Related papers: Challenges in structural variant calling in low-co…
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.…
Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing requires the integration of multiple alignment signals including read-pair, split-read and read-depth. However, owing to inherent technical…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
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…
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
In this paper, we show that the projective Reed-Muller~(PRM) codes form a family of locally correctable codes~(LCC) in the regime of low query complexities. A PRM code is specified by the alphabet size $q$, the number of variables $m$, and…
We report multi-frequency Very Large Array observations of three massive star formation regions (MSFRs) containing radio continuum components that were identified as broad radio recombination line (RRL) sources and hypercompact (HC) H II…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
We report the detection of three compact ($< 0.001$ pc) radio sources (CRSs) at K$_{a}$-band (0.9 cm) in the \uchiirs G040.54+2.59 (two CRSs) and G034.13+0.47 (one CRS). These CRSs have weak flux densities and are located at the center of…
Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…
Variant calling, the problem of estimating whether a position in a DNA sequence differs from a reference sequence, given noisy, redundant, overlapping short sequences that cover that position, is fundamental to genomics. We propose a deep…
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…
We introduce a family of balanced locally repairable codes (BLRCs) $[n, k, d]$ for arbitrary values of $n$, $k$ and $d$. Similar to other locally repairable codes (LRCs), the presented codes are suitable for applications that require a low…
In this work, we give locally repairable regenerating code (LRRC) [1]-[3], [5], [6] constructions that can protect the file size promised by the graph analysis of the modified family helper selection (MFHS) scheme [1] at the…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Multi-segment reconstruction (MSR) problem consists of recovering a signal from noisy segments with unknown positions of the observation windows. One example arises in DNA sequence assembly, which is typically solved by matching short reads…
Radiology reports are critical for clinical decision-making but often lack a standardized format, limiting both human interpretability and machine learning (ML) applications. While large language models (LLMs) have shown strong capabilities…