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Measures of RNA abundance are important for many areas of biology and often obtained from high-throughput RNA sequencing methods such as Illumina sequence data. These measures need to be normalized to remove technical biases inherent in the sequencing approach, most notably the length of the RNA species and the sequencing depth of a sample. These biases are(More)
The power of deep sequencing technology to reliably detect single RNA reads leads to a paradoxical problem of high sensitivity. In hybridization or PCR based methods for RNA quantification, the concern is low sensitivity, i.e., the problem that the signal from truly expressed genes might not be distinguishable from noise. In contrast, the problem with(More)
A challenge of genome annotation is the identification of genes performing specific biological functions. Here, we propose a phylogenetic approach that utilizes RNA-seq data to infer the historical relationships among cell types and to trace the pattern of gene-expression changes on the tree. The hypothesis is that gene-expression changes coincidental with(More)
Molecular phylogenetic studies suggest that the hemochorial placentation and decidualization are ancestral traits of eutherian mammals. While the origin of the placental tissue is well understood, the origin of the decidual cells is unclear. Here we address the origin of decidual cells by examining the expression patterns of six transcription factors (TFs)(More)
The endometrial stromal fibroblast (ESF) is a cell type present in the uterine lining of therian mammals. In the stem lineage of eutherian mammals, ESF acquired the ability to differentiate into decidual cells in order to allow embryo implantation. We call the latter cell type "neo-ESF" in contrast to "paleo-ESF" which is homologous to eutherian ESF but is(More)
Reproduction in eutherian mammals is characterized by extended intrauterine retention of the fetus after implantation. We summarize evolutionary innovations that enable this form of vivipary, including early maternal recognition of pregnancy, invasive placentation, and emergence of the decidual cell type. We first review the structure of the marsupial(More)
Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription(More)
  • Koryu Kin
  • Journal of experimental zoology. Part B…
  • 2015
Multicellular organisms are composed of distinct cell types that have specific roles in the body. Each cell type is a product of two kinds of historical processes-development and evolution. Although the concept of a cell type is difficult to define, the cell type concept based on the idea of the core regulatory network (CRN), a gene regulatory network that(More)
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