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This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
Motivation: Array-based comparative genomic hybridization (arrayCGH) has recently become a popular tool to identify DNA copy number variations along the genome. These profiles are starting to be used as markers to improve prognosis or…
Parallel sentences are a relatively scarce but extremely useful resource for many applications including cross-lingual retrieval and statistical machine translation. This research explores our methodology for mining such data from…
Approximate Bayesian Computation (ABC) methods have become essential tools for performing inference when likelihood functions are intractable or computationally prohibitive. However, their scalability remains a major challenge in…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
Summary: The AptaBlocks Web Interface is focused on providing graphical, intuitive, and platform independent access to AptaBlocks, an experimentally validated algorithmic approach for the in-silico design of oligonucleotide sticky bridges.…
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Recent advances in methods and techniques enable us to develop an interactive overlay to the global map of science based on aggregated citation relations among the 9,162 journals contained in the Science Citation Index and Social Science…
Knowledge graphs are freely aggregated, published, and edited in the Web of data, and thus may overlap. Hence, a key task resides in aligning (or matching) their content. This task encompasses the identification, within an aggregated…
Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
Understanding and comparing distributions of data (e.g., regarding their modes, shapes, or outliers) is a common challenge in many scientific disciplines. Typically, this challenge is addressed using side-by-side comparisons of histograms…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
An increasing amount of data is published on the Web according to the Linked Open Data (LOD) principles. End users would like to browse these data in a flexible manner. In this paper we focus on similarity-based browsing and we introduce a…
Feature upsampling is a fundamental and indispensable ingredient of almost all current network structures for dense prediction tasks. Recently, a popular similarity-based feature upsampling pipeline has been proposed, which utilizes a…