A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
… represent biologicalgraph theory concepts and the various graph types, as well as the
available data structures for storing and reading graphs. In addition, we describe several network

A conceptual map of invasion biology: Integrating hypotheses into a consensus network

M Enders, F Havemann, F Ruland… - Global Ecology and …, 2020 - Wiley Online Library
… Although useful for providing a first overview, these previous approaches to creating
hypothesis networks in invasion biology had several limitations that were overcome by our …

Computational network biology: data, models, and applications

C Liu, Y Ma, J Zhao, R Nussinov, YC Zhang, F Cheng… - Physics Reports, 2020 - Elsevier
… have long been central to our understanding of biological systems, in the form of linkage …
network biology, first introducing various types of biological networks and network structural …

The structure of ecological networks across levels of organization

PR Guimaraes Jr - Annual Review of Ecology, Evolution, and …, 2020 - annualreviews.org
… in ecological networks across multiple levels of biological … basic patterns predicted by
network theory emerge at the … Finally, I discuss the implications of network structures for our …

Revisiting the functional anatomy of the human brain: toward a meta-networking theory of cerebral functions

G Herbet, H Duffau - Physiological Reviews, 2020 - journals.physiology.org
… We discuss the major implications of this approach in fundamental neurosciences as well …
basic principles of DTI are based on the biological constraints imposed by cerebral tissues on …

Percolation on complex networks: Theory and application

M Li, RR Liu, L Lü, MB Hu, S Xu, YC Zhang - Physics Reports, 2021 - Elsevier
… In the last two decades, network science has blossomed and influenced various fields, such
as statistical physics, computer science, biology and sociology, from the perspective of the …

Construction and optimization of an ecological network based on morphological spatial pattern analysis and circuit theory

Y An, S Liu, Y Sun, F Shi, R Beazley - Landscape Ecology, 2021 - Springer
… These graph theory-based indexes, which are important for … for the development and
reproduction of biological species. … has a considerable impact on ecological network construction. …

Molecular networks in Network Medicine: Development and applications

EK Silverman, HHHW Schmidt… - … : Systems Biology …, 2020 - Wiley Online Library
… Based on graph theory, networks provide a … cell biology, understanding the impact of sample
collection and storage protocols on the Omics data utilized for building molecular networks

Lack of theory building and testing impedes progress in the factor and network literature

EI Fried - Psychological Inquiry, 2020 - Taylor & Francis
… the problem of weak theories and its consequences in the … Network theory is based on the
guiding principle that … to theoretical biology, theoretical physics, or theoretical economics, all of …

Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
… through the use of graph theory, machine learning and deep learning techniques. … to define
biological networks at different levels of detail. Besides the graph representation of biological