Systems Biology (Methods in Molecular Biology)

Chapter 14 A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data Stephen A. Ramsey Abstract In this methods ...

ortholog pairs across species [10], but that approach has been criticized as insufficiently accounting for species-specific effe ...

management system based on the Comprehensive R Archive Network (CRAN) [17]. The R installation should have the following softwar ...

For each species, raw counts and normalized counts of aligned mRNA-seq reads for each gene, based on Ensembl gene iden- tifiers ...

Sample group information for the mRNA-seq datasets for each species. For each species, the sample group information should be c ...

workflow involve performing identical transformations on the data sets for individual species, and thus, for those steps I show ...

has a benefit of reducing the number of hypothesis tests per- formed for individual-gene-level differential expression analy- si ...

genes_exp_dog <- rsc_maxexp_dog$gene[which(rsc_maxexp_dog$max_exp >= cutoff_dog)] rsc_exp_dog <- rsc_dog[genes_exp_dog, ...

For each species, map the gene expression data to gene function-based expression index levels (specifically, enrichment scores ...

gsva_merged <- merge(gsva_dog_c5$es.obs, gsva_human_c5$es.obs, by.x=0, by.y=0) >dim(gsva_merged) [1] 1452 443 sample_data_ ...

In the above R command, the "t" function returns the transpose of its argument, and the "cmdscale" function returns a list objec ...

library(DESeq2) deg_dog_df <- results(DESeq(DESeqDataSetFromMatrix(countData=rsc_exp_dog, colData=data.frame(condition=factor ...

per-gene differential expression testing; and the "results" func- tion returns the results of the differential expression testin ...

two species (although given the very large TCGA cohort size, some overlap between cancer and normal is seen for the TCGA dataset ...

Fowles JS, Brown KC, Hess AM et al (2016) Intra- and interspecies gene expression models for predicting drug response in canine ...

Chapter 15 Multi-agent Simulations of Population Behavior: A Promising Tool for Systems Biology Alfredo Colosimo Abstract This c ...

appearing of computational strategies appropriate to reproduce complex functions and collective behavior of interacting agents. ...

systems’ behavior under the influence of environmental factors [10, 11].In particular, it allows representing such factors in th ...

The unifying element in the above cases was the presence of force-fields affecting the dynamic behavior of the agents. The field ...

and D, respectively, wherek 1 rules the yellow!blue rate. In panel D the global time course of the considered process is reporte ...