相关论文: Identifying DNA motifs based on match and mismatch…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…

Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…

In ecology it has become common to apply DNA barcoding to biological samples leading to datasets containing a large number of nucleotide sequences. The focus is then on inferring the taxonomic placement of each of these sequences by…

Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…

Identifying molecular signatures from complex disease patients with underlying symptomatic similarities is a significant challenge in the analysis of high dimensional multi-omics data. Topological data analysis (TDA) provides a way of…

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…

Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…

Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…

The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…

Patent examiners need to solve a complex information retrieval task when they assess the novelty and inventive step of claims made in a patent application. Given a claim, they search for prior art, which comprises all relevant publicly…

Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…

The discovery of discriminatory bias in human or automated decision making is a task of increasing importance and difficulty, exacerbated by the pervasive use of machine learning and data mining. Currently, discrimination discovery largely…

Medical image synthesis generates additional imaging modalities that are costly, invasive or harmful to acquire, which helps to facilitate the clinical workflow. When training pairs are substantially misaligned (e.g., lung MRI-CT pairs with…

Inferring from inconsistency and making decisions are two problems which have always been treated separately by researchers in Artificial Intelligence. Consequently, different models have been proposed for each category. Different…

In the last fifteen years, data series motif and discord discovery have emerged as two useful and well-used primitives for data series mining, with applications to many domains, including robotics, entomology, seismology, medicine, and…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…

The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…