J, Verschaffelt P, Webel H, Willems S* EuPA Open Proteomics 2020, 24:1-6
[ Paper ]

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 ]

2019


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 ]

Proteomic profiling of the thrombin-activated canine platelet secretome (CAPS)

Cremer SE*, Catalfamo JL, Goggs R, Seemann SE, Kristensen AT, Brooks MB PLoS One. 2019 Nov 13;14(11):e0224891. 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 ]

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P*, Jensen LJ*, Mering CV* Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
[ 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 ]

2018


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 ]

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

Cook HV, Doncheva NT, Szklarczyk D, von Mering C, Jensen LJ* Viruses. 2018 Sep 23;10(10):519
[ PubMed | Paper ]

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 ]

2017


The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P*, Jensen LJ*, von Mering C* Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. Epub 2016 Oct 18
[ PubMed | Paper ]

DotAligner: identification and clustering of RNA structure motifs

Smith MA*, Seemann SE, Quek XC, Mattick JS Genome Biol. 2017 Dec 28;18(1):244
[ PubMed | Paper ]

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 ]

2016


SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

Damas ND, Marcatti M, Come C, Christensen LL, Nielsen MM, Baumgartner R, Gylling HM, Maglieri G, Rundsten CF, Seemann SE, Rapin N, Thezenas S, Vang S, Orntoft 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 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 ]

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 RS, Folkersen L, Kvist PH, Jackerott M, Fleckner J, Vilien M, Knudsen LB, Heding A, Frederiksen KS Inflamm Bowel Dis. 2016 Sep;22(9):2078-97
[ 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 ]

MicroRNAs as regulators of beta-cell function and dysfunction

Osmai M, Osmai Y, Bang-Berthelsen CH, Pallesen EM, 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

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 ]

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(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 AC, Bang-Bertelsen CH, Grunnet LG, Pociot F, Beck-Nielsen H, Ozanne SE, 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 AM, 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. 2014 Sep 1;37(9):1525-33
[ PubMed | Paper ]

Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference

Lopes M, Kutlu B, Miani M, Bang-Berthelsen CH, Storling 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 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 ]

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

* RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin J, Ruzzo WL (Ed.), Methods in Molecular Biology 2014
[ Book ]

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 ]

2013


LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF*, Reiche*, 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, Honer zu Siederdissen C, 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, 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 ]

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 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 ]

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, Brondum-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, Sorensen K, Bang-Berthelsen CH, Hansen L, Andersen ML, Hougaard P, Juul A, Zhang CY, 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 CM, Henriksen KF, Hjalgrim H, Kirchhoff M, Bijlsma EK, Nielsen M, den Hollander NS, Ruivenkamp CA, Isidor B, Le Caignec C, Zannolli R, Mucciolo M, Renieri A, Mari F, Anderlid BM, 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*, Ekstrom 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*, 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 ]

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 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 ]

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, 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, Floyel 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 ]

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 ]

Genome browsers

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

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 ]

Conference Papers


A folding algorithm for extended RNA secondary structures

Honer zu Siederdissen C*, Bernhart SH, Stadler PF, Hofacker IL Bioinformatics. 2011 Jul 1;27(13):i129-36
[ 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 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 ]

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 NB, Moller BL, 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 PF* 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 PF, Mang Y, Tommerup N, Gilchrist MJ, Nygard AB, Cirera S, Jorgensen CB, Fredholm M, Gorodkin J* Comput Biol Chem. 2009 Apr;33(2):121-36. Epub 2008 Dec 6
[ PubMed | Paper | Dataresource | Sup ]

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Anandam P, Torarinsson E, Ruzzo WL* Bioinformatics. 2009 Mar 1;25(5):668-9. Epub 2009 Jan 9
[ PubMed | Paper | Sup ]

Structural profiles of human miRNA families from pairwise clustering

Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, 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 ]

WAR: Webserver for aligning structural RNAs

Torarinsson E, Lindgreen S* Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W79-84. Epub 2008 May 20
[ PubMed | Paper | Webserver ]

SNP-finding in pig mitochondrial ESTs

Scheibye-Alsing K, Cirera S, Gilchrist MJ, 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 ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, 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 ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, 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 LB, Hoj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, 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 ZL, Gorodkin J, Reecy JM, 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 ]

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, Jorgensen 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, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshoj 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 JH, 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 JH, Enstero M, Sawera M, Jensen P, Ohman 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 CB, 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, Jorgensen 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 JH, Lyngso RB, 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, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj 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 JH*, Lyngso RB, Stormo GD, 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 ES, 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


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 ]

Conference Papers


A mini-greedy algorithm for faster structural RNA stem-loop search

Gorodkin J, Lyngso RB, Stormo GD* Genome Inform. 2001;12:184-93
[ PubMed ]

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 | Webserver ]

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 1997, 75(3):269-275
[ 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 ]