A practical tool for maximal information coefficient analysis

Albanese, Davide; Riccadonna, Samantha; Donati, Claudio; Franceschi, Pietro

doi:10.1093/gigascience/giy032

Cited by 80 publications

(42 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The threshold of 0.6 was utilized for the linear Pearson correlation analysis to identify the highly-correlated variables, which is in line with previous research (Kobelo et al 2008). Moreover, with respect to the nonlinear correlation, one of the mutual information based measures, maximal information coefficient (MIC) was also employed to identify the nonlinear association between two variables (Albanese et al 2018). As suggested by Albanese et al (2018), the threshold of MIC was chosen to be 0.7.…”

Section: Data Preparationmentioning

confidence: 78%

“…Moreover, with respect to the nonlinear correlation, one of the mutual information based measures, maximal information coefficient (MIC) was also employed to identify the nonlinear association between two variables (Albanese et al 2018). As suggested by Albanese et al (2018), the threshold of MIC was chosen to be 0.7. Above all, the highly correlated pairs of variables were selected based on two criteria: the Pearson correlation coefficient is greater than 0.6 or the MIC is greater than 0.7.…”

Section: Data Preparationmentioning

confidence: 99%

See 1 more Smart Citation

Approach-level real-time crash risk analysis for signalized intersections

Yuan

Abdel-Aty

2018

Accident Analysis & Prevention

105

View full text Add to dashboard Cite

Intersections are among the most dangerous roadway facilities due to the complex traffic conflicting movements and frequent stop-and-go traffic. However, previous intersection safety analyses were conducted based on static and highly aggregated data (e.g., annual average daily traffic (AADT), annual crash frequency). These aggregated data may result in unreliable findings simply because they are averages and cannot represent the real conditions at the time of crash occurrence. This study attempts to investigate the relationship between crash occurrence at signalized intersections and real-time traffic, signal timing, and weather characteristics based on 23 signalized intersections in Central Florida. The intersection and intersection-related crashes were collected and then divided into two types, i.e., within intersection crashes and intersection entrance crashes. Bayesian conditional logistic models were developed for these two kinds of crashes, respectively. For the within intersection models, the model results showed that the through volume from "A" approach (the traveling approach of at-fault vehicle), the left turn volume from "B" approach (near-side crossing approach), and the overall average flow ratio (OAFR) from "D" approach (far-side crossing approach), were found to have significant positive effects on the odds of crash occurrence. Moreover, the increased adaptability for the left turn signal timing of "B" approach and more priority for "A" approach could significantly decrease the odds of crash occurrence. For the intersection entrance models, average speed was found to have significant negative effect on the odds of crash occurrence. The longer average green time and longer average waiting time for the left turn phase, higher green ratio for the through phase, and higher adaptability for the through phase can significantly improve the safety performance of intersection entrance area. In addition, the average queue length on the through lanes was found to have positive effect on the odds of crash occurrence. These results are important in real-time safety applications at signalized intersections in the context of proactive traffic management.

show abstract

Section: Data Preparationmentioning

confidence: 78%

Section: Data Preparationmentioning

confidence: 99%

Approach-level real-time crash risk analysis for signalized intersections

Yuan

Abdel-Aty

2018

Accident Analysis & Prevention

105

View full text Add to dashboard Cite

show abstract

“…By combining available bacterial and fungal sequencing data from the same fecal samples, intradomain correlation analyses were performed using MICtools (119). All comparisons of relationships (i.e., bacterium-bacterium, fungus-fungus, fungus-bacterium within host species and forest) were assessed based on the relative abundance of bacterial and fungal SVs.…”

Section: Methodsmentioning

confidence: 99%

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance

et al. 2020

Self Cite

View full text Add to dashboard Cite

Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.

show abstract

“…In that case, we would not be able to detect them using Spearman’s or Pearson’s correlation coefficients. We used instead MICtools package ( Albanese et al. 2018 ), which is able to identify a wider range of relationships in large data sets and assess their statistical significance.…”

Section: Methodsmentioning

confidence: 99%

Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition

Arroyo

Iannes

Bapteste

et al. 2020

Genome Biology and Evolution

View full text Add to dashboard Cite

The Holozoa clade comprises animals and several unicellular lineages (choanoflagellates, filastereans and teretosporeans). Understanding their full diversity is essential to address the origins of animals and other evolutionary questions. However, they are poorly known. To provide more insights into the real diversity of holozoans and check for undiscovered diversity, we here analysed 18S rDNA metabarcoding data from the global Tara Oceans expedition. To overcome the low phylogenetic information contained in the metabarcoding dataset (composed of sequences from the short V9 region of the gene), we used similarity networks by combining two datasets: unknown environmental sequences from Tara Oceans and known reference sequences from GenBank. We then calculated network metrics to compare environmental to reference sequences. These metrics reflected the divergence between both types of sequences and provided an effective way to search for evolutionary relevant diversity, further validated by phylogenetic placements. Our results showed that the percentage of unicellular holozoan diversity remains hidden. We found novelties in several lineages, especially in Acanthoecida choanoflagellates. We also identified a potential new holozoan group that could not be assigned to any of the described extant clades. Data on geographical distribution showed that, although ubiquitous, each unicellular holozoan lineage exhibits a different distribution pattern. We also identified a positive association between new animal hosts and the ichthyosporean symbiont Creolimax fragrantissima, as well as for other holozoans previously reported as free-living. Overall, our analyses provide a fresh perspective into the diversity and ecology of unicellular holozoans, highlighting the amount of undescribed diversity.

show abstract

A practical tool for maximal information coefficient analysis

Cited by 80 publications

References 22 publications

Approach-level real-time crash risk analysis for signalized intersections

Approach-level real-time crash risk analysis for signalized intersections

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance

Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition

Contact Info

Product

Resources

About