Related papers: Accelerating Genome Analysis via Algorithm-Archite…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
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…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
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…
Gradient porous structured materials possess significant potential of being applied in many engineering fields. To accelerate the design process of infill graded microstructures, a novel asymptotic homogenisation topology optimisation…
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and…
Recent applications of machine learning and statistical inference provide case studies demonstrating how such approaches can accelerate the discovery process in physical chemistry and related fields. Examples discussed in this review…
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…
As high-throughput sequencers become standard equipment outside of sequencing centers, there is an increasing need for efficient methods for pre-processing and primary analysis. While a vast literature proposes methods for HTS data…
Embedded systems continue to rapidly proliferate in diverse fields, including medical devices, autonomous vehicles, and more generally, the Internet of Things (IoT). Many embedded systems require application-specific hardware components to…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
In the past decade, the heterogeneous information network (HIN) has become an important methodology for modern recommender systems. To fully leverage its power, manually designed network templates, i.e., meta-structures, are introduced to…
Quantum computing is a promising paradigm that may overcome the current computational power bottlenecks. The increasing maturity of quantum processors provides more possibilities for the development and implementation of quantum algorithms.…
A major public health issue is the growing resistance of bacteria to antibiotics. An important part of the needed response is the discovery and development of new antimicrobial strategies. These require the screening of potential new drugs,…
Neural architectures and hardware accelerators have been two driving forces for the progress in deep learning. Previous works typically attempt to optimize hardware given a fixed model architecture or model architecture given fixed…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…