15 papers · ranked by Valyu relevance
Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva, Reinhard Schneider
'Reinhard Schneider'] The quantities of data obtained by the new high-throughput technologies, such as microarrays or ChIP-Chip arrays, and the large-scale OMICS-approaches, such as genomics, proteomics and transcriptomics, are becoming vast. Sequencing technologies become cheaper and easier to use and, thus…
Dominik Seidel
The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic…
François Chevenet, Christine Brun, Anne-Laure Bañuls, Bernard Jacq + 1 more
'Richard Christen'] Background Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as…
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available…
Yi-Sen Peng, Bai-You Cheng, Tung-Chi Liu, Jinzhi Zhang
Trees are complex and dynamic living structures, where structural stability is essential for survival and for public safety in urban environments. Tree forks, as structural junctions, are key to tree integrity but are prone to failure under stress. The specific mechanical contributions of their internal conical…
Philippe Gouret, Julie D Thompson, Pierre Pontarotti
Background To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted. Results Here, we…
Yi Lin, Miao Jiang, Petri Pellikka, Janne Heiskanen
Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the…
Pierre Dutilleul, Nishan Mudalige, Louis-Paul Rivest, Esmaiel Jabbari
'Esmaiel Jabbari'] The increasingly large size of the graphical and numerical data sets collected with modern technologies requires constant update and upgrade of the statistical models, methods and procedures to be used for their analysis in order to optimize learning and maximize knowledge and understanding. This is…
Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang + 1 more
'Tatsuya Akutsu'] Background Many tree structures are found in nature and organisms. Such trees are believed to be constructed on the basis of certain rules. We have previously developed grammar-based compression methods for ordered and unordered single trees, based on bisection-type tree grammars. Here, these methods…
Petr Novotný, Jan Wild
The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures…
Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita + 1 more
'Tatsuya Akutsu'] Background Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely used measures for comparison of tree structured data. However, it is known that…
Juan Zhang, Wei Xu, Zhiqiang Dou, Liuyi Pan + 5 more
'Zhifang Yang' 'Yuliang Cai' 'Ali Akbar Ghasemi-Soloklui'] Different tree shapes (TSs) directly influence canopy structure, light interception, and photosynthetic activity, impacting fruit quality and yield. This study investigated the effects of light interception efficiency (LIE) on the quality and yield of “Jimei”…
Rasa Meskauskiene, Oliver Laule, Nikolai V Ivanov, Florian Martin + 3 more
'Markus Wyss' 'Wilhelm Gruissem' 'Philip Zimmermann'] Background It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a…
Pengyu Liu, Jacob Lusk, Nataša Jonoska, Mariel Vázquez + 1 more
'Shi-Jie Chen'] R-loops are a class of non-canonical nucleic acid structures that typically form during transcription when the nascent RNA hybridizes the DNA template strand, leaving the non-template DNA strand unpaired. These structures are abundant in nature and play important physiological and pathological roles.…
Michela Quadrini, Luca Tesei, Emanuela Merelli
Background RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free structures due to their inherent tree representation. Results In this work, we introduce an algebraic…