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Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
$\textbf{scqubits}$ is an open-source Python package for simulating and analyzing superconducting circuits. It provides convenient routines to obtain energy spectra of common superconducting qubits, such as the transmon, fluxonium, flux,…
Machine learning (ML) models for code clone detection determine whether two pieces of code are semantically equivalent, which in turn is a key building block for software-engineering tasks like refactoring and security tasks like…
The capability of accurately determining code similarity is crucial in many tasks related to software development. For example, it might be essential to identify code duplicates for performing software maintenance. This research introduces…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Recent advances in large language models (LLMs) have significantly accelerated progress in code translation, enabling more accurate and efficient transformation across programming languages. While originally developed for natural language…
A freely available Python code for modelling SNR evolution has been created. This software is intended for two purposes: to understand SNR evolution; and to use in modelling observations of SNR for obtaining good estimates of SNR…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
The detection of nuclei and cells in histology images is of great value in both clinical practice and pathological studies. However, multiple reasons such as morphological variations of nuclei or cells make it a challenging task where…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
Similarity-driven multi-view linear reconstruction (SiMLR) is an algorithm that exploits inter-modality relationships to transform large scientific datasets into smaller, more well-powered and interpretable low-dimensional spaces. SiMLR…
The direct detection and characterization of planetary and substellar companions at small angular separations is a rapidly advancing field. Dedicated high-contrast imaging instruments deliver unprecedented sensitivity, enabling detailed…