Related papers: Efficient network-guided multi-locus association m…

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. In this paper we combine an experimental design for multiple independent detections of the genetic causes of a phenotype, with a high-throughput…

Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is…

This paper addresses the path selection problem from a known source to the destination in dense networks. The proposed solution for route discovery uses the genetic algorithm approach for a QoS based network. The multi point crossover and…

Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…

We present an alternative method for genome-wide association studies (GWAS) that is more powerful than the regular GWAS method for locus detection. The regular GWAS method suffers from a substantial multiple-testing burden because of the…

Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…

Network-oriented research has been increasingly popular in many scientific areas. In neuroscience research, imaging-based network connectivity measures have become the key for understanding brain organizations, potentially serving as…

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an…

Graph mining analyzes real-world graphs to find core substructures (connected subgraphs) in applications modeled as graphs. Substructure discovery is a process that involves identifying meaningful patterns, structures, or components within…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

The shortest path problem is related to many dynamic processes on networks, ranging from routing in communication networks to signaling in molecular interaction networks. When the network is fully known, the shortest path problem can be…

Motivation. Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…

Determining whether nodes can be localized, called localizability detection, is essential for wireless sensor networks (WSNs). This step is required for localizing nodes, achieving low-cost deployments, and identifying prerequisites in…

Few-Shot Medical Image Segmentation (FSMIS) aims to segment novel classes of medical objects using only a few labeled images. Prototype-based methods have made significant progress in addressing FSMIS. However, they typically generate a…

Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…

The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…

Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named…