scholarly journals Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

2009 ◽  
Vol 2009 ◽  
pp. 1-12 ◽  
Author(s):  
Sandra Andorf ◽  
Tanja Gärtner ◽  
Matthias Steinfath ◽  
Hanna Witucka-Wall ◽  
Thomas Altmann ◽  
...  
Keyword(s):  
Systems Biology ◽  
Network Structure ◽  
Molecular Network

The next step in systems biology: simulating the temporospatial dynamics of molecular network

BioEssays ◽  
2003 ◽  
Vol 26 (1) ◽  
pp. 68-72 ◽  
Author(s):  
Hao Zhu ◽  
Sui Huang ◽  
Pawan Dhar
Keyword(s):  
Systems Biology ◽  
Molecular Network

scholarly journals Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm

RSC Advances ◽  
2017 ◽  
Vol 7 (37) ◽  
pp. 23222-23233 ◽  
Author(s):  
Wei Liu ◽  
Wen Zhu ◽  
Bo Liao ◽  
Haowen Chen ◽  
Siqi Ren ◽  
...  
Keyword(s):  
Systems Biology ◽  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Network Structure ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Central Problem ◽  
Expression Data ◽  
Redundancy Reduction ◽  
Gene Regulatory

Inferring gene regulatory networks from expression data is a central problem in systems biology.

scholarly journals SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

2021 ◽  
Author(s):  
Adrien Rougny ◽  
Vasundra Touré ◽  
John Albanese ◽  
Dagmar Waltemath ◽  
Denis Shirshov ◽  
...  
Keyword(s):  
Systems Biology ◽  
Semantic Annotation ◽  
Formal Analysis ◽  
Molecular Network ◽  
Molecular Networks ◽  
Scientific Publications ◽  
Graphical Notation ◽  
Biological Concepts ◽  
Scientific Results ◽  
Semantic Layer

Abstract A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.

scholarly journals Preparation and properties of a new type of flexible epoxy resin based on a molecular network structure

2021 ◽  
Vol 15 (11) ◽  
pp. 1032-1040
Author(s):  
X. F. Zhang ◽  
T. Cao ◽  
T. H. Zhao ◽  
C. Ma ◽  
P. Y. Liu
Keyword(s):  
Epoxy Resin ◽  
Network Structure ◽  
Molecular Network ◽  
New Type

Moderate conformational transition promotes the formation of a self-reinforced highly oriented silk fibroin network structure

Soft Matter ◽  
2021 ◽  
Author(s):  
Ting Shu ◽  
Jing Cui ◽  
Zhuochen Lv ◽  
Leitao Cao ◽  
Jing Ren ◽  
...  
Keyword(s):  
Silk Fibroin ◽  
Network Structure ◽  
Conformational Transition ◽  
Molecular Network ◽  
Low Density ◽  
Conformation Transition ◽  
The Way

Moderate conformation transition promotes the formation of low-density crosslinking molecular network and further rearrangement of amorphous proteins to form the highly oriented molecular network structure, which paved the way for achieving mechanical-enhanced silk fibroin materials.

3D molecular network and magnetic ordering, formed by multi-dentate magnetic couplers, bis(benzene)chromium(i) and [1,2,5]thiadiazolo[3,4-c][1,2,5]thiadiazolidyl

2018 ◽  
Vol 47 (29) ◽  
pp. 9897-9902 ◽  
Author(s):  
Yoshiaki Shuku ◽  
Yuta Hirai ◽  
Nikolay A. Semenov ◽  
Evgeny Kadilenko ◽  
Nina P. Gritsan ◽  
...  
Keyword(s):  
Network Structure ◽  
Radical Anion ◽  
Magnetic Ordering ◽  
Molecular Network ◽  
3D Network ◽  
Ordered State ◽  
Magnetically Ordered

The bis(benzene)chromium(i) salt of [1,2,5]thiadiazolo[3,4-c][1,2,5]thiadiazolyl radical-anion formed a 3D network structure and realized a magnetically ordered state below 8 K.

scholarly journals A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Tomas Hruz ◽  
Markus Wyss ◽  
Christoph Lucas ◽  
Oliver Laule ◽  
Peter von Rohr ◽  
...  
Keyword(s):  
Complex System ◽  
Systems Biology ◽  
Complex Networks ◽  
Network Structure ◽  
Biological Networks ◽  
Large Graphs ◽  
Layout Algorithm ◽  
Underlying Network ◽  
Visualization Algorithms ◽  
Edge Crossings

Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ-clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs.

Abstract 357: A systems biology approach for rational molecular network inference

2014 ◽  
Author(s):  
Megan E. Egbert ◽  
Michelle L. Wynn ◽  
Zhi Fen Wu ◽  
Rabia A. Gilani ◽  
Santiago Schnell ◽  
...  
Keyword(s):  
Systems Biology ◽  
Network Inference ◽  
Molecular Network
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