Related papers: Recent advancement in Next Generation Sequencing t…
Next-Generation Sequencing (NGS) has become a cornerstone of genomic research, yet the complexity of downstream analysis-ranging from differential expression gene (DEG) identification to biological interpretations-remains a significant…
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…
The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production,…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a…
Early detection is crucial for successful cancer treatment and increasing survivability rates, particularly in the most common forms. Ten different cancers have been identified in most of these advances that effectively use CNNs…
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…
Nested sampling (NS) computes parameter posterior distributions and makes Bayesian model comparison computationally feasible. Its strengths are the unsupervised navigation of complex, potentially multi-modal posteriors until a well-defined…
Retrieval-Augmented Generation (RAG) represents a major advancement in natural language processing (NLP), combining large language models (LLMs) with information retrieval systems to enhance factual grounding, accuracy, and contextual…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Neural networks are trained by minimizing a loss function that defines the discrepancy between the predicted model output and the target value. The selection of the loss function is crucial to achieve task-specific behaviour and highly…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
An emerging computing paradigm, so-called next-generation reservoir computing (NG-RC) is investigated. True to its namesake, NG-RC requires no actual reservoirs for input data mixing but rather computing the polynomial terms directly from…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…