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Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…

Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…

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…

A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…

Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…

This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the…

The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…

Scikit-network is a Python package inspired by scikit-learn for the analysis of large graphs. Graphs are represented by their adjacency matrix in the sparse CSR format of SciPy. The package provides state-of-the-art algorithms for ranking,…

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…

Within the context of topological data analysis, the problems of identifying topological significance and matching signals across datasets are important and useful inferential tasks in many applications. The limitation of existing solutions…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…

Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…

Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…

Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…

We introduce NetworKit, an open-source software package for analyzing the structure of large complex networks. Appropriate algorithmic solutions are required to handle increasingly common large graph data sets containing up to billions of…

Interactive line chart visualizations greatly enhance the effective exploration of large time series. Although downsampling has emerged as a well-established approach to enable efficient interactive visualization of large datasets, it is…

Detecting the occlusion from stereo images or video frames is important to many computer vision applications. Previous efforts focus on bundling it with the computation of disparity or optical flow, leading to a chicken-and-egg problem. In…

PyTransport constitutes a straightforward code written in C++ together with Python scripts which automatically edit, compile and run the C++ code as a Python module. It has been written for Unix-like systems (OS X and Linux). Primarily the…

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…