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PLoS computational biology, ISSN 1553-7358, 08/2018, Volume 14, Issue 8, p. e1006341
The investigation of RNA-based regulation of cellular processes is becoming an increasingly important part of biological or medical research. For the analysis... 
Journal Article
BIOINFORMATICS, ISSN 1367-4803, 08/2019, Volume 35, Issue 16, pp. 2862 - 2864
A Summary: Experimental structure probing data has been shown to improve thermodynamics-based RNA secondary structure prediction. To this end, chemical... 
SHAPE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Applications Notes
Journal Article
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, ISSN 0219-7200, 10/2019, Volume 17, Issue 5
Efficient computational tools for the identification of putative target RNAs regulated by prokaryotic sRNAs rely on thermodynamic models of RNA secondary... 
BIOINFORMATICS | seed | constrained helix-length | ACCESSIBILITY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | steric constraints | RNA-RNA interaction prediction | canonical helix | BINDING | TOOLS
Journal Article
Procedia Computer Science, ISSN 1877-0509, 2018, Volume 135, pp. 570 - 578
A growth of city can be a benefit both for the government and the citizen its self. In addition, if the growth are not accompany with the advantages of the... 
Smart City | Urban Development | Integration Suggestion System | IoT
Journal Article
Bioinformatics, ISSN 1367-4803, 07/2019, Volume 35, Issue 14, pp. i354 - i359
Abstract Summary SHAPE experiments are used to probe the structure of RNA molecules. We present ShaKer to predict SHAPE data for RNA using a graph-kernel-based... 
SECONDARY STRUCTURE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Eccb 2019 Conference Proceedings | Ismb
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 07/2018, Volume 46, Issue W1, pp. W25 - W29
Abstract The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and... 
DESIGN | ALIGNMENT | RECOGNITION | CYANOBACTERIA | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | INFO-RNA | INTARNA | TARGET PREDICTION | DOMAINS | WEB SERVER | Web Server Issue
Journal Article
by Dale, Ryan and Grüning, Björn and Sjödin, Andreas and Rowe, Jillian and Chapman, Brad A and Tomkins-Tinch, Christopher H and Valieris, Renan and Batut, Bérénice and Caprez, Adam and Cokelaer, Thomas and Yusuf, Dilmurat and Beauchamp, Kyle A and Brinda, Karel and Wollmann, Thomas and Corguillé, Gildas Le and Ryan, Devon and Bretaudeau, Anthony and Hoogstrate, Youri and Pedersen, Brent S and Heeringen, Simon van and Raden, Martin and Luna-Valero, Sebastian and Soranzo, Nicola and Smet, Matthias De and Kuster, Greg Von and Kirchner, Rory and Pantano, Lorena and Charlop-Powers, Zachary and Thornton, Kevin and Martin, Marcel and Beek, Marius van den and Maticzka, Daniel and Miladi, Milad and Will, Sebastian and Gravouil, Kévin and Unneberg, Per and Brueffer, Christian and Blank, Clemens and Piro, Vitor C and Wolff, Joachim and Antao, Tiago and Gladman, Simon and Shlyakhter, Ilya and Hollander, Mattias de and Mabon, Philip and Shen, Wei and Boekel, Jorrit and Holtgrewe, Manuel and Bouvier, Dave and de Ruiter, Julian R and Cabral, Jennifer and Choudhary, Saket and Harding, Nicholas and Kleinkauf, Robert and Enns, Eric and Eggenhofer, Florian and Brown, Joseph and Cock, Peter J. A and Timm, Henning and Thomas, Cristel and Zhang, Xiao-Ou and Chambers, Matt and Turaga, Nitesh and Seiler, Enrico and Brislawn, Colin and Pruesse, Elmar and Fallmann, Jörg and Kelleher, Jerome and Nguyen, Hai and Parsons, Lance and Fang, Zhuoqing and Stovner, Endre Bakken and Stoler, Nicholas and Ye, Simon and Wohlers, Inken and Farouni, Rick and Freeberg, Mallory and Johnson, James E and Bargull, Marcel and Kensche, Philip Reiner and Webster, Timothy H and Eppley, John M and Stahl, Christoph and Rose, Alexander S and Reynolds, Alex and Wang, Liang-Bo and Garnier, Xavier and Dirmeier, Simon and Knudsen, Michael and Taylor, James and Srivastava, Avi and Rai, Vivek and Agren, Rasmus and Junge, Alexander and Guimera, Roman Valls and Khan, Aziz and Schmeier, Sebastian and He, Guowei and Pinello, Luca and Hägglund, Emil and ... and Bioconda Team and The Bioconda Team and Umeå universitet and Teknisk-naturvetenskapliga fakulteten and Kemiska institutionen
Nature Methods, ISSN 1548-7091, 07/2018, Volume 15, Issue 7, pp. 475 - 476
Journal Article
International journal of molecular sciences, ISSN 1422-0067, 05/2020, Volume 21, Issue 11, p. 3852
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution.... 
mutation | RNA-RNA interaction | compensatory mutation | design | sRNA
Journal Article
BIOINFORMATICS, ISSN 1367-4803, 01/2020, Volume 36, Issue 2, pp. 462 - 469
Motivation: The folding dynamics of ribonucleic acids (RNAs) are typically studied via coarse-grained models of the underlying energy landscape to face the... 
PATHWAYS | FUNNELS | STATES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | KINETICS | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SECONDARY STRUCTURE
Journal Article
BMC BIOINFORMATICS, ISSN 1471-2105, 01/2020, Volume 21, Issue 1, pp. 1 - 11
Background Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction.... 
Constraints | RNA-RNA interaction | Accessibility | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Seed | sRNA | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SECONDARY | Target prediction | PROBABILITIES | TOOL | Accuracy | Parameters | Seeds | Energy | Fines & penalties | Computer applications | Probability | Hybridization | Trends | Ribonucleic acid--RNA | Investigations
Journal Article
Nucleic acids research, ISSN 0305-1048, 05/2020, Volume 48, Issue W1, pp. W287 - W291
RNA molecules fold into complex structures as a result of intramolecular interactions between their nucleotides. The function of many non-coding RNAs and some... 
Journal Article
Journal Article
BMC bioinformatics, 01/2020, Volume 21, Issue 1, p. 15
Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently,... 
Bacteria - metabolism | Computational Biology - methods | Bacteria - chemistry | RNA, Bacterial - chemistry | RNA, Small Untranslated - chemistry | RNA, Bacterial - genetics | RNA, Small Untranslated - genetics | Bacteria - genetics | RNA, Bacterial - metabolism | RNA, Small Untranslated - metabolism
Journal Article
Dendrochronologia, ISSN 1125-7865, 04/2020, Volume 60, p. 125679
The crossdating of tree-ring series is typically based on tree-ring width sequences, which is a crude abstraction of the growth signal stored in tree rings. In... 
Tree ring | Crossdating | Microdensitometry | Picea abies | Intra-annual | Wood density profile | PROFILES | RECONSTRUCTION | WIDTH | WOOD DENSITY | GEOGRAPHY, PHYSICAL | TEMPERATURE | ALIGNMENT | FLUCTUATIONS | GROWTH | HIGH-FREQUENCY DENSITOMETRY | FORESTRY | CLIMATE
Journal Article
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