Related papers: GenHap: A Novel Computational Method Based on Gene…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
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…
(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…
Sparse compiler is a promising solution for sparse tensor algebra optimization. In compiler implementation, reduction in sparse-dense hybrid algebra plays a key role in performance. Though GPU provides various reduction semantics that can…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Reproducibility in genome-wide association studies (GWAS) is crucial for ensuring reliable genomic research outcomes. However, limited access to original genomic datasets (mainly due to privacy concerns) prevents researchers from…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
A two-layer neural network model that systematically includes correlations among input variables to arbitrary order and is designed to implement Bayes inference has been adapted to classify breast cancer tumors as malignant or benign,…
An inherently parallel algorithm is proposed that efficiently performs selection: finding the K-th largest member of a set of N members. Selection is a common component of many more complex algorithms and therefore is a widely studied…
We present HARP, a novel method for learning low dimensional embeddings of a graph's nodes which preserves higher-order structural features. Our proposed method achieves this by compressing the input graph prior to embedding it, effectively…
Neuro-encoded expression programming(NEEP) that aims to offer a novel continuous representation of combinatorial encoding for genetic programming methods is proposed in this paper. Genetic programming with linear representation uses…
The Matrix Bandwidth Minimization Problem (MBMP) seeks for a simultaneous reordering of the rows and the columns of a square matrix such that the nonzero entries are collected within a band of small width close to the main diagonal. The…
Background: Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
Real-world physical systems are inherently complex, often involving the coupling of multiple physics, making their simulation both highly valuable and challenging. Many mainstream approaches face challenges when dealing with decoupled data.…
Exploration of task mappings plays a crucial role in achieving high performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms. The problem of optimally mapping a set of tasks onto a set of given heterogeneous processors…
A growing number of problems in computational mathematics can be reduced to the solution of many linear systems that are related, often depending smoothly or slowly on a parameter $p$, that is, $A(p)x(p)=b(p)$. We introduce an efficient…