Computational network biology: data, models, and applications
Biological entities are involved in intricate and complex interactions, in which uncovering the
biological information from the network concepts are of great significance. Benefiting from …
biological information from the network concepts are of great significance. Benefiting from …
The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil
M Ebadi, Q Bafort, E Mizrachi… - Proceedings of the …, 2023 - National Acad Sciences
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas
some view WGD mainly as detrimental and an evolutionary dead end, there is growing …
some view WGD mainly as detrimental and an evolutionary dead end, there is growing …
Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management
Network models of soil and plant microbiomes provide new opportunities for enhancing
disease management, but also challenges for interpretation. We present a framework for …
disease management, but also challenges for interpretation. We present a framework for …
Counting graphlets: Space vs time
Counting graphlets is a well-studied problem in graph mining and social network analysis.
Recently, several papers explored very simple and natural approaches based on Monte …
Recently, several papers explored very simple and natural approaches based on Monte …
Linc: a motif counting algorithm for uncertain graphs
In graph applications (eg, biological and social networks), various analytics tasks (eg,
clustering and community search) are carried out to extract insight from large and complex …
clustering and community search) are carried out to extract insight from large and complex …
Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton
Y Yang, X Wen, Z Wu, K Wang, Y Zhu - Science China Life Sciences, 2023 - Springer
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains
approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii …
approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii …
Motif counting beyond five nodes
Counting graphlets is a well-studied problem in graph mining and social network analysis.
Recently, several papers explored very simple and natural algorithms based on Monte Carlo …
Recently, several papers explored very simple and natural algorithms based on Monte Carlo …
Motivo: fast motif counting via succinct color coding and adaptive sampling
The randomized technique of color coding is behind state-of-the-art algorithms for estimating
graph motif counts. Those algorithms, however, are not yet capable of scaling well to very …
graph motif counts. Those algorithms, however, are not yet capable of scaling well to very …
Probgraph: High-performance and high-accuracy graph mining with probabilistic set representations
Important graph mining problems such as Clustering are computationally demanding. To
significantly accelerate these problems, we propose ProbGraph: a graph representation that …
significantly accelerate these problems, we propose ProbGraph: a graph representation that …
Understanding the mechanisms behind the response to environmental perturbation in microbial mats: a metagenomic-network based approach
To date, it remains unclear how anthropogenic perturbations influence the dynamics of
microbial communities, what general patterns arise in response to disturbance, and whether …
microbial communities, what general patterns arise in response to disturbance, and whether …