Related papers: Comparative Assembly Hubs: Web Accessible Browsers…
Assembly-based tools provide a powerful modeling paradigm for non-expert shape designers. However, choosing a component from a large shape repository and aligning it to a partial assembly can become a daunting task. In this paper we…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
The extended structural context has made scientific paper summarization a challenging task. This paper proposes CHANGES, a contrastive hierarchical graph neural network for extractive scientific paper summarization. CHANGES represents a…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data…
We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both…
Selecting between different dependency structures of hidden Markov random field can be very challenging, due to the intractable normalizing constant in the likelihood. We answer this question with approximate Bayesian computation (ABC)…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
Graph convolutional networks (GCNs) have gained popularity due to high performance achievable on several downstream tasks including node classification. Several architectural variants of these networks have been proposed and investigated…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Scientific articles are long text documents organized into sections, each describing aspects of the research. Analyzing scientific production has become progressively challenging due to the increase in the number of available articles.…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Network alignment, the process of finding correspondences between nodes in different graphs, has many scientific and industrial applications. Existing unsupervised network alignment methods find suboptimal alignments that break up node…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotype. The phenotype can be…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…
Scholars frequently employ relatedness measures to estimate the similarity between two different items (e.g., documents, authors, and institutes). Such relatedness measures are commonly based on overlapping references ($\textit{i.e.}$,…
Similarity measures are fundamental tools for quantifying the alignment between artificial and biological systems. However, the diversity of similarity measures and their varied naming and implementation conventions makes it challenging to…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…