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1

De novo prediction of structured RNAs from genomic sequences

Jan Gorodkin, Ivo L. Hofacker, Elfar Torarinsson, Zizhen Yao, Jakob H. Havgaard, Walter L. Ruzzo

Journal:

Trends in Biotechnology

Year:

2010

Language:

english

File:

PDF, 795 KB

english, 2010

2

Structured RNAs and synteny regions in the pig genome

Christian Anthon,Hakim Tafer,Jakob H Havgaard,Bo Thomsen…

Journal:

Year:

2014

Language:

english

File:

PDF, 810 KB

english, 2014

3

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

Havgaard, Jakob H., Torarinsson, Elfar, Gorodkin, Jan

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 396 KB

english, 2007

4

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

Sundfeld, Daniel, Havgaard, Jakob H., de Melo, Alba C. M. A., Gorodkin, Jan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.01 MB

english, 2015

5

Optimizing RNA structures by sequence extensions using RNAcop

Hecker, Nikolai, Christensen-Dalsgaard, Mikkel, Seemann, Stefan E., Havgaard, Jakob H., Stadler, Peter F., Hofacker, Ivo L., Nielsen, Henrik, Gorodkin, Jan

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.14 MB

english, 2015

6

Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia

Junge, Alexander, Zandi, Roza, Havgaard, Jakob Hull, Gorodkin, Jan, Cowland, Jack Bernard

Journal:

Year:

2017

Language:

english

File:

PDF, 731 KB

english, 2017

7

[IEEE 2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) - St. Petersburg, Russia (2017.3.6-2017.3.8)] 2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) - CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment

Sundfeld, Daniel, Havgaard, Jakob H., Gorodkin, Jan, Melo, Alba C. M. A. de

Year:

2017

Language:

english

File:

PDF, 565 KB

english, 2017

8

RNAscClust : clustering RNA sequences using structure conservation and graph based motifs

Miladi, Milad, Junge, Alexander, Costa, Fabrizio, Seemann, Stefan E., Havgaard, Jakob Hull, Gorodkin, Jan, Backofen, Rolf

Journal:

Year:

2017

Language:

english

File:

PDF, 410 KB

english, 2017

9

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

Kato, Yuki, Gorodkin, Jan, Havgaard, Jakob Hull

Journal:

Year:

2017

Language:

english

File:

PDF, 663 KB

english, 2017

10

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

Alkan, Ferhat, Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull, Gorodkin, Jan

Journal:

Year:

2018

Language:

english

File:

PDF, 1.33 MB

english, 2018

11

Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities

Sundfeld, Daniel, Teodoro, George, Havgaard, Jakob H., Gorodkin, Jan, Melo, Alba C. M. A.

Journal:

Concurrency and Computation: Practice and Experience

Year:

2019

Language:

english

File:

PDF, 1.04 MB

english, 2019

12

Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism

Jacobsen, Mette Juul, Havgaard, Jakob H., Anthon, Christian, Mentzel, Caroline M. Junker, Cirera, Susanna, Krogh, Poula Maltha, Pundhir, Sachin, Karlskov-Mortensen, Peter, Bruun, Camilla S., Lesnik, P

Journal:

Frontiers in Genetics

Year:

2019

File:

PDF, 2.64 MB

2019