Genomics
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…
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
Identifying the mutations that drive cancer growth is key in clinical decision making and precision oncology. As driver mutations confer selective advantage and thus have an increased likelihood of occurrence, frequency-based statistical…
In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden…
Deep learning has empowered analysis for single-cell sequencing data in many ways and has generated deep understanding about a range of complex cellular systems. As the booming single-cell sequencing technologies brings the surge of high…
We investigated the data-driven relationship between features in the tumor microenvironment (TME) and the overall and 5-year survival in triple-negative breast cancer (TNBC) and non-TNBC (NTNBC) patients by using Explainable Artificial…
Identifying subgroups and properties of cancer biopsy samples is a crucial step towards obtaining precise diagnoses and being able to perform personalized treatment of cancer patients. Recent data collections provide a comprehensive…
The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies - a crucial step…
COVID-19 patients show varying severity of the disease ranging from asymptomatic to requiring intensive care. Although a number of SARS-CoV-2 specific monoclonal antibodies have been identified, we still lack an understanding of the overall…
Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…
Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact…
Linked-Reads technologies, such as 10x Genomics, combine both the high-quality and low cost of short-reads sequencing and a long-range information, through the use of barcodes able to tag reads which originate from a common long DNA…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
This paper introduces the Gene Mover's Distance, a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of the proposed distance is to interpret…
Graph network science is becoming increasingly popular, notably in big-data perspective where understanding individual entities for individual functional roles is complex and time consuming. It is likely when a set of genes are regulated by…
A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers.…
Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects. With increasing numbers of datasets being deposited in public…
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing…
Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…