Masked conditional variational autoencoders for chromosome straightening [PDF]
arXiv, 2023 Karyotyping is of importance for detecting chromosomal aberrations in human disease. However, chromosomes easily appear curved in microscopic images, which prevents cytogeneticists from analyzing chromosome types. To address this issue, we propose a framework for chromosome straightening, which comprises a preliminary processing algorithm and a ...
arxiv
Rasch-based high-dimensionality data reduction and class prediction with applications to microarray gene expression data [PDF]
Expert Systems with Applications, 2010;37(7):5178-5185, 2010 Class prediction is an important application of microarray gene expression data analysis. The high-dimensionality of microarray data, where number of genes (variables) is very large compared to the number of samples (obser- vations), makes the application of many prediction techniques (e.g., logistic regression, discriminant analysis) difficult.
arxiv +1 more source
AutoKary2022: A Large-Scale Densely Annotated Dataset for Chromosome Instance Segmentation [PDF]
arXiv, 2023 Automated chromosome instance segmentation from metaphase cell microscopic images is critical for the diagnosis of chromosomal disorders (i.e., karyotype analysis). However, it is still a challenging task due to lacking of densely annotated datasets and the complicated morphologies of chromosomes, e.g., dense distribution, arbitrary orientations, and ...
arxiv
Unified theory of human genome reveals a constrained spatial chromosomal arrangement in interphase nuclei [PDF]
, 2015 We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across all pairs of chromosomes in the genome to derive an extrinsic parameter called effective gene density.
arxiv +1 more source
Size and location of radish 1 chromosome regions carrying the fertility restorer Rfk1 gene in spring turnip rape [PDF]
Chromosome Research 2012, 20(3): 353-361, 2012 In spring turnip rape (Brassica rapa L. spp. oleifera) the most promising F1 hybrid system would be the Ogu-INRA CMS/Rf system. A Kosena fertility restorer gene Rfk1, homologue of the Ogura restorer gene Rfo, was successfully transferred from oilseed rape into turnip rape and that restored the fertility in female lines carrying Ogura cms. The trait was,
arxiv +1 more source
DMseg: a Python algorithm for de novo detection of differentially or variably methylated regions [PDF]
arXiv, 2023 Detecting and assessing statistical significance of differentially methylated regions (DMRs) is a fundamental task in methylome association studies. While the average differential methylation in different phenotype groups has been the inferential focus, methylation changes in chromosomal regions may also present as differential variability, i.e ...
arxiv
A statistical framework for the analysis of microarray probe-level data [PDF]
Annals of Applied Statistics 2007, Vol. 1, No. 2, 333-357, 2007 In microarray technology, a number of critical steps are required to convert the raw measurements into the data relied upon by biologists and clinicians. These data manipulations, referred to as preprocessing, influence the quality of the ultimate measurements and studies that rely upon them.
arxiv +1 more source
Detecting Breakage Fusion Bridge cycles in tumor genomes -- an algorithmic approach [PDF]
, 2013 Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids. When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions where duplicated segments are ...
arxiv +1 more source
Robust cDNA microarray image segmentation and analysis technique based on Hough circle transform [PDF]
HFSP JOURNAL ISSN:1955-2068,Vol.9, Issue.7, part.1 Human Frontier
Science Program , HFSP JOURNAL ISSN:1955-2068, 2016 One of the most challenging tasks in microarray image analysis is spot segmentation. A solution to this problem is to provide an algorithm than can be used to find any spot within the microarray image. Circular Hough Transformation (CHT) is a powerful feature extraction technique used in image analysis, computer vision, and digital image processing ...
arxiv
A Geometric Approach For Fully Automatic Chromosome Segmentation [PDF]
arXiv, 2011 A fundamental task in human chromosome analysis is chromosome segmentation. Segmentation plays an important role in chromosome karyotyping. The first step in segmentation is to remove intrusive objects such as stain debris and other noises. The next step is detection of touching and overlapping chromosomes, and the final step is separation of such ...
arxiv