Related papers: FastRemap: A Tool for Quickly Remapping Reads betw…
With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…
Recently we proposed an algorithm for the fast reconstruction of compact context-specific metabolic networks (FASTCORE) that allowed dropping the reconstruction time to the time order of seconds (Vlassis et al.,2014). This extremely low…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
Fast 3D data analysis and steering of a tomographic experiment by changing environmental conditions or acquisition parameters require fast, close to real-time, 3D reconstruction of large data volumes. Here we present a performance-optimized…
Exploratory analysis of high-dimensional data rarely stops at a single embedding. In practice, analysts rerun dimensionality reduction after changing preprocessing, subsets, or hyperparameters, and standard nonlinear methods can quickly…
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…
Accelerating Magnetic Resonance Imaging (MRI) by taking fewer measurements has the potential to reduce medical costs, minimize stress to patients and make MRI possible in applications where it is currently prohibitively slow or expensive.…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Transformer-based models have made tremendous impacts in natural language generation. However the inference speed is a bottleneck due to large model size and intensive computing involved in auto-regressive decoding process. We develop…
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative…
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…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
Evaluation beyond aggregate performance metrics, e.g. F1-score, is crucial to both establish an appropriate level of trust in machine learning models and identify future model improvements. In this paper we demonstrate CrossCheck, an…