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Inference of Ancient Polyploidy Using Transcriptome Data
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and...
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Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing
Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human...
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Transcriptome analysis in abiotic stress conditions in higher plants
Drought, high salinity, and low temperature are major environmental factors that limit plant productivity. Plants respond and adapt to these stresses...
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Integrating Single-Cell Methylome and Transcriptome Data with MAPLE
As a mechanism of epigenetic gene regulation, DNA methylation has crucial roles in developmental and differentiation programs. Thanks to the recently...
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Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq
Poly(A) tails are added to most eukaryotic mRNA and have essential regulatory functions. However, due to its homopolymeric nature, the sequence...
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The Pineal Transcriptome Webpage
The pineal transcriptome webpage is described, which provides access to the transcript expression profile of the vertebrate pineal gland and, in many...
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Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail...
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Transcriptome Analysis of Aquatic Species Exposed to Endocrine Disruptors
Animals and humans both have normal endocrine systems that are affected by endocrine-disrupting chemicals (EDCs). Numerous substances found in...
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Transcriptome Sequencing and Analysis of Seabuckthorn (Hippophae Sp.)
Seabuckthorn (Hippophae Sp.) is known for its immense medicinal, nutritional, and agronomical properties and has been utilized for centuries as...
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Multi-slice spatial transcriptome domain analysis with SpaDo
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and...
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The Complexity of the Mammalian Transcriptome
Draft genome assemblies for multiple mammalian species combined with new technologies to map transcripts from diverse RNA samples to these genomes...
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Analysis of the Plant Mitochondrial Transcriptome
Transcriptome analyses are widely performed, but the analysis of organelle genome expression is often overlooked. In this chapter, we describe three...
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GTax: improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a...
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What Is the Transcriptome and How It Is Evaluated
The concept of the transcriptome revolves around the complete set of transcripts present in a given cell type, tissue, or organ and encompasses both...
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Transcriptome in Human Mycoses
Mycoses are infectious diseases caused by fungi, which incidence has increased in recent decades due to the increasing number of immunocompromised...
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CRISPR technologies for genome, epigenome and transcriptome editing
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome,...
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Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia
Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML...
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Droplet-based transcriptome profiling of individual synapses
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological...
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Single Cell Transcriptome Analysis During Development in Dictyostelium
Dictyostelium represents a stripped-down model for understanding how cells make decisions during development. The complete life cycle takes around a...
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Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq
The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and...
