Related papers: Copy Number Variants and Segmental Duplications Sh…

An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…

DNA Copy number variation (CNV) has recently gained considerable interest as a source of genetic variation that likely influences phenotypic differences. Many statistical and computational methods have been proposed and applied to detect…

Core-collapse supernova remnants (CCSNRs) are crucial for understanding the final stages of massive star evolution, as they reflect the imprints of their progenitors' pre-explosion activities. However, the evolution of CCSNRs, particularly…

Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Frozen self-supervised representations often transfer well with only a few labels across many semantic tasks. We argue that a single geometric quantity, \emph{directional} CDNV (decision-axis variance), sits at the core of two favorable…

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…

Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…

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…

Convolutional neural networks (CNN) have made great progress for synthetic aperture radar (SAR) images change detection. However, sampling locations of traditional convolutional kernels are fixed and cannot be changed according to the…

The self-consistent field (SCF) generation of the three-dimensional (3D) electron density distribution ($\rho$) represents a fundamental aspect of density functional theory (DFT) and related first-principles calculations, and how one can…

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…

Many supernova remnants (SNRs) are considered to evolve in molecular environments, but the associations between SNRs and molecular clouds (MCs) are often unclear. Being aware of such ambiguous case, we report our study on the molecular…

We present two results about using allele-count (AC) burdens of rare SNPs discovered in a case-control sequencing study for prediction or validation in an external prospective study. When genotyping only the SNPs polymorphic in the sequence…

Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are…

Motivated by the problem of learning with small sample sizes, this paper shows how to incorporate into support-vector machines (SVMs) those properties that have made convolutional neural networks (CNNs) successful. Particularly important is…

Supernova remnants (SNR) are now widely believed to be a source of cosmic rays (CRs) up to an energy of 1 PeV. The magnetic fields required to accelerate CRs to sufficiently high energies need to be much higher than can result from…

Deleterious genetic variants can be evaluated as quantitative traits using information theory-based sequence analysis of recognition sites. To assess the effect of such variants, fitness and genetic load of SNPs which alter binding site…

We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…

We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…