Related papers: Just-DNA-Seq, open-source personal genomics platfo…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although…
Personalized diagnoses have not been possible due to sear amount of data pathologists have to bear during the day-to-day routine. This lead to the current generalized standards that are being continuously updated as new findings are…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…
In the last years, especially since the COVID-19 pandemic, precision medicine platforms emerged as useful tools for supporting new tests like the ones that detect the presence of antibodies and antigens with better sensitivity and…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Glioblastoma is a highly aggressive form of brain cancer characterized by rapid progression and poor prognosis. Despite advances in treatment, the underlying genetic mechanisms driving this aggressiveness remain poorly understood. In this…
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…
The integration of knowledge graphs and graph machine learning (GML) in genomic data analysis offers several opportunities for understanding complex genetic relationships, especially at the RNA level. We present a comprehensive approach for…
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially…
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
Ultra high-throughput sequencing of transcriptomes (RNA-Seq) is a widely used method for quantifying gene expression levels due to its low cost, high accuracy and wide dynamic range for detection. However, the nature of RNA-Seq makes it…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI…
In this paper, we consider the problem of answering count queries for genomic data subject to perfect privacy constraints. Count queries are often used in applications that collect aggregate (population-wide) information from biomedical…
Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…
The genetic etiologies of common diseases are highly complex and heterogeneous. Classic statistical methods, such as linear regression, have successfully identified numerous genetic variants associated with complex diseases. Nonetheless,…