Bipartite graphs in systems biology and medicine: a survey of methods and applications
The latest advances in high-throughput techniques during the past decade allowed the
systems biology field to expand significantly. Today, the focus of biologists has shifted from …
systems biology field to expand significantly. Today, the focus of biologists has shifted from …
Current breathomics—a review on data pre-processing techniques and machine learning in metabolomics breath analysis
We define breathomics as the metabolomics study of exhaled air. It is a strongly emerging
metabolomics research field that mainly focuses on health-related volatile organic …
metabolomics research field that mainly focuses on health-related volatile organic …
A comprehensive evaluation of module detection methods for gene expression data
A critical step in the analysis of large genome-wide gene expression datasets is the use of
module detection methods to group genes into co-expression modules. Because of …
module detection methods to group genes into co-expression modules. Because of …
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Background In the post-genomic era, the rapid increase in high-throughput data calls for
computational tools capable of integrating data of diverse types and facilitating recognition …
computational tools capable of integrating data of diverse types and facilitating recognition …
Comparing the performance of biomedical clustering methods
C Wiwie, J Baumbach, R Röttger - Nature methods, 2015 - nature.com
Identifying groups of similar objects is a popular first step in biomedical data analysis, but it
is error-prone and impossible to perform manually. Many computational methods have been …
is error-prone and impossible to perform manually. Many computational methods have been …
The African turquoise killifish genome provides insights into evolution and genetic architecture of lifespan
Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in
nature, but the mechanisms underlying the evolution of lifespan differences remain elusive …
nature, but the mechanisms underlying the evolution of lifespan differences remain elusive …
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
Although the concept of botanical carnivory has been known since Darwin's time, the
molecular mechanisms that allow animal feeding remain unknown, primarily due to a …
molecular mechanisms that allow animal feeding remain unknown, primarily due to a …
Using anticlustering to partition data sets into equivalent parts.
M Papenberg, GW Klau - Psychological Methods, 2021 - psycnet.apa.org
Numerous applications in psychological research require that a pool of elements is
partitioned into multiple parts. While many applications seek groups that are well-separated …
partitioned into multiple parts. While many applications seek groups that are well-separated …
Adept: a domain independent sequence alignment strategy for gpu architectures
Background Bioinformatic workflows frequently make use of automated genome assembly
and protein clustering tools. At the core of most of these tools, a significant portion of …
and protein clustering tools. At the core of most of these tools, a significant portion of …
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape
M Utriainen, JH Morris - BMC bioinformatics, 2023 - Springer
Background Since the initial publication of clusterMaker, the need for tools to analyze large
biological datasets has only increased. New datasets are significantly larger than a decade …
biological datasets has only increased. New datasets are significantly larger than a decade …