Related papers: Centromere reference models for human chromosomes …
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Oceania and Island Southeast Asia have a rich, yet understudied, human genomic landscape. This region encompasses some of the first areas inhabited by humans following the out-of-Africa expansion, includes populations with the highest…
We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the…
Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation…
We present a novel method for identification of the boundary of embryonic cells (blastomeres) in Hoffman Modulation Contrast (HMC) microscopic images that are taken between day one to day three. Identification of boundaries of blastomeres…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
The paternally inherited Y chromosome has been widely used in population genetic studies to understand relationships among human populations. Our interpretation of Y chromosomal evidence about population history and genetics has rested on…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
Recently, scientists from The Craig J. Venter Institute reported construction of very long DNA molecules using a variety of experimental procedures adopting a number of working hypotheses. Finding a mathematical rule for generation of such…
Binary stars are prevalent yet challenging to detect. We present a novel approach using convolutional neural networks (CNNs) to identify binary stars from low-resolution spectra obtained by the LAMOST survey. The CNN is trained on a dataset…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Predicting the impacts of coronal mass ejections (CMEs) is a major focus of current space weather forecasting efforts. Typically, CME properties are reconstructed from stereoscopic coronal images and then used to forward model a CME's…
Despite advances in data augmentation and transfer learning, convolutional neural networks (CNNs) difficultly generalise to unseen domains. When segmenting brain scans, CNNs are highly sensitive to changes in resolution and contrast: even…