Related papers: Meraculous-2D: Haplotype-sensitive Assembly of Hig…
We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using "bubble" structures within the de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Fabrication of custom-built heterostructures based on stacked 2D materials provides an effective method to controllably tune electronic and optical properties. To that end, optimizing fabrication techniques for building these…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources. In this study, we present an efficient de…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…
We have developed a new geometrical method for identifying and reconstructing a homogeneous and highly complete set of galaxy groups in the next generation of deep, flux-limited redshift surveys. Our method combines information from the…
Many recent advances in our understanding of two-dimensional (2D) electron systems stem from van der Waals (vdW) heterostructures. The assembly process relies on the weak bonding across interfaces between layered vdW compounds, making it…
Computing haplotypes from sequencing data, i.e. haplotype assembly, is an important component of molecular and population genetics problems, including interpreting the effects of genetic variation on complex traits and reconstructing…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Accurate segmentation of tubular structures in medical images, such as vessels and airway trees, is crucial for computer-aided diagnosis, radiotherapy, and surgical planning. However, significant challenges exist in algorithm design when…
Defect-free single atom array in optical tweezers is a promising platform for scalable quantum computing, quantum simulation, and quantum metrology. Extending single-species array to mixed-species one promise to offer new possibilities. In…
Enlarged lymph nodes (LNs) can provide important information for cancer diagnosis, staging, and measuring treatment reactions, making automated detection a highly sought goal. In this paper, we propose a new algorithm representation of…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Two-dimensional (2D) heterojunctions display a remarkable potential for application in high performance, low power electro-optical systems. p-n junctions based on vertically stacked heterostructures have shown very promising performance as…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…