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Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…

Comparable corpus is a set of topic aligned documents in multiple languages, which are not necessarily translations of each other. These documents are useful for multilingual natural language processing when there is no parallel text…

Atomic ensembles, comprising clouds of atoms addressed by laser fields, provide an attractive system for both the storage of quantum information, and the coherent conversion of quantum information between atomic and optical degrees of…

Motivation: The rapid growth in genome-wide association studies (GWAS) in plants and animals has brought about the need for a central resource that facilitates i) performing GWAS, ii) accessing data and results of other GWAS, and iii)…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

We present Digital Collections Explorer, a web-based, open-source exploratory search platform that leverages CLIP (Contrastive Language-Image Pre-training) for enhanced visual discovery of digital collections. Our Digital Collections…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

(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…

Query sensitive summarization aims at providing the users with the summary of the contents of single or multiple web pages based on the search query. This paper proposes a novel idea of generating a comparative summary from a set of URLs…

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…

Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority…

GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…

We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…

Navigating the vast and rapidly increasing sea of academic publications to identify institutional synergies, benchmark research contributions and pinpoint key research contributions has become an increasingly daunting task, especially with…

Entity alignment has always had significant uses within a multitude of diverse scientific fields. In particular, the concept of matching entities across networks has grown in significance in the world of social science as communicative…

Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…

To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…

Visual comparison is an important task in the analysis of multivariate graphs. However, comparison of topological features of a graph with respect to its data attributes for different portions of the data remains challenging because there…