Results 1 to 10 of about 500,832 (45)

Visualizing dimensionality reduction of systems biology data [PDF]

Data Mining and Knowledge Discovery Vol 10 (1), 2012, 2012
One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after application of such a method the data is projected and visualized in the new coordinate system, using scatter plots or ...
arxiv   +1 more source

Copy-number-variation and copy-number-alteration region detection by cumulative plots [PDF]

BMC Bioinformatics, 10(suppl 1):S67 (2009), 2009
Background: Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutation and are larger-scaled than the single nucleotide polymorphisms.
arxiv   +1 more source

Identifying down and up-regulated chromosome regions using RNA-Seq data [PDF]

, 2017
The number of studies dealing with RNA-Seq data analysis has experienced a fast increase in the past years making this type of gene expression a strong competitor to the DNA microarrays. This paper proposes a Bayesian model to detect down and up-regulated chromosome regions using RNA-Seq data.
arxiv   +1 more source

ChrSNet: Chromosome Straightening using Self-attention Guided Networks [PDF]

arXiv, 2022
Karyotyping is an important procedure to assess the possible existence of chromosomal abnormalities. However, because of the non-rigid nature, chromosomes are usually heavily curved in microscopic images and such deformed shapes hinder the chromosome analysis for cytogeneticists.
arxiv  

Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences [PDF]

, 2012
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in E. coli.
arxiv   +1 more source

A Bayesian Generalized CAR Model for Correlated Signal Detection [PDF]

, 2015
Over the last decade, large-scale multiple testing has found itself at the forefront of modern data analysis. In many applications data are correlated, so that the observed test statistic used for detecting a non-null case, or signal, at each location in a dataset carries some information about the chances of a true signal at other locations.
arxiv   +1 more source

Identification of significant features in DNA microarray data [PDF]

WIREs Comp Stat, 2013, 5(4): 309-325, 2013
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA microarray experiments is to identify genes associated with biological processes of interest.
arxiv   +1 more source

Chromosome Oscillations in Mitosis [PDF]

, 2005
Successful cell division requires a tight regulation of chromosome motion via the activity of molecular motors. Many of the key players at the origin of the forces generating the movement have been identified, but their spatial and temporal organization remains elusive.
arxiv   +1 more source

Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays [PDF]

Annals of Applied Statistics 2008, Vol. 2, No. 2, 687-713, 2008
Chromosomal DNA is characterized by variation between individuals at the level of entire chromosomes (e.g., aneuploidy in which the chromosome copy number is altered), segmental changes (including insertions, deletions, inversions, and translocations), and changes to small genomic regions (including single nucleotide polymorphisms).
arxiv   +1 more source

Chromosome Segmentation Analysis Using Image Processing Techniques and Autoencoders [PDF]

arXiv, 2022
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic diseases and disorders.
arxiv